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Conserved domains on  [gi|1720387542|ref|XP_030105084|]
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nectin-3 isoform X3 [Mus musculus]

Protein Classification

Ig and TM_EGFR-like domain-containing protein( domain architecture ID 10309443)

Ig and TM_EGFR-like domain-containing protein

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 ...
1-53 2.21e-27

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 cd07704:

Pssm-ID: 448366  Cd Length: 96  Bit Score: 102.98  E-value: 2.21e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1720387542   1 MESSTTSFPNETATIVSQYKLFPTRFARGRRITCVVKHPALEKDIRYSFILDI 53
Cdd:cd07704    44 MESSRTFEHNRTATVTSEYHLVPTRFANGRPLTCVVSHPALQQDIRITHILDV 96
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
57-143 7.18e-16

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 cd20930:

Pssm-ID: 448366  Cd Length: 86  Bit Score: 71.83  E-value: 7.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720387542  57 PEVSVTGYDGNWFVGRKGVNLKCNADANPPPFKSVWSRLDGQWPDGLLASDNTLhFVHPLTVNYSGVYVCKVSNSLGQRS 136
Cdd:cd20930     1 PEVSISGYDDNWYLGRNEATLTCDVRSNPEPTGYDWSTTSGPFPTSAVAQGPQL-LIHSVDRLVNTTFICTVTNAVGTGR 79

                  ....*..
gi 1720387542 137 DQKVIYI 143
Cdd:cd20930    80 AEQTIFV 86
TM_EGFR-like cd12087
Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine ...
190-220 4.09e-03

Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases; PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. They are activated by ligand-induced dimerization, resulting in the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Collectively, they can recognize a variety of ligands including EGF, TGFalpha, and neuregulins, among others. All four subfamily members can form homo- or heterodimers. HER3 contains an impaired kinase domain and depends on its heterodimerization partner for activation. EGFR subfamily members are involved in signaling pathways leading to a broad range of cellular responses including cell proliferation, differentiation, migration, growth inhibition, and apoptosis. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of EGFR family RTKs have been associated with increased breast cancer risk.


:

Pssm-ID: 213052  Cd Length: 38  Bit Score: 34.43  E-value: 4.09e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1720387542 190 IGTIIASVVGGALFLVLVSilAGVFCYRRRR 220
Cdd:cd12087     5 TTSIAAGVVGGLLVLVILG--LIVFLFRRRR 33
 
Name Accession Description Interval E-value
IgC1_2_Nectin-3-4_like cd07704
Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related ...
1-53 2.21e-27

Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3 or cluster of differentiation (CD) 113) and nectin-4 (poliovirus receptor related protein 4). Nectin-3 and nectin-4 belong to the nectin family comprised of four transmembrane glycoproteins (nectin-1 through -4). 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. Nectin-3 has also been shown to form a heterophilic trans-interaction with nectin-1 in ciliary epithelia, establishing the apex-apex adhesion between the pigment and non-pigment cell layers. Nectin-4 has recently been identified in several types of breast carcinoma and can be used as a histological and serological marker for breast cancer.


Pssm-ID: 409501  Cd Length: 96  Bit Score: 102.98  E-value: 2.21e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1720387542   1 MESSTTSFPNETATIVSQYKLFPTRFARGRRITCVVKHPALEKDIRYSFILDI 53
Cdd:cd07704    44 MESSRTFEHNRTATVTSEYHLVPTRFANGRPLTCVVSHPALQQDIRITHILDV 96
Ig3_Nectin-5_like cd20930
Third immunoglobulin domain of Nectin-like Protein-5, and similar domains; The members here ...
57-143 7.18e-16

Third immunoglobulin domain of Nectin-like Protein-5, and similar domains; The members here are composed of the third immunoglobulin domain of Nectin-like Protein-5 (also known as Cluster of Differentiation 155 (CD155)). Nectin-like Protein-5 mediates NK (Natural Killer) cell adhesion and triggers NK cell effector functions. CD155 binds two different NK cell receptors: CD96 and CD226. These interactions accumulate at the cell-cell contact site, leading to the formation of a mature immunological synapse between NK cell and target cell. This may trigger adhesion and secretion of lytic granules and IFN-gamma and activate cytotoxicity of activated NK cells. CD155 may also promote NK cell-target cell modular exchange, and PVR transfer to the NK cell. This transfer is more important in some tumor cells expressing a lot of PVR, and may trigger fratricide NK cell activation, providing tumors with a mechanism of immunoevasion. Moreover, CD155 plays a role in mediating tumor cell invasion and migration.


Pssm-ID: 409524  Cd Length: 86  Bit Score: 71.83  E-value: 7.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720387542  57 PEVSVTGYDGNWFVGRKGVNLKCNADANPPPFKSVWSRLDGQWPDGLLASDNTLhFVHPLTVNYSGVYVCKVSNSLGQRS 136
Cdd:cd20930     1 PEVSISGYDDNWYLGRNEATLTCDVRSNPEPTGYDWSTTSGPFPTSAVAQGPQL-LIHSVDRLVNTTFICTVTNAVGTGR 79

                  ....*..
gi 1720387542 137 DQKVIYI 143
Cdd:cd20930    80 AEQTIFV 86
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
1-45 1.48e-09

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


Pssm-ID: 400489  Cd Length: 89  Bit Score: 54.35  E-value: 1.48e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1720387542   1 MESSTTSFPNETATIVSQYKLFPTRFARGRRITCVVKHPALEKDI 45
Cdd:pfam08205  45 ETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQVSYGALRGSI 89
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
75-136 2.23e-06

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: 45.19  E-value: 2.23e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1720387542   75 VNLKCNADANPPPFKSvWSRLDGQW---PDGLLASDNTLHFV---HPLTVNYSGVYVCKVSNSLGQRS 136
Cdd:smart00410  12 VTLSCEASGSPPPEVT-WYKQGGKLlaeSGRFSVSRSGSTSTltiSNVTPEDSGTYTCAATNSSGSAS 78
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
75-130 1.48e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 433584 [Multi-domain]  Cd Length: 75  Bit Score: 39.49  E-value: 1.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720387542  75 VNLKCNADANPPPfkSVWSRLDGQW----PDGLLASDNTLHfVHPLTVNYSGVYVCKVSN 130
Cdd:pfam13927  19 VTLTCEASGSPPP--TITWYKNGGKlssgRTSLVGGNGTLT-ISNVTREDSGTYTCTASN 75
TM_EGFR-like cd12087
Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine ...
190-220 4.09e-03

Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases; PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. They are activated by ligand-induced dimerization, resulting in the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Collectively, they can recognize a variety of ligands including EGF, TGFalpha, and neuregulins, among others. All four subfamily members can form homo- or heterodimers. HER3 contains an impaired kinase domain and depends on its heterodimerization partner for activation. EGFR subfamily members are involved in signaling pathways leading to a broad range of cellular responses including cell proliferation, differentiation, migration, growth inhibition, and apoptosis. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of EGFR family RTKs have been associated with increased breast cancer risk.


Pssm-ID: 213052  Cd Length: 38  Bit Score: 34.43  E-value: 4.09e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1720387542 190 IGTIIASVVGGALFLVLVSilAGVFCYRRRR 220
Cdd:cd12087     5 TTSIAAGVVGGLLVLVILG--LIVFLFRRRR 33
 
Name Accession Description Interval E-value
IgC1_2_Nectin-3-4_like cd07704
Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related ...
1-53 2.21e-27

Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3 or cluster of differentiation (CD) 113) and nectin-4 (poliovirus receptor related protein 4). Nectin-3 and nectin-4 belong to the nectin family comprised of four transmembrane glycoproteins (nectin-1 through -4). 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. Nectin-3 has also been shown to form a heterophilic trans-interaction with nectin-1 in ciliary epithelia, establishing the apex-apex adhesion between the pigment and non-pigment cell layers. Nectin-4 has recently been identified in several types of breast carcinoma and can be used as a histological and serological marker for breast cancer.


Pssm-ID: 409501  Cd Length: 96  Bit Score: 102.98  E-value: 2.21e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1720387542   1 MESSTTSFPNETATIVSQYKLFPTRFARGRRITCVVKHPALEKDIRYSFILDI 53
Cdd:cd07704    44 MESSRTFEHNRTATVTSEYHLVPTRFANGRPLTCVVSHPALQQDIRITHILDV 96
IgC1_2_PVR_like cd05719
Second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and Necl-5), ...
1-53 2.54e-21

Second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and Necl-5), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (Necl-5)) and similar proteins. Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), these result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted, while CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" and has a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the second Ig-like domain of nectin-1, also known as poliovirus receptor related protein(PVRL)1 or CD111.


Pssm-ID: 409384  Cd Length: 96  Bit Score: 86.78  E-value: 2.54e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1720387542   1 MESSTTSFP-NETATIVSQYKLFPTRFARGRRITCVVKHPALEKDIRYSFILDI 53
Cdd:cd05719    43 EASTTQVRGsNGTVTVTSRYRLVPSREADGQPLTCVVEHPSLEKDQRISVTLNV 96
Ig3_Nectin-5_like cd20930
Third immunoglobulin domain of Nectin-like Protein-5, and similar domains; The members here ...
57-143 7.18e-16

Third immunoglobulin domain of Nectin-like Protein-5, and similar domains; The members here are composed of the third immunoglobulin domain of Nectin-like Protein-5 (also known as Cluster of Differentiation 155 (CD155)). Nectin-like Protein-5 mediates NK (Natural Killer) cell adhesion and triggers NK cell effector functions. CD155 binds two different NK cell receptors: CD96 and CD226. These interactions accumulate at the cell-cell contact site, leading to the formation of a mature immunological synapse between NK cell and target cell. This may trigger adhesion and secretion of lytic granules and IFN-gamma and activate cytotoxicity of activated NK cells. CD155 may also promote NK cell-target cell modular exchange, and PVR transfer to the NK cell. This transfer is more important in some tumor cells expressing a lot of PVR, and may trigger fratricide NK cell activation, providing tumors with a mechanism of immunoevasion. Moreover, CD155 plays a role in mediating tumor cell invasion and migration.


Pssm-ID: 409524  Cd Length: 86  Bit Score: 71.83  E-value: 7.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720387542  57 PEVSVTGYDGNWFVGRKGVNLKCNADANPPPFKSVWSRLDGQWPDGLLASDNTLhFVHPLTVNYSGVYVCKVSNSLGQRS 136
Cdd:cd20930     1 PEVSISGYDDNWYLGRNEATLTCDVRSNPEPTGYDWSTTSGPFPTSAVAQGPQL-LIHSVDRLVNTTFICTVTNAVGTGR 79

                  ....*..
gi 1720387542 137 DQKVIYI 143
Cdd:cd20930    80 AEQTIFV 86
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
1-45 1.48e-09

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


Pssm-ID: 400489  Cd Length: 89  Bit Score: 54.35  E-value: 1.48e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1720387542   1 MESSTTSFPNETATIVSQYKLFPTRFARGRRITCVVKHPALEKDI 45
Cdd:pfam08205  45 ETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQVSYGALRGSI 89
IgC1_2_Nectin-2_Necl-5_like cd07703
Second immunoglobulin (Ig) domain of Nectin-2 and Nectin-like protein 5, and similar domains; ...
2-44 3.15e-07

Second immunoglobulin (Ig) domain of Nectin-2 and Nectin-like protein 5, and similar domains; member of the C1-set of the Ig superfamily (IgSF) 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: 409500  Cd Length: 97  Bit Score: 47.78  E-value: 3.15e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1720387542   2 ESSTTSFPNETATIVSQYKLFPTRFARGRRITCVVKHPALEKD 44
Cdd:cd07703    45 TTQVPGPDSGTVTVTSEYSLVPTPEANGKEVTCKVEHETLEEP 87
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
75-136 2.23e-06

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: 45.19  E-value: 2.23e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1720387542   75 VNLKCNADANPPPFKSvWSRLDGQW---PDGLLASDNTLHFV---HPLTVNYSGVYVCKVSNSLGQRS 136
Cdd:smart00410  12 VTLSCEASGSPPPEVT-WYKQGGKLlaeSGRFSVSRSGSTSTltiSNVTPEDSGTYTCAATNSSGSAS 78
Ig cd00096
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
75-133 4.51e-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: 4.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720387542  75 VNLKCNADANPPPfKSVWSR------LDGQWPDGLLASDNTLHFvHPLTVNYSGVYVCKVSNSLG 133
Cdd:cd00096     1 VTLTCSASGNPPP-TITWYKngkplpPSSRDSRRSELGNGTLTI-SNVTLEDSGTYTCVASNSAG 63
IgI_3_Robo cd05725
Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
75-134 1.15e-04

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


Pssm-ID: 409390 [Multi-domain]  Cd Length: 83  Bit Score: 40.07  E-value: 1.15e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720387542  75 VNLKCNADANPPPfKSVWSRLDGQWPDGL--LASDNTLHFVHpLTVNYSGVYVCKVSNSLGQ 134
Cdd:cd05725    15 AEFQCEVGGDPVP-TVRWRKEDGELPKGRyeILDDHSLKIRK-VTAGDMGSYTCVAENMVGK 74
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
75-130 1.48e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 433584 [Multi-domain]  Cd Length: 75  Bit Score: 39.49  E-value: 1.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720387542  75 VNLKCNADANPPPfkSVWSRLDGQW----PDGLLASDNTLHfVHPLTVNYSGVYVCKVSN 130
Cdd:pfam13927  19 VTLTCEASGSPPP--TITWYKNGGKlssgRTSLVGGNGTLT-ISNVTREDSGTYTCTASN 75
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
75-134 8.39e-04

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


Pssm-ID: 395002  Cd Length: 86  Bit Score: 37.94  E-value: 8.39e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1720387542  75 VNLKCNADANPPPFKSVWSRLDGQWPDGLLA-------SDNTLHFVhPLTVNYSGVYVCKVSNSLGQ 134
Cdd:pfam00047  14 ATLTCSASTGSPGPDVTWSKEGGTLIESLKVkhdngrtTQSSLLIS-NVTKEDAGTYTCVVNNPGGS 79
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
12-48 1.27e-03

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


Pssm-ID: 409428  Cd Length: 100  Bit Score: 37.86  E-value: 1.27e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1720387542  12 TATIVSQYKLFPTRFARGRRITCVVKHPALEKDIRYS 48
Cdd:cd05771    64 TYSISSYLTLEPGTENRGATYTCRVTHVSLEEPLSVS 100
I-set pfam07679
Immunoglobulin I-set domain;
75-136 1.29e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 37.24  E-value: 1.29e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720387542  75 VNLKCNADANPPPfKSVWSRlDGQwpdgLLASDNTLHF----------VHPLTVNYSGVYVCKVSNSLGQRS 136
Cdd:pfam07679  18 ARFTCTVTGTPDP-EVSWFK-DGQ----PLRSSDRFKVtyeggtytltISNVQPDDSGKYTCVATNSAGEAE 83
IgC2_CEACAM5-like cd20948
Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell ...
76-140 1.37e-03

Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains; member of the C2-set IgSF domains; The members here are composed of the fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar 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. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), also known as CD66e (Cluster of Differentiation 66e), is a cell surface glycoprotein that plays a role in cell adhesion, intracellular signaling and tumor progression. Diseases associated with CEACAM5 include lung cancer and rectum cancer. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand.


Pssm-ID: 409540  Cd Length: 76  Bit Score: 37.09  E-value: 1.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1720387542  76 NLKCNADANPPPFKSvWSrldgqWPDGLLASDNTLhFVHPLTVNYSGVYVCKVSNSLGQRSDQKV 140
Cdd:cd20948    14 NLSCHAASNPPAQYS-WT-----INGTFQTSSQEL-FLPAITENNEGTYTCSAHNSLTGKNISLV 71
TM_EGFR-like cd12087
Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine ...
190-220 4.09e-03

Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases; PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. They are activated by ligand-induced dimerization, resulting in the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Collectively, they can recognize a variety of ligands including EGF, TGFalpha, and neuregulins, among others. All four subfamily members can form homo- or heterodimers. HER3 contains an impaired kinase domain and depends on its heterodimerization partner for activation. EGFR subfamily members are involved in signaling pathways leading to a broad range of cellular responses including cell proliferation, differentiation, migration, growth inhibition, and apoptosis. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of EGFR family RTKs have been associated with increased breast cancer risk.


Pssm-ID: 213052  Cd Length: 38  Bit Score: 34.43  E-value: 4.09e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1720387542 190 IGTIIASVVGGALFLVLVSilAGVFCYRRRR 220
Cdd:cd12087     5 TTSIAAGVVGGLLVLVILG--LIVFLFRRRR 33
Ig_DSCAM cd05734
Immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM); The members ...
73-144 4.58e-03

Immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM); The members here are composed of the immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the intellectual disability phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion.


Pssm-ID: 409397 [Multi-domain]  Cd Length: 97  Bit Score: 35.93  E-value: 4.58e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1720387542  73 KGVNLKCNADANPPPfKSVWSRLDG-----QWPDGLLA------SDNTLHFVHPLTVNySGVYVCKVSNSLGqrSD-QKV 140
Cdd:cd05734    17 KAVVLNCSADGYPPP-TIVWKHSKGsgvpqFQHIVPLNgriqllSNGSLLIKHVLEED-SGYYLCKVSNDVG--ADiSKS 92

                  ....
gi 1720387542 141 IYIS 144
Cdd:cd05734    93 MYLT 96
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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