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Conserved domains on  [gi|311641796|emb|CBX46829|]
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unnamed protein product [synthetic construct]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
266-370 7.00e-68

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd05858:

Pssm-ID: 472250  Cd Length: 105  Bit Score: 220.60  E-value: 7.00e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANTTDKELEVLSLHNVTFE 345
Cdd:cd05858    1 PILQAGLPANTSVVVGTDAEFVCKVYSDAQPHIQWLKHVEKNGSKYGPDGLPYVEVLKTAGVNTTDKEIEVLYLRNVTFE 80
                         90       100
                 ....*....|....*....|....*
gi 311641796 346 DAGEYTCLAGNSIGFSHHSAWLVVL 370
Cdd:cd05858   81 DAGEYTCLAGNSIGISHHSAWLTVL 105
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
632-740 1.00e-63

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


:

Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 209.47  E-value: 1.00e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 632 QLLESGGGLVQPGGSLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVISPSGGDTWYADSVKGRFTISRDNSKNTLYLQ 711
Cdd:cd04981    1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 311641796 712 MNSLRAEDTAVYYCATAG--------DYWGQGTLVTV 740
Cdd:cd04981   81 LNSLTSEDTAVYYCARGLggygysyfDYWGQGTTVTV 117
IgI_2_FGFR cd05857
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of ...
164-258 7.65e-62

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, FGFR2, FGFR3, FGFR4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three IG-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans.


:

Pssm-ID: 409443 [Multi-domain]  Cd Length: 95  Bit Score: 203.55  E-value: 7.65e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd05857    1 PYWTNPEKMEKKLHAVPAANTVKFRCPAAGNPTPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVV 80
                         90
                 ....*....|....*
gi 311641796 244 ENKFGSIRQTYTLDV 258
Cdd:cd05857   81 ENEYGSINHTYHLDV 95
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
770-876 3.00e-58

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


:

Pssm-ID: 409373  Cd Length: 105  Bit Score: 194.22  E-value: 3.00e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 770 VLTQPPSASGTPGQRVTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGSKSGTSASLAISGLQSE 849
Cdd:cd04984    1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80
                         90       100
                 ....*....|....*....|....*..
gi 311641796 850 DEADYYCAAWDDslNGVVFGGGTKLTV 876
Cdd:cd04984   81 DEADYYCQVWDS--NSYVFGGGTKLTV 105
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
519-612 4.93e-46

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


:

Pssm-ID: 409425  Cd Length: 105  Bit Score: 159.81  E-value: 4.93e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 595
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80
                         90
                 ....*....|....*..
gi 311641796 596 FSCSVMHEALHNHYTQK 612
Cdd:cd05768   81 FSCVVGHEALPLQFTQK 97
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
411-510 9.78e-40

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


:

Pssm-ID: 409493  Cd Length: 98  Bit Score: 141.82  E-value: 9.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPKPKDTLMiSRTPEVTCVVVDVShEDPEVKFNWYV-DGVEVHnAKTKPREEQYNSTYRVVSVLTVLHQDWLNG 489
Cdd:cd07696    1 VSVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNG 77
                         90       100
                 ....*....|....*....|.
gi 311641796 490 KEYKCKVSNKALPSSIEKTIS 510
Cdd:cd07696   78 KTFKCKVTHPDLPSPIVKSIQ 98
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
50-122 6.43e-07

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd04973:

Pssm-ID: 472250  Cd Length: 94  Bit Score: 48.35  E-value: 6.43e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796  50 EVPGPEPGQQEQLVFGSGDAVELSCPPPGGGPMGPtvWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSC 122
Cdd:cd04973    7 APPTYQISEVESYSAHPGDLLQLRCRLRDDVQSIN--WTKDGVQLGENNRTRITGEEVQIKDAVPRDSGLYAC 77
 
Name Accession Description Interval E-value
IgI_3_FGFR2 cd05858
Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor 2 (FGFR2); member ...
266-370 7.00e-68

Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor 2 (FGFR2); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain of human fibroblast growth factor receptor 2 (FGFR2). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs. FGFR2 is required for male sex determination. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409444  Cd Length: 105  Bit Score: 220.60  E-value: 7.00e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANTTDKELEVLSLHNVTFE 345
Cdd:cd05858    1 PILQAGLPANTSVVVGTDAEFVCKVYSDAQPHIQWLKHVEKNGSKYGPDGLPYVEVLKTAGVNTTDKEIEVLYLRNVTFE 80
                         90       100
                 ....*....|....*....|....*
gi 311641796 346 DAGEYTCLAGNSIGFSHHSAWLVVL 370
Cdd:cd05858   81 DAGEYTCLAGNSIGISHHSAWLTVL 105
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
632-740 1.00e-63

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 209.47  E-value: 1.00e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 632 QLLESGGGLVQPGGSLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVISPSGGDTWYADSVKGRFTISRDNSKNTLYLQ 711
Cdd:cd04981    1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 311641796 712 MNSLRAEDTAVYYCATAG--------DYWGQGTLVTV 740
Cdd:cd04981   81 LNSLTSEDTAVYYCARGLggygysyfDYWGQGTTVTV 117
IgI_2_FGFR cd05857
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of ...
164-258 7.65e-62

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, FGFR2, FGFR3, FGFR4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three IG-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans.


Pssm-ID: 409443 [Multi-domain]  Cd Length: 95  Bit Score: 203.55  E-value: 7.65e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd05857    1 PYWTNPEKMEKKLHAVPAANTVKFRCPAAGNPTPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVV 80
                         90
                 ....*....|....*
gi 311641796 244 ENKFGSIRQTYTLDV 258
Cdd:cd05857   81 ENEYGSINHTYHLDV 95
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
770-876 3.00e-58

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 194.22  E-value: 3.00e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 770 VLTQPPSASGTPGQRVTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGSKSGTSASLAISGLQSE 849
Cdd:cd04984    1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80
                         90       100
                 ....*....|....*....|....*..
gi 311641796 850 DEADYYCAAWDDslNGVVFGGGTKLTV 876
Cdd:cd04984   81 DEADYYCQVWDS--NSYVFGGGTKLTV 105
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
519-612 4.93e-46

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 159.81  E-value: 4.93e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 595
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80
                         90
                 ....*....|....*..
gi 311641796 596 FSCSVMHEALHNHYTQK 612
Cdd:cd05768   81 FSCVVGHEALPLQFTQK 97
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
411-510 9.78e-40

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409493  Cd Length: 98  Bit Score: 141.82  E-value: 9.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPKPKDTLMiSRTPEVTCVVVDVShEDPEVKFNWYV-DGVEVHnAKTKPREEQYNSTYRVVSVLTVLHQDWLNG 489
Cdd:cd07696    1 VSVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNG 77
                         90       100
                 ....*....|....*....|.
gi 311641796 490 KEYKCKVSNKALPSSIEKTIS 510
Cdd:cd07696   78 KTFKCKVTHPDLPSPIVKSIQ 98
C1-set pfam07654
Immunoglobulin C1-set domain;
521-605 1.86e-35

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 129.29  E-value: 1.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  521 VYTLPPSRDELtKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCS 599
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79

                  ....*.
gi 311641796  600 VMHEAL 605
Cdd:pfam07654  80 VEHEGL 85
IGv smart00406
Immunoglobulin V-Type;
646-727 1.22e-33

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 124.03  E-value: 1.22e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796   646 SLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVISpSGGDTWYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYC 725
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIG-SNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79

                   ..
gi 311641796   726 AT 727
Cdd:smart00406  80 AV 81
IGc1 smart00407
Immunoglobulin C-Type;
535-608 3.28e-31

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 116.64  E-value: 3.28e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796   535 QVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH 608
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
413-501 2.70e-22

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 91.54  E-value: 2.70e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  413 VFLFPPKPKDTlmiSRTPEVTCVVVDVSHedPEVKFNWYVDGVEVHN-AKTKPREEQYNSTYRVVSVLTVLHQDWLNGKE 491
Cdd:pfam07654   1 VYVFPPSPEEL---GKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE 75
                          90
                  ....*....|
gi 311641796  492 YKCKVSNKAL 501
Cdd:pfam07654  76 YTCRVEHEGL 85
IGv smart00406
Immunoglobulin V-Type;
785-857 3.67e-18

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 79.73  E-value: 3.67e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796   785 VTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIY----GDNQRPSGVPDRFSGSK--SGTSASLAISGLQSEDEADYYCA 857
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYigsnGSSYYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCA 80
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
772-877 2.35e-17

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 78.27  E-value: 2.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  772 TQPPSASGTPGQRVTISCSGSSS-NIGRNPVNWYQQLPGTAPKLLI--YGDNQRPSGVPDRFSGSK--SGTSASLAISGL 846
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSGRGdpSNGDGSLTIQNL 80
                          90       100       110
                  ....*....|....*....|....*....|.
gi 311641796  847 QSEDEADYYCAAWDDslNGVVFGGGTKLTVL 877
Cdd:pfam07686  81 TLSDSGTYTCAVIPS--GEGVFGKGTRLTVL 109
I-set pfam07679
Immunoglobulin I-set domain;
184-258 1.97e-14

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 69.59  E-value: 1.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796  184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:pfam07679  17 SARFTCTVTGTPDPEVSWFKDGQPLRSSDRF-KVTYEGGTYTLTISNVQPDDSGKYTCVATNSAGEAEASAELTV 90
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
184-258 4.65e-14

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 68.30  E-value: 4.65e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796   184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:smart00410  11 SVTLSCEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNSSGSASSGTTLTV 85
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
273-369 6.41e-13

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 64.83  E-value: 6.41e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796   273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKHvevNGSKVGPDGTPYVTVLKTAGanttdkeleVLSLHNVTFEDAGEYTC 352
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQ---GGKLLAESGRFSVSRSGSTS---------TLTISNVTPEDSGTYTC 68
                           90
                   ....*....|....*..
gi 311641796   353 LAGNSIGFSHHSAWLVV 369
Cdd:smart00410  69 AATNSSGSASSGTTLTV 85
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
640-740 1.15e-11

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 62.09  E-value: 1.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  640 LVQPGGSLRLSCAASGFTFSGYI-MWWVRQAPGKGLEWVSVISPSGGDTwyaDSVKGRFTISRDNSKNTLYLQMNSLRAE 718
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEASTsVYWYRQPPGKGPTFLIAYYSNGSEE---GVKKGRFSGRGDPSNGDGSLTIQNLTLS 83
                          90       100
                  ....*....|....*....|....*
gi 311641796  719 DTAVYYCATAGD---YWGQGTLVTV 740
Cdd:pfam07686  84 DSGTYTCAVIPSgegVFGKGTRLTV 108
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
273-356 3.25e-10

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 57.19  E-value: 3.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYVTVLKTAGanttdkeleVLSLHNVTFEDAGEYTC 352
Cdd:pfam13927   8 PSSVTVREGETVTLTCEATGSPPPTITWYK----NGEPISSGSTRSRSLSGSNS---------TLTISNVTRSDAGTYTC 74

                  ....
gi 311641796  353 LAGN 356
Cdd:pfam13927  75 VASN 78
IgI_1_FGFR cd04973
First immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of ...
50-122 6.43e-07

First immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for all FGFs.


Pssm-ID: 409362  Cd Length: 94  Bit Score: 48.35  E-value: 6.43e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796  50 EVPGPEPGQQEQLVFGSGDAVELSCPPPGGGPMGPtvWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSC 122
Cdd:cd04973    7 APPTYQISEVESYSAHPGDLLQLRCRLRDDVQSIN--WTKDGVQLGENNRTRITGEEVQIKDAVPRDSGLYAC 77
IGc1 smart00407
Immunoglobulin C-Type;
432-503 5.98e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.92  E-value: 5.98e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796   432 VTCVVVDVSHEDPEVKfnWYVDGVEVH-NAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPS 503
Cdd:smart00407   4 LVCLVSGFYPPDITVT--WLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKE 74
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
61-123 5.10e-04

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 39.87  E-value: 5.10e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796   61 QLVFGSGDAVELSCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQR-----LQVLNASHEDSGAYSCR 123
Cdd:pfam00047   5 TVTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIESLKVKHDNGRttqssLLISNVTKEDAGTYTCV 72
 
Name Accession Description Interval E-value
IgI_3_FGFR2 cd05858
Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor 2 (FGFR2); member ...
266-370 7.00e-68

Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor 2 (FGFR2); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain of human fibroblast growth factor receptor 2 (FGFR2). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs. FGFR2 is required for male sex determination. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409444  Cd Length: 105  Bit Score: 220.60  E-value: 7.00e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANTTDKELEVLSLHNVTFE 345
Cdd:cd05858    1 PILQAGLPANTSVVVGTDAEFVCKVYSDAQPHIQWLKHVEKNGSKYGPDGLPYVEVLKTAGVNTTDKEIEVLYLRNVTFE 80
                         90       100
                 ....*....|....*....|....*
gi 311641796 346 DAGEYTCLAGNSIGFSHHSAWLVVL 370
Cdd:cd05858   81 DAGEYTCLAGNSIGISHHSAWLTVL 105
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
632-740 1.00e-63

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 209.47  E-value: 1.00e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 632 QLLESGGGLVQPGGSLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVISPSGGDTWYADSVKGRFTISRDNSKNTLYLQ 711
Cdd:cd04981    1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80
                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 311641796 712 MNSLRAEDTAVYYCATAG--------DYWGQGTLVTV 740
Cdd:cd04981   81 LNSLTSEDTAVYYCARGLggygysyfDYWGQGTTVTV 117
IgI_2_FGFR cd05857
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of ...
164-258 7.65e-62

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, FGFR2, FGFR3, FGFR4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three IG-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans.


Pssm-ID: 409443 [Multi-domain]  Cd Length: 95  Bit Score: 203.55  E-value: 7.65e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd05857    1 PYWTNPEKMEKKLHAVPAANTVKFRCPAAGNPTPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVV 80
                         90
                 ....*....|....*
gi 311641796 244 ENKFGSIRQTYTLDV 258
Cdd:cd05857   81 ENEYGSINHTYHLDV 95
IgI_3_FGFR cd04974
Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of ...
266-367 2.34e-58

Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409363  Cd Length: 102  Bit Score: 194.18  E-value: 2.34e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANtTDKELEVLSLHNVTFE 345
Cdd:cd04974    1 PILQAGLPANQTVVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKYGPDGLPYVTVLKVAGVN-TTGEENTLTISNVTFD 79
                         90       100
                 ....*....|....*....|..
gi 311641796 346 DAGEYTCLAGNSIGFSHHSAWL 367
Cdd:cd04974   80 DAGEYICLAGNSIGLSFHSAWL 101
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
770-876 3.00e-58

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 194.22  E-value: 3.00e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 770 VLTQPPSASGTPGQRVTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGSKSGTSASLAISGLQSE 849
Cdd:cd04984    1 VLTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80
                         90       100
                 ....*....|....*....|....*..
gi 311641796 850 DEADYYCAAWDDslNGVVFGGGTKLTV 876
Cdd:cd04984   81 DEADYYCQVWDS--NSYVFGGGTKLTV 105
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
519-612 4.93e-46

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 159.81  E-value: 4.93e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP--ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 595
Cdd:cd05768    1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPlpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80
                         90
                 ....*....|....*..
gi 311641796 596 FSCSVMHEALHNHYTQK 612
Cdd:cd05768   81 FSCVVGHEALPLQFTQK 97
IgI_2_FGFR_like cd05729
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor, and similar ...
164-258 2.10e-42

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor, and similar domains; member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, FGFR2, FGFR3, FGFR4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three Ig-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans. This group also contains fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors.


Pssm-ID: 409393 [Multi-domain]  Cd Length: 95  Bit Score: 149.29  E-value: 2.10e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd05729    1 PRFTDTEKMEEREHALPAANKVRLECGAGGNPMPNITWLKDGKEFKKEHRIGGTKVEEKGWSLIIERAIPRDKGKYTCIV 80
                         90
                 ....*....|....*
gi 311641796 244 ENKFGSIRQTYTLDV 258
Cdd:cd05729   81 ENEYGSINHTYDVDV 95
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
411-510 9.78e-40

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409493  Cd Length: 98  Bit Score: 141.82  E-value: 9.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPKPKDTLMiSRTPEVTCVVVDVShEDPEVKFNWYV-DGVEVHnAKTKPREEQYNSTYRVVSVLTVLHQDWLNG 489
Cdd:cd07696    1 VSVFLIPPSPKDLFL-TKSAKVTCLVVDLT-SIEEVNVTWSReDGNEVL-ASTTNPEKHYNATLSVVSTLTVCADDWDNG 77
                         90       100
                 ....*....|....*....|.
gi 311641796 490 KEYKCKVSNKALPSSIEKTIS 510
Cdd:cd07696   78 KTFKCKVTHPDLPSPIVKSIQ 98
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
770-876 5.16e-37

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409369  Cd Length: 106  Bit Score: 134.44  E-value: 5.16e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 770 VLTQPP-SASGTPGQRVTISCsGSSSNIGRNPVNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGSKSGTSASLAISGLQS 848
Cdd:cd04980    2 VMTQSPaSLSVSPGERVTISC-KASQSISSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80
                         90       100
                 ....*....|....*....|....*...
gi 311641796 849 EDEADYYCAAWDDSLngVVFGGGTKLTV 876
Cdd:cd04980   81 EDAAVYYCQQGYTFP--YTFGGGTKLEI 106
C1-set pfam07654
Immunoglobulin C1-set domain;
521-605 1.86e-35

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 129.29  E-value: 1.86e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  521 VYTLPPSRDELtKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCS 599
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79

                  ....*.
gi 311641796  600 VMHEAL 605
Cdd:pfam07654  80 VEHEGL 85
IGv smart00406
Immunoglobulin V-Type;
646-727 1.22e-33

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 124.03  E-value: 1.22e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796   646 SLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVISpSGGDTWYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYC 725
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIG-SNGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79

                   ..
gi 311641796   726 AT 727
Cdd:smart00406  80 AV 81
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
771-876 3.91e-33

Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E and, D strands in one sheet and A', G, F, C, C', and C" strands in the other.


Pssm-ID: 409355 [Multi-domain]  Cd Length: 111  Bit Score: 123.60  E-value: 3.91e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 771 LTQPP-SASGTPGQRVTISCSGSSSNIGrNPVNWYQQLPGTAPKLLIYGD---NQRPSGVPDRFSGSKSG-TSASLAISG 845
Cdd:cd00099    1 VTQSPrSLSVQEGESVTLSCEVSSSFSS-TYIYWYRQKPGQGPEFLIYLSsskGKTKGGVPGRFSGSRDGtSSFSLTISN 79
                         90       100       110
                 ....*....|....*....|....*....|..
gi 311641796 846 LQSEDEADYYCAAWDDSLNG-VVFGGGTKLTV 876
Cdd:cd00099   80 LQPEDSGTYYCAVSESGGTDkLTFGSGTRLTV 111
IGc1 smart00407
Immunoglobulin C-Type;
535-608 3.28e-31

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 116.64  E-value: 3.28e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796   535 QVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH 608
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEvTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
413-501 2.70e-22

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 91.54  E-value: 2.70e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  413 VFLFPPKPKDTlmiSRTPEVTCVVVDVSHedPEVKFNWYVDGVEVHN-AKTKPREEQYNSTYRVVSVLTVLHQDWLNGKE 491
Cdd:pfam07654   1 VYVFPPSPEEL---GKPNTLTCLVTGFYP--PDITVTWLKNGQEVTEgVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE 75
                          90
                  ....*....|
gi 311641796  492 YKCKVSNKAL 501
Cdd:pfam07654  76 YTCRVEHEGL 85
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
520-605 3.75e-22

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 91.75  E-value: 3.75e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 520 QVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSC 598
Cdd:cd00098    1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTsGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTC 80

                 ....*..
gi 311641796 599 SVMHEAL 605
Cdd:cd00098   81 VVTHESL 87
IgI_2_FGFRL1-like cd05856
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1 ...
164-258 2.07e-20

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1); member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 is comprised of a signal peptide, three extracellular Ig-like modules, a transmembrane segment, and a short intracellular domain. FGFRL1 is expressed preferentially in skeletal tissues. Similar to FGF receptors, the expressed protein interacts specifically with heparin and with FGF2. FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors.


Pssm-ID: 409442  Cd Length: 92  Bit Score: 86.45  E-value: 2.07e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRgEHRIGgiKLRHQQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd05856    1 PRFTQPAKMRRRVIARPVGSSVRLKCVASGNPRPDITWLKDNKPLT-PPEIG--ENKKKKWTLSLKNLKPEDSGKYTCHV 77
                         90
                 ....*....|....*
gi 311641796 244 ENKFGSIRQTYTLDV 258
Cdd:cd05856   78 SNRAGEINATYKVDV 92
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
640-740 5.00e-20

Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E and, D strands in one sheet and A', G, F, C, C', and C" strands in the other.


Pssm-ID: 409355 [Multi-domain]  Cd Length: 111  Bit Score: 86.23  E-value: 5.00e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 640 LVQPGGSLRLSCAASGFtFSGYIMWWVRQAPGKGLEWVSVISPSGGDTwyADSVKGRFTISRDnSKNTLYLQMNSLRAED 719
Cdd:cd00099    9 SVQEGESVTLSCEVSSS-FSSTYIYWYRQKPGQGPEFLIYLSSSKGKT--KGGVPGRFSGSRD-GTSSFSLTISNLQPED 84
                         90       100
                 ....*....|....*....|....*..
gi 311641796 720 TAVYYCATAG------DYWGQGTLVTV 740
Cdd:cd00099   85 SGTYYCAVSEsggtdkLTFGSGTRLTV 111
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
772-876 6.05e-20

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 85.79  E-value: 6.05e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 772 TQPPSA-SGTPGQRVTISCSGSSSNIgrNPVNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGS--KSGTSASLAISGLQS 848
Cdd:cd04983    2 TQSPQSlSVQEGENVTLNCNYSTSTF--YYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQL 79
                         90       100
                 ....*....|....*....|....*....
gi 311641796 849 EDEADYYCAAWDDSLNG-VVFGGGTKLTV 876
Cdd:cd04983   80 SDSAVYFCALSESGGTGkLTFGKGTRLTV 108
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
518-605 3.63e-19

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409496  Cd Length: 99  Bit Score: 83.27  E-value: 3.63e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 518 EPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 596
Cdd:cd07699    1 APSVTIFPPSSEELSSGKATLVCLINKFYPGFATVTWKVDGSTvSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVY 80

                 ....*....
gi 311641796 597 SCSVMHEAL 605
Cdd:cd07699   81 TCEVTHEGL 89
IGv smart00406
Immunoglobulin V-Type;
785-857 3.67e-18

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 79.73  E-value: 3.67e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796   785 VTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIY----GDNQRPSGVPDRFSGSK--SGTSASLAISGLQSEDEADYYCA 857
Cdd:smart00406   2 VTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYigsnGSSYYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCA 80
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
771-876 3.85e-18

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigens as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain the standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409371  Cd Length: 117  Bit Score: 80.87  E-value: 3.85e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 771 LTQPP-SASGTPGQRVTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIY----GDNQRPSG-VPDRFSGSK-SGTSAS-LA 842
Cdd:cd04982    1 LEQPQlSITREESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYvsstSAVRKDSGkTKNKFEARKdVGKSTStLT 80
                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 311641796 843 ISGLQSEDEADYYCAAWDDSLNGV--VFGGGTKLTV 876
Cdd:cd04982   81 ITNLEKEDSATYYCAYWESGSGYYikVFGSGTKLIV 116
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
771-876 4.48e-18

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here are composed of the immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409480  Cd Length: 110  Bit Score: 80.40  E-value: 4.48e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 771 LTQPPSAS-GTPGQRVTISCSgssSNIGRNPVNWYQQLPGTAPKLLIY---GDNQRPSGVP-DRFSGSK-SGTSASLAIS 844
Cdd:cd05899    1 VTQSPRYLiKRRGQSVTLRCS---QKSGHDNMYWYRQDPGKGLQLLFYsygGGLNEEGDLPgDRFSASRpSLTRSSLTIK 77
                         90       100       110
                 ....*....|....*....|....*....|...
gi 311641796 845 GLQSEDEADYYCAAWDDSL-NGVVFGGGTKLTV 876
Cdd:cd05899   78 SAEPEDSAVYLCASSLGGGaDEAYFGPGTRLTV 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
772-877 2.35e-17

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 78.27  E-value: 2.35e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  772 TQPPSASGTPGQRVTISCSGSSS-NIGRNPVNWYQQLPGTAPKLLI--YGDNQRPSGVPDRFSGSK--SGTSASLAISGL 846
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSGRGdpSNGDGSLTIQNL 80
                          90       100       110
                  ....*....|....*....|....*....|.
gi 311641796  847 QSEDEADYYCAAWDDslNGVVFGGGTKLTVL 877
Cdd:pfam07686  81 TLSDSGTYTCAVIPS--GEGVFGKGTRLTVL 109
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
411-515 1.25e-16

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 76.22  E-value: 1.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPkPKDTLMISRTPEVTCVVVDVSHEDPEVKfnWYVDGVEVHNAK---TKPREEQyNSTYRVVSVLTVLHQDWL 487
Cdd:cd05768    1 PSVYLLPP-PEEELSLNETVTLTCLVKGFYPEDIFVS--WLQNGEPLPSADyktTAPVPES-DGSFFVYSKLNVSTADWN 76
                         90       100
                 ....*....|....*....|....*....
gi 311641796 488 NGKEYKCKVSNKALPS-SIEKTISKAKGQ 515
Cdd:cd05768   77 SGDVFSCVVGHEALPLqFTQKSIDKSPGK 105
IgI_4_hemolin-like cd20978
Fourth immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set ...
164-258 7.09e-16

Fourth immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fourth immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The fourth Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409570 [Multi-domain]  Cd Length: 88  Bit Score: 73.58  E-value: 7.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPErmdKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGehRIGGIKLrhQQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd20978    1 PKFIQKP---EKNVVVKGGQDVTLPCQVTGVPQPKITWLHNGKPLQG--PMERATV--EDGTLTIINVQPEDTGYYGCVA 73
                         90
                 ....*....|....*
gi 311641796 244 ENKFGSIRQTYTLDV 258
Cdd:cd20978   74 TNEIGDIYTETLLHV 88
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
519-607 1.28e-15

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 73.20  E-value: 1.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNG---QPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGN 594
Cdd:cd16093    2 PTVSLHAPSREEFLGNRtATFVCLATGFSPKTISFKWLRNGkevTSSTGAVVEEPKEDGKTLYSATSFLTITESEWKSQT 81
                         90
                 ....*....|...
gi 311641796 595 VFSCSVMHEALHN 607
Cdd:cd16093   82 EFTCEFKHKGEIV 94
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
630-740 2.74e-15

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409514  Cd Length: 115  Bit Score: 72.59  E-value: 2.74e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 630 EVQLLESGGGLVQPGGSLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVIspsggDTWYADSVKGRFTISRDNSKNTLY 709
Cdd:cd16095    1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSL-----DHISTKVSEDRITSSREDTNSQIF 75
                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 311641796 710 LQMNSLRAEDTAVYYCA-TAGD-------YWGQGTLVTV 740
Cdd:cd16095   76 LQIKGLGLRDSGQYHCArRVGYgddtdklIFGPGTDVIV 114
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
412-509 9.57e-15

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 70.57  E-value: 9.57e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 412 SVFLFPPKPKDTLmiSRTPEVTCVVVDVSHEDpeVKFNWYVDGVEVHNAKTKPRE-EQYNSTYRVVSVLTVLHQDWLNGK 490
Cdd:cd00098    1 TVTLLPPSPEEKG--GGKVTLVCLVSGFYPKD--ITVTWLKNGVPLTSGVSTSSPvEPNDGTYSVTSSLTVPPSDWDEGA 76
                         90
                 ....*....|....*....
gi 311641796 491 EYKCKVSNKALPSSIEKTI 509
Cdd:cd00098   77 TYTCVVTHESLKSPLSKTW 95
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
519-604 1.97e-14

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of epsilon and gamma chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409622  Cd Length: 94  Bit Score: 69.40  E-value: 1.97e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESnGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWqQGNVFSC 598
Cdd:cd21817    2 PSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNS-GSLTSGVKTFPAVLQSSGLYTTSSQVTVPSSSW-GSQTFTC 79

                 ....*.
gi 311641796 599 SVMHEA 604
Cdd:cd21817   80 NVEHKP 85
I-set pfam07679
Immunoglobulin I-set domain;
184-258 1.97e-14

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 69.59  E-value: 1.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796  184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:pfam07679  17 SARFTCTVTGTPDPEVSWFKDGQPLRSSDRF-KVTYEGGTYTLTISNVQPDDSGKYTCVATNSAGEAEASAELTV 90
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
774-876 2.07e-14

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 69.07  E-value: 2.07e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796   774 PPSASGTPGQRVTISCSGSSSNIGRnpVNWYQQlpgtAPKLLIYgdnqrpsgvPDRFSGSKSGTSASLAISGLQSEDEAD 853
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPE--VTWYKQ----GGKLLAE---------SGRFSVSRSGSTSTLTISNVTPEDSGT 65
                           90       100
                   ....*....|....*....|...
gi 311641796   854 YYCAAWDDSlnGVVFgGGTKLTV 876
Cdd:smart00410  66 YTCAATNSS--GSAS-SGTTLTV 85
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
642-732 3.01e-14

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigens as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain the standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409371  Cd Length: 117  Bit Score: 69.70  E-value: 3.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 642 QPGGSLRLSCAASGFTFSGYIMWWVRQAPGKGLEWVSVISPSGGDTWYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTA 721
Cdd:cd04982   11 EESKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLTITNLEKEDSA 90
                         90
                 ....*....|.
gi 311641796 722 VYYCAtagdYW 732
Cdd:cd04982   91 TYYCA----YW 97
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
184-258 4.65e-14

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 68.30  E-value: 4.65e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796   184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:smart00410  11 SVTLSCEASGSPPPEVTWYKQGGKLLAESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNSSGSASSGTTLTV 85
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
519-605 5.58e-14

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta, and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 68.21  E-value: 5.58e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPS-RDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 596
Cdd:cd05847    1 PTVQILHSScASTLTSETIQLLCLISGYTPSTIEVEWLVDGQVaTLSAASTAPQKEEGGTFSTTSKLNVTQEDWKSGKTY 80

                 ....*....
gi 311641796 597 SCSVMHEAL 605
Cdd:cd05847   81 TCKVTHQGT 89
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
636-740 1.12e-13

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 67.15  E-value: 1.12e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796   636 SGGGLVQPGGSLRLSCAASGFtfSGYIMWWVRQapgkGLEWVSVispsggdtwyadsvKGRFTISRDNskNTLYLQMNSL 715
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGS--PPPEVTWYKQ----GGKLLAE--------------SGRFSVSRSG--STSTLTISNV 58
                           90       100
                   ....*....|....*....|....*...
gi 311641796   716 RAEDTAVYYCA---TAGDYWGqGTLVTV 740
Cdd:smart00410  59 TPEDSGTYTCAatnSSGSASS-GTTLTV 85
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
185-255 1.95e-13

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409353 [Multi-domain]  Cd Length: 70  Bit Score: 65.81  E-value: 1.95e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGREFRGEHRiGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYT 255
Cdd:cd00096    1 VTLTCSASGNPPPTITWYKNGKPLPPSSR-DSRRSELGNGTLTISNVTLEDSGTYTCVASNSAGGSASASV 70
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
273-369 6.41e-13

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 64.83  E-value: 6.41e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796   273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKHvevNGSKVGPDGTPYVTVLKTAGanttdkeleVLSLHNVTFEDAGEYTC 352
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQ---GGKLLAESGRFSVSRSGSTS---------TLTISNVTPEDSGTYTC 68
                           90
                   ....*....|....*..
gi 311641796   353 LAGNSIGFSHHSAWLVV 369
Cdd:smart00410  69 AATNSSGSASSGTTLTV 85
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
519-604 7.24e-13

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409374  Cd Length: 98  Bit Score: 65.30  E-value: 7.24e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEW--ESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 596
Cdd:cd04985    2 PTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWqkNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVY 81

                 ....*...
gi 311641796 597 SCSVMHEA 604
Cdd:cd04985   82 KCQVQHSA 89
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
517-606 8.93e-13

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 65.48  E-value: 8.93e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 517 REPQVYTLPPSRDELTKNQ-VSLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFF-LYSKLTVDKSRWQQ- 592
Cdd:cd05769    1 TPPTVALFPPSEAEIRNKRkATLVCLATGFYPDHVSLSWKVNGKEvKDGVATDPQALRENTSTYsLSSRLRVSATEWFNp 80
                         90
                 ....*....|....
gi 311641796 593 GNVFSCSVMHEALH 606
Cdd:cd05769   81 RNTFTCIVKFYGGT 94
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
184-245 4.01e-12

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 62.58  E-value: 4.01e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 311641796  184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQwSLVMESVVPSDRGNYTCVVEN 245
Cdd:pfam13927  18 TVTLTCEATGSPPPTITWYKNGEPISSGSTRSRSLSGSNS-TLTISNVTRSDAGTYTCVASN 78
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
640-740 4.77e-12

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here are composed of the immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409480  Cd Length: 110  Bit Score: 63.46  E-value: 4.77e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 640 LVQPGGSLRLSCAASgftfSGY-IMWWVRQAPGKGLEWVsVISPSGGDTWYADSVKGRFTISRdNSKNTLYLQMNSLRAE 718
Cdd:cd05899    9 IKRRGQSVTLRCSQK----SGHdNMYWYRQDPGKGLQLL-FYSYGGGLNEEGDLPGDRFSASR-PSLTRSSLTIKSAEPE 82
                         90       100
                 ....*....|....*....|....*...
gi 311641796 719 DTAVYYCATAGD------YWGQGTLVTV 740
Cdd:cd05899   83 DSAVYLCASSLGggadeaYFGPGTRLTV 110
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
640-740 1.15e-11

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 62.09  E-value: 1.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  640 LVQPGGSLRLSCAASGFTFSGYI-MWWVRQAPGKGLEWVSVISPSGGDTwyaDSVKGRFTISRDNSKNTLYLQMNSLRAE 718
Cdd:pfam07686   7 TVALGGSVTLPCTYSSSMSEASTsVYWYRQPPGKGPTFLIAYYSNGSEE---GVKKGRFSGRGDPSNGDGSLTIQNLTLS 83
                          90       100
                  ....*....|....*....|....*
gi 311641796  719 DTAVYYCATAGD---YWGQGTLVTV 740
Cdd:pfam07686  84 DSGTYTCAVIPSgegVFGKGTRLTV 108
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
641-740 1.26e-11

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 61.90  E-value: 1.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 641 VQPGGSLRLSCAASGFTFSgYIMWWvRQAPGKGLEWVSVISpsggdTWYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 720
Cdd:cd04983   10 VQEGENVTLNCNYSTSTFY-YLFWY-RQYPGQGPQFLIYIS-----SDSGNKKKGRFSATLDKSRKSSSLHISAAQLSDS 82
                         90       100
                 ....*....|....*....|....*.
gi 311641796 721 AVYYCATAGDYW------GQGTLVTV 740
Cdd:cd04983   83 AVYFCALSESGGtgkltfGKGTRLTV 108
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
775-876 7.29e-11

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409503  Cd Length: 112  Bit Score: 59.84  E-value: 7.29e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 775 PSASGTPGQRVTISCSGSSSNigRNP-VNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGS--KSGTSASLAISGLQSEDE 851
Cdd:cd07706    7 PDVSVQVGEEVTLNCRYETSW--TNYyLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNfqKAQKSISLTISALQLEDS 84
                         90       100
                 ....*....|....*....|....*....
gi 311641796 852 ADYYCAAWD----DSLngvVFGGGTKLTV 876
Cdd:cd07706   85 AKYFCALSLpydtDKL---IFGKGTRLTV 110
Ig4_Contactin-2-like cd05728
Fourth Ig domain of the neural cell adhesion molecule contactin-2, and similar domains; The ...
184-258 9.48e-11

Fourth Ig domain of the neural cell adhesion molecule contactin-2, and similar domains; The members here are composed of the fourth Ig domain of the neural cell adhesion molecule contactin-2. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (also called TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. The first four Ig domains form the intermolecular binding fragment which arranges as a compact U-shaped module by contacts between Ig domains 1 and 4, and domains 2 and 3. It has been proposed that a linear zipper-like array forms, from contactin-2 molecules alternatively provided by the two apposed membranes.


Pssm-ID: 143205 [Multi-domain]  Cd Length: 85  Bit Score: 58.77  E-value: 9.48e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRI---GGiKLRHQQWSLvmesvvpSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05728   16 SLRWECKASGNPRPAYRWLKNGQPLASENRIeveAG-DLRITKLSL-------SDSGMYQCVAENKHGTIYASAELAV 85
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
410-511 1.19e-10

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409496  Cd Length: 99  Bit Score: 59.01  E-value: 1.19e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 410 APSVFLFPPKPKDtlMISRTPEVTCVVVDVSHEDPEVkfNWYVDGVEVHNA-KTKPREEQYNSTYRVVSVLTVLHQDWLN 488
Cdd:cd07699    1 APSVTIFPPSSEE--LSSGKATLVCLINKFYPGFATV--TWKVDGSTVSSGvTTSKTEQQSDNTYSMSSYLTLSSSDWNK 76
                         90       100
                 ....*....|....*....|...
gi 311641796 489 GKEYKCKVSNKALPSSIEKTISK 511
Cdd:cd07699   77 HKVYTCEVTHEGLSSTITKSFNR 99
IgC1_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of ...
411-501 1.50e-10

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta, and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 409434  Cd Length: 97  Bit Score: 58.58  E-value: 1.50e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPKPKDTLMiSRTPEVTCVVVdvSHEDPEVKFNWYVDGVEVHN--AKTKPREEQyNSTYRVVSVLTVLHQDWLN 488
Cdd:cd05847    1 PTVQILHSSCASTLT-SETIQLLCLIS--GYTPSTIEVEWLVDGQVATLsaASTAPQKEE-GGTFSTTSKLNVTQEDWKS 76
                         90
                 ....*....|...
gi 311641796 489 GKEYKCKVSNKAL 501
Cdd:cd05847   77 GKTYTCKVTHQGT 89
IgI_3_Robo cd05725
Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
273-369 1.97e-10

Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, and Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409390 [Multi-domain]  Cd Length: 83  Bit Score: 57.79  E-value: 1.97e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVgPDGTpyVTVLKtaganttDKELEvlsLHNVTFEDAGEYTC 352
Cdd:cd05725    4 PQNQVVLVDDSAEFQCEVGGDPVPTVRWRK----EDGEL-PKGR--YEILD-------DHSLK---IRKVTAGDMGSYTC 66
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd05725   67 VAENMVGKIEASATLTV 83
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
640-740 2.64e-10

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409497  Cd Length: 116  Bit Score: 58.61  E-value: 2.64e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 640 LVQPGGSLRLSCAASGFTFSGYIMWW-VRQAPGKG--LEWVSVISPSGGDTwYADSVKG-RFTISRDNSKNTLYLQMNSL 715
Cdd:cd07700    9 LVQTNQTVKMSCEAKTSPKNTRIYWLrQRQAPSKDshFEFLASWDPSKGIV-YGEGVDQeKLIILSDSDSSRYILSLMSV 87
                         90       100
                 ....*....|....*....|....*...
gi 311641796 716 RAEDTAVYYCATAGD---YWGQGTLVTV 740
Cdd:cd07700   88 KPEDSGTYFCMTVGSpelIFGTGTKLSV 115
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
273-356 3.25e-10

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 57.19  E-value: 3.25e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYVTVLKTAGanttdkeleVLSLHNVTFEDAGEYTC 352
Cdd:pfam13927   8 PSSVTVREGETVTLTCEATGSPPPTITWYK----NGEPISSGSTRSRSLSGSNS---------TLTISNVTRSDAGTYTC 74

                  ....
gi 311641796  353 LAGN 356
Cdd:pfam13927  75 VASN 78
IgI_3_Robo cd05725
Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
178-258 3.83e-10

Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, and Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409390 [Multi-domain]  Cd Length: 83  Bit Score: 57.02  E-value: 3.83e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 178 AVPAANTVRFRCPAAGNPTPSISWLKNGrefrGEHRIGGIKLRHQQwSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLD 257
Cdd:cd05725    8 VVLVDDSAEFQCEVGGDPVPTVRWRKED----GELPKGRYEILDDH-SLKIRKVTAGDMGSYTCVAENMVGKIEASATLT 82

                 .
gi 311641796 258 V 258
Cdd:cd05725   83 V 83
I-set pfam07679
Immunoglobulin I-set domain;
273-369 1.11e-09

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 55.73  E-value: 1.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDgtPYVTVLKTAGANTtdkelevLSLHNVTFEDAGEYTC 352
Cdd:pfam07679   7 PKDVEVQEGESARFTCTVTGTPDPEVSWFK----DGQPLRSS--DRFKVTYEGGTYT-------LTISNVQPDDSGKYTC 73
                          90
                  ....*....|....*..
gi 311641796  353 LAGNSIGFSHHSAWLVV 369
Cdd:pfam07679  74 VATNSAGEAEASAELTV 90
IgI_5_Robo cd20952
Fifth Ig-like domain of Roundabout (Robo) homolog 1/2, and similar domains; a member of the ...
179-258 1.99e-09

Fifth Ig-like domain of Roundabout (Robo) homolog 1/2, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fifth Ig-like domain of Roundabout (Robo) homolog 1/2 and similar domains. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagonizes slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be is the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. The fifth Ig-like domain of Robo 1 and 2 is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors


Pssm-ID: 409544 [Multi-domain]  Cd Length: 87  Bit Score: 55.20  E-value: 1.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGREFRGEH-RIGGIklrhQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLD 257
Cdd:cd20952   11 VAVGGTVVLNCQATGEPVPTISWLKDGVPLLGKDeRITTL----ENGSLQIKGAEKSDTGEYTCVALNLSGEATWSAVLD 86

                 .
gi 311641796 258 V 258
Cdd:cd20952   87 V 87
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
527-605 2.06e-09

Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Cluster of Differentiation (CD) 1. CD1 family of transmembrane glycoproteins, are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. They mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes (CD1a, CD1b, CD1c, CD1d, and CD1e) organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. CD1a localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. C1-set Ig domains have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409620  Cd Length: 93  Bit Score: 55.41  E-value: 2.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 527 SRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVL-DSDGSFFLYSKLTVDKsrwQQGNVFSCSVMHEAL 605
Cdd:cd21029    9 SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGTQSGGILpNHDGTYQLRKTLDIAP---GEGAGYSCRVDHSSL 85
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
534-603 3.16e-09

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity.


Pssm-ID: 409507  Cd Length: 96  Bit Score: 54.74  E-value: 3.16e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 534 NQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHE 603
Cdd:cd16085   16 NQVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTVNKDGTYNWTSWLLVNVSAHREDVVLTCQVEHD 85
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
411-510 3.55e-09

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 54.71  E-value: 3.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPkPKDTLMISRTPEVTCVVVDVSHEDPEVKfnWYVDGVEVHNAKTKPREEQYNS---TYRVVSVLTVLHQDWL 487
Cdd:cd16093    2 PTVSLHAP-SREEFLGNRTATFVCLATGFSPKTISFK--WLRNGKEVTSSTGAVVEEPKEDgktLYSATSFLTITESEWK 78
                         90       100
                 ....*....|....*....|...
gi 311641796 488 NGKEYKCKVSNKAlpSSIEKTIS 510
Cdd:cd16093   79 SQTEFTCEFKHKG--EIVEKNAS 99
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
776-876 5.56e-09

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 54.62  E-value: 5.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 776 SASGT--PGQRVTISCSGSSSNIGRNPVNWYQQLPGTAPKLL--IYGDNQRP---SGVPDRFSGS--KSGTSASLAISGL 846
Cdd:cd04981    5 SGPGLvkPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIglIYPGGGDTyyaDSFKGRFTITrdTSKSTAYLQLNSL 84
                         90       100       110
                 ....*....|....*....|....*....|...
gi 311641796 847 QSEDEADYYCA---AWDDSLNGVVFGGGTKLTV 876
Cdd:cd04981   85 TSEDTAVYYCArglGGYGYSYFDYWGQGTTVTV 117
IgI_LRIG1-like cd05763
Immunoglobulin (Ig)-like ectodomain of the LRIG1 (Leucine-rich Repeats And Immunoglobulin-like ...
177-259 5.88e-09

Immunoglobulin (Ig)-like ectodomain of the LRIG1 (Leucine-rich Repeats And Immunoglobulin-like Domains Protein 1) and similar proteins; member of the I-set of IgSF domains; The members here are composed of subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. The ectodomain of LRIG1 has two distinct regions: the proposed 15 LRRs and three Ig-like domains closer to the membrane. LRIG1 has been reported to interact with many receptor tyrosine kinases, GDNF/c-Ret, E-cadherin, JAK/STAT, c-Met, and the EGFR family signaling systems. Immunoglobulin Superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The structure of the LRIG1 extracellular Ig domain lacks a C" strand and thus is better described as a member of the I-set of IgSF domains.


Pssm-ID: 409420 [Multi-domain]  Cd Length: 91  Bit Score: 53.78  E-value: 5.88e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNG-------REFRgehriggIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGS 249
Cdd:cd05763    9 ITIRAGSTARLECAATGHPTPQIAWQKDGgtdfpaaRERR-------MHVMPEDDVFFIVDVKIEDTGVYSCTAQNSAGS 81
                         90
                 ....*....|
gi 311641796 250 IRQTYTLDVL 259
Cdd:cd05763   82 ISANATLTVL 91
IgC1_CH1_IgM cd21819
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; ...
532-604 6.50e-09

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of mu chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409624  Cd Length: 95  Bit Score: 53.87  E-value: 6.50e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 311641796 532 TKNQVSLTCLVKGFYPSDIAVEWESNGQPE-NNYKTTPPVLdSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEA 604
Cdd:cd21819   14 TSDPVTVGCLATDFLPDSITFSWTDDNNSLtTGVKTYPSVL-TGGTYTASSQLQVPESEWKSKENFYCKVEHPG 86
IgI_Titin_like cd05747
Immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins; member of the ...
167-256 6.61e-09

Immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the fifth immunoglobulin (Ig)-like domain from the C-terminus of human titin x and similar proteins. Titin (also called connectin) is a fibrous sarcomeric protein specifically found in vertebrate striated muscle. Titin is gigantic; depending on isoform composition it ranges from 2970 to 3700 kDa, and is of a length that spans half a sarcomere. Titin largely consists of multiple repeats of Ig-like and fibronectin type 3 (FN-III)-like domains. Titin connects the ends of myosin thick filaments to Z disks and extends along the thick filament to the H zone and appears to function similar to an elastic band, keeping the myosin filaments centered in the sarcomere during muscle contraction or stretching. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 143224 [Multi-domain]  Cd Length: 92  Bit Score: 53.90  E-value: 6.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 167 TRPERMdkkllAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQwSLVMESVVPSDRGNYTCVVENK 246
Cdd:cd05747    8 TKPRSL-----TVSEGESARFSCDVDGEPAPTVTWMREGQIIVSSQRHQITSTEYKS-TFEISKVQMSDEGNYTVVVENS 81
                         90
                 ....*....|
gi 311641796 247 FGSIRQTYTL 256
Cdd:cd05747   82 EGKQEAQFTL 91
Ig3_L1-CAM_like cd05731
Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar ...
183-258 6.96e-09

Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar domains; The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, and spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM and human neurofascin.


Pssm-ID: 409394 [Multi-domain]  Cd Length: 83  Bit Score: 53.57  E-value: 6.96e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 183 NTVRFRCPAAGNPTPSISWLKNGrefrGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05731   11 GVLLLECIAEGLPTPDIRWIKLG----GELPKGRTKFENFNKTLKIENVSEADSGEYQCTASNTMGSARHTISVTV 82
IgI_5_Dscam cd20958
Fifth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
177-258 9.55e-09

Fifth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fifth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409550 [Multi-domain]  Cd Length: 89  Bit Score: 53.34  E-value: 9.55e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRiggiKLRHQQWSLVMESVVP-SDRGNYTCVVENKFG-SIRQTY 254
Cdd:cd20958   10 LTAVAGQTLRLHCPVAGYPISSITWEKDGRRLPLNHR----QRVFPNGTLVIENVQRsSDEGEYTCTARNQQGqSASRSV 85

                 ....
gi 311641796 255 TLDV 258
Cdd:cd20958   86 FVKV 89
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
284-364 9.91e-09

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409353 [Multi-domain]  Cd Length: 70  Bit Score: 52.72  E-value: 9.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 284 VEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYVTVLKTAGanttdkeleVLSLHNVTFEDAGEYTCLAGNSIGFSHH 363
Cdd:cd00096    1 VTLTCSASGNPPPTITWYK----NGKPLPPSSRDSRRSELGNG---------TLTISNVTLEDSGTYTCVASNSAGGSAS 67

                 .
gi 311641796 364 S 364
Cdd:cd00096   68 A 68
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
520-605 1.18e-08

Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted.


Pssm-ID: 409427  Cd Length: 94  Bit Score: 53.25  E-value: 1.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 520 QVYTLPPSrDELTKNQvsLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFL--YSKLTVDKsrwqqGNVFS 597
Cdd:cd05770    6 QVYSRFPA-ENGKPNV--LNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSFSKDWTFYLlkYTEFTPTK-----GDEYA 77

                 ....*...
gi 311641796 598 CSVMHEAL 605
Cdd:cd05770   78 CRVRHNTL 85
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
519-605 1.27e-08

Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 409428  Cd Length: 100  Bit Score: 53.27  E-value: 1.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEW--ESNGQPE-----NNYKTTPPVLDSDGSFFLYSKLTVDKSRWQ 591
Cdd:cd05771    1 PRV-RLSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWlrEEPGGSEsqvsrDGVSLSSHRQSVDGTYSISSYLTLEPGTEN 79
                         90
                 ....*....|....
gi 311641796 592 QGNVFSCSVMHEAL 605
Cdd:cd05771   80 RGATYTCRVTHVSL 93
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
519-605 1.40e-08

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409424  Cd Length: 95  Bit Score: 53.08  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTKNQVsLTCLVKGFYPSDIAVEWESNGQP-ENNYKTTPPVLDSDGSFFLYSKLTVDKSRwqqGNVFS 597
Cdd:cd05767    3 PEVTVFPKSPVELGEPNT-LICFVDNFFPPVINVTWLRNGQPvTDGVSETVFLPREDHSFRKFSYLPFTPSE---GDIYD 78

                 ....*...
gi 311641796 598 CSVMHEAL 605
Cdd:cd05767   79 CRVEHWGL 86
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
519-602 1.56e-08

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409623  Cd Length: 94  Bit Score: 52.89  E-value: 1.56e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVY--TLPPSRdelTKNQVSLTCLVKGFYPSDIAVEWESNGQpENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVF 596
Cdd:cd21818    2 PTVFplSLCPSL---SSDPVVIGCLVQGFFPEPVNVTWNYSGK-GGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAY 77

                 ....*.
gi 311641796 597 SCSVMH 602
Cdd:cd21818   78 KCSVQH 83
IgI_4_hemolin-like cd20978
Fourth immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set ...
266-369 2.98e-08

Fourth immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fourth immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The fourth Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409570 [Multi-domain]  Cd Length: 88  Bit Score: 51.62  E-value: 2.98e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLkHvevNGSKV-GPDGTPYVTvlktagANTtdkelevLSLHNVTF 344
Cdd:cd20978    1 PKFIQKPEKNVVVKGGQDVTLPCQVTGVPQPKITWL-H---NGKPLqGPMERATVE------DGT-------LTIINVQP 63
                         90       100
                 ....*....|....*....|....*
gi 311641796 345 EDAGEYTCLAGNSIGFSHHSAWLVV 369
Cdd:cd20978   64 EDTGYYGCVATNEIGDIYTETLLHV 88
IgC1_MHC_II_beta_HLA-DQ_I-A cd21001
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
518-605 4.14e-08

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of human histocompatibility antigen (HLA) DQ and mouse I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E have the same basic features insofar as peptide loading and presentation, they differ in that each interacts with distinctly different sets of peptides, and in the incidence of deletion of their genes. A structural understanding of the similarities and differences between I-A and I-E may help with understanding their roles in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. Human HLA-DR, -DQ, and -DP are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. HLA-DQ is involved in the autoimmune diseases celiac disease and diabetes mellitus type. DQ is one of several antigens involved in rejection of organ transplants. DQ2 is encoded by the HLA-DQB1*02 allele group. DQ6 is encoded by the HLA-DQB1*06 allele group. DQ2 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. These isoforms, nicknamed DQ2.2 and DQ2.5, are also encoded by the DQA1*0201 and DQA1*0501 genes, respectively. DQ6 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. For DQ6, however, cis-isoform pairing only occurs with DQ1 alpha-chains. There are many haplotypes of DQ6. Susceptibility to Leptospirosis infection was found associated with undifferentiated DQ6. DQ8 is determined by the antibody recognition of beta8 and this generally detects the gene product of DQB1*0302. DQ8 is commonly linked to autoimmune disease in the human population. DQ8 is the second most predominant isoform linked to celiac disease and the DQ most linked to Type 1 diabetes. DQ8 increases the risk for rheumatoid arthritis and is linked to the primary risk locus for RA, HLA-DR4. DR4 also plays an important role in Type 1 diabetes. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune response. They are expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice, and induced in nonprofessional APCs, such as keratinocyctes; they are expressed on the surface of activated human T cells and on T cells from other species. MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes; these peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC, and bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409592  Cd Length: 97  Bit Score: 51.65  E-value: 4.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 518 EPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKLTVDKsrwQQGNVF 596
Cdd:cd21001    3 EPTV-TISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETaGVVSTPLIRNGDWTFQILVMLEMTP---QRGDVY 78

                 ....*....
gi 311641796 597 SCSVMHEAL 605
Cdd:cd21001   79 TCHVEHPSL 87
IgC_1_Robo cd07693
First immunoglobulin (Ig)-like constant domain in Robo (roundabout) receptors, and similar ...
177-251 5.07e-08

First immunoglobulin (Ig)-like constant domain in Robo (roundabout) receptors, and similar domains; The members here are composed of the first immunoglobulin (Ig)-like domain in Roundabout (Robo) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit1, Slit2, Slit3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit1, Slit2,and Slit3 are expressed at the ventral midline. Robo3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be is the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site.


Pssm-ID: 409490 [Multi-domain]  Cd Length: 99  Bit Score: 51.40  E-value: 5.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFR------GEHRI---GGiklrhqqwSLVMESVVP-----SDRGNYTCV 242
Cdd:cd07693   10 LIVSKGDPATLNCKAEGRPTPTIQWLKNGQPLEtdkddpRSHRIvlpSG--------SLFFLRVVHgrkgrSDEGVYVCV 81

                 ....*....
gi 311641796 243 VENKFGSIR 251
Cdd:cd07693   82 AHNSLGEAV 90
IgI_telokin-like cd20973
immunoglobulin-like domain of telokin and similar proteins; a member of the I-set of IgSF ...
177-258 5.51e-08

immunoglobulin-like domain of telokin and similar proteins; a member of the I-set of IgSF domains; The members here are composed of the immunoglobulin (Ig) domain in telokin, the C-terminal domain of myosin light chain kinase which is identical to telokin, and similar proteins. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the telokin Ig domain lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409565 [Multi-domain]  Cd Length: 88  Bit Score: 51.04  E-value: 5.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTL 256
Cdd:cd20973    7 KEVVEGSAARFDCKVEGYPDPEVKWMKDDNPIVESRRFQIDQDEDGLCSLIISDVCGDDSGKYTCKAVNSLGEATCSAEL 86

                 ..
gi 311641796 257 DV 258
Cdd:cd20973   87 TV 88
Ig5_Contactin cd04969
Fifth immunoglobulin (Ig) domain of contactin; The members here are composed of the fifth ...
174-258 7.01e-08

Fifth immunoglobulin (Ig) domain of contactin; The members here are composed of the fifth immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma.


Pssm-ID: 409358 [Multi-domain]  Cd Length: 89  Bit Score: 50.92  E-value: 7.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 174 KKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRhqqwSLVMESVVPSDRGNYTCVVENKFGSIRQT 253
Cdd:cd04969    9 KKKILAAKGGDVIIECKPKASPKPTISWSKGTELLTNSSRICILPDG----SLKIKNVTKSDEGKYTCFAVNFFGKANST 84

                 ....*
gi 311641796 254 YTLDV 258
Cdd:cd04969   85 GSLSV 89
IgI_Myotilin_C_like cd05744
Immunoglobulin (Ig)-like domain of myotilin, palladin, and myopalladin; member of the I-set of ...
177-258 7.34e-08

Immunoglobulin (Ig)-like domain of myotilin, palladin, and myopalladin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in myotilin, palladin, and myopalladin. Myotilin, palladin, and myopalladin function as scaffolds that regulate actin organization. Myotilin and myopalladin are most abundant in skeletal and cardiac muscle; palladin is ubiquitously expressed in the organs of developing vertebrates and plays a key role in cellular morphogenesis. The three family members each interact with specific molecular partners with all three binding to alpha-actinin; In addition, palladin also binds to vasodilator-stimulated phosphoprotein (VASP) and ezrin, myotilin binds to filamin and actin, and myopalladin also binds to nebulin and cardiac ankyrin repeat protein (CARP). This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409405 [Multi-domain]  Cd Length: 91  Bit Score: 50.96  E-value: 7.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTL 256
Cdd:cd05744   10 LEVQEGRLCRFDCKVSGLPTPDLFWQLNGKPVRPDSAHKMLVRENGRHSLIIEPVTKRDAGIYTCIARNRAGENSFNAEL 89

                 ..
gi 311641796 257 DV 258
Cdd:cd05744   90 VV 91
IgI_5_Robo cd20952
Fifth Ig-like domain of Roundabout (Robo) homolog 1/2, and similar domains; a member of the ...
273-369 9.60e-08

Fifth Ig-like domain of Roundabout (Robo) homolog 1/2, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fifth Ig-like domain of Roundabout (Robo) homolog 1/2 and similar domains. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagonizes slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be is the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. The fifth Ig-like domain of Robo 1 and 2 is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors


Pssm-ID: 409544 [Multi-domain]  Cd Length: 87  Bit Score: 50.19  E-value: 9.60e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevngskvgpDGTPyvtvLKTAGANTTDKELEVLSLHNVTFEDAGEYTC 352
Cdd:cd20952    6 PQNQTVAVGGTVVLNCQATGEPVPTISWLK-----------DGVP----LLGKDERITTLENGSLQIKGAEKSDTGEYTC 70
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd20952   71 VALNLSGEATWSAVLDV 87
Ig3_L1-CAM cd05876
Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM); The members here ...
184-258 1.07e-07

Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM); The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM.


Pssm-ID: 409460 [Multi-domain]  Cd Length: 83  Bit Score: 49.91  E-value: 1.07e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHrigGIKLRHQQWsLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05876   12 SLVLECIAEGLPTPTVKWLRPSGPLPPDR---VKYQNHNKT-LQLLNVGESDDGEYVCLAENSLGSARHAYYVTV 82
Ig_Pro_neuregulin cd05750
Immunoglobulin (Ig)-like domain in neuregulins; The members here are composed of the ...
188-258 1.37e-07

Immunoglobulin (Ig)-like domain in neuregulins; The members here are composed of the immunoglobulin (Ig)-like domain in neuregulins (NRGs). NRGs are signaling molecules which participate in cell-cell interactions in the nervous system, breast, heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. There are four members of the neuregulin gene family (NRG-1, NRG-2, NRG-3, and NRG-4). The NRG-1 protein, binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. The other NRGs proteins bind one or the other or both of these ErbBs. NRG-1 has multiple functions: in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors, while in the peripheral nervous system NRG-1 regulates processes such as target cell differentiation, and Schwann cell survival. There are many NRG-1 isoforms which arise from the alternative splicing of mRNA. Less is known of the functions of the other NRGs. NRG-2 and NRG-3 are expressed predominantly in the nervous system. NRG-2 is expressed by motor neurons and terminal Schwann cells, and is concentrated near synaptic sites and may be a signal that regulates synaptic differentiation. NRG-4 has been shown to direct pancreatic islet cell development towards the delta-cell lineage.


Pssm-ID: 409408 [Multi-domain]  Cd Length: 92  Bit Score: 50.20  E-value: 1.37e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 311641796 188 RCPAAG-NPTPSISWLKNGREFrGEHRIGGIKLRHQQWS--LVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05750   20 KCEATSeNPSPRYRWFKDGKEL-NRKRPKNIKIRNKKKNseLQINKAKLEDSGEYTCVVENILGKDTVTGNVTV 92
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
174-249 2.25e-07

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 49.12  E-value: 2.25e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796  174 KKLLAVPAANTVRFRCPA-AGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGS 249
Cdd:pfam00047   3 PPTVTVLEGDSATLTCSAsTGSPGPDVTWSKEGGTLIESLKVKHDNGRTTQSSLLISNVTKEDAGTYTCVVNNPGGS 79
IgI_4_MYLK-like cd20976
Fourth Ig-like domain from smooth muscle myosin light chain kinase and similar domains ; a ...
188-258 2.98e-07

Fourth Ig-like domain from smooth muscle myosin light chain kinase and similar domains ; a member of the I-set of IgSF domains; The members here are composed of the fourth immunoglobulin (Ig)-like domain from smooth muscle myosin light chain kinase (MYLK) and similar domains. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of this group shows that the fourth Ig-like domain from myosin light chain kinase lacks this strand and thus belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409568 [Multi-domain]  Cd Length: 90  Bit Score: 49.17  E-value: 2.98e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796 188 RCPAAGNPTPSISWLKNGRE--FRGEHriggIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd20976   22 QCSARGKPVPRITWIRNAQPlqYAADR----STCEAGVGELHIQDVLPEDHGTYTCLAKNAAGQVSCSAWVTV 90
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
780-876 3.07e-07

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409580  Cd Length: 114  Bit Score: 49.86  E-value: 3.07e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 780 TPGQRVTISCSGSSSNIGRNPVNWYQQLPGTApKLLIY--GDNQRPsGVPDRFSGS--KSGTSASLAISGLQSEDEADYY 855
Cdd:cd20988   11 SVGKPVTLKCSMKGEAISNYYINWYRKTQGNT-MTFIYreGGIYGP-GFKDNFRGDidSSNNLAVLKILEASERDEGSYY 88
                         90       100
                 ....*....|....*....|....*.
gi 311641796 856 CAAwDDSLNG-----VVFGGGTKLTV 876
Cdd:cd20988   89 CAS-DTPGGGreydpLIFGKGTYLTV 113
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
519-610 3.16e-07

Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409495  Cd Length: 92  Bit Score: 49.15  E-value: 3.16e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDEltkNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVL-DSDGSFFLYSKLTVDKSRWQqgnVFS 597
Cdd:cd07698    3 PKVHVTHHPRSD---GESTLRCWALGFYPAEITLTWQRDGEDQTQDMELVETRpNGDGTFQKWAAVVVPSGEEQ---RYT 76
                         90
                 ....*....|...
gi 311641796 598 CSVMHEALHNHYT 610
Cdd:cd07698   77 CHVQHEGLPEPLT 89
IgI_2_Follistatin_like cd05736
Second immunoglobulin (Ig)-like domain of a Follistatin-related protein 5, and similar domains; ...
273-369 3.66e-07

Second immunoglobulin (Ig)-like domain of a Follistatin-related protein 5, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain found in human Follistatin-related protein 5 (FSTL5) and a follistatin-like molecule encoded by the CNS-related Mahya gene. Mahya genes have been retained in certain Bilaterian branches during evolution. They are conserved in Hymenoptera and Deuterostomes, but are absent from other metazoan species such as fruit fly and nematode. Mahya proteins are secretory, with a follistatin-like domain (Kazal-type serine/threonine protease inhibitor domain and EF-hand calcium-binding domain), two Ig-like domains, and a novel C-terminal domain. Mahya may be involved in learning and memory and in processing of sensory information in Hymenoptera and vertebrates. Follistatin is a secreted, multidomain protein that binds activins with high affinity and antagonizes their signaling.


Pssm-ID: 409399 [Multi-domain]  Cd Length: 93  Bit Score: 48.80  E-value: 3.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYVTVLktagANTTDkelevLSLHNVTFEDAGEYTC 352
Cdd:cd05736    7 PEFQAKEPGVEASLRCHAEGIPLPRVQWLK----NGMDINPKLSKQLTLI----ANGSE-----LHISNVRYEDTGAYTC 73
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd05736   74 IAKNEGGVDEDISSLFV 90
IgI_4_MYLK-like cd20976
Fourth Ig-like domain from smooth muscle myosin light chain kinase and similar domains ; a ...
270-369 4.49e-07

Fourth Ig-like domain from smooth muscle myosin light chain kinase and similar domains ; a member of the I-set of IgSF domains; The members here are composed of the fourth immunoglobulin (Ig)-like domain from smooth muscle myosin light chain kinase (MYLK) and similar domains. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of this group shows that the fourth Ig-like domain from myosin light chain kinase lacks this strand and thus belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409568 [Multi-domain]  Cd Length: 90  Bit Score: 48.40  E-value: 4.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 270 AGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevngskvgpDGTPyvtvLKTAGANTT-DKELEVLSLHNVTFEDAG 348
Cdd:cd20976    5 SSVPKDLEAVEGQDFVAQCSARGKPVPRITWIR-----------NAQP----LQYAADRSTcEAGVGELHIQDVLPEDHG 69
                         90       100
                 ....*....|....*....|.
gi 311641796 349 EYTCLAGNSIGFSHHSAWLVV 369
Cdd:cd20976   70 TYTCLAKNAAGQVSCSAWVTV 90
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
517-605 4.95e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain has two globular domains (N- and C-terminal) and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409423  Cd Length: 96  Bit Score: 48.48  E-value: 4.95e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 517 REPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN---NYKTTPPVLDsdgsfFLYSKLTVDKSRWQQG 593
Cdd:cd05766    2 VQPSV-KVSPTKTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEETagvVSTELIPNGD-----WTFQILVMLETTPRRG 75
                         90
                 ....*....|..
gi 311641796 594 NVFSCSVMHEAL 605
Cdd:cd05766   76 DVYTCQVEHSSL 87
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
518-605 5.31e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR. HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. HLA-DR is also involved in several autoimmune conditions, disease susceptibility, and disease resistance including seronegative-rheumatoid arthritis, penicillamine-induced myasthenia, schizophrenia, Goodpasture syndrome, systemic lupus erythematosus, Alzheimers, tuberculoid leprosy, and Hashimoto's thyroiditis. HLA-DR molecules are upregulated in response to signaling. HLA-DR is an alphabeta heterodimer cell surface receptor, each subunit of which contains two extracellular domains, a membrane-spanning domain, and a cytoplasmic tail. Both alpha and beta chains are anchored in the membrane. The DR beta chain is encoded by 4 loci, however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. Sometimes an individual may only possess 2 copies of the same locus, DRB1*. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53 specificity, has some variation, and is associated with certain HLA-DRB1 types. The HLA-DRB5 locus encodes the HLA-DR51 specificity, which is typically invariable, and is linked to the HLA-DR2 types. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409591  Cd Length: 96  Bit Score: 48.46  E-value: 5.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 518 EPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKL-TVDKSrwqqGNV 595
Cdd:cd21000    3 EPKV-TVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKaGVVSTGLIQNGDWTFQTLVMLeTVPRS----GEV 77
                         90
                 ....*....|
gi 311641796 596 FSCSVMHEAL 605
Cdd:cd21000   78 YTCQVEHPSV 87
IgI_VEGFR cd04976
Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor (VEGFR); member ...
171-259 5.76e-07

Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor (VEGFR); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor (VEGFR). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1), and VEGFR-3 (Flt-4). VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angiogenic, and microvascular permeability-enhancing effects of VEGF-A. VEGFR-1 may play an inhibitory part in these processes by binding VEGF and interfering with its interaction with VEGFR-2. VEGFR-1 has a signaling role in mediating monocyte chemotaxis. VEGFR-1 and VEGFR-2 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. VEGFR-3 has been shown to be involved in tumor angiogenesis and growth. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409365  Cd Length: 90  Bit Score: 48.36  E-value: 5.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 171 RMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRiggiklRHQQWSLVMESVVPSDRGNYTCVVENKFGSI 250
Cdd:cd04976    7 RKQQVLEATAGKRSVRLPMKVKAYPPPEVVWYKDGLPLTEKAR------YLTRHSLIIKEVTEEDTGNYTILLSNKQSNV 80

                 ....*....
gi 311641796 251 RQTYTLDVL 259
Cdd:cd04976   81 FKNLTATLV 89
IgI_1_FGFR cd04973
First immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of ...
50-122 6.43e-07

First immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for all FGFs.


Pssm-ID: 409362  Cd Length: 94  Bit Score: 48.35  E-value: 6.43e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796  50 EVPGPEPGQQEQLVFGSGDAVELSCPPPGGGPMGPtvWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSC 122
Cdd:cd04973    7 APPTYQISEVESYSAHPGDLLQLRCRLRDDVQSIN--WTKDGVQLGENNRTRITGEEVQIKDAVPRDSGLYAC 77
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
532-605 7.89e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409593  Cd Length: 97  Bit Score: 48.00  E-value: 7.89e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 532 TKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDG--SFFLYSKLTVDKSrwqQGNVFSCSVMHEAL 605
Cdd:cd21002   16 TREPVMLACHVWGFYPADVTITWLKNGDPVAPHSSAPKTAQPNGdwTYQTQVTLAVTPS---PGDTYTCSVQHASL 88
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
518-605 9.04e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP. HLA class II histocompatibility antigen, DP(W2) beta chain is a protein that in humans is encoded by the HLA-DPB1 gene. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DP is an alphabeta heterodimer cell-surface receptor. Each DP subunit (alpha-subunit, beta-subunit) is composed of a alpha-helical N-terminal domain, an IgG-like beta sheet, a membrane spanning domain, and a cytoplasmic domain. The alpha-helical domain forms the sides of the peptide binding groove. The beta sheet regions form the base of the binding groove and the bulk of the molecule as well as the inter-subunit (non-covalent) binding region. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409594  Cd Length: 96  Bit Score: 47.83  E-value: 9.04e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 518 EPQVYtLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN-NYKTTPPVLDSDGSFFLYSKLTVDKsrwQQGNVF 596
Cdd:cd21003    3 QPKVN-VSPSKKGPLQHHNLLVCHVTDFYPGNIQVRWFLNGQEETaGVVSTNLIHNGDWTFQILVMLEMTP---QQGDVY 78

                 ....*....
gi 311641796 597 SCSVMHEAL 605
Cdd:cd21003   79 TCQVEHPSL 87
IgC2_3_Dscam cd20957
Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
177-253 9.36e-07

Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the Constant 2 (C2)-set of IgSF domains; The members here are composed of the third immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C, and C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand.


Pssm-ID: 409549 [Multi-domain]  Cd Length: 88  Bit Score: 47.53  E-value: 9.36e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRhqqwSLVMESVVPSDRGNYTCVVENKFGSIRQT 253
Cdd:cd20957   11 QTVDFGRTAVFNCSVTGNPIHTVLWMKDGKPLGHSSRVQILSED----VLVIPSVKREDKGMYQCFVRNDGDSAQAT 83
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
641-740 9.83e-07

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409503  Cd Length: 112  Bit Score: 48.28  E-value: 9.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 641 VQPGGSLRLSCAASGfTFSGYIMWWVRQAPGKglEWVSVISpsgGDTWYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 720
Cdd:cd07706   11 VQVGEEVTLNCRYET-SWTNYYLFWYKQLPSG--EMTFLIR---QDSSEQNAKSGRYSVNFQKAQKSISLTISALQLEDS 84
                         90       100
                 ....*....|....*....|....*.
gi 311641796 721 AVYYCATAGDY------WGQGTLVTV 740
Cdd:cd07706   85 AKYFCALSLPYdtdkliFGKGTRLTV 110
IgI_1_Contactin-5 cd05848
First immunoglobulin (Ig) domain of contactin-5; member of the I-set of Ig superfamily domains; ...
185-250 1.29e-06

First immunoglobulin (Ig) domain of contactin-5; member of the I-set of Ig superfamily domains; The members here are composed of the first immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-5. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains, anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. In rats, a lack of contactin-5 (NB-2) results in an impairment of the neuronal activity in the auditory system. Contactin-5 is expressed specifically in the postnatal nervous system, peaking at about 3 weeks postnatal. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala; lower levels of expression have been detected in the corpus callosum, caudate nucleus, and spinal cord. This group belongs to the I-set of IgSF domains.


Pssm-ID: 409435  Cd Length: 96  Bit Score: 47.24  E-value: 1.29e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGREFRGEHRIggiklrhqQWSLVMESVVPS------DRGNYTCVVENKFGSI 250
Cdd:cd05848   22 VILNCEARGNPVPTYRWLRNGTEIDTESDY--------RYSLIDGNLIISnpsevkDSGRYQCLATNSIGSI 85
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
768-876 1.36e-06

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409514  Cd Length: 115  Bit Score: 47.94  E-value: 1.36e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 768 QSVLTQPPSASGTPGQRVTISCSGSSSNIGRNPVNWYQQLPGTAPKLLIYGDNQRPSGVPDRFSGSKSGTSA--SLAISG 845
Cdd:cd16095    1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHISTKVSEDRITSSREDTNSqiFLQIKG 80
                         90       100       110
                 ....*....|....*....|....*....|....
gi 311641796 846 LQSEDEADYYCA---AWDDSLNGVVFGGGTKLTV 876
Cdd:cd16095   81 LGLRDSGQYHCArrvGYGDDTDKLIFGPGTDVIV 114
IgI_3_Contactin cd04968
Third immunoglobulin (Ig) domain of contactin; member of the I-set of Ig superfamily (IgSF) ...
266-369 1.85e-06

Third immunoglobulin (Ig) domain of contactin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains.


Pssm-ID: 409357 [Multi-domain]  Cd Length: 88  Bit Score: 46.77  E-value: 1.85e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevngskvgPDGTPYVT-VLKTAGAnttdkeleVLSLHNVTF 344
Cdd:cd04968    1 PSIKVRFPADTYALKGQTVTLECFALGNPVPQIKWRK----------VDGSPSSQwEITTSEP--------VLEIPNVQF 62
                         90       100
                 ....*....|....*....|....*
gi 311641796 345 EDAGEYTCLAGNSIGFSHHSAWLVV 369
Cdd:cd04968   63 EDEGTYECEAENSRGKDTVQGRIIV 87
IgI_titin_I1-like cd20951
Immunoglobulin domain I1 of the titin I-band and similar proteins; a member of the I-set of ...
179-258 2.07e-06

Immunoglobulin domain I1 of the titin I-band and similar proteins; a member of the I-set of IgSF domains; The members here are composed of the immunoglobulin domain I1 of the titin I-band and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The Ig I1 domain of the titin I-band is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409543 [Multi-domain]  Cd Length: 94  Bit Score: 46.64  E-value: 2.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQW--SLVMESVVPSDRGNYTCVVENKFGSIRQTYTL 256
Cdd:cd20951   12 VWEKSDAKLRVEVQGKPDPEVKWYKNGVPIDPSSIPGKYKIESEYGvhVLHIRRVTVEDSAVYSAVAKNIHGEASSSASV 91

                 ..
gi 311641796 257 DV 258
Cdd:cd20951   92 VV 93
IgI_NCAM-1_like cd05732
Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1) and similar ...
275-369 2.66e-06

Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1) and similar proteins; The members here are composed of the fourth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule (NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-non-NCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. Also included in this group is NCAM-2 (also known as OCAM/mamFas II and RNCAM) NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE). One of the unique features of I-set domains is the lack of a C" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains.


Pssm-ID: 409395 [Multi-domain]  Cd Length: 96  Bit Score: 46.36  E-value: 2.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 275 NQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVG-PDGtpYVTVLKTAGANTtdkelevLSLHNVTFEDAGEYTCL 353
Cdd:cd05732   10 NQTAVELEQITLTCEAEGDPIPEITWRRATRGISFEEGdLDG--RIVVRGHARVSS-------LTLKDVQLTDAGRYDCE 80
                         90
                 ....*....|....*.
gi 311641796 354 AGNSIGFSHHSAWLVV 369
Cdd:cd05732   81 ASNRIGGDQQSMYLEV 96
IgI_1_MuSK cd20970
agrin-responsive first immunoglobulin-like domains (Ig1) of the MuSK ectodomain; a member of ...
185-258 2.69e-06

agrin-responsive first immunoglobulin-like domains (Ig1) of the MuSK ectodomain; a member of the I-set of IgSF domains; The members here are composed of the first immunoglobulin-like domains (Ig1) of the Muscle-specific kinase (MuSK). MuSK is a receptor tyrosine kinase specifically expressed in skeletal muscle, where it plays a central role in the formation and maintenance of the neuromuscular junction (NMJ). MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. The activation of MUSK in myotubes regulates the formation of NMJs through the regulation of different processes including the specific expression of genes in subsynaptic nuclei, the reorganization of the actin cytoskeleton and the clustering of the acetylcholine receptors (AChR) in the postsynaptic membrane. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the MuSK lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409562 [Multi-domain]  Cd Length: 92  Bit Score: 46.35  E-value: 2.69e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 185 VRFRCPAAGNPTPSISWLKNG---REFRGEHRIGGIKLrhqqwSLVMESVVPSDRGNYTCVVENK-FGSIRQTYTLDV 258
Cdd:cd20970   20 ATFMCRAEGSPEPEISWTRNGnliIEFNTRYIVRENGT-----TLTIRNIRRSDMGIYLCIASNGvPGSVEKRITLQV 92
IgI_M-protein_C cd05891
C-terminal immunoglobulin (Ig)-like domain of M-protein; member of the I-set of Ig superfamily ...
172-248 2.80e-06

C-terminal immunoglobulin (Ig)-like domain of M-protein; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of M-protein (also known as myomesin-2). M-protein is a structural protein localized to the M-band, a transverse structure in the center of the sarcomere, and is a candidate for M-band bridges. M-protein is modular consisting mainly of repetitive IG-like and fibronectin type III (FnIII) domains and has a muscle-type specific expression pattern. M-protein is present in fast fibers.


Pssm-ID: 143299  Cd Length: 92  Bit Score: 46.44  E-value: 2.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 172 MDKKllavpaanTVRFRCPAAGNPTPSISWLKNGREFR-GEHRIggIKLRHQQW-SLVMESVVPSDRGNYTCVVENKFG 248
Cdd:cd05891   14 MEGK--------TLNLTCTVFGNPDPEVIWFKNDQDIElSEHYS--VKLEQGKYaSLTIKGVTSEDSGKYSINVKNKYG 82
IgI_Myomesin_like_C cd05737
C-terminal immunoglobulin (Ig)-like domain of myomesin and M-protein; member of the I-set of ...
184-258 2.99e-06

C-terminal immunoglobulin (Ig)-like domain of myomesin and M-protein; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of myomesin and M-protein (also known as myomesin-2). Myomesin and M-protein are both structural proteins localized to the M-band, a transverse structure in the center of the sarcomere, and are candidates for M-band bridges. Both proteins are modular, consisting mainly of repetitive Ig-like and fibronectin type III (FnIII) domains. Myomesin is expressed in all types of vertebrate striated muscle; M-protein has a muscle-type specific expression pattern. Myomesin is present in both slow and fast fibers; M-protein is present only in fast fibers. It has been suggested that myomesin acts as a molecular spring with alternative splicing as a means of modifying its elasticity.


Pssm-ID: 319300  Cd Length: 92  Bit Score: 46.43  E-value: 2.99e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQW-SLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05737   18 TLNLTCNVWGDPPPEVSWLKNDQALAFLDHC-NLKVEAGRTvYFTINGVSSEDSGKYGLVVKNKYGSETSDVTVSV 92
Ig3_L1-CAM_like cd05731
Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar ...
275-369 3.13e-06

Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar domains; The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, and spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM and human neurofascin.


Pssm-ID: 409394 [Multi-domain]  Cd Length: 83  Bit Score: 45.86  E-value: 3.13e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 275 NQTAVLGSDVEFHCKVYSDAQPHIQWLKhveVNGSkvgpdgTPyvtvlktAGANTTDKELEVLSLHNVTFEDAGEYTCLA 354
Cdd:cd05731    4 STMVLRGGVLLLECIAEGLPTPDIRWIK---LGGE------LP-------KGRTKFENFNKTLKIENVSEADSGEYQCTA 67
                         90
                 ....*....|....*
gi 311641796 355 GNSIGFSHHSAWLVV 369
Cdd:cd05731   68 SNTMGSARHTISVTV 82
IgI_2_Palladin_C cd20990
Second C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig ...
177-259 4.30e-06

Second C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of palladin. Palladin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to this family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Palladin binds to alpha-actinin ezrin, vasodilator-stimulated phosphoprotein VASP, SPIN90 (also known as DIP or mDia interacting protein), and Src. Palladin also binds F-actin directly, via its Ig3 domain. Palladin is expressed as several alternatively spliced isoforms, having various combinations of Ig-like domains, in a cell-type-specific manner. It has been suggested that palladin's different Ig-like domains may be specialized for distinct functions. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409582  Cd Length: 91  Bit Score: 45.86  E-value: 4.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGsiRQTYTL 256
Cdd:cd20990   10 LTVQEGKLCRMDCKVSGLPTPDLSWQLDGKPIRPDSAHKMLVRENGVHSLIIEPVTSRDAGIYTCIATNRAG--QNSFNL 87

                 ...
gi 311641796 257 DVL 259
Cdd:cd20990   88 ELV 90
IgI_titin_I1-like cd20951
Immunoglobulin domain I1 of the titin I-band and similar proteins; a member of the I-set of ...
276-369 4.56e-06

Immunoglobulin domain I1 of the titin I-band and similar proteins; a member of the I-set of IgSF domains; The members here are composed of the immunoglobulin domain I1 of the titin I-band and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The Ig I1 domain of the titin I-band is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409543 [Multi-domain]  Cd Length: 94  Bit Score: 45.87  E-value: 4.56e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 276 QTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYVTVLKTAGAnttdkeLEVLSLHNVTFEDAGEYTCLAG 355
Cdd:cd20951   10 HTVWEKSDAKLRVEVQGKPDPEVKWYK----NGVPIDPSSIPGKYKIESEYG------VHVLHIRRVTVEDSAVYSAVAK 79
                         90
                 ....*....|....
gi 311641796 356 NSIGFSHHSAWLVV 369
Cdd:cd20951   80 NIHGEASSSASVVV 93
Ig4_L1-NrCAM_like cd04978
Fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), ...
184-259 4.58e-06

Fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), and NrCAM (Ng-CAM-related); The members here are composed of the fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), and NrCAM (Ng-CAM-related). These proteins belong to the L1 subfamily of cell adhesion molecules (CAMs) and are comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. These molecules are primarily expressed in the nervous system. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth.


Pssm-ID: 409367 [Multi-domain]  Cd Length: 89  Bit Score: 45.52  E-value: 4.58e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQqwSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDVL 259
Cdd:cd04978   16 TGELICEAEGNPQPTITWRLNGVPIEPAPEDMRRTVDGR--TLIFSNLQPNDTAVYQCNASNVHGYLLANAFLHVL 89
IgI_2_MuSK cd20968
agrin-responsive second immunoglobulin-like domains (Ig2) of the Muscle-specific kinase (MuSK) ...
189-249 4.94e-06

agrin-responsive second immunoglobulin-like domains (Ig2) of the Muscle-specific kinase (MuSK) ectodomain; a member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin-like (Ig) domains of the Muscle-specific kinase (MuSK) ectodomain. MuSK is a receptor tyrosine kinase specifically expressed in skeletal muscle, where it plays a central role in the formation and maintenance of the neuromuscular junction (NMJ). MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. The activation of MUSK in myotubes regulates the formation of NMJs through the regulation of different processes including the specific expression of genes in subsynaptic nuclei, the reorganization of the actin cytoskeleton and the clustering of the acetylcholine receptors (AChR) in the postsynaptic membrane. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the MuSK lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409560 [Multi-domain]  Cd Length: 88  Bit Score: 45.70  E-value: 4.94e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 311641796 189 CPAAGNPTPSISWLKNGREFRGEHRIGGIklrhQQWSLVMESVVPSDRGNYTCVVENKFGS 249
Cdd:cd20968   21 CTTMGNPKPSVSWIKGDDLIKENNRIAVL----ESGSLRIHNVQKEDAGQYRCVAKNSLGI 77
IgI_2_RPTP_IIa_LAR_like cd05738
Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F; ...
172-249 5.14e-06

Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F; member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain found in the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. LAR belongs to the RPTP type IIa subfamily. Members of this subfamily are cell adhesion molecule-like proteins involved in central nervous system (CNS) development. They have large extracellular portions comprised of multiple Ig-like domains and two to nine fibronectin type III (FNIII) domains and a cytoplasmic portion having two tandem phosphatase domains.


Pssm-ID: 409400 [Multi-domain]  Cd Length: 91  Bit Score: 45.77  E-value: 5.14e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 172 MDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRhQQWSLVMESVVPSDRGNYTCVVENKFGS 249
Cdd:cd05738    4 MGPQLKVVEKARTATMLCAASGNPDPEISWFKDFLPVDTATSNGRIKQL-RSGALQIENSEESDQGKYECVATNSAGT 80
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
516-610 5.33e-06

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409590  Cd Length: 99  Bit Score: 45.92  E-value: 5.33e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 516 PR--EPQVyTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN-YKTTPPVLDSDGSFflySKLTVDKSRWQQ 592
Cdd:cd20998    2 PRrvEPTV-TVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTgIVSTGLVRNGDWTF---QTLVMLETVPQS 77
                         90
                 ....*....|....*...
gi 311641796 593 GNVFSCSVMHEALHNHYT 610
Cdd:cd20998   78 GEVYTCQVEHPSLTDPVT 95
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
513-605 5.43e-06

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the C1-set of Ig superfamily (IgSF) domains; The non-classical mouse MHC class I (MHC-I) molecule Qa-1b is a non-polymorphic MHC molecule with an important function in innate immunity. It binds and presents signal peptides of classical MHC-I molecules at the cell surface and, as such, act as an indirect sensor for the normal expression of MHC-I molecules. This signal peptide dominantly accommodated in the groove of Qa-1b is called Qdm, for Qa-1 determinant modifier, and its amino acid sequence AMAPRTLLL is highly conserved among mammalian species. The Qdm/Qa-1b complex serves as a ligand for the germ-line encoded heterodimeric CD94/NKG2A receptors expressed on natural killer (NK) cells and activated CD8+ T cells and transduces inhibitory signals to these lymphocytes. Thus, upon binding, Qa-1b signals NK cells not to engage in cell lysis. The molecular basis of Qa-1b function is unclear.


Pssm-ID: 409625  Cd Length: 98  Bit Score: 45.91  E-value: 5.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 513 KGQPREPQVYTLPPSRDELTknqvsLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKS 588
Cdd:cd21820    2 RSDPPKAHVTHHPRSEDEVT-----LRCWALGFYPADITLTWQLNGeeltQDMELVETRPA---GDGTFQKWAAVVVPLG 73
                         90
                 ....*....|....*..
gi 311641796 589 RWQqgnVFSCSVMHEAL 605
Cdd:cd21820   74 KEQ---YYTCHVYHEGL 87
IgI_3_WFIKKN-like cd05765
Third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz ...
178-258 5.57e-06

Third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz and NTR domain-containing protein), and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz and NTR domain-containing protein) and similar proteins. WFIKKN is a secreted protein that consists of multiple types of protease inhibitory modules, including two tandem Kunitz-type protease inhibitor-domains. The Ig superfamily is a heterogenous group of proteins built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409422 [Multi-domain]  Cd Length: 95  Bit Score: 45.62  E-value: 5.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 178 AVPAANTVRFRCPAAGNPTPSISWLKN--GRE---FRGEHRIGGIKLRHQQwSLVMESVVPSDRGNYTCVVENKFGSIRQ 252
Cdd:cd05765   11 TVKVGETASFHCDVTGRPQPEITWEKQvpGKEnliMRPNHVRGNVVVTNIG-QLVIYNAQPQDAGLYTCTARNSGGLLRA 89

                 ....*.
gi 311641796 253 TYTLDV 258
Cdd:cd05765   90 NFPLSV 95
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
782-858 5.57e-06

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 45.94  E-value: 5.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 782 GQRVTISCSgsSSNIGRNPVNWYQQLPGTAPK---LLIYGDNQRPSGVPD----RFSGSKSGTSASLAISGLQSEDEADY 854
Cdd:cd05720   13 GQKVELVCE--VLNSVPQGCSWLFQPRGSAPQptfLLYLSSSNKTKWAEGldskRFSGSRSGSSYVLTLKDFRKEDEGYY 90

                 ....
gi 311641796 855 YCAA 858
Cdd:cd05720   91 FCSV 94
IgI_6_Dscam cd20959
Sixth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
193-258 5.87e-06

Sixth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the sixth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409551  Cd Length: 94  Bit Score: 45.56  E-value: 5.87e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 193 GNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd20959   29 GDLPLNIRWTLDGQPISDDLGITVSRLGRRSSILSIDSLEASHAGNYTCHARNSAGSASYTAPLTV 94
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
410-522 6.30e-06

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 45.83  E-value: 6.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 410 APSVFLFPPKPKDtlmISRTPEVTCVVVdVSHEDPE-VKFNWYVDGVEVH-NAKTKP---REEqyNSTYRVVSVLTVLHQ 484
Cdd:cd05769    2 PPTVALFPPSEAE---IRNKRKATLVCL-ATGFYPDhVSLSWKVNGKEVKdGVATDPqalREN--TSTYSLSSRLRVSAT 75
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 311641796 485 DWLN-GKEYKCKVS--NKALPSSIEKTISKAKGQPREPQVY 522
Cdd:cd05769   76 EWFNpRNTFTCIVKfyGGTDTDTWTQGIAGPVTCGVSAEEL 116
IgI_2_Titin_Z1z2-like cd20972
Second Ig-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk, and ...
169-249 6.67e-06

Second Ig-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the titin Z1z2 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409564 [Multi-domain]  Cd Length: 91  Bit Score: 45.27  E-value: 6.67e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 169 PERMDKKL--LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQWSLVMESVVPSDRGNYTCVVENK 246
Cdd:cd20972    1 PPQFIQKLrsQEVAEGSKVRLECRVTGNPTPVVRWFCEGKELQNSPDI-QIHQEGDLHSLIIAEAFEEDTGRYSCLATNS 79

                 ...
gi 311641796 247 FGS 249
Cdd:cd20972   80 VGS 82
IgI_2_Robo cd05724
Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
190-248 7.33e-06

Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of the Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit-2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409389 [Multi-domain]  Cd Length: 87  Bit Score: 45.08  E-value: 7.33e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 190 PAAGNPTPSISWLKNGREFRGEHRigGIKLRHQQwSLVMESVVPSDRGNYTCVVENKFG 248
Cdd:cd05724   21 PPRGHPEPTVSWRKDGQPLNLDNE--RVRIVDDG-NLLIAEARKSDEGTYKCVATNMVG 76
IgC1_CH1_IgD cd16092
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member ...
536-604 7.86e-06

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of delta chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 319341  Cd Length: 96  Bit Score: 45.22  E-value: 7.86e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 311641796 536 VSLTCLVKGFYPSDIAVEWE--SNGQPEnnyKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNvFSCSVMHEA 604
Cdd:cd16092   20 VVLACLITGYHPTSVTVTWYmgTQSQPQ---RTFPEIQRRDSYYMTSSQLSTPLQQWRQGE-YKCVVQHTA 86
IgI_3_NCAM-1 cd05730
Third immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule 1 (NCAM-1); member of ...
184-258 8.52e-06

Third immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule 1 (NCAM-1); member of the I-set of IgSF domains; The members here are composed of the third immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule (NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-non-NCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions) through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain.


Pssm-ID: 143207 [Multi-domain]  Cd Length: 95  Bit Score: 44.92  E-value: 8.52e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRigGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05730   20 SVTLACDADGFPEPTMTWTKDGEPIESGEE--KYSFNEDGSEMTILDVDKLDEAEYTCIAENKAGEQEAEIHLKV 92
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
532-605 8.53e-06

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld. H-2Ld complexed with peptide QL9 (or p2Ca) and complexed with influenza virus peptide NP366-374 (ASNEN-METM), respectively are high-affinity alloantigens for the 2C T cell receptor (TCR). The a1-a2 super domains of H-2Ld, H-2Db, and H-2Kb closely superimpose. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409609  Cd Length: 95  Bit Score: 45.12  E-value: 8.53e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 532 TKNQVSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21018   16 SKGEVTLRCWALGFYPADITLTWQLNGeeltQDMELVETRPA---GDGTFQKWASVVVPLGKEQN---YTCRVYHEGL 87
IgI_3_WFIKKN-like cd05765
Third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz ...
273-359 9.07e-06

Third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz and NTR domain-containing protein), and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz and NTR domain-containing protein) and similar proteins. WFIKKN is a secreted protein that consists of multiple types of protease inhibitory modules, including two tandem Kunitz-type protease inhibitor-domains. The Ig superfamily is a heterogenous group of proteins built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409422 [Multi-domain]  Cd Length: 95  Bit Score: 44.85  E-value: 9.07e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVevngskvgPDGTPYVTVLKTAGANTTDKELEVLSLHNVTFEDAGEYTC 352
Cdd:cd05765    7 PTHQTVKVGETASFHCDVTGRPQPEITWEKQV--------PGKENLIMRPNHVRGNVVVTNIGQLVIYNAQPQDAGLYTC 78

                 ....*..
gi 311641796 353 LAGNSIG 359
Cdd:cd05765   79 TARNSGG 85
IgI_4_Neogenin_like cd05723
Fourth immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set ...
273-369 9.79e-06

Fourth immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the fourth immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC which is deleted in colorectal carcinoma. DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409388  Cd Length: 84  Bit Score: 44.49  E-value: 9.79e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPdgTPYVTVLKtaganttDKELEVLSLhnvTFEDAGEYTC 352
Cdd:cd05723    4 PSNIYAHESMDIVFECEVTGKPTPTVKWVK----NGDVVIP--SDYFKIVK-------EHNLQVLGL---VKSDEGFYQC 67
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd05723   68 IAENDVGNAQASAQLII 84
IgC1_CH2_IgD cd16084
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; ...
521-605 1.03e-05

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin constant domain (IgC) in delta heavy chains. The IgC family includes immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409506  Cd Length: 97  Bit Score: 44.74  E-value: 1.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 521 VYTLPPSRDEL-TKNQVSLTCLVKGFYPSDIAVEWESNGQ-PENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSC 598
Cdd:cd16084    2 VYLLTPAVQDLwLRDKATFTCFVVGSDLKDAHLTWEVAGKvPTGGVEEGLLERHSNGSQSQHSRLTLPRSLWNAGTSVTC 81

                 ....*..
gi 311641796 599 SVMHEAL 605
Cdd:cd16084   82 TLNHPSL 88
Ig_2 pfam13895
Immunoglobulin domain; This domain contains immunoglobulin-like domains.
179-255 1.27e-05

Immunoglobulin domain; This domain contains immunoglobulin-like domains.


Pssm-ID: 464026 [Multi-domain]  Cd Length: 79  Bit Score: 43.92  E-value: 1.27e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796  179 VPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRiggiklrhqqwsLVMESVVPSDRGNYTCVVENKFGSIRQTYT 255
Cdd:pfam13895  11 VTEGEPVTLTCSAPGNPPPSYTWYKDGSAISSSPN------------FFTLSVSAEDSGTYTCVARNGRGGKVSNPV 75
IgI_NCAM-1 cd05869
Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1); The members ...
178-258 1.29e-05

Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1); The members here are composed of the fourth Ig domain of Neural Cell Adhesion Molecule 1(NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM) and heterophilic (NCAM-non-NCAM) interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. One of the unique features of I-set domains is the lack of a C" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains.


Pssm-ID: 143277 [Multi-domain]  Cd Length: 97  Bit Score: 44.59  E-value: 1.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 178 AVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRI--GGIKLRH--QQWSLVMESVVPSDRGNYTCVVENKFGSIRQT 253
Cdd:cd05869   13 AMELEEQITLTCEASGDPIPSITWRTSTRNISSEEKTldGHIVVRShaRVSSLTLKYIQYTDAGEYLCTASNTIGQDSQS 92

                 ....*
gi 311641796 254 YTLDV 258
Cdd:cd05869   93 MYLEV 97
Ig_Titin_like cd05748
Immunoglobulin (Ig)-like domain of titin and similar proteins; The members here are composed ...
179-258 1.48e-05

Immunoglobulin (Ig)-like domain of titin and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain found in titin-like proteins and similar proteins. Titin (also called connectin) is a fibrous sarcomeric protein specifically found in vertebrate striated muscle. Titin is a giant protein; depending on isoform composition, it ranges from 2970 to 3700 kDa, and is of a length that spans half a sarcomere. Titin largely consists of multiple repeats of Ig-like and fibronectin type 3 (FN-III)-like domains. Titin connects the ends of myosin thick filaments to Z disks and extends along the thick filament to the H zone. It appears to function similarly to an elastic band, keeping the myosin filaments centered in the sarcomere during muscle contraction or stretching. Within the sarcomere, titin is also attached to or is associated with myosin binding protein C (MyBP-C). MyBP-C appears to contribute to the generation of passive tension by titin and like titin has repeated Ig-like and FN-III domains. Also included in this group are worm twitchin and insect projectin, thick filament proteins of invertebrate muscle which also have repeated Ig-like and FN-III domains.


Pssm-ID: 409406 [Multi-domain]  Cd Length: 82  Bit Score: 44.12  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05748    4 VRAGESLRLDIPIKGRPTPTVTWSKDGQPLKETGRV-QIETTASSTSLVIKNAKRSDSGKYTLTLKNSAGEKSATINVKV 82
IgI_2_Dscam cd20953
Second immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
175-248 1.62e-05

Second immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. DSCAM is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409545  Cd Length: 95  Bit Score: 44.45  E-value: 1.62e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 175 KLLAVPAANTVRFRCPAAGNPTPSISWLKNgreFRGEHRIGGIKL--RHQQWS--LVMESVVPSDRGNYTCVVENKFG 248
Cdd:cd20953   11 QPLTVSSASSIALLCPAQGYPAPSFRWYKF---IEGTTRKQAVVLndRVKQVSgtLIIKDAVVEDSGKYLCVVNNSVG 85
Ig3_Peroxidasin cd05745
Third immunoglobulin (Ig)-like domain of peroxidasin; The members here are composed of the ...
184-258 1.92e-05

Third immunoglobulin (Ig)-like domain of peroxidasin; The members here are composed of the third immunoglobulin (Ig)-like domain in peroxidasin. Peroxidasin has a peroxidase domain and interacting extracellular motifs containing four Ig-like domains. It has been suggested that peroxidasin is secreted and has functions related to the stabilization of the extracellular matrix. It may play a part in various other important processes such as removal and destruction of cells which have undergone programmed cell death and protection of the organism against non-self.


Pssm-ID: 143222 [Multi-domain]  Cd Length: 74  Bit Score: 43.39  E-value: 1.92e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFrgehrigGIKLRHQQWS---LVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05745    4 TVDFLCEAQGYPQPVIAWTKGGSQL-------SVDRRHLVLSsgtLRISRVALHDQGQYECQAVNIVGSQRTVAQLTV 74
IgI_NCAM-1 cd05869
Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1); The members ...
275-369 2.14e-05

Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1); The members here are composed of the fourth Ig domain of Neural Cell Adhesion Molecule 1(NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM) and heterophilic (NCAM-non-NCAM) interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. One of the unique features of I-set domains is the lack of a C" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains.


Pssm-ID: 143277 [Multi-domain]  Cd Length: 97  Bit Score: 43.82  E-value: 2.14e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 275 NQTAV-LGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGP-DGTPYVTvlktagantTDKELEVLSLHNVTFEDAGEYTC 352
Cdd:cd05869   10 NQTAMeLEEQITLTCEASGDPIPSITWRTSTRNISSEEKTlDGHIVVR---------SHARVSSLTLKYIQYTDAGEYLC 80
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd05869   81 TASNTIGQDSQSMYLEV 97
IgC1_MHC_Ib_Qa-1 cd21013
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar ...
513-605 2.29e-05

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins. Qa-1 presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides derived from the TCR Vbeta8.2 of activated T cells also activates CD8+ regulatory T cells to control autoimmunity and maintain self-tolerance. Four allotypes of Qa-1 (Qa-1a-d) are expressed that are highly conserved in sequence but have several variations that could affect peptide binding to Qa-1 or TCR recognition. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409604  Cd Length: 97  Bit Score: 43.96  E-value: 2.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 513 KGQPREPQVYTLPPSRDELTknqvsLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSR 589
Cdd:cd21013    1 RSDPPKAHVTHHPRSEGYVT-----LRCWALGFYPADITLTWQLNGEEltqDMEFVETRPA--GDGTFQKWASVVVPLGK 73
                         90
                 ....*....|....*.
gi 311641796 590 WQQgnvFSCSVMHEAL 605
Cdd:cd21013   74 EQK---YTCHVEHEGL 86
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
410-509 2.69e-05

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409374  Cd Length: 98  Bit Score: 43.73  E-value: 2.69e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 410 APSVFLFPPKPKDTlmISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNG 489
Cdd:cd04985    1 APTVFPLQSATKSQ--SNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSG 78
                         90       100
                 ....*....|....*....|
gi 311641796 490 KEYKCKVSNKALPSSIEKTI 509
Cdd:cd04985   79 EVYKCQVQHSASNSKQEKDV 98
IgI_NCAM-1_like cd05732
Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1) and similar ...
189-258 3.39e-05

Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1) and similar proteins; The members here are composed of the fourth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule (NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-non-NCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. Also included in this group is NCAM-2 (also known as OCAM/mamFas II and RNCAM) NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE). One of the unique features of I-set domains is the lack of a C" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains.


Pssm-ID: 409395 [Multi-domain]  Cd Length: 96  Bit Score: 43.28  E-value: 3.39e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 189 CPAAGNPTPSISWLKNGREFRGEH-----RIgGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05732   23 CEAEGDPIPEITWRRATRGISFEEgdldgRI-VVRGHARVSSLTLKDVQLTDAGRYDCEASNRIGGDQQSMYLEV 96
IgI_2_Follistatin_like cd05736
Second immunoglobulin (Ig)-like domain of a Follistatin-related protein 5, and similar domains; ...
184-260 3.63e-05

Second immunoglobulin (Ig)-like domain of a Follistatin-related protein 5, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain found in human Follistatin-related protein 5 (FSTL5) and a follistatin-like molecule encoded by the CNS-related Mahya gene. Mahya genes have been retained in certain Bilaterian branches during evolution. They are conserved in Hymenoptera and Deuterostomes, but are absent from other metazoan species such as fruit fly and nematode. Mahya proteins are secretory, with a follistatin-like domain (Kazal-type serine/threonine protease inhibitor domain and EF-hand calcium-binding domain), two Ig-like domains, and a novel C-terminal domain. Mahya may be involved in learning and memory and in processing of sensory information in Hymenoptera and vertebrates. Follistatin is a secreted, multidomain protein that binds activins with high affinity and antagonizes their signaling.


Pssm-ID: 409399 [Multi-domain]  Cd Length: 93  Bit Score: 43.40  E-value: 3.63e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFrGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDVLE 260
Cdd:cd05736   17 EASLRCHAEGIPLPRVQWLKNGMDI-NPKLSKQLTLIANGSELHISNVRYEDTGAYTCIAKNEGGVDEDISSLFVED 92
IgI_hNeurofascin_like cd05875
Immunoglobulin (Ig)-like domain of human neurofascin (NF); member of the I-set of Ig ...
189-249 3.79e-05

Immunoglobulin (Ig)-like domain of human neurofascin (NF); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin (Ig)-like domain of human neurofascin (NF). NF belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and a cytoplasmic domain. NF has many alternatively spliced isoforms having different temporal expression patterns during development. NF participates in axon subcellular targeting and synapse formation, however little is known of the functions of the different isoforms. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lacks a C" strand.


Pssm-ID: 409459  Cd Length: 95  Bit Score: 43.43  E-value: 3.79e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 189 CPAAGNPTPSISWLKNGREFrgehRIGG---IKLRHQQWSLVMESV---VPSD-RGNYTCVVENKFGS 249
Cdd:cd05875   23 CEAKGNPVPTFHWTRNGKFF----NVAKdprVSMRRRSGTLVIDFRgggRPEDyEGEYQCFARNKFGT 86
IgI_4_Neogenin_like cd05723
Fourth immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set ...
185-256 3.81e-05

Fourth immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the fourth immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC which is deleted in colorectal carcinoma. DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409388  Cd Length: 84  Bit Score: 42.95  E-value: 3.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGR--------EFRGEHriggiklrhqqwSLVMESVVPSDRGNYTCVVENKFGSIRQTYTL 256
Cdd:cd05723   15 IVFECEVTGKPTPTVKWVKNGDvvipsdyfKIVKEH------------NLQVLGLVKSDEGFYQCIAENDVGNAQASAQL 82
Ig_C5_MyBP-C cd05894
C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C); The members here ...
179-258 3.83e-05

C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C); The members here are composed of the C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C). MyBP-C consists of repeated domains, Ig and fibronectin type 3, and various linkers. Three isoforms of MYBP-C exist: slow-skeletal (ssMyBP-C), fast-skeletal (fsMyBP-C), and cardiac (cMyBP-C). cMYBP-C has insertions between and inside domains and an additional cardiac-specific Ig domain at the N-terminus. For cMYBP_C an interaction has been demonstrated between this C5 domain and the Ig C8 domain.


Pssm-ID: 409475  Cd Length: 86  Bit Score: 42.90  E-value: 3.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGREFR-GEHRIgGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLD 257
Cdd:cd05894    7 VVAGNKLRLDVPISGEPAPTVTWSRGDKAFTaTEGRV-RVESYKDLSSFVIEGAEREDEGVYTITVTNPVGEDHASLFVK 85

                 .
gi 311641796 258 V 258
Cdd:cd05894   86 V 86
IgI_4_Dscam cd20956
Fourth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
184-258 4.67e-05

Fourth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fourth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409548 [Multi-domain]  Cd Length: 96  Bit Score: 42.93  E-value: 4.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHRIggiklRHQQW--------SLV-MESVVPSDRGNYTCVVENKFGSIRQTY 254
Cdd:cd20956   18 SVSLKCVASGNPLPQITWTLDGFPIPESPRF-----RVGDYvtsdgdvvSYVnISSVRVEDGGEYTCTATNDVGSVSHSA 92

                 ....
gi 311641796 255 TLDV 258
Cdd:cd20956   93 RINV 96
IgC1_MHC_Ia_H-2Kb cd21019
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the ...
519-605 4.74e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb. H-2Kb is an alloantigen for the 2C T cell receptor (TCR). H-2Kb forms a complex with beta-2-microglobulin, and a peptide, including VSV-8 (RGYVYNGL), SEV-9 (FAPGNYPAL), and OVA-8 (SIINFEKL). Comparison of the OVA-8, VSV-8, and SEV-9 complexes with H-2Kb indicates that four side chains (Lys-66, Glu-152, Arg-155, and Trp-167) adopt peptide-specific conformations. H-2Kb paralogs include H-2Db, H-2Kbml and H-2KbI1s. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409610  Cd Length: 94  Bit Score: 42.79  E-value: 4.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDEltkNQVSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQqgn 594
Cdd:cd21019    5 PKAHVTHHSRPE---DKVTLRCWALGFYPADITLTWQLNGeeliQDMELVETRPA---GDGTFQKWASVVVPLGKEQ--- 75
                         90
                 ....*....|.
gi 311641796 595 VFSCSVMHEAL 605
Cdd:cd21019   76 YYTCHVYHQGL 86
IgI_L1-CAM_like cd05733
Immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins; ...
175-249 5.28e-05

Immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains NrCAM [Ng(neuronglia)CAM-related cell adhesion molecule], which is primarily expressed in the nervous system, and human neurofascin. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lacks a C" strand.


Pssm-ID: 409396 [Multi-domain]  Cd Length: 94  Bit Score: 42.78  E-value: 5.28e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796 175 KLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQWSLVME--SVVPSD-RGNYTCVVENKFGS 249
Cdd:cd05733    9 KDYIVDPRDNITIKCEAKGNPQPTFRWTKDGKFFDPAKDP-RVSMRRRSGTLVIDnhNGGPEDyQGEYQCYASNELGT 85
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
273-370 5.38e-05

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 43.22  E-value: 5.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  273 PANQTAVLGSDVEFHCKV---YSDAQPHIQWLKHVEVNGSKV-----GPDGTPYVTVLKTAGANTTDKELEVLSLHNVTF 344
Cdd:pfam07686   3 PREVTVALGGSVTLPCTYsssMSEASTSVYWYRQPPGKGPTFliayySNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLTL 82
                          90       100
                  ....*....|....*....|....*..
gi 311641796  345 EDAGEYTC-LAGNSIGFSHHSAWLVVL 370
Cdd:pfam07686  83 SDSGTYTCaVIPSGEGVFGKGTRLTVL 109
Ig4_L1-CAM_like cd05867
Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM); The members ...
165-250 5.54e-05

Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM); The members here are composed of the fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, and spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM.


Pssm-ID: 409453 [Multi-domain]  Cd Length: 89  Bit Score: 42.57  E-value: 5.54e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 165 YWTRpeRMDKKLLAvpAANTVRFRCPAAGNPTPSISWLKNGREFRGehrIGGIKLRH-QQWSLVMESVVPSDRGNYTCVV 243
Cdd:cd05867    1 YWTR--RPQSHLYG--PGETARLDCQVEGIPTPNITWSINGAPIEG---TDPDPRRHvSSGALILTDVQPSDTAVYQCEA 73

                 ....*..
gi 311641796 244 ENKFGSI 250
Cdd:cd05867   74 RNRHGNL 80
IGc1 smart00407
Immunoglobulin C-Type;
432-503 5.98e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.92  E-value: 5.98e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796   432 VTCVVVDVSHEDPEVKfnWYVDGVEVH-NAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPS 503
Cdd:smart00407   4 LVCLVSGFYPPDITVT--WLRNGQEVTeGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKE 74
Ig4_Peroxidasin cd05746
Fourth immunoglobulin (Ig)-like domain of peroxidasin; The members here are composed of the ...
185-249 6.18e-05

Fourth immunoglobulin (Ig)-like domain of peroxidasin; The members here are composed of the fourth immunoglobulin (Ig)-like domain in peroxidasin. Peroxidasin has a peroxidase domain and interacting extracellular motifs containing four Ig-like domains. It has been suggested that peroxidasin is secreted, and has functions related to the stabilization of the extracellular matrix. It may play a part in various other important processes such as removal and destruction of cells which have undergone programmed cell death and protection of the organism against non-self.


Pssm-ID: 143223  Cd Length: 69  Bit Score: 41.78  E-value: 6.18e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGREF--RGEHRIGgiklrhQQWSLVMESVVPSDRGNYTCVVENKFGS 249
Cdd:cd05746    1 VQIPCSAQGDPEPTITWNKDGVQVteSGKFHIS------PEGYLAIRDVGVADQGRYECVARNTIGY 61
IgI_3_Contactin-1 cd05851
Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) ...
278-369 6.83e-05

Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains.


Pssm-ID: 143259  Cd Length: 88  Bit Score: 42.32  E-value: 6.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 278 AVLGSDVEFHCKVYSDAQPHIQWLKHVEvngskvgpdGTPYVTVLKTAGAnttdkeleVLSLHNVTFEDAGEYTCLAGNS 357
Cdd:cd05851   13 ALKGQNVTLECFALGNPVPVIRWRKILE---------PMPATAEISMSGA--------VLKIFNIQPEDEGTYECEAENI 75
                         90
                 ....*....|..
gi 311641796 358 IGFSHHSAWLVV 369
Cdd:cd05851   76 KGKDKHQARVYV 87
IgI_VEGFR-2 cd05864
Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 2 (VEGFR-2); ...
170-259 7.92e-05

Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 2 (VEGFR-2); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 2 (VEGFR-2). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGFR-2 (KDR/Flk-1) is a major mediator of the mitogenic, angiogenic and microvascular permeability-enhancing effects of VEGF-A; VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGF-A also interacts with VEGFR-1, which it binds more strongly than VEGFR-2. VEGFR-1 and VEGFR-2 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409450  Cd Length: 89  Bit Score: 42.22  E-value: 7.92e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 170 ERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRiggIKLRHqqwSLVMESVVPSDRGNYTCVVENKFGS 249
Cdd:cd05864    5 GSGMESLVEAKVGERVRIPVKYLGYPPPEIKWYKNGIPIESNHT---IKAGH---VLTIMEVTEKDAGNYTVVLTNPISK 78
                         90
                 ....*....|
gi 311641796 250 IRQTYTLDVL 259
Cdd:cd05864   79 EKQRHTFSLV 88
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
631-736 8.41e-05

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409369  Cd Length: 106  Bit Score: 42.38  E-value: 8.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 631 VQLLESGGGL-VQPGGSLRLSCAASGFTFSGYIMWWvRQAPGKglewvsviSP----SGGDTwYADSVKGRFTISrdNSK 705
Cdd:cd04980    1 IVMTQSPASLsVSPGERVTISCKASQSISSNYLAWY-QQKPGQ--------APklliYYAST-LHSGVPSRFSGS--GSG 68
                         90       100       110
                 ....*....|....*....|....*....|....
gi 311641796 706 NTLYLQMNSLRAEDTAVYYCATAGDY---WGQGT 736
Cdd:cd04980   69 TDFTLTISSVEPEDAAVYYCQQGYTFpytFGGGT 102
IgI_2_MuSK cd20968
agrin-responsive second immunoglobulin-like domains (Ig2) of the Muscle-specific kinase (MuSK) ...
273-359 9.27e-05

agrin-responsive second immunoglobulin-like domains (Ig2) of the Muscle-specific kinase (MuSK) ectodomain; a member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin-like (Ig) domains of the Muscle-specific kinase (MuSK) ectodomain. MuSK is a receptor tyrosine kinase specifically expressed in skeletal muscle, where it plays a central role in the formation and maintenance of the neuromuscular junction (NMJ). MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. The activation of MUSK in myotubes regulates the formation of NMJs through the regulation of different processes including the specific expression of genes in subsynaptic nuclei, the reorganization of the actin cytoskeleton and the clustering of the acetylcholine receptors (AChR) in the postsynaptic membrane. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the MuSK lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409560 [Multi-domain]  Cd Length: 88  Bit Score: 41.84  E-value: 9.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVevngskvgpdgtpyvTVLKtagANTTDKELEV--LSLHNVTFEDAGEY 350
Cdd:cd20968    6 PTNVTIIEGLKAVLPCTTMGNPKPSVSWIKGD---------------DLIK---ENNRIAVLESgsLRIHNVQKEDAGQY 67

                 ....*....
gi 311641796 351 TCLAGNSIG 359
Cdd:cd20968   68 RCVAKNSLG 76
IgC1_MHC_Ia_RT1-Aa cd21015
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the ...
533-612 9.91e-05

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa. While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, RT1-Aa and RT1-A1c, which are associated with TAP-A and TAP-B. The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409606  Cd Length: 95  Bit Score: 42.06  E-value: 9.91e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 533 KNQVSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEALHNH 608
Cdd:cd21015   16 EGDVTLRCWALGFYPADITLTWQLNGedltQDMELVETRPA---GDGTFQKWASVVVPLGKEQN---YTCRVEHEGLPKP 89

                 ....
gi 311641796 609 YTQK 612
Cdd:cd21015   90 LSQR 93
IgI_Lingo-1 cd20969
Immunoglobulin I-set domain of the Leucine-rich repeat and immunoglobin-like domain-containing ...
179-258 1.10e-04

Immunoglobulin I-set domain of the Leucine-rich repeat and immunoglobin-like domain-containing protein 1 (Lingo-1); The members here are composed of the immunoglobulin I-set (IgI) domain of the Leucine-rich repeat and immunoglobin-like domain-containing protein 1 (Lingo-1). Human Lingo-1 is a central nervous system-specific transmembrane glycoprotein also known as LERN-1, which functions as a negative regulator of neuronal survival, axonal regeneration, and oligodendrocyte differentiation and myelination. Lingo-1 is a key component of the Nogo receptor signaling complex (RTN4R/NGFR) in RhoA activation responsible for some inhibition of axonal regeneration by myelin-associated factors. The ligand-binding ectodomain of human Lingo-1 contains a bimodular, kinked structure composed of leucine-rich repeat (LRR) and immunoglobulin (Ig)-like modules. Diseases associated with Lingo-1 include mental retardation, autosomal recessive 64 and essential tremor. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the Lingo-1 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409561  Cd Length: 92  Bit Score: 41.99  E-value: 1.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGR-----EFRGEHRI---GGIKLRHQQwslvmesvvPSDRGNYTCVVENKFGSI 250
Cdd:cd20969   14 VDEGHTVQFVCRADGDPPPAILWLSPRKhlvsaKSNGRLTVfpdGTLEVRYAQ---------VQDNGTYLCIAANAGGND 84

                 ....*...
gi 311641796 251 RQTYTLDV 258
Cdd:cd20969   85 SMPAHLHV 92
IgI_TrKABC_d5 cd04971
Fifth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB, and TrkC; member of the I-set ...
193-253 1.31e-04

Fifth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB, and TrkC; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the fifth domain of Trk receptors TrkA, TrkB, and TrkC, an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share significant sequence homology and domain organization. The first three domains are leucine-rich domains while the fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrkA, TrkB, and TrkC mediate the trophic effects of the neurotrophin Nerve Growth Factor (NGF) family. TrkA is recognized by NGF. TrkB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. TrkC is recognized by NT-3. NT-3 is promiscuous as in some cell systems it activates TrkA and TrkB receptors. TrkA is a receptor found in all major NGF targets, including the sympathetic, trigeminal, and dorsal root ganglia, cholinergic neurons of the basal forebrain, and the striatum. TrKB transcripts are found throughout multiple structures of the central and peripheral nervous systems. The TrkC gene is expressed throughout the mammalian nervous system. This group belongs to the I-set of IgSF domains.


Pssm-ID: 409360  Cd Length: 96  Bit Score: 41.62  E-value: 1.31e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796 193 GNPTPSISWLKNGREFR-GEH---RIGGIKLRHQQWSLVMESVVPS--DRGNYTCVVENKFGSIRQT 253
Cdd:cd04971   24 GNPKPTLTWYHNGAVLNeSDYirtEIHYEAATPTEYHGCLKFDNPThvNNGNYTLVASNEYGQDSKS 90
Ig_Perlecan_like cd05743
Immunoglobulin (Ig)-like domain of the human basement membrane heparan sulfate proteoglycan ...
184-250 1.61e-04

Immunoglobulin (Ig)-like domain of the human basement membrane heparan sulfate proteoglycan perlecan and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain of the human basement membrane heparan sulfate proteoglycan perlecan, also known as HSPG2, and similar proteins. Perlecan consists of five domains: domain I has three putative heparan sulfate attachment sites, domain II has four LDL receptor-like repeats, and one Ig-like repeat, domain III resembles the short arm of laminin chains, domain IV has multiple Ig-like repeats (21 repeats in human perlecan), and domain V resembles the globular G domain of the laminin A chain and internal repeats of EGF. Perlecan may participate in a variety of biological functions including cell binding, LDL-metabolism, basement membrane assembly and selective permeability, calcium binding, and growth- and neurite-promoting activities.


Pssm-ID: 143220  Cd Length: 78  Bit Score: 40.94  E-value: 1.61e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFrGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSI 250
Cdd:cd05743    3 TVEFTCVATGVPTPIINWRLNWGHV-PDSARVSITSEGGYGTLTIRDVKESDQGAYTCEAINTRGMV 68
Ig5_Contactin cd04969
Fifth immunoglobulin (Ig) domain of contactin; The members here are composed of the fifth ...
278-369 1.66e-04

Fifth immunoglobulin (Ig) domain of contactin; The members here are composed of the fifth immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma.


Pssm-ID: 409358 [Multi-domain]  Cd Length: 89  Bit Score: 41.29  E-value: 1.66e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 278 AVLGSDVEFHCKVYSDAQPHIQWLKHVE--VNGSKVG--PDGTpyvtvlktaganttdkelevLSLHNVTFEDAGEYTCL 353
Cdd:cd04969   14 AAKGGDVIIECKPKASPKPTISWSKGTEllTNSSRICilPDGS--------------------LKIKNVTKSDEGKYTCF 73
                         90
                 ....*....|....*.
gi 311641796 354 AGNSIGFSHHSAWLVV 369
Cdd:cd04969   74 AVNFFGKANSTGSLSV 89
IgI_1_Contactin-1 cd05849
First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains; ...
185-253 1.66e-04

First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains; The members here are composed of the first immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains.


Pssm-ID: 409436 [Multi-domain]  Cd Length: 95  Bit Score: 41.48  E-value: 1.66e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGrefrgehriGGIKLRHQQWSLVMESVVPS------DRGNYTCVVENKFGSIRQT 253
Cdd:cd05849   22 VSVNCRARANPFPIYKWRKNN---------LDIDLTNDRYSMVGGNLVINnpdkykDAGRYVCIVSNIYGKVRSR 87
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
525-605 1.67e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of the murine H-2T-encoded T10, T22, and similar proteins. T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. Classical MHC class I (class Ia) molecules participate in immune responses by presenting peptide antigens to cytolytic alpha beta T cells. Many nonclassical MHC class I (class Ib) molecules have distinct antigen-binding capabilities, suggesting that they have evolved for specific tasks that are distinct from those of MHC class Ia. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409607  Cd Length: 97  Bit Score: 41.62  E-value: 1.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 525 PP----SRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSRWQQgnvFS 597
Cdd:cd21016    5 PPkahvTRHPRPEGDVTLRCWALGFYPADITLTWQKDGEEltqDMEFVETRPA--GDGTFQKWAAVVVPLGKEQS---YT 79

                 ....*...
gi 311641796 598 CSVMHEAL 605
Cdd:cd21016   80 CHVYHEGL 87
Ig4_NrCAM cd05868
Fourth immunoglobulin (Ig)-like domain of NrCAM (NgCAM-related cell adhesion molecule); The ...
165-259 2.44e-04

Fourth immunoglobulin (Ig)-like domain of NrCAM (NgCAM-related cell adhesion molecule); The members here are composed of the fourth immunoglobulin (Ig)-like domain of NrCAM (NgCAM-related cell adhesion molecule). NrCAM belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six IG-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. NrCAM is primarily expressed in the nervous system.


Pssm-ID: 409454  Cd Length: 89  Bit Score: 40.73  E-value: 2.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 165 YWTRPERmdkKLLAVPAANTVRFrCPAAGNPTPSISWLKNGREFR-----GEHRIGGIklrhqqwSLVMESVVPSDRGNY 239
Cdd:cd05868    1 YWITAPT---NLVLSPGEDGTLI-CRANGNPKPSISWLTNGVPIEiaptdPSRKVDGD-------TIIFSKVQERSSAVY 69
                         90       100
                 ....*....|....*....|
gi 311641796 240 TCVVENKFGSIRQTYTLDVL 259
Cdd:cd05868   70 QCNASNEYGYLLANAFVNVL 89
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
531-605 2.83e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) F; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen alpha chain F (HLA-F). HLA-F, encoded by the HLA-F gene in humans, belongs to the non-classical HLA class I heavy chain paralogs. This class I molecule mainly exists as a heterodimer associated with the invariant light chain beta-2-microglobulin. HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409614  Cd Length: 98  Bit Score: 40.95  E-value: 2.83e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 531 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21023   15 ISDHEATLRCWALGFYPAEITLTWQRDGEEQTQdtelVETRPA---GDGTFQKWAAVVVPPGEEQR---YTCHVQHEGL 87
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
533-605 3.00e-04

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd. Mouse MHC is composed of 11 subclasses. It includes the classical MHC class I (MHC-Ia) that comprises H-2D, H-2K and H-2L subclasses, the non-classical MHC class I (MHCIb) that comprises H-2Q, H-2M and H-2T subclasses, the classical MHC class II (MHC-IIa) that includes H-2A(I-A) and H-2E(I-E) subclasses, and the non-classical MHC class II (MHC-IIb) comprises H-2M and H-2O. H-2K, H-2D, and H-2L are 80 to 90% homologous at the amino acid level yet appear to be involved in different recognition reactions and are differentially expressed on lymphoid cells. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409611  Cd Length: 95  Bit Score: 40.90  E-value: 3.00e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 533 KNQVSLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21020   17 EGDVTLRCWALGFYPADITLTWQLNGEEltqEMELVETRPA--GDGTFQKWASVVVPLGKEQK---YTCHVEHEGL 87
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
411-509 3.02e-04

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant-1 set domain (IgC) of alpha heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409375  Cd Length: 96  Bit Score: 40.83  E-value: 3.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 411 PSVFLFPPKPKDtLMISRTPEVTCVVVDVshEDPE-VKFNWYVDGVEvhNAKTKPREEQYNSTYRVVSVLTVLHQDWLNG 489
Cdd:cd04986    2 PRLSLQRPALED-LLLGSNASLTCTLSGL--KDPEgATFTWEPSGGK--EAIQGPPERDSCGCYSVSSVLPGCAEPWNSG 76
                         90       100
                 ....*....|....*....|
gi 311641796 490 KEYKCKVSNKALPSSIEKTI 509
Cdd:cd04986   77 DTFSCTVTHPESKGTLTATI 96
IgI_Twitchin_like cd20949
C-terminal immunoglobulin-like domain of the myosin-associated giant protein kinase Twitchin, ...
187-248 3.15e-04

C-terminal immunoglobulin-like domain of the myosin-associated giant protein kinase Twitchin, and similar domains; member of the I-set IgSF domains; The members here are composed of the C-terminal immunoglobulin-like domain of the myosin-associated giant protein kinase Twitchin and similar proteins, including Caenorhabditis elegans and Aplysia californica Twitchin, Drosophila melanogaster Projectin, and similar proteins. These are very large muscle proteins containing multiple immunoglobulin (Ig)-like and fibronectin type III (FN3) domains and a single kinase domain near the C-terminus. In humans these proteins are called Titin. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The Ig-like domain of the Twitchin is a member of the I-set IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins (titin, telokin, and twitchin), the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D.


Pssm-ID: 409541 [Multi-domain]  Cd Length: 89  Bit Score: 40.39  E-value: 3.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 311641796 187 FRCPAAGNPTPSISWLKNGREFRGEHRIGGiKLRHQQWSLVMESVVPSDRGNYTCVVENKFG 248
Cdd:cd20949   19 ILCEVKGEPQPNVTWHFNGQPISASVADMS-KYRILADGLLINKVTQDDTGEYTCRAYQVNS 79
IgI_Myotilin_C_like cd05744
Immunoglobulin (Ig)-like domain of myotilin, palladin, and myopalladin; member of the I-set of ...
273-369 3.56e-04

Immunoglobulin (Ig)-like domain of myotilin, palladin, and myopalladin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in myotilin, palladin, and myopalladin. Myotilin, palladin, and myopalladin function as scaffolds that regulate actin organization. Myotilin and myopalladin are most abundant in skeletal and cardiac muscle; palladin is ubiquitously expressed in the organs of developing vertebrates and plays a key role in cellular morphogenesis. The three family members each interact with specific molecular partners with all three binding to alpha-actinin; In addition, palladin also binds to vasodilator-stimulated phosphoprotein (VASP) and ezrin, myotilin binds to filamin and actin, and myopalladin also binds to nebulin and cardiac ankyrin repeat protein (CARP). This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409405 [Multi-domain]  Cd Length: 91  Bit Score: 40.17  E-value: 3.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLkhveVNGSKVGPDGTpYVTVLKTAGANTtdkelevLSLHNVTFEDAGEYTC 352
Cdd:cd05744    7 PGDLEVQEGRLCRFDCKVSGLPTPDLFWQ----LNGKPVRPDSA-HKMLVRENGRHS-------LIIEPVTKRDAGIYTC 74
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd05744   75 IARNRAGENSFNAELVV 91
IgI_3_hemolin-like cd20977
Third immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set ...
169-248 3.59e-04

Third immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the third immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The third Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM).


Pssm-ID: 409569  Cd Length: 93  Bit Score: 40.45  E-value: 3.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 169 PERMDKKLLAVPAANTVRFrCPAAGNPTPSISWLKNGREF--RGEHRIGgiklRHQQWS---LVMESVVPSDRGNYTCVV 243
Cdd:cd20977    3 PQYVSKDMMAKAGDVTMIY-CMYGSNPTAHPNYFKNGKDVngNPEDRIT----RHNRTSgkrLLFKTTLPEDEGVYTCEV 77

                 ....*
gi 311641796 244 ENKFG 248
Cdd:cd20977   78 DNGVG 82
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
516-607 3.64e-04

Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 2 (C1 repeat 1). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains, a single V-set and two C1-set IgSF domains. Their cytoplasmic tails contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47, but with much less affinity.


Pssm-ID: 409429  Cd Length: 102  Bit Score: 40.77  E-value: 3.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 516 PREPQVyTLPPSRDELTKnQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTT-PPVLDSDgSFFLYSKLTVDKSRWQQGN 594
Cdd:cd05772    2 PSQPLV-SGPSGRATPGQ-TVSFTCKSHGFSPRDITLKWFKNGNELSALQTTvFPEGDSV-SYSVSSTVQVVLTKDDVHS 78
                         90
                 ....*....|...
gi 311641796 595 VFSCSVMHEALHN 607
Cdd:cd05772   79 QLTCEVAHVTLQA 91
IgI_2_FGFRL1-like cd05856
Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1 ...
280-359 3.83e-04

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1); member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 is comprised of a signal peptide, three extracellular Ig-like modules, a transmembrane segment, and a short intracellular domain. FGFRL1 is expressed preferentially in skeletal tissues. Similar to FGF receptors, the expressed protein interacts specifically with heparin and with FGF2. FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors.


Pssm-ID: 409442  Cd Length: 92  Bit Score: 40.23  E-value: 3.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 280 LGSDVEFHCKVYSDAQPHIQWLKhvevngskvgpDGTPYVTvlKTAGANTTDKEleVLSLHNVTFEDAGEYTCLAGNSIG 359
Cdd:cd05856   18 VGSSVRLKCVASGNPRPDITWLK-----------DNKPLTP--PEIGENKKKKW--TLSLKNLKPEDSGKYTCHVSNRAG 82
IgI_2_KIRREL3-like cd05759
Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar ...
404-510 4.36e-04

Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and Drosophila RST (irregular chiasm C-roughest) protein. These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development.


Pssm-ID: 409416  Cd Length: 98  Bit Score: 40.13  E-value: 4.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 404 APEAEGAPSVFLFPPKPKDtlmisrtpeVTCVVvdvSHEDPEVKFNWYVDGVEVHNA---KTKPREEQYNSTyrvVSVLT 480
Cdd:cd05759    1 DPVIEGGPVISLQAGVPYN---------LTCRA---RGAKPAAEIIWFRDGEQLEGAvysKELLKDGKRETT---VSTLL 65
                         90       100       110
                 ....*....|....*....|....*....|
gi 311641796 481 VLHQDWLNGKEYKCKVSNKALPSSIEKTIS 510
Cdd:cd05759   66 ITPSDLDTGRTFTCRARNEAIPNGKETSIT 95
IgI_1_Neogenin_like cd05722
First immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set of ...
164-250 4.52e-04

First immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC which is deleted in colorectal carcinoma. DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409387  Cd Length: 97  Bit Score: 40.15  E-value: 4.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 164 PYWTRPERMDkkLLAVPAANTVrFRCPAAGNPTPSISWLKNgrefrGEHRIGGIKLRHQQW---SLVMESVVPS-----D 235
Cdd:cd05722    1 ELYFLSEPSD--IVAMRGGPVV-LNCSAESDPPPKIEWKKD-----GVLLNLVSDERRQQLpngSLLITSVVHSkhnkpD 72
                         90
                 ....*....|....*.
gi 311641796 236 RGNYTCVVENK-FGSI 250
Cdd:cd05722   73 EGFYQCVAQNEsLGSI 88
IgC1_CH2_IgA cd04986
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
518-602 4.87e-04

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant-1 set domain (IgC) of alpha heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409375  Cd Length: 96  Bit Score: 40.06  E-value: 4.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 518 EPQVYTLPPS-RDELTKNQVSLTCLVKGFYPSDIAV-EWESNGqpENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNV 595
Cdd:cd04986    1 QPRLSLQRPAlEDLLLGSNASLTCTLSGLKDPEGATfTWEPSG--GKEAIQGPPERDSCGCYSVSSVLPGCAEPWNSGDT 78

                 ....*..
gi 311641796 596 FSCSVMH 602
Cdd:cd04986   79 FSCTVTH 85
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
61-123 5.10e-04

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 39.87  E-value: 5.10e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 311641796   61 QLVFGSGDAVELSCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQR-----LQVLNASHEDSGAYSCR 123
Cdd:pfam00047   5 TVTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIESLKVKHDNGRttqssLLISNVTKEDAGTYTCV 72
IgI_5_Dscam cd20958
Fifth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
274-364 5.83e-04

Fifth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fifth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409550 [Multi-domain]  Cd Length: 89  Bit Score: 39.47  E-value: 5.83e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 274 ANQTAVLGSDVEFHCKV-----YSdaqphIQWLKhvevNGS--------KVGPDGTpyvtvlktaganttdkelevLSLH 340
Cdd:cd20958    8 GNLTAVAGQTLRLHCPVagypiSS-----ITWEK----DGRrlplnhrqRVFPNGT--------------------LVIE 58
                         90       100
                 ....*....|....*....|....*
gi 311641796 341 NVTF-EDAGEYTCLAGNSIGFSHHS 364
Cdd:cd20958   59 NVQRsSDEGEYTCTARNQQGQSASR 83
IgC1_MHC_Ib_Qa-2 cd21014
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the ...
536-605 6.02e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of QA-2. Qa-2 is a nonclassical MHC Ib antigen, which has been implicated in both innate and adaptive immune responses, as well as embryonic development. Qa-2 has an unusual peptide binding specificity in that it requires two dominant C-terminal anchor residues and is capable of associating with a substantially more diverse array of peptide sequences than other nonclassical MHC. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409605  Cd Length: 94  Bit Score: 39.73  E-value: 6.02e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 311641796 536 VSLTCLVKGFYPSDIAVEWESNG----QPENNYKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21014   19 VTLRCWALGFYPADITLTWQLNGeeltQDMELVETRPA---GDGTFQKWASVVVPLGKEQN---YTCHVNHEGL 86
IgC1_MHC_H-2_TLA cd21012
H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of ...
536-605 6.05e-04

H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the major histocompatibility complex (MHC) H-2 class I histocompatibility complex TLA (thymus leukemia antigen). The murine MHC class I histocompatibility TLA (Thymus leukemia antigen), which is encoded in the T region by T3 and T18 genes, is expressed mainly by intestinal epithelial cells and thymocytes. The murine TLAs are class I, beta-2-microglobulin-associated glycoproteins. The TLA function is not defined by antigen presentation, but rather by its relatively high affinity binding to CD8-alpha-alpha compared with CD8-alpha-beta. The existence of a human homolog for murine TLA remains unresolved. This group is a member of the C1-set Ig domains, which have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409603  Cd Length: 95  Bit Score: 39.71  E-value: 6.05e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 311641796 536 VSLTCLVKGFYPSDIAVEWESNGQP---ENNYKTTPPVldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21012   20 VTLRCWALGFYPAHITLTWQLNGEEliqDTELVETRPA--GDGTFQKWAAVVVPSGEEQK---YTCHVYHEGL 87
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
523-606 6.70e-04

CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.


Pssm-ID: 400489  Cd Length: 89  Bit Score: 39.32  E-value: 6.70e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796  523 TLPPSRDELTKNQVSLTCLVKGFYPsDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMH 602
Cdd:pfam08205   4 EPPASLLEGEGPEVVATCSSAGGKP-APRITWYLDGKPLEAAETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQVSY 82

                  ....
gi 311641796  603 EALH 606
Cdd:pfam08205  83 GALR 86
IgI_telokin-like cd20973
immunoglobulin-like domain of telokin and similar proteins; a member of the I-set of IgSF ...
275-369 7.28e-04

immunoglobulin-like domain of telokin and similar proteins; a member of the I-set of IgSF domains; The members here are composed of the immunoglobulin (Ig) domain in telokin, the C-terminal domain of myosin light chain kinase which is identical to telokin, and similar proteins. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the telokin Ig domain lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409565 [Multi-domain]  Cd Length: 88  Bit Score: 39.48  E-value: 7.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 275 NQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevngskvgpDGTPyvtvLKTAGANTTDKE---LEVLSLHNVTFEDAGEYT 351
Cdd:cd20973    6 DKEVVEGSAARFDCKVEGYPDPEVKWMK-----------DDNP----IVESRRFQIDQDedgLCSLIISDVCGDDSGKYT 70
                         90
                 ....*....|....*...
gi 311641796 352 CLAGNSIGFSHHSAWLVV 369
Cdd:cd20973   71 CKAVNSLGEATCSAELTV 88
IgI_2_Palladin_C cd20990
Second C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig ...
263-369 7.92e-04

Second C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of palladin. Palladin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to this family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Palladin binds to alpha-actinin ezrin, vasodilator-stimulated phosphoprotein VASP, SPIN90 (also known as DIP or mDia interacting protein), and Src. Palladin also binds F-actin directly, via its Ig3 domain. Palladin is expressed as several alternatively spliced isoforms, having various combinations of Ig-like domains, in a cell-type-specific manner. It has been suggested that palladin's different Ig-like domains may be specialized for distinct functions. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409582  Cd Length: 91  Bit Score: 39.31  E-value: 7.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 263 PHrpILQAglPANQTAVLGSDVEFHCKVYSDAQPHIQWlkhvEVNGSKVGPDgTPYVTVLKTAGANTtdkelevLSLHNV 342
Cdd:cd20990    1 PH--FLQA--PGDLTVQEGKLCRMDCKVSGLPTPDLSW----QLDGKPIRPD-SAHKMLVRENGVHS-------LIIEPV 64
                         90       100
                 ....*....|....*....|....*..
gi 311641796 343 TFEDAGEYTCLAGNSIGFSHHSAWLVV 369
Cdd:cd20990   65 TSRDAGIYTCIATNRAGQNSFNLELVV 91
IgI_1_Contactin cd04967
First immunoglobulin (Ig) domain of contactin; member of the I-set of (Ig) superfamily domains; ...
185-253 8.20e-04

First immunoglobulin (Ig) domain of contactin; member of the I-set of (Ig) superfamily domains; The members here are composed of the first immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains.


Pssm-ID: 409356 [Multi-domain]  Cd Length: 96  Bit Score: 39.53  E-value: 8.20e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGREFRGEhriggiklRHQQWSLVMESVVPS------DRGNYTCVVENKFGSIRQT 253
Cdd:cd04967   22 VALNCRARANPVPSYRWLMNGTEIDLE--------SDYRYSLVDGTLVISnpskakDAGHYQCLATNTVGSVLSR 88
Ig2_PTK7 cd05760
Second immunoglobulin (Ig)-like domain of protein tyrosine kinase (PTK) 7; The members here ...
184-260 8.80e-04

Second immunoglobulin (Ig)-like domain of protein tyrosine kinase (PTK) 7; The members here are composed of the second immunoglobulin (Ig)-like domain in protein tyrosine kinase (PTK) 7, also known as CCK4. PTK7 is a subfamily of the receptor protein tyrosine kinase family, and is referred to as an RPTK-like molecule. RPTKs transduce extracellular signals across the cell membrane and play important roles in regulating cell proliferation, migration, and differentiation. PTK7 is organized as an extracellular portion having seven Ig-like domains, a single transmembrane region, and a cytoplasmic tyrosine kinase-like domain. PTK7 is considered a pseudokinase as it has several unusual residues in some of the highly conserved tyrosine kinase (TK) motifs; it is predicted to lack TK activity. PTK7 may function as a cell-adhesion molecule. PTK7 mRNA is expressed at high levels in placenta, melanocytes, liver, lung, pancreas, and kidney. PTK7 is overexpressed in several cancers, including melanoma and colon cancer lines.


Pssm-ID: 409417  Cd Length: 95  Bit Score: 39.53  E-value: 8.80e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 184 TVRFRCPAAGNPTPSISWLKNGREFRGEHriGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSI--RQTYTLDVLE 260
Cdd:cd05760   18 RVTLRCHIDGHPRPTYQWFRDGTPLSDGQ--GNYSVSSKERTLTLRSAGPDDSGLYYCCAHNAFGSVcsSQNFTLSIID 94
Ig2_IL1R-like cd05757
Second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains; ...
194-243 9.89e-04

Second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains; The members here are composed of the second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R; also known as cluster of differentiation (CD) 121). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three IG-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. This group also contains ILIR-like 1 (IL1R1L) which maps to the same chromosomal location as IL1R1 and IL1R2.


Pssm-ID: 409415  Cd Length: 92  Bit Score: 39.23  E-value: 9.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 311641796 194 NPTPSISWLKNGREFRGEHRIGGIKLRhqqwsLVMESVVPSDRGNYTCVV 243
Cdd:cd05757   27 NVLPPIQWYKDCKPLQGDKRFIPKGSK-----LLIQNVTEEDAGNYTCKF 71
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
642-730 9.92e-04

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 39.78  E-value: 9.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 642 QPGGSLRLSCAASGFTFSGyiMWWVRQAPG--KGLEWVSVISPSGGDTWYADSVKGRFTISRDNSKNTLYLqmNSLRAED 719
Cdd:cd05720   11 QLGQKVELVCEVLNSVPQG--CSWLFQPRGsaPQPTFLLYLSSSNKTKWAEGLDSKRFSGSRSGSSYVLTL--KDFRKED 86
                         90
                 ....*....|.
gi 311641796 720 TAVYYCATAGD 730
Cdd:cd05720   87 EGYYFCSVISN 97
IgV_1_MRC-OX-2_like cd05846
First immunoglobulin (Ig) variable (V) domain of rat MRC OX-2 antigen, and similar domains; ...
275-353 1.03e-03

First immunoglobulin (Ig) variable (V) domain of rat MRC OX-2 antigen, and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200) and similar proteins. MRC OX-2 is a membrane glycoprotein expressed in a variety of lymphoid and non-lymphoid cells in rats. It has a similar broad distribution pattern in humans. MRC OX-2 may regulate myeloid cell activity. The protein has an extracellular portion containing two Ig-like domains, a transmembrane portion, and a cytoplasmic portion.


Pssm-ID: 409433  Cd Length: 108  Bit Score: 39.64  E-value: 1.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 275 NQTAVLGSDVEFHCKvYSDAQPHIQ--WLKHVEV-----------NGSKVGPdgtPYV--TVLKTAGANTTdkeleVLSL 339
Cdd:cd05846    7 DTRAVLGGNATLSCN-LTLPEEVLQvtWQKIKASspenivtyskkYGVKIQP---SYVrrISFTSSGLNST-----SITI 77
                         90
                 ....*....|....
gi 311641796 340 HNVTFEDAGEYTCL 353
Cdd:cd05846   78 WNVTLEDEGCYKCL 91
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
531-605 1.09e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-A gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. HLA-A2 is associated with spontaneous abortions, HIV, and Hodgkin lymphoma. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409618  Cd Length: 95  Bit Score: 39.05  E-value: 1.09e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 531 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21027   15 VSDHEATLRCWALSFYPAEITLTWQRDGEDQTQdtelVETRPA---GDGTFQKWAAVVVPSGQEQR---YTCHVQHEGL 87
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
641-740 1.16e-03

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409580  Cd Length: 114  Bit Score: 39.46  E-value: 1.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 641 VQPGGSLRLSCAASGFTFSGYIMWWVRQAPGKGLewvSVISPSGGDtwYADSVKGRFTISRDNSKNTLYLQMNSLRAEDT 720
Cdd:cd20988   10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTM---TFIYREGGI--YGPGFKDNFRGDIDSSNNLAVLKILEASERDE 84
                         90       100
                 ....*....|....*....|....*....
gi 311641796 721 AVYYCAT-----AGDY----WGQGTLVTV 740
Cdd:cd20988   85 GSYYCASdtpggGREYdpliFGKGTYLTV 113
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
531-605 1.19e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4. HLA-C belongs to the MHC class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and beta-2-microglobulin. The mature C chain is anchored in the membrane. MHC Class I molecules, like HLA-C, are expressed in nearly all cells, and present small peptides to the immune system which surveys for non-self peptides. HLA-C is a locus on chromosome 6, which encodes for a large number of HLA-C alleles that are Class-I MHC receptors. Class Ib histocompatibility leukocyte antigens (HLA)-Cw3 and (HLA)-Cw4 are ligands for the natural killer (NK) cell inhibitory receptors KIR2DL2 and KIR2DL1, respectively. HLA-Cw3 and related alleles (HLA-Cw1, -Cw7, and -Cw8) contain Ser77 and Asn80 and interact with KIR that are reactive with the GL183 antibody Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. HLA-Cw4 and related alleles (HLA-Cw2, -Cw5, and -Cw6) have Asn77 and Lys80 and are recognized by KIR reactive with the EB6 15 or HP-3E4 16 antibody. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409616  Cd Length: 96  Bit Score: 39.02  E-value: 1.19e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 531 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21025   15 VSDHEATLRCWALGFYPAEITLTWQWDGEDQTQdtelVETRPA---GDGTFQKWAAVVVPSGEEQR---YTCHVQHEGL 87
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
531-605 1.27e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E. HLA-E is the first human class Ib major histocompatibility complex molecule to be crystallized. Like other MHC class I molecules, HLA-E is a heterodimer consisting of an a heavy chain and light chain beta-2-microglobulin. HLA-E is highly conserved and almost nonpolymorphic, and has recently been shown to be the first specialized ligand for natural killer cell receptors. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409615  Cd Length: 95  Bit Score: 39.00  E-value: 1.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 531 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQqgnVFSCSVMHEAL 605
Cdd:cd21024   15 ISDHEATLRCWALGFYPAEITLTWQQDGEGHTQdtelVETRPA---GDGTFQKWAAVVVPSGEEQ---RYTCHVQHEGL 87
Ig4_Peroxidasin cd05746
Fourth immunoglobulin (Ig)-like domain of peroxidasin; The members here are composed of the ...
284-361 1.31e-03

Fourth immunoglobulin (Ig)-like domain of peroxidasin; The members here are composed of the fourth immunoglobulin (Ig)-like domain in peroxidasin. Peroxidasin has a peroxidase domain and interacting extracellular motifs containing four Ig-like domains. It has been suggested that peroxidasin is secreted, and has functions related to the stabilization of the extracellular matrix. It may play a part in various other important processes such as removal and destruction of cells which have undergone programmed cell death and protection of the organism against non-self.


Pssm-ID: 143223  Cd Length: 69  Bit Score: 37.93  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 284 VEFHCKVYSDAQPHIQWLKH-VEVNGS---KVGPDGTpyvtvlktaganttdkelevLSLHNVTFEDAGEYTCLAGNSIG 359
Cdd:cd05746    1 VQIPCSAQGDPEPTITWNKDgVQVTESgkfHISPEGY--------------------LAIRDVGVADQGRYECVARNTIG 60

                 ..
gi 311641796 360 FS 361
Cdd:cd05746   61 YA 62
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
535-605 1.40e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409613  Cd Length: 94  Bit Score: 38.97  E-value: 1.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 535 QVSLTCLVKGFYPSDIAVEWESNGQPENN----YKTTPPvldSDGSFFLYSKLTVDKSRWQQgnvFSCSVMHEAL 605
Cdd:cd21022   18 EATLRCWALGFYPAEIILTWQRDGEDQTQdvelVETRPA---GDGTFQKWAAVVVPSGEEQR---YTCHVQHEGL 86
IgI_4_Dscam cd20956
Fourth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
266-369 1.50e-03

Fourth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the fourth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409548 [Multi-domain]  Cd Length: 96  Bit Score: 38.70  E-value: 1.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 266 PILQAGLPaNQTAVLGSDVEFHCKVYSDAQPHIQWLkhveVNGSKVGPDG----TPYVTVLKtaganttdkelEVLSLHN 341
Cdd:cd20956    2 PVLLETFS-EQTLQPGPSVSLKCVASGNPLPQITWT----LDGFPIPESPrfrvGDYVTSDG-----------DVVSYVN 65
                         90       100       110
                 ....*....|....*....|....*....|.
gi 311641796 342 VT---FEDAGEYTCLAGNSIGFSHHSAWLVV 369
Cdd:cd20956   66 ISsvrVEDGGEYTCTATNDVGSVSHSARINV 96
Ig5_Contactin-1 cd05852
Fifth immunoglobulin (Ig) domain of contactin-1; The members here are composed of the fifth ...
172-258 1.55e-03

Fifth immunoglobulin (Ig) domain of contactin-1; The members here are composed of the fifth immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma.


Pssm-ID: 409438  Cd Length: 89  Bit Score: 38.44  E-value: 1.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 172 MDKKLLAVPAANTVrFRCPAAGNPTPSISWLKNGREFRGEHRIggikLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIR 251
Cdd:cd05852    8 MKKKILAAKGGRVI-IECKPKAAPKPKFSWSKGTELLVNNSRI----SIWDDGSLEILNITKLDEGSYTCFAENNRGKAN 82

                 ....*..
gi 311641796 252 QTYTLDV 258
Cdd:cd05852   83 STGVLSV 89
Ig_Sema3 cd05871
Immunoglobulin (Ig)-like domain of class III semaphorin Sema3; The members here are composed ...
195-261 1.63e-03

Immunoglobulin (Ig)-like domain of class III semaphorin Sema3; The members here are composed of the immunoglobulin (Ig)-like domain of Sema3 and similar proteins. Semaphorins are classified based on structural features additional to the Sema domain. Sema3 is a Class III semaphorin that is secreted. It is a vertebrate class having a Sema domain, an Ig domain, a short basic domain. They have been shown to be axonal guidance cues and have a part in the regulation of the cardiovascular, immune, and respiratory systems. Sema3A, the prototype member of this class III subfamily, induces growth cone collapse and is an inhibitor of axonal sprouting. In perinatal rat cortex, it acts as a chemoattractant and functions to direct the orientated extension of apical dendrites. It may play a role, prior to the development of apical dendrites, in signaling the radial migration of newborn cortical neurons towards the upper layers. Sema3A selectively inhibits vascular endothelial growth factor receptor (VEGF)-induced angiogenesis and induces microvascular permeability. This group also includes Sema3B, -C, -D, -E, -G.


Pssm-ID: 409455  Cd Length: 92  Bit Score: 38.48  E-value: 1.63e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 195 PTPSISWLKN-GREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCV-VENKFGSIRQTYTLDVLER 261
Cdd:cd05871   24 PQATVKWLFQrGGDQRKEEVKSEERLIVTDRGLLLRSLQRSDAGVYTCQaVEHGFSQTLVKIRLHVIEP 92
Ig4_Contactin-2-like cd05728
Fourth Ig domain of the neural cell adhesion molecule contactin-2, and similar domains; The ...
273-369 1.92e-03

Fourth Ig domain of the neural cell adhesion molecule contactin-2, and similar domains; The members here are composed of the fourth Ig domain of the neural cell adhesion molecule contactin-2. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (also called TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. The first four Ig domains form the intermolecular binding fragment which arranges as a compact U-shaped module by contacts between Ig domains 1 and 4, and domains 2 and 3. It has been proposed that a linear zipper-like array forms, from contactin-2 molecules alternatively provided by the two apposed membranes.


Pssm-ID: 143205 [Multi-domain]  Cd Length: 85  Bit Score: 37.96  E-value: 1.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYVTvlktAGAnttdkelevLSLHNVTFEDAGEYTC 352
Cdd:cd05728    6 ISDTEADIGSSLRWECKASGNPRPAYRWLK----NGQPLASENRIEVE----AGD---------LRITKLSLSDSGMYQC 68
                         90
                 ....*....|....*..
gi 311641796 353 LAGNSIGFSHHSAWLVV 369
Cdd:cd05728   69 VAENKHGTIYASAELAV 85
IgI_1_Palladin_C cd05893
First C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig ...
185-258 2.18e-03

First C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of palladin. Palladin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to this family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Palladin binds to alpha-actinin ezrin, vasodilator-stimulated phosphoprotein VASP, SPIN90 (also known as DIP or mDia interacting protein), and Src. Palladin also binds F-actin directly, via its Ig3 domain. Palladin is expressed as several alternatively spliced isoforms, having various combinations of Ig-like domains, in a cell-type-specific manner. It has been suggested that palladin's different Ig-like domains may be specialized for distinct functions. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409474  Cd Length: 92  Bit Score: 38.15  E-value: 2.18e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGREF--RGEHRIGGIKLrHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05893   18 VTFTCRVAGNPKPKIYWFKDGKQIspKSDHYTIQRDL-DGTCSLHTTASTLDDDGNYTIMAANPQGRISCTGRLMV 92
IgI_1_NCAM-1_like cd04977
First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1, and similar ...
273-359 2.20e-03

First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1, and similar domains; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM) and heterophilic (NCAM-nonNCAM) interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. Also included in this group is NCAM-2 (also known as OCAM/mamFas II and RNCAM). NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE). This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409366  Cd Length: 95  Bit Score: 38.39  E-value: 2.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQpHIQWlkhVEVNGSKVGPDGTPYVTVLKtaganttDKELEVLSLHNVTFEDAGEYTC 352
Cdd:cd04977    7 PSYAEISVGESKFFLCKVSGDAK-NINW---VSPNGEKVLTKHGNLKVVNH-------GSVLSSLTIYNANINDAGIYKC 75

                 ....*..
gi 311641796 353 LAGNSIG 359
Cdd:cd04977   76 VATNGKG 82
IgI_NCAM-2 cd05870
Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 2 (NCAM-2); The members ...
189-258 2.30e-03

Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 2 (NCAM-2); The members here are composed of the fourth Ig domain of Neural Cell Adhesion Molecule NCAM-2 (also known as OCAM/mamFas II and RNCAM). NCAM-2 is organized similarly to NCAM, including five N-terminal Ig-like domains and two fibronectin type III domains. NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE), and may function like NCAM, as an adhesion molecule. One of the unique features of I-set domains is the lack of a C" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains.


Pssm-ID: 143278 [Multi-domain]  Cd Length: 98  Bit Score: 38.42  E-value: 2.30e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 311641796 189 CPAAGNPTPSISWLK--NGREF-RGEHRIGG---IKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDV 258
Cdd:cd05870   23 CKAEGEPIPEITWKRasDGHTFsEGDKSPDGrieVKGQHGESSLHIKDVKLSDSGRYDCEAASRIGGHQKSMYLDI 98
Ig3_L1-CAM cd05876
Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM); The members here ...
316-369 2.33e-03

Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM); The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM.


Pssm-ID: 409460 [Multi-domain]  Cd Length: 83  Bit Score: 37.97  E-value: 2.33e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 311641796 316 TPYVTVLKTAGANTTDKEL-----EVLSLHNVTFEDAGEYTCLAGNSIGFSHHSAWLVV 369
Cdd:cd05876   24 TPTVKWLRPSGPLPPDRVKyqnhnKTLQLLNVGESDDGEYVCLAENSLGSARHAYYVTV 82
IgI_VEGFR-3 cd05863
Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3); ...
185-259 2.36e-03

Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3); member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGFR-3 (Flt-4) binds two members of the VEGF family (VEGF-C and VEGF-D) and is involved in tumor angiogenesis and growth. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409449  Cd Length: 88  Bit Score: 37.99  E-value: 2.36e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 311641796 185 VRFRCPAAGNPTPSISWLKNGRefrgehrigGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDVL 259
Cdd:cd05863   22 VKLPVKVAAYPPPEFQWYKDGK---------LISGKHSPHSLQIKDVTEASAGTYTLVLWNSAAGLEKRISLELI 87
IgI_1_hemolin-like cd20979
First immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set ...
200-248 2.55e-03

First immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the first immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The first Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand. I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM).


Pssm-ID: 409571  Cd Length: 91  Bit Score: 37.93  E-value: 2.55e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 311641796 200 SWLKNGREFR-GEHRIGgikLRHQQWSLVMESVVPSDRGNYTCVVENKFG 248
Cdd:cd20979   34 SWLKDGKSFNwQEHNVA---QRKDEGSLVFLKPQASDEGQYQCFAETPAG 80
IgC1_CD80 cd16083
Immunoglobulin constant (IgC)-like domain of antigen receptor Cluster of Differentiation (CD) ...
180-210 2.84e-03

Immunoglobulin constant (IgC)-like domain of antigen receptor Cluster of Differentiation (CD) 80; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin constant (IgC)-like domain of the antigen receptor Cluster of Differentiation (CD) 80. CD80 (also known as glycoprotein B7-1) and CD86 (also known as glycoprotein B7-2) are expressed on antigen-presenting cells and deliver the co-stimulatory signal through CD28 and CTLA-4 (CD152) on T cells. signaling through CD28 augments the T-cell response, whereas CTLA-4 signaling attenuates it. CD80 contains two Ig-like domains, an amino-terminal immunoglobulin variable (IgV)-like domain characteristic of adhesion molecules, and a membrane proximal immunoglobulin constant (IgC)-like domain similar to the constant domains of antigen receptors. Members of the Ig family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409505  Cd Length: 91  Bit Score: 37.82  E-value: 2.84e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 311641796 180 PAANTVRFRCPAAGN-PTPSISWLKNGREFRG 210
Cdd:cd16083   12 PSPNIKRIICSTSGGfPEPRLSWLENGEELNA 43
IgI_1_Palladin_C cd05893
First C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig ...
281-359 3.29e-03

First C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of palladin. Palladin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to this family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Palladin binds to alpha-actinin ezrin, vasodilator-stimulated phosphoprotein VASP, SPIN90 (also known as DIP or mDia interacting protein), and Src. Palladin also binds F-actin directly, via its Ig3 domain. Palladin is expressed as several alternatively spliced isoforms, having various combinations of Ig-like domains, in a cell-type-specific manner. It has been suggested that palladin's different Ig-like domains may be specialized for distinct functions. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409474  Cd Length: 92  Bit Score: 37.77  E-value: 3.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 281 GSDVEFHCKVYSDAQPHIQWLKhvevNGSKVGPDGTPYvtvlktaganTTDKELE-VLSLHNV--TFEDAGEYTCLAGNS 357
Cdd:cd05893   15 GMPVTFTCRVAGNPKPKIYWFK----DGKQISPKSDHY----------TIQRDLDgTCSLHTTasTLDDDGNYTIMAANP 80

                 ..
gi 311641796 358 IG 359
Cdd:cd05893   81 QG 82
IgI_Perlecan_like cd05754
Immunoglobulin (Ig)-like domain found in Perlecan and similar proteins; member of the I-set of ...
173-256 3.96e-03

Immunoglobulin (Ig)-like domain found in Perlecan and similar proteins; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the third immunoglobulin (Ig)-like domain found in Perlecan. Perlecan is a large multi-domain heparin sulfate proteoglycan, important in tissue development and organogenesis. Perlecan can be represented as 5 major portions; its fourth major portion (domain IV) is a tandem repeat of immunoglobulin-like domains (Ig2-Ig15) which can vary in size due to alternative splicing. Perlecan binds many cellular and extracellular ligands. Its domain IV region has many binding sites. Some of these have been mapped at the level of individual Ig-like domains, including a site restricted to the Ig5 domain for heparin/sulfatide, a site restricted to the Ig3 domain for nidogen-1 and nidogen-2, a site restricted to Ig4-5 for fibronectin, and sites restricted to Ig2 and to Ig13-15 for fibulin-2. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409412  Cd Length: 85  Bit Score: 37.15  E-value: 3.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 173 DKKLLAVPAANTVRFRCPA-AGNPTPSISWLK-NGREFRGEHRIGGIklrhqqwsLVMESVVPSDRGNYTCVVENKFGSI 250
Cdd:cd05754    7 EPRSQEVRPGADVSFICRAkSKSPAYTLVWTRvNGTLPSRAMDFNGI--------LTIRNVQLSDAGTYVCTGSNMLDTD 78

                 ....*.
gi 311641796 251 RQTYTL 256
Cdd:cd05754   79 EATATL 84
IgI_7_Dscam cd20954
Seventh immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar ...
273-359 4.08e-03

Seventh immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains; The members here are composed of the seventh immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C" strand.


Pssm-ID: 409546 [Multi-domain]  Cd Length: 96  Bit Score: 37.29  E-value: 4.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 273 PANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVevnGSKVGP----DGTPYVTVLktagANTTdkelevLSLHNVTFEDAG 348
Cdd:cd20954    8 PVDANVAAGQDVMLHCQADGFPTPTVTWKKAT---GSTPGEykdlLYDPNVRIL----PNGT------LVFGHVQKENEG 74
                         90
                 ....*....|.
gi 311641796 349 EYTCLAGNSIG 359
Cdd:cd20954   75 HYLCEAKNGIG 85
IgC1_TCR_gamma cd07697
T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig ...
519-607 4.31e-03

T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) constant (C) domain of the gamma chain of gamma-delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 409494  Cd Length: 98  Bit Score: 37.62  E-value: 4.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 519 PQVYTLPPSRDELTK-NQVSLTCLVKGFYPSDIAVEWESNG------QPENNykttpPVLDSDgSFFLYSKLTVDKSrwQ 591
Cdd:cd07697    2 PKPTIFLPSIAETEKqKAGTYLCLLENFFPDVIKIHWREKKsdtileSQEGN-----TEKTKD-TYMKFSWLTVPKK--S 73
                         90
                 ....*....|....*.
gi 311641796 592 QGNVFSCSVMHEALHN 607
Cdd:cd07697   74 LGKEHRCIYKHENNKN 89
IgI_1_Titin_Z1z2-like cd20974
First Ig-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and ...
179-259 4.76e-03

First Ig-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and similar proteins; a member of the I-set of IgSF domains; The members here are composed of the first immunoglobulin (Ig)-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C" strand. The structure of the titin Z1z2 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis.


Pssm-ID: 409566 [Multi-domain]  Cd Length: 93  Bit Score: 37.33  E-value: 4.76e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGrEFRGEHRIGGIKL--RHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTL 256
Cdd:cd20974   12 VLEGSTATFEAHVSGKPVPEVSWFRDG-QVISTSTLPGVQIsfSDGRAKLSIPAVTKANSGRYSLTATNGSGQATSTAEL 90

                 ...
gi 311641796 257 DVL 259
Cdd:cd20974   91 LVL 93
IgI_4_Robo cd05726
Fourth immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
179-258 7.14e-03

Fourth immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; Members here are composed the fourth immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, Robo3), and three mammalian Slit homologs (Slit-1, Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, and Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409391 [Multi-domain]  Cd Length: 98  Bit Score: 36.86  E-value: 7.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 179 VPAANTVRFRCPAAGNPTPSISWLKNGRE---FRGEHRIGGIKLR-HQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTY 254
Cdd:cd05726   11 VALGRTVTFQCETKGNPQPAIFWQKEGSQnllFPYQPPQPSSRFSvSPTGDLTITNVQRSDVGYYICQALNVAGSILAKA 90

                 ....
gi 311641796 255 TLDV 258
Cdd:cd05726   91 QLEV 94
Ig1_Tyro3_like cd20961
First immunoglobulin (Ig)-like domain of Tyro3 receptor tyrosine kinase (RTK), and similar ...
177-245 7.86e-03

First immunoglobulin (Ig)-like domain of Tyro3 receptor tyrosine kinase (RTK), and similar domains; The members here are composed of the first immunoglobulin (Ig)-like domain of Tyro3 receptor tyrosine kinase (RTK). Tyro3 together with Axl and Mer form the Axl/Tyro3 family of receptor tyrosine kinases (RTKs). This family includes Axl (also known as Ark, Ufo, and Tyro7), Tyro3 (also known as Sky, Rse, Brt, Dtk, and Tif), and Mer (also known as Nyk, c-Eyk, and Tyro12). Axl/Tyro3 family receptors have an extracellular portion with two Ig-like domains followed by two fibronectin-types III (FNIII) domains, a membrane-spanning single helix, and a cytoplasmic tyrosine kinase domain. Axl, Tyro3 and Mer are widely expressed in adult tissues, though they show higher expression in the brain, in the lymphatic and vascular systems, and in the testis. Axl, Tyro3, and Mer bind the vitamin K dependent protein Gas6 with high affinity, and in doing so activate their tyrosine kinase activity. Axl/Gas6 signaling may play a part in cell adhesion processes, prevention of apoptosis, and cell proliferation.


Pssm-ID: 409553  Cd Length: 87  Bit Score: 36.27  E-value: 7.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 311641796 177 LAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIgGIKLRHQQWS--LVMESVVPSDRGNYTCVVEN 245
Cdd:cd20961    3 LTVSQGQPVKLNCSVEGMEEPDIQWVKDGAVVQNLDQL-YIPVSEQHWIgfLSLKSVERSDAGRYWCQVED 72
IgC1_CH1_IgEG cd21817
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and ...
410-509 8.21e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of epsilon and gamma chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409622  Cd Length: 94  Bit Score: 36.66  E-value: 8.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 410 APSVFLFPPKPKDTLMISRTpeVTCVVVDVSHEDPEVKFNwyvDGVEVHNAKTKPREEQYNSTYRVVSVLTVlHQDWLNG 489
Cdd:cd21817    1 APSVFPLAPCCKSTNGSSVT--LGCLVTGYFPEPVTVTWN---SGSLTSGVKTFPAVLQSSGLYTTSSQVTV-PSSSWGS 74
                         90       100
                 ....*....|....*....|
gi 311641796 490 KEYKCKVSNKALPSSIEKTI 509
Cdd:cd21817   75 QTFTCNVEHKPSSTKVDKKI 94
IgC_TCR_delta cd07687
Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors ...
531-610 9.37e-03

Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs); The members here are composed of the constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 409484  Cd Length: 80  Bit Score: 35.94  E-value: 9.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 311641796 531 LTKNQVSLTCLVKGFYPSDIAVEWESNGQPennYKTTP-PVLDSDGSfflYSklTVDKSRWQQGNVFSCSVMHEALHNHY 609
Cdd:cd07687    6 VMKNGTNVACLVKNFYPKEVTISLSSSKKI---IEFDPaIVISPNGK---YS--AVKLGKYGDSDSVTCSVQHSNKTVHS 77

                 .
gi 311641796 610 T 610
Cdd:cd07687   78 T 78
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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