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Conserved domains on  [gi|47605684|sp|Q86UW8|]
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RecName: Full=Hyaluronan and proteoglycan link protein 4; AltName: Full=Brain link protein 2; Flags: Precursor

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 ...
 50-165 3.56e-50

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 cd05877:

Pssm-ID: 472250  Cd Length: 117  Bit Score: 164.81  E-value: 3.56e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  50 QTAPGQVVSHRGGTIVLPCRYHYEAAAHGHDGVRLKWTKV-VDPLAFTDVFVALGPQHRAFGSYRGRAELQGDGPGDASL 128
Cdd:cd05877   1 ETVQAKVFSHRGGNVTLPCRYHYEPELSAPRKIRVKWTKLeVDYAKEEDVLVAIGTRHKSYGSYQGRVFLRRADDLDASL 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 47605684 129 VLRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05877  81 VITDLRLEDYGRYRCEVIDGLEDESVVVALRLRGVVF 117
Link_Domain super family cl02612
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 163-267 5.94e-47

The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules.


The actual alignment was detected with superfamily member cd03518:

Pssm-ID: 470631  Cd Length: 95  Bit Score: 155.66  E-value: 5.94e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 163 VVFPYHPRGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsagGG 242
Cdd:cd03518   1 VVFPYQPRLGRYNLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPC----------GG 70

                        90       100
                ....*....|....*....|....*
gi 47605684 243 GDANGGLRNYGYRHNAEERYDAFCF 267
Cdd:cd03518  71 KRTVPGLRSYGERDKMLSRYDAFCF 95
Link_Domain super family cl02612
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 274-364 1.69e-39

The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules.


The actual alignment was detected with superfamily member cd03519:

Pssm-ID: 470631  Cd Length: 91  Bit Score: 136.01  E-value: 1.69e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 274 RVFFLKPLRPVPFSGAARACAARGAAVAKVGQLFAAWKLQLLDRCTAGWLADGSARYPIVNPRARCGGRRPGVRSLGFPD 353
Cdd:cd03519   1 GVFYLLHPGKLTFSEAVAACQRDGAQIAKVGQLFAAWKFHGLDRCDAGWLADGSVRYPISRPRPRCGPLEPGVRSFGFPD 80

                        90
                ....*....|.
gi 47605684 354 ATRRLFGVYCY 364
Cdd:cd03519  81 KKHKLYGVYCY 91
 
Name Accession Description Interval E-value
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
 50-165 3.56e-50

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. 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.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 164.81  E-value: 3.56e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  50 QTAPGQVVSHRGGTIVLPCRYHYEAAAHGHDGVRLKWTKV-VDPLAFTDVFVALGPQHRAFGSYRGRAELQGDGPGDASL 128
Cdd:cd05877   1 ETVQAKVFSHRGGNVTLPCRYHYEPELSAPRKIRVKWTKLeVDYAKEEDVLVAIGTRHKSYGSYQGRVFLRRADDLDASL 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 47605684 129 VLRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05877  81 VITDLRLEDYGRYRCEVIDGLEDESVVVALRLRGVVF 117
Link_domain_HAPLN_module_1 cd03518
Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins ...
 163-267 5.94e-47

Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239595  Cd Length: 95  Bit Score: 155.66  E-value: 5.94e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 163 VVFPYHPRGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsagGG 242
Cdd:cd03518   1 VVFPYQPRLGRYNLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPC----------GG 70

                        90       100
                ....*....|....*....|....*
gi 47605684 243 GDANGGLRNYGYRHNAEERYDAFCF 267
Cdd:cd03518  71 KRTVPGLRSYGERDKMLSRYDAFCF 95
Link_domain_HAPLN_module_2 cd03519
Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins ...
 274-364 1.69e-39

Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239596  Cd Length: 91  Bit Score: 136.01  E-value: 1.69e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 274 RVFFLKPLRPVPFSGAARACAARGAAVAKVGQLFAAWKLQLLDRCTAGWLADGSARYPIVNPRARCGGRRPGVRSLGFPD 353
Cdd:cd03519   1 GVFYLLHPGKLTFSEAVAACQRDGAQIAKVGQLFAAWKFHGLDRCDAGWLADGSVRYPISRPRPRCGPLEPGVRSFGFPD 80

                        90
                ....*....|.
gi 47605684 354 ATRRLFGVYCY 364
Cdd:cd03519  81 KKHKLYGVYCY 91
Xlink pfam00193
Extracellular link domain;
163-267 1.01e-36

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 128.84  E-value: 1.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684   163 VVFPYHPRGgRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsaggg 242
Cdd:pfam00193   1 GVFHLESPG-RYKLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNC------------ 67

                          90       100
                  ....*....|....*....|....*
gi 47605684   243 GDANGGLRNYGYRHNAEERYDAFCF 267
Cdd:pfam00193  68 GGNMPGVRQYGFRDPLSERYDAYCY 92
LINK smart00445
Link (Hyaluronan-binding);
161-268 1.39e-30

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 112.82  E-value: 1.39e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684    161 EGVVFPYHPRGgRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsag 240
Cdd:smart00445   1 DGGVFHVEKNG-RYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRC---------- 69

                           90       100
                   ....*....|....*....|....*...
gi 47605684    241 ggGDANGGLRNYGYRHNaEERYDAFCFT 268
Cdd:smart00445  70 --GGNLPGVRQYGFPDP-TSRYDAYCFN 94
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 53-158 1.27e-08

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: 51.74  E-value: 1.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684     53 PGQVVSHRGGTIVLPCRyhyeaaAHGHDGVRLKWTKvvdplaftdvfvalgpQHRAFGSYRGRAELQGDGpGDASLVLRN 132
Cdd:smart00410   1 PPSVTVKEGESVTLSCE------ASGSPPPEVTWYK----------------QGGKLLAESGRFSVSRSG-STSTLTISN 57

                           90       100
                   ....*....|....*....|....*.
gi 47605684    133 VTLQDYGRYECEVTNELEDDAGMVKL 158
Cdd:smart00410  58 VTPEDSGTYTCAATNSSGSASSGTTL 83
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 48-147 1.07e-06

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 46.02  E-value: 1.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684    48 VVQTAPGQVVSHRGGTIVLPCRyhyeaaAHGHDGVRLKWTKvvdplaftdvfvalGPQHRAFGSYRGRAELQGDGpgdaS 127
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCE------ATGSPPPTITWYK--------------NGEPISSGSTRSRSLSGSNS----T 58

                          90       100
                  ....*....|....*....|
gi 47605684   128 LVLRNVTLQDYGRYECEVTN 147
Cdd:pfam13927  59 LTISNVTRSDAGTYTCVASN 78
 
Name Accession Description Interval E-value
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
 50-165 3.56e-50

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. 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.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 164.81  E-value: 3.56e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  50 QTAPGQVVSHRGGTIVLPCRYHYEAAAHGHDGVRLKWTKV-VDPLAFTDVFVALGPQHRAFGSYRGRAELQGDGPGDASL 128
Cdd:cd05877   1 ETVQAKVFSHRGGNVTLPCRYHYEPELSAPRKIRVKWTKLeVDYAKEEDVLVAIGTRHKSYGSYQGRVFLRRADDLDASL 80

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 47605684 129 VLRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05877  81 VITDLRLEDYGRYRCEVIDGLEDESVVVALRLRGVVF 117
Link_domain_HAPLN_module_1 cd03518
Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins ...
 163-267 5.94e-47

Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239595  Cd Length: 95  Bit Score: 155.66  E-value: 5.94e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 163 VVFPYHPRGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsagGG 242
Cdd:cd03518   1 VVFPYQPRLGRYNLNFHEAQQACEEQDATLASFEQLYQAWTEGLDWCNAGWLSDGTVQYPITKPREPC----------GG 70

                        90       100
                ....*....|....*....|....*
gi 47605684 243 GDANGGLRNYGYRHNAEERYDAFCF 267
Cdd:cd03518  71 KRTVPGLRSYGERDKMLSRYDAFCF 95
Link_domain_HAPLN_module_2 cd03519
Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins ...
 274-364 1.69e-39

Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.


Pssm-ID: 239596  Cd Length: 91  Bit Score: 136.01  E-value: 1.69e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 274 RVFFLKPLRPVPFSGAARACAARGAAVAKVGQLFAAWKLQLLDRCTAGWLADGSARYPIVNPRARCGGRRPGVRSLGFPD 353
Cdd:cd03519   1 GVFYLLHPGKLTFSEAVAACQRDGAQIAKVGQLFAAWKFHGLDRCDAGWLADGSVRYPISRPRPRCGPLEPGVRSFGFPD 80

                        90
                ....*....|.
gi 47605684 354 ATRRLFGVYCY 364
Cdd:cd03519  81 KKHKLYGVYCY 91
Xlink pfam00193
Extracellular link domain;
163-267 1.01e-36

Extracellular link domain;


Pssm-ID: 459706  Cd Length: 92  Bit Score: 128.84  E-value: 1.01e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684   163 VVFPYHPRGgRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsaggg 242
Cdd:pfam00193   1 GVFHLESPG-RYKLTFQEAQAACAALGATLATPEQLYAAWKAGLDTCDAGWLADGTVRYPITTPRPNC------------ 67

                          90       100
                  ....*....|....*....|....*
gi 47605684   243 GDANGGLRNYGYRHNAEERYDAFCF 267
Cdd:pfam00193  68 GGNMPGVRQYGFRDPLSERYDAYCY 92
LINK smart00445
Link (Hyaluronan-binding);
161-268 1.39e-30

Link (Hyaluronan-binding);


Pssm-ID: 214667  Cd Length: 94  Bit Score: 112.82  E-value: 1.39e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684    161 EGVVFPYHPRGgRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsag 240
Cdd:smart00445   1 DGGVFHVEKNG-RYKLTFAEAREACRAQGATLATVGQLYAAWQDGFDTCDAGWLADGSVRYPIITPRPRC---------- 69

                           90       100
                   ....*....|....*....|....*...
gi 47605684    241 ggGDANGGLRNYGYRHNaEERYDAFCFT 268
Cdd:smart00445  70 --GGNLPGVRQYGFPDP-TSRYDAYCFN 94
Link_Domain cd01102
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 163-267 7.49e-28

The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules.


Pssm-ID: 238534  Cd Length: 92  Bit Score: 105.19  E-value: 7.49e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 163 VVFPYHPRGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsaggg 242
Cdd:cd01102   1 VVFHLESQNGRYKLTFAEAALACKARGAHLATPGQLEAAWQDGFDVCTAGWLADGSVRYPIVTSRPNC------------ 68

                        90       100
                ....*....|....*....|....*
gi 47605684 243 GDANGGLRNYGyRHNAEERYDAFCF 267
Cdd:cd01102  69 GGRNPGVRSYG-NPAPSGRYDAYCF 92
Link_domain_CSPGs_modules_2_4 cd03520
Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules ...
 303-364 3.31e-24

Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan 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.


Pssm-ID: 239597  Cd Length: 96  Bit Score: 95.46  E-value: 3.31e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47605684 303 VGQLFAAWKlQLLDRCTAGWLADGSARYPIVNPRARCGGRRPGVRSL-------GFPDATRRlFGVYCY 364
Cdd:cd03520  30 TGQLYAAWR-QGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTLyrfpnqtGFPDPHSR-FDAYCF 96
Link_Domain cd01102
The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive ...
 274-364 4.62e-24

The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules.


Pssm-ID: 238534  Cd Length: 92  Bit Score: 95.18  E-value: 4.62e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 274 RVFFLKP---LRPVPFSGAARACAARGAAVAKVGQLFAAWKLqLLDRCTAGWLADGSARYPIVNPRARCGGRRPGVRSLG 350
Cdd:cd01102   1 VVFHLESqngRYKLTFAEAALACKARGAHLATPGQLEAAWQD-GFDVCTAGWLADGSVRYPIVTSRPNCGGRNPGVRSYG 79

                        90
                ....*....|....
gi 47605684 351 FPdATRRLFGVYCY 364
Cdd:cd01102  80 NP-APSGRYDAYCF 92
Link_domain_CSPGs_modules_1_3 cd03517
Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third ...
 163-267 8.35e-24

Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. 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.


Pssm-ID: 239594  Cd Length: 95  Bit Score: 94.40  E-value: 8.35e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 163 VVFPYHPRGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsaGGG 242
Cdd:cd03517   1 VVFHYRDATARYALTFPRAQRACLDISAQIATPEQLLAAYEDGFEQCDAGWLADQTVRYPIQTPREGC---------YGD 71

                        90       100
                ....*....|....*....|....*
gi 47605684 243 GDANGGLRNYGYRhNAEERYDAFCF 267
Cdd:cd03517  72 MDGFPGVRNYGVR-DPDELYDVYCY 95
Ig_CSPGs_LP_like cd05714
Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage ...
 54-165 1.76e-22

Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP). Included in this group are the CSPGs aggrecan, 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. There is considerable evidence that HA-binding CSPGs are involved in developmental processes in the central nervous system. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409379  Cd Length: 123  Bit Score: 91.89  E-value: 1.76e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  54 GQVVSHRGGTIVLPCRYHYE--AAAHGHDGVRLKWTKV-VDP--LAFTDVFVALGPQHRAFGSYRGRAEL--QGDGPGDA 126
Cdd:cd05714   5 AKVFSHLGGNVTLPCKFYRDptAFGSGIHKIRIKWTKLtSDSgyLKEVDVLVAMGNVVYHKKTYGGRVSVplKPGSDSDA 84

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 47605684 127 SLVLRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05714  85 SLVITDLTASDYGLYRCEVIEGIEDDQDVVALDVQGVVF 123
Link_domain_CSPGs_modules_2_4 cd03520
Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules ...
 175-267 9.91e-21

Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan 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.


Pssm-ID: 239597  Cd Length: 96  Bit Score: 86.21  E-value: 9.91e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 175 KLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCGGLGGTGSAGgggdangglrnygY 254
Cdd:cd03520  10 KFTFQEARAECRSLGAVLATTGQLYAAWRQGLDQCDPGWLADGSVRYPISTPRPQCGGGLPGVRTL-------------Y 76

                        90       100
                ....*....|....*....|
gi 47605684 255 RH-------NAEERYDAFCF 267
Cdd:cd03520  77 RFpnqtgfpDPHSRFDAYCF 96
Link_domain_TSG_6_like cd03515
This is the extracellular link domain of the type found in human TSG-6. The link domain is a ...
 164-267 5.67e-18

This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accumulate in vascular tissues during aging and diabetes, these receptors may be implicated in the pathologies of these states. Both stabilins are present in the early endocytic pathway in hepatic sinusoidal epithelium associating with clathrin/AP-2. Stabilin-1 is expressed in macrophages. Stabilin-2 is absent from the latter. In macrophages: stabilin-1 is involved in trafficking between early/sorting endosomes and the trans-Golgi network. Stabilin-1 has also been implicated in angiogenesis and possibly leucocyte trafficking. Both stabilins bind gram-positive and gram-negative bacteria. TSG-6 and stabilins contain a single link module which supports high affinity binding to HA.


Pssm-ID: 239592  Cd Length: 93  Bit Score: 78.27  E-value: 5.67e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 164 VFPYHPRGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsagggG 243
Cdd:cd03515   2 VFHLRSRSGKYKLTYTEAKAACEAEGAHLATYSQLSAAQQLGFHLCAAGWLAKGRVGYPIVFPSANC------------G 69

                        90       100
                ....*....|....*....|....
gi 47605684 244 DANGGLRNYGYRHNAEERYDAFCF 267
Cdd:cd03515  70 FGHVGIVDYGPRLNLSERWDAYCY 93
Ig_Versican cd05901
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 62-165 2.48e-10

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican. In CSPGs, the 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, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Like aggrecan, versican has a wide distribution in connective tissue and extracellular matrices. 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.


Pssm-ID: 409482  Cd Length: 128  Bit Score: 58.05  E-value: 2.48e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  62 GTIVLPCRYHYEAAAHG-----HDGVRLKWTKVVDPLAFTD-----VFVALGPQHRAFGSYRGRAEL--QGDGPGDASLV 129
Cdd:cd05901  13 GSVVLPCRFSTLPTLPPsynitSEFLRIKWTKIQVDKNGKDhkettVLVAQNGIIKIGQEYMGRVSVpsHPEDQGDASLT 92

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 47605684 130 LRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05901  93 IVKLRASDAGVYRCEVMHGIEDTQDTVSLDVSGVVF 128
IgV_CRIg cd16089
Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin ...
 51-146 3.70e-10

Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg); The members here are composed of the immunoglobulin variable (IgV) region of the complement receptor of the immunoglobulin superfamily (CRIg). The N-terminal domain of CRIg (also known as Z39Ig and V-set and Ig domain-containing 4 (VSIG4) belongs to the IgV family of immunoglobulin-like domains while the C-terminal domain of CRIg belongs to the IgC family of immunoglobulin-like domains. Like all members of this family, the CRIg domain contains two beta-sheets: one composed of strands A', G, F, C, C' and C", and the other of strands B, E and D. The complement system is an important part of the innate immune system and is required for removal of pathogens from the bloodstream. After exposure to pathogens, the third component of the complement system, C3, is cleaved to C3b which, after recruitment of factor B, initiates formation of the alternative pathway convertases. CRIg, a complement receptor expressed on macrophages, binds to C3b and iC3b mediating phagocytosis of the particles. It is also a potent inhibitor of the alternative pathway convertases and a negative regulator of T cell activation. 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, 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.


Pssm-ID: 409510  Cd Length: 117  Bit Score: 57.15  E-value: 3.70e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  51 TAPGQVVSHRGGTIVLPCRYHYEAaahGHDGVRLKWTKVVDPLAFTdVFVALGP-QHRAFGSYRGRAELQGDGPGDASLV 129
Cdd:cd16089   4 EGPESITGPWKGSVNLPCTYVPEE---GYTQVLVKWLVQRDSDPVT-IFLRDSSgDHIQQAKYRGRLEVSKDTPGDVSLQ 79

                        90
                ....*....|....*..
gi 47605684 130 LRNVTLQDYGRYECEVT 146
Cdd:cd16089  80 LDTLEMDDRGHYTCQVT 96
Ig_Aggrecan_like cd05878
Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core ...
 53-165 4.21e-10

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.


Pssm-ID: 409462  Cd Length: 125  Bit Score: 57.24  E-value: 4.21e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  53 PGQVVSHRGGTIVLPCRY----HYEAAAHGHDGVRLKWTKV---VDPLAFTDVFVALGPQHRAFGSYRGRAELQG--DGP 123
Cdd:cd05878   4 SSPVRVLLGTSVTLPCYFidppHPVTPSTAPLAPRIKWSKVsvdGKKEKEVVLLVATEGRVRVNSAYQGRVSLPNypAIP 83

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 47605684 124 GDASLVLRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05878  84 SDATLEVQSLRASDSGLYRCEVMHGIEDSQDTVELVVKGVVF 125
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 53-158 1.27e-08

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: 51.74  E-value: 1.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684     53 PGQVVSHRGGTIVLPCRyhyeaaAHGHDGVRLKWTKvvdplaftdvfvalgpQHRAFGSYRGRAELQGDGpGDASLVLRN 132
Cdd:smart00410   1 PPSVTVKEGESVTLSCE------ASGSPPPEVTWYK----------------QGGKLLAESGRFSVSRSG-STSTLTISN 57

                           90       100
                   ....*....|....*....|....*.
gi 47605684    133 VTLQDYGRYECEVTNELEDDAGMVKL 158
Cdd:smart00410  58 VTPEDSGTYTCAATNSSGSASSGTTL 83
Ig_Neurocan cd05902
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 54-165 8.49e-08

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan. In CSPGs, the 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, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Unlike aggrecan which is widely distributed 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.


Pssm-ID: 409483  Cd Length: 121  Bit Score: 50.60  E-value: 8.49e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  54 GQVVSHRGGTIVLPCRYHYEAAAHG-HDGVRLKWTKVVDPLAFTD--VFVALGPQHRAFGSYRGRAELQGDgPG---DAS 127
Cdd:cd05902   5 PPVRRPLSSSVLLPCVFTLPPSASSpPEGPRIKWTKLSTSGGQQQrpVLVARDNVVRVAKAFQGRVSLPGY-PKnryNAS 83

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 47605684 128 LVLRNVTLQDYGRYECEVTNELEDDAGMVKLDLEGVVF 165
Cdd:cd05902  84 LVLSRLRYSDSGTYRCEVVLGINDEQDTVPLEVTGVVF 121
IgV_VCBP cd20963
Immunoglobulin Variable region-containing chitin-binding proteins; an immunoglobulin V-set ...
 48-167 1.15e-07

Immunoglobulin Variable region-containing chitin-binding proteins; an immunoglobulin V-set domain; The members here are composed of the immunoglobulin variable (IgV) region-containing chitin-binding proteins (VCBPs). VCBPs are secreted, immune-type molecules that have been identified in both amphioxus and sea squirt (Ciona intestinalis). VCBPs, which consist of a leader peptide, two tandem N-terminal immunoglobulin V-type domains and a single C-terminal chitin-binding domain, belong to a multigene family encoding secreted proteins. The VCBPs were identified first in the cephalochordate Branchiostoma floridae and show structural similarities with V-type domains of immunoglobulins and T cell receptors, suggesting that VCBPs represent a unique gut-associated form of innate immune proteins. 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, 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. 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 V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C" in the other.


Pssm-ID: 409555  Cd Length: 123  Bit Score: 50.31  E-value: 1.15e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  48 VVQTAPGQVVSHRGGTIVLPCRYHYEAAAHGHdgvRLKWTKVVDP-------LAFTDVFVALGPQHRAFGSYRGRAELQG 120
Cdd:cd20963   4 VTVPSYTRTDPTWGNRVELPCSYTISPAAQPP---TITWLKGISVdraevvfKGFKYWNETSSSGEVYFGDYAGRASVAS 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 47605684 121 -DGPgdaSLVLRNVTLQDYGRYECEVTNE-LEDDAGmvkLDLEGVVFPY 167
Cdd:cd20963  81 lTQP---TLVLTDLKFDDWGRYWCRVANWsQRDEFG---TDAESMLLWI 123
Link_domain_TSG_6_like cd03515
This is the extracellular link domain of the type found in human TSG-6. The link domain is a ...
 305-364 1.94e-07

This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accumulate in vascular tissues during aging and diabetes, these receptors may be implicated in the pathologies of these states. Both stabilins are present in the early endocytic pathway in hepatic sinusoidal epithelium associating with clathrin/AP-2. Stabilin-1 is expressed in macrophages. Stabilin-2 is absent from the latter. In macrophages: stabilin-1 is involved in trafficking between early/sorting endosomes and the trans-Golgi network. Stabilin-1 has also been implicated in angiogenesis and possibly leucocyte trafficking. Both stabilins bind gram-positive and gram-negative bacteria. TSG-6 and stabilins contain a single link module which supports high affinity binding to HA.


Pssm-ID: 239592  Cd Length: 93  Bit Score: 48.61  E-value: 1.94e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 305 QLFAAWKLQLlDRCTAGWLADGSARYPIVNPRARCGGRRPGVRSLGFPDATRRLFGVYCY 364
Cdd:cd03515  35 QLSAAQQLGF-HLCAAGWLAKGRVGYPIVFPSANCGFGHVGIVDYGPRLNLSERWDAYCY 93
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 48-147 1.07e-06

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 46.02  E-value: 1.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684    48 VVQTAPGQVVSHRGGTIVLPCRyhyeaaAHGHDGVRLKWTKvvdplaftdvfvalGPQHRAFGSYRGRAELQGDGpgdaS 127
Cdd:pfam13927   3 VITVSPSSVTVREGETVTLTCE------ATGSPPPTITWYK--------------NGEPISSGSTRSRSLSGSNS----T 58

                          90       100
                  ....*....|....*....|
gi 47605684   128 LVLRNVTLQDYGRYECEVTN 147
Cdd:pfam13927  59 LTISNVTRSDAGTYTCVASN 78
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 51-145 2.11e-06

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: 46.30  E-value: 2.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684    51 TAPGQVVSHRGGTIVLPCRYHYEaaaHGHDGVRLKWTKVvDPLAFTDVFVALGPQHRAFGSYRGRAELQGDGP-GDASLV 129
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSS---MSEASTSVYWYRQ-PPGKGPTFLIAYYSNGSEEGVKKGRFSGRGDPSnGDGSLT 76

                          90
                  ....*....|....*.
gi 47605684   130 LRNVTLQDYGRYECEV 145
Cdd:pfam07686  77 IQNLTLSDSGTYTCAV 92
IgV_HHLA2 cd16091
Immunoglobulin Variable (IgV) domain in HERV-H LTR-associating 2 (HHLA2); The members here are ...
 110-158 3.35e-06

Immunoglobulin Variable (IgV) domain in HERV-H LTR-associating 2 (HHLA2); The members here are composed of the immunoglobulin variable (IgV) region in HERV-H LTR-associating 2 (HHLA2; also known as B7-H7/B7 homolog 7). HHLA2 is a member of the B7 family of immune regulatory proteins. Mature human HHLA2 consists of an extracellular domain (ECD) with three immunoglobulin-like domains, a transmembrane segment, and a cytoplasmic domain. HHLA2 is widely expressed in human cancers including non-small cell lung carcinoma (NSCLS), triple negative breast cancer (TNBC), and melanoma, but has limited expression on normal tissues. Interestingly, unlike other members of B7 family, HHLA2 is not expressed in mice or rats. HHLA2 functions as a T cell coinhibitory molecules as it inhibits the proliferation of activated CD4(+) and CD8(+) T cells and their cytokine production. Furthermore, HHLA2 is constitutively expressed on the surface of human monocytes and is induced on B cells after stimulation, however it is not inducible on T cells.


Pssm-ID: 409512  Cd Length: 107  Bit Score: 45.46  E-value: 3.35e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 47605684 110 GSYRGRAELQGD--GPGDASLVLRNVTLQDYGRYECEVTNELEDDAGMVKL 158
Cdd:cd16091  55 QRYRNRTSLFKDqiSNGNASLLLRRVQLQDEGRYKCYTSTIIGNQESFVNL 105
Link_domain_CD44_like cd03516
This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates ...
 170-269 1.80e-05

This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It also plays an important role in arteriogenesis. The functional HA-binding domain of CD44 is an extended domain comprised of a single link module flanked with N-and C- extensions. These extensions are essential for folding and for functional activity. This group also contains the cell surface retention sequence (CRS) binding protein-1 (CRSBP-1) and lymph vessel endothelial receptor-1 (LYVE-1). CRSBP-1 is a cell surface binding protein for the CRS motif of PDGF-BB (platelet-derived growth factor-BB) and is responsible for the cell surface retention of PDGF-BB in SSV-transformed cells. CRSBP-1 may play a role in autocrine regulation of cell growth mediated by CRS containing growth regulators. LYVE-1 is preferentially expressed on the lymphatic endothelium and is used as a molecular marker for the detection and characterization of lymphatic vessels in tumors.


Pssm-ID: 239593  Cd Length: 144  Bit Score: 44.37  E-value: 1.80e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684 170 RGGRYKLTFAEAQRACAEQDGILASAEQLHAAWRDGLDWCNAGWLRDGSVQYPVNRPREPCgglggtgsaggggdanggL 249
Cdd:cd03516  13 KNGRYSLNFTEAKEACRALGLTLASKAQVETALKFGFETCRYGWVEDGFVVIPRIDPNPLC------------------G 74

                        90       100
                ....*....|....*....|....
gi 47605684 250 RNY-GY---RHNAEERYDAFCFTS 269
Cdd:cd03516  75 KNGtGVyilNSNLSSRYDAYCYNS 98
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 64-150 4.49e-05

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: 41.16  E-value: 4.49e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  64 IVLPCRyhyeaaAHGHDGVRLKWTKVVDPLAFTDVFValgpqhrafgsyrgraelQGDGPGDASLVLRNVTLQDYGRYEC 143
Cdd:cd00096   1 VTLTCS------ASGNPPPTITWYKNGKPLPPSSRDS------------------RRSELGNGTLTISNVTLEDSGTYTC 56


                ....*..
gi 47605684 144 EVTNELE 150
Cdd:cd00096  57 VASNSAG 63
IgV_1_JAM1-like cd20946
First Ig-like domain of Junctional adhesion molecule-1 (JAM1)and similar domains; a member of ...
 49-152 4.73e-05

First Ig-like domain of Junctional adhesion molecule-1 (JAM1)and similar domains; a member of the V-set of IgSF domains; The members here are composed of the first Ig-like domain of Junctional Adhesion Molecule-1 (JAM1)and similar domains. 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 first Ig-like domain of JAM1 is a member of the V-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C'-C" in the other.


Pssm-ID: 409538  Cd Length: 102  Bit Score: 42.14  E-value: 4.73e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  49 VQTAPGQVVSHRGGTIVLPCRYHYEAAAHghdgvRLKWTKVVDPLAFTDVFvalgpQHRAFGSYRGRAELQGdgpgdASL 128
Cdd:cd20946   2 VPSSQQVVTVVENQEVILSCKTPKKTSSP-----RVEWKKLQRDVTFVVFQ-----NNKIQGDYKGRAEILG-----TNI 66

                        90       100
                ....*....|....*....|....*....
gi 47605684 129 VLRNVTLQDYGRYECEVT-----NELEDD 152
Cdd:cd20946  67 TIKNVTRSDSGKYRCEVSarsdgQNLGEV 95
Ig_Aggrecan cd05900
Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), ...
 83-165 8.14e-05

Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan; The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan. In CSPGs, the 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 HA. These aggregates contribute to the tissue's load bearing properties. Aggrecan has a wide distribution in connective tissue and extracellular matrices. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409481  Cd Length: 123  Bit Score: 41.85  E-value: 8.14e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  83 RLKWTKVVDPlAFTDVFVALGPQHRAFGSYRGRAELQGDG--PGDASLVLRNVTLQDYGRYECEVTNELEDDAGMVKLDL 160
Cdd:cd05900  40 RIKWSFISKE-KESVLLVATEGKVRVNTEYLDRVSLPNYPaiPSDATLEITELRSNDSGTYRCEVMHGIEDNYDTVEVQV 118


                ....*
gi 47605684 161 EGVVF 165
Cdd:cd05900 119 KGIVF 123
IGv smart00406
Immunoglobulin V-Type;
63-145 1.43e-04

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 40.06  E-value: 1.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684     63 TIVLPCRYHYEAAAhghdGVRLKWTKVvDPLAFTDVFVALGPQHRAFG--SYRGRAELQGDG-PGDASLVLRNVTLQDYG 139
Cdd:smart00406   1 SVTLSCKFSGSTFS----SYYVSWVRQ-PPGKGLEWLGYIGSNGSSYYqeSYKGRFTISKDTsKNDVSLTISNLRVEDTG 75


                   ....*.
gi 47605684    140 RYECEV 145
Cdd:smart00406  76 TYYCAV 81
IgV_1_Nectin-4_like cd05888
First immunoglobulin (Ig) domain of nectin-4, and similar domains; The members here are ...
 61-145 2.83e-04

First immunoglobulin (Ig) domain of nectin-4, and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of nectin-4 (also known as poliovirus receptor related protein 4 or LNIR receptor). Nectin-4 belongs to the nectin family, which is comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which participate in adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. For example nectin-4 trans-interacts with nectin-1. Nectin-4 has also been shown to interact with the actin filament-binding protein, afadin. Unlike the other nectins, which are widely expressed in adult tissues, nectin-4 is mainly expressed during embryogenesis, and is not detected in normal adult tissue or in serum. Nectin-4 is re-expressed in breast carcinoma, and patients having metastatic breast cancer have a circulating form of nectin-4 formed from the ectodomain


Pssm-ID: 409471  Cd Length: 108  Bit Score: 39.88  E-value: 2.83e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  61 GGTIVLPCRYHYEAaahGHDGVRLKWTKVVDPLAFTDVFVALGPQ-HRAFGSYRGRAELQGDG-PGDASLVLRNVTLQDY 138
Cdd:cd05888   8 GQDAKLPCFYRGDS---GEQVGQVAWARVDAGEGAQEIALLHSKYgLHVFPAYEGRVEQPPPPrPADGSVLLRNAVQADE 84


                ....*..
gi 47605684 139 GRYECEV 145
Cdd:cd05888  85 GEYECRV 91
IgI_NCAM-2 cd05870
Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 2 (NCAM-2); The members ...
 56-149 3.15e-04

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: 39.57  E-value: 3.15e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  56 VVSHRGGTIVLPCRyhyeaaAHGHDGVRLKWTKVVDPLAFTDvfvalGPQhrafgSYRGRAELQGDGpGDASLVLRNVTL 135
Cdd:cd05870  11 ETTVENGAATLSCK------AEGEPIPEITWKRASDGHTFSE-----GDK-----SPDGRIEVKGQH-GESSLHIKDVKL 73

                        90
                ....*....|....
gi 47605684 136 QDYGRYECEVTNEL 149
Cdd:cd05870  74 SDSGRYDCEAASRI 87
IgV_CD33 cd05712
Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic ...
 51-141 3.32e-04

Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic acid-binding Ig-like lectins); The members here are composed of the immunoglobulin (Ig) domain at the N-terminus of Cluster of Differentiation (CD) 33 and related Siglecs (sialic acid-binding Ig-like lectins). Siglec refers to a structurally related protein family that specifically recognizes sialic acid in oligosaccharide chains of glycoproteins and glycolipids. Siglecs are type I transmembrane proteins, organized as an extracellular module composed of Ig-like domains, an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains, followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG, the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11.


Pssm-ID: 409377  Cd Length: 119  Bit Score: 40.07  E-value: 3.32e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  51 TAPGQVVSHRGGTIVLPCRYHYEAAAHGHDGVRLKWTKVVDPLAFTDVFVALGPQHRAFGSYRGRAELQGD-GPGDASLV 129
Cdd:cd05712   4 QMPKSVTVQEGLCVLIPCSFSYPADYWVSNPVHGYWYRGGPYPKYRPPVATNNRTREVHESTQGRFRLLGDpGKKNCSLS 83

                        90
                ....*....|..
gi 47605684 130 LRNVTLQDYGRY 141
Cdd:cd05712  84 ISDARPEDSGKY 95
IgV_1_Nectin-2_NecL-5_like_CD112_CD155 cd20989
First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar ...
 47-144 6.03e-04

First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar domains; The members here are composed of the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or Cluster of Differentiation 112 (CD112)), nectin-like protein 5 (CD155), and similar proteins. Nectins and Nectin-like molecules are a family of Ca(2+)-independent immunoglobulin-like transmembrane glycoproteins belonging to the class of adhesion receptors, consisting of nine members (nectins 1 through 4 and nectin-like proteins 1 through 5). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. CD155 is the fifth member in the nectin-like molecule family, and functions as the receptor of poliovirus; therefore, CD155 is also referred to as Necl-5, or PVR. In contrast to all other family members, CD155 lacks self-adhesion capacity, yet it shares with nectins the feature to interact with other nectins. For instance, CD155 heterophilically trans-interacts with nectin-3, thereby contributing significantly to the establishment of adherens junctions between epithelial cells. This group belongs to the Constant 1 (C1)-set of IgSF domains, which has one beta-sheet that is formed by strands A-B-E-D and the other strands by G-F-C-C'.


Pssm-ID: 409581  Cd Length: 112  Bit Score: 39.10  E-value: 6.03e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  47 VVVQtAPGQVVSHRGGTIVLPCryHYEAAAHGHDGVRLKWTKVvDPLAFTDVF-VALGPQHR-----AFGSYRGRAELQg 120
Cdd:cd20989   1 VRVQ-VPPEVRGFLGGSVTLPC--HLLPPNMVTHVSQVTWQRH-DEHGSVAVFhPKQGPSFPeserlSFVAARLGAELR- 75

                        90       100
                ....*....|....*....|....
gi 47605684 121 dgpgDASLVLRNVTLQDYGRYECE 144
Cdd:cd20989  76 ----NASLAMFGLRVEDEGNYTCE 95
IgV_CD2_like_N cd05775
N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; ...
 76-148 9.57e-04

N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain (or domain 1) of T-cell surface antigen Clusters of Differentiation (CD) 2 and similar proteins. CD2 is a T-cell specific surface glycoprotein and is critically important for mediating adhesion between T cells and antigen-presenting cells or between cytolytic T cells and target cells. CD2 is located on chromosome 1 at 1p13 in humans and on chromosome 3 in mice. CD2 contains an extracellular domain with two or Ig-like domains, a single transmembrane segment, and a cytoplasmic region rich in proline and basic residues.


Pssm-ID: 409431  Cd Length: 98  Bit Score: 38.10  E-value: 9.57e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 47605684  76 AHGHDGVRLKWTKVVDPLAftDVFVALGPqhRAFGSYRGRAELQgdgPGDASLVLRNVTLQDYGRYECEVTNE 148
Cdd:cd05775  19 SLQDDIDEIKWKKTKDKIV--EWENNIGP--TYFGSFKDRVLLD---KESGSLTIKNLTKEDSGTYELEITST 84
IgV_MOG_like cd05713
Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here ...
 112-143 1.33e-03

Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG); The members here are composed of the immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). MOG, a minor component of the myelin sheath, is an important CNS-specific autoantigen, linked to the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). It is a transmembrane protein having an extracellular Ig domain. MOG is expressed in the CNS on the outermost lamellae of the myelin sheath, and on the surface of oligodendrocytes, and may participate in the completion, compaction, and/or maintenance of myelin. This group also includes butyrophilin (BTN). BTN is the most abundant protein in bovine milk-fat globule membrane (MFGM).


Pssm-ID: 409378  Cd Length: 114  Bit Score: 38.33  E-value: 1.33e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 47605684 112 YRGRAELQGDG--PGDASLVLRNVTLQDYGRYEC 143
Cdd:cd05713  63 YRGRTELLKDAiaEGSVALRIHNVRPSDEGQYTC 96
IgV_CEACAM_like cd05741
Immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion ...
 105-148 1.35e-03

Immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and related domains. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions: it is a cell adhesion molecule and a signaling molecule that regulates the growth of tumor cells, an angiogenic factor, and a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two (D1, D4) or four (D1-D4) Ig-like domains on the cell surface. This family corresponds to the D1 Ig-like domain. Also belonging to this group is the N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84-like family. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. SLAM family proteins are organized as an extracellular domain with having two or four Ig-like domains, a single transmembrane segment, and a cytoplasmic region having Tyr-based motifs. The extracellular domain is organized as a membrane-distal Ig variable (IgV) domain that is responsible for ligand recognition and a membrane-proximal truncated Ig constant-2 (IgC2) domain.


Pssm-ID: 409403  Cd Length: 102  Bit Score: 37.88  E-value: 1.35e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 47605684 105 QHRAFGSYRGRAELQGDGpgdaSLVLRNVTLQDYGRYECEVTNE 148
Cdd:cd05741  50 EFRAGSAFSGREYIYTNG----SLLIQNITLSDTGFYTLESTNI 89
IgV_B7-H4 cd20984
Immunoglobulin Variable (IgV) domain of B7-H4; The members here are composed of the ...
 57-147 1.78e-03

Immunoglobulin Variable (IgV) domain of B7-H4; The members here are composed of the immunoglobulin variable (IgV) domain of B7-H4 (also known as B7-S1, B7x, or Vtcn1). B7-H4 is one of the B7 family of immune-regulatory ligands that act as negative regulators of T cell function; it contains one IgV domain and one IgC domain. The B7-family consists of structurally related cell-surface protein ligands, which bind to receptors on lymphocytes that regulate immune responses. The binding of B7-H4 to unidentified receptors results in the inhibition of TCR-mediated T cell proliferation, cell-cycle progression and IL-2 production. As a co-inhibitory molecule, B7-H4 is widely expressed in tumor tissues and its expression is significantly associated with poor prognosis in human cancers such as glioma, pancreatic cancer, oral squamous cell carcinoma, renal cell carcinoma, and lung cancer.


Pssm-ID: 409576  Cd Length: 110  Bit Score: 37.96  E-value: 1.78e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684  57 VSHRGGTIVLPCRYHYEAAAHGHDgvrLKWTKVVDP---LAFTDVFVALGPQHRAFgsyRGRAELQGDG--PGDASLVLR 131
Cdd:cd20984   8 AGNIGEDGILSCTFTPDIKLSDIV---IQWLKEGDSglvHEFKEGKDELSRQSPMF---RGRTSLFADQvhVGNASLRLK 81

                        90
                ....*....|....*.
gi 47605684 132 NVTLQDYGRYECEVTN 147
Cdd:cd20984  82 NVQLTDAGTYLCIISN 97
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 52-149 2.01e-03

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: 37.17  E-value: 2.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47605684    52 APGQVVSHRGGTIVLPCRYHyeaaaHGHDGVRLKWTKvvdplafTDVFVALGPQHraFGSYRGRaelqgdgpGDASLVLR 131
Cdd:pfam00047   2 APPTVTVLEGDSATLTCSAS-----TGSPGPDVTWSK-------EGGTLIESLKV--KHDNGRT--------TQSSLLIS 59

                          90
                  ....*....|....*...
gi 47605684   132 NVTLQDYGRYECEVTNEL 149
Cdd:pfam00047  60 NVTKEDAGTYTCVVNNPG 77
IgV_PDl1 cd20947
Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1); The members here ...
 102-146 8.24e-03

Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1); The members here are composed of the immunoglobulin variable (IgV) domain of Programmed death ligand 1 (PD-L1; also known as Cluster of Differentiation 274 (CD274)). PD-L1 is a cell-surface ligand that competes with PD-L2 for binding to the immunosuppressive receptor programmed death-1 (PD-1). PD-1 is a member of the B7 family that plays an important role in negatively regulating immune responses upon interaction with its two ligands, PD-L1 or PD-L2. Like PD-L2, PD-L1 interacts with PD-1 and suppresses T cell proliferation and cytokine production. The PD-1 receptor is expressed on the surface of activated T cells, while PD-L1 is expressed on cancer cells. When PD-1 and PD-L1 bind together, they form a molecular shield protecting tumor cells from being destroyed by the immune system. Thus, inhibiting the binding of PD-L1 to PD-1 with an antibody leads to killing of tumor cells by T cells. PD-1 inhibitors (such as Pembrolizumab, Nivolumab, and Cemiplimab) and PD-L1 inhibitors (such as Atezolizumab, Avelumab, and Durvalumab ) are an emerging class of immunotherapy that stimulate lymphocytes against tumor cells.


Pssm-ID: 409539  Cd Length: 110  Bit Score: 36.06  E-value: 8.24e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 47605684 102 LGPQHrafGSYRGRAELQGDG--PGDASLVLRNVTLQDYGRYECEVT 146
Cdd:cd20947  54 LKVQH---SSYRQRARLLKDQlsLGNAALQITDVKLQDAGVYRCMIS 97
 
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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