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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041  97 DARGRCSWTSESPWeegkwPDVEAVKGT---LDGQQAELQIYFSQGGQAVA-IGQFKDRITGSNDPG--NASITISHMQP 170
Cdd:cd05715   16 DVRLTCTFTSCYTV-----GDAFSVTWTyqpEGGNTTESMFHYSKGKPYILkVGRFKDRVSWAGNPSkkDASIVISNLQF 90

                         90
                 ....*....|....*....
gi 530422041 171 ADSGIYICDVNNPPDFLGQ 189
Cdd:cd05715   91 SDNGTYTCDVKNPPDIVGG 109

Procyclic acidic repetitive protein (PARP); This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041  364 TLPSSIHETGPDTIQEPDYEPKPTQEPAPEPAPGSEPMAVPDLDIELELEPETQSELEPE 423
Cdd:pfam05887  47 TKVSDDDTNGTDPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPE 106

Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041  97 DARGRCSWTSESPWeegkwPDVEAVKGT---LDGQQAELQIYFSQGGQAVA-IGQFKDRITGSNDPG--NASITISHMQP 170
Cdd:cd05715   16 DVRLTCTFTSCYTV-----GDAFSVTWTyqpEGGNTTESMFHYSKGKPYILkVGRFKDRVSWAGNPSkkDASIVISNLQF 90

                         90
                 ....*....|....*....
gi 530422041 171 ADSGIYICDVNNPPDFLGQ 189
Cdd:cd05715   91 SDNGTYTCDVKNPPDIVGG 109

Immunoglobulin V-Type;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 530422041   127 GQQAELQIYFSQGGQAVAIGQFKDRITGSNDPGN--ASITISHMQPADSGIYICDV 180
Cdd:smart00406  26 GKGLEWLGYIGSNGSSYYQESYKGRFTISKDTSKndVSLTISNLRVEDTGTYYCAV 81

Immunoglobulin domain; This family contains immunoglobulin-like domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041  204 KPLCSVQGRPET---GHTISLSClSALGTPSPVYYWHKlEGRDIVPV---KENFNPTTGILVIGNLTNFEQGYYQCTAIN 277
Cdd:pfam13927   1 KPVITVSPSSVTvreGETVTLTC-EATGSPPPTITWYK-NGEPISSGstrSRSLSGSNSTLTISNVTRSDAGTYTCVASN 78

Second Ig-like domain of Junctional adhesion molecule-1 (JAM1); a member of the I-set of IgSF domains; The members here are composed of the second Ig-like domain of Junctional adhesion molecule-1 (JAM1). JAM1 is an immunoglobulin superfamily (IgSF) protein with two Ig-like domains in its extracellular region; it plays a role in the formation of endothelial and epithelial tight junction and acts as a receptor for mammalian reovirus sigma-1. The 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 second Ig-like domain of JAM1 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, the A strand of the I-set is discontinuous but lacks 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041 205 PLCSVQGRPETGHTISLSCLSALGTPSPVYYWHKlegrDIVPVKEN-------------FNPTTGILVIGNLTNFEQGYY 271
Cdd:cd20950    1 PTVNIPSSATIGNRAVLTCSEPDGSPPSEYTWFK----DGVVMPTNpkstrafsnssysLDPTTGELVFDPLSASDTGEY 76

                 ....*....
gi 530422041 272 QCTAINRLG 280
Cdd:cd20950   77 SCEARNGYG 85

MSCRAMM family adhesin clumping factor ClfB; Clumping factor B is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 530422041 375 DTIQEPDYEPKPTQEPAPEPAPGSEPMAVPD 405
Cdd:NF033845 545 DPTPGPPVDPEPSPEPEPEPTPDPEPSPDPD 575

Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041  97 DARGRCSWTSESPWeegkwPDVEAVKGT---LDGQQAELQIYFSQGGQAVA-IGQFKDRITGSNDPG--NASITISHMQP 170
Cdd:cd05715   16 DVRLTCTFTSCYTV-----GDAFSVTWTyqpEGGNTTESMFHYSKGKPYILkVGRFKDRVSWAGNPSkkDASIVISNLQF 90

                         90
                 ....*....|....*....
gi 530422041 171 ADSGIYICDVNNPPDFLGQ 189
Cdd:cd05715   91 SDNGTYTCDVKNPPDIVGG 109

Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are composed of the immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA 1). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule and may play a role in the structural organization of the thymus and early lymphocyte development.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041  97 DARGRCSWTSESPWeegkwPDVEAVKGT---LDGQQAELQIYFSQGGQAVAIGQFKDRITGSNDP--GNASITISHMQPA 171
Cdd:cd05880   16 DVRLKCTFSSSAPI-----GDTLVITWNfrpLDGGREESVFYYHKRPYPPPDGRFKGRVVWDGNImrRDASILIWQLQPT 90

                         90
                 ....*....|....*..
gi 530422041 172 DSGIYICDVNNPPDFLG 188
Cdd:cd05880   91 DNGTYTCQVKNPPDVHG 107

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530422041   216 GHTISLSClSALGTPSPVYYWHKlEGRDIVPVKENF----NPTTGILVIGNLTNFEQGYYQCTAINRLGNSSCEIDLT 289
Cdd:smart00410   9 GESVTLSC-EASGSPPPEVTWYK-QGGKLLAESGRFsvsrSGSTSTLTISNVTPEDSGTYTCAATNSSGSASSGTTLT 84

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041   127 GQQAELQIYFS-----------QGGQAVAigqFKDRITGSNDPGNASITISHMQPADSGIYICDVNNPpdfLGQNQGILN 195
Cdd:smart00410   9 GESVTLSCEASgspppevtwykQGGKLLA---ESGRFSVSRSGSTSTLTISNVTPEDSGTYTCAATNS---SGSASSGTT 82

                   ...
gi 530422041   196 VSV 198
Cdd:smart00410  83 LTV 85

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530422041 127 GQQAELQIYFSQGGQAVAiGQFKDRITGSNDPGN-ASITISHMQPADSGIYIC 178
Cdd:cd00099   39 GQGPEFLIYLSSSKGKTK-GGVPGRFSGSRDGTSsFSLTISNLQPEDSGTYYC 90

Second Ig-like domain of Junctional adhesion molecule-1 (JAM1); a member of the I-set of IgSF domains; The members here are composed of the second Ig-like domain of Junctional adhesion molecule-1 (JAM1). JAM1 is an immunoglobulin superfamily (IgSF) protein with two Ig-like domains in its extracellular region; it plays a role in the formation of endothelial and epithelial tight junction and acts as a receptor for mammalian reovirus sigma-1. The 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 second Ig-like domain of JAM1 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, the A strand of the I-set is discontinuous but lacks 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041 205 PLCSVQGRPETGHTISLSCLSALGTPSPVYYWHKlegrDIVPVKEN-------------FNPTTGILVIGNLTNFEQGYY 271
Cdd:cd20950    1 PTVNIPSSATIGNRAVLTCSEPDGSPPSEYTWFK----DGVVMPTNpkstrafsnssysLDPTTGELVFDPLSASDTGEY 76

                 ....*....
gi 530422041 272 QCTAINRLG 280
Cdd:cd20950   77 SCEARNGYG 85

Procyclic acidic repetitive protein (PARP); This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 530422041  379 EPDYEPKPTQEPAPEPAPGSEPMAVPDLDIELELEPETQSELEPEPEPEPESEPGV-----VVEPLSEDEKGVVKA 449
Cdd:pfam05887  58 DPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPGAatlksVALPFAIAAVGLVAA 133

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 530422041 228 GTPSPVYYWhKLEG-------RDIVPVKENFNPTtgiLVIGNLTNFEQGYYQCTAINRLGNSSCEIDL 288
Cdd:cd05744   26 GLPTPDLFW-QLNGkpvrpdsAHKMLVRENGRHS---LIIEPVTKRDAGIYTCIARNRAGENSFNAEL 89

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530422041 219 ISLSClSALGTPSPVYYWHKlEGRDIVP---VKENFNPTTGILVIGNLTNFEQGYYQCTAINRLG 280
Cdd:cd00096    1 VTLTC-SASGNPPPTITWYK-NGKPLPPssrDSRRSELGNGTLTISNVTLEDSGTYTCVASNSAG 63

DNA polymerase III subunit gamma/tau;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530422041 329 ERNSKTIAELEPM----TKINPRgeSEAMPREDATQ--LEVTLPSSIHETGPDTIQEPDYEPKPTQEPAPEPAPGSEPM 401
Cdd:PRK14960 373 QQNGQAEVGLNSQaqtaQEITPV--SAVQPVEVISQpaMVEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPEPQPNQDLM 449

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 530422041 216 GHTISLSClSALGTPSPVYYWHKleGRDIVPV-KENFNPTTGILVIGNLTNFEQGYYQCTAINRLGNSSCEIDLT 289
Cdd:cd05745    2 GQTVDFLC-EAQGYPQPVIAWTK--GGSQLSVdRRHLVLSSGTLRISRVALHDQGQYECQAVNIVGSQRTVAQLT 73

Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core protein (CSPG); The members here are composed of the immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core proteins (CSPGs). Included in this group are the Ig domains of other CSPGs: versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 530422041 114 KWPDVEavkgTLDGQQAELQIYFSQGGQaVAIGQ-FKDRITGSNDP---GNASITISHMQPADSGIYICDV 180
Cdd:cd05878   40 KWSKVS----VDGKKEKEVVLLVATEGR-VRVNSaYQGRVSLPNYPaipSDATLEVQSLRASDSGLYRCEV 105

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.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 530422041 150 DRITGSNDPGNASITISHMQPADSGIYICDV 180
Cdd:cd04984   59 DRFSGSKSGNTASLTISGAQTEDEADYYCQV 89

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 530422041 126 DGQQAELQIYFSQGGQAVAIGQFKDRITGS-NDPGNASITISHMQPADSGIYIC 178
Cdd:cd05899   36 PGKGLQLLFYSYGGGLNEEGDLPGDRFSASrPSLTRSSLTIKSAEPEDSAVYLC 89

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.

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 530422041 147 QFKDRITGSNDPGNASITISHMQPADSGIYICDVNNP 183
Cdd:cd00096   25 PPSSRDSRRSELGNGTLTISNVTLEDSGTYTCVASNS 61

MSCRAMM family adhesin clumping factor ClfB; Clumping factor B is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 530422041 375 DTIQEPDYEPKPTQEPAPEPAPGSEPMAVPD 405
Cdd:NF033845 545 DPTPGPPVDPEPSPEPEPEPTPDPEPSPDPD 575

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530422041 214 ETGHTISLSCLsALGTPSPVYYWHK-LEG---RDIVPVKENFNPTTGILVIGNLTNFEQGYYQCTAINRLGNSSCEIDLT 289
Cdd:cd20953   16 SSASSIALLCP-AQGYPAPSFRWYKfIEGttrKQAVVLNDRVKQVSGTLIIKDAVVEDSGKYLCVVNNSVGGESVETVLT 94