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Conserved domains on  [gi|1187631538|ref|XP_020768864|]
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programmed cell death protein 1 [Odocoileus virginianus texanus]

Protein Classification

IgV_PD1 domain-containing protein( domain architecture ID 11610716)

IgV_PD1 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 3.06e-77

Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.


:

Pssm-ID: 409509  Cd Length: 112  Bit Score: 230.09  E-value: 3.06e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  34 ALTFSPARLVVPEGANATFTCSFSSKPEHFVLNWYRMSPSNQTDKLAAFPEDRSQPGRDQRFRVTPLPDGQHFLMSVVAA 113
Cdd:cd16088     1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1187631538 114 QRNDSGVYFCGAIYLPPRTQINESHPAELTVT 145
Cdd:cd16088    81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 3.06e-77

Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.


Pssm-ID: 409509  Cd Length: 112  Bit Score: 230.09  E-value: 3.06e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  34 ALTFSPARLVVPEGANATFTCSFSSKPEHFVLNWYRMSPSNQTDKLAAFPEDRSQPGRDQRFRVTPLPDGQHFLMSVVAA 113
Cdd:cd16088     1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1187631538 114 QRNDSGVYFCGAIYLPPRTQINESHPAELTVT 145
Cdd:cd16088    81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-145 6.40e-16

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: 71.72  E-value: 6.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  38 SPARLVVPEGANATFTCSFSS--KPEHFVLNWYRMSPSNQTDKL-AAFPEDRSQPGRDQRFRVTPLPDGQHFLMSVVAAQ 114
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSsmSEASTSVYWYRQPPGKGPTFLiAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1187631538 115 RNDSGVYFCGAIylpPRTQINESHPAELTVT 145
Cdd:pfam07686  82 LSDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 39-144 2.08e-09

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: 53.28  E-value: 2.08e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538   39 PARLVVPEGANATFTCSFSSKPEHFVlNWYRmspsnqtdklaafpEDRSQPGRDQRFRVTPLPDGQHFLMSvvAAQRNDS 118
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEV-TWYK--------------QGGKLLAESGRFSVSRSGSTSTLTIS--NVTPEDS 63

                           90       100
                   ....*....|....*....|....*.
gi 1187631538  119 GVYFCGAIYlpprTQINESHPAELTV 144
Cdd:smart00410  64 GTYTCAATN----SSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 3.06e-77

Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.


Pssm-ID: 409509  Cd Length: 112  Bit Score: 230.09  E-value: 3.06e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  34 ALTFSPARLVVPEGANATFTCSFSSKPEHFVLNWYRMSPSNQTDKLAAFPEDRSQPGRDQRFRVTPLPDGQHFLMSVVAA 113
Cdd:cd16088     1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1187631538 114 QRNDSGVYFCGAIYLPPRTQINESHPAELTVT 145
Cdd:cd16088    81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-145 6.40e-16

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: 71.72  E-value: 6.40e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  38 SPARLVVPEGANATFTCSFSS--KPEHFVLNWYRMSPSNQTDKL-AAFPEDRSQPGRDQRFRVTPLPDGQHFLMSVVAAQ 114
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSsmSEASTSVYWYRQPPGKGPTFLiAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1187631538 115 RNDSGVYFCGAIylpPRTQINESHPAELTVT 145
Cdd:pfam07686  82 LSDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 35-123 2.34e-11

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


Pssm-ID: 409355 [Multi-domain]  Cd Length: 111  Bit Score: 59.66  E-value: 2.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  35 LTFSPARLVVPEGANATFTCSFSSKPEHFVLNWYRMSPSNQtdklaafPE---------DRSQPGRDQRFRVTpLPDGQH 105
Cdd:cd00099     1 VTQSPRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKPGQG-------PEfliylssskGKTKGGVPGRFSGS-RDGTSS 72

                          90
                  ....*....|....*...
gi 1187631538 106 FLMSVVAAQRNDSGVYFC 123
Cdd:cd00099    73 FSLTISNLQPEDSGTYYC 90
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 39-144 2.08e-09

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: 53.28  E-value: 2.08e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538   39 PARLVVPEGANATFTCSFSSKPEHFVlNWYRmspsnqtdklaafpEDRSQPGRDQRFRVTPLPDGQHFLMSvvAAQRNDS 118
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEV-TWYK--------------QGGKLLAESGRFSVSRSGSTSTLTIS--NVTPEDS 63

                           90       100
                   ....*....|....*....|....*.
gi 1187631538  119 GVYFCGAIYlpprTQINESHPAELTV 144
Cdd:smart00410  64 GTYTCAATN----SSGSASSGTTLTV 85
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 38-125 1.93e-07

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


Pssm-ID: 409480  Cd Length: 110  Bit Score: 48.43  E-value: 1.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  38 SPARLVVPEGANATFTCSFSSkpEHFVLNWYRMSP------------SNQTDKlAAFPEDRSQPGRdqrfrvtplPDGQH 105
Cdd:cd05899     4 SPRYLIKRRGQSVTLRCSQKS--GHDNMYWYRQDPgkglqllfysygGGLNEE-GDLPGDRFSASR---------PSLTR 71

                          90       100
                  ....*....|....*....|
gi 1187631538 106 FLMSVVAAQRNDSGVYFCGA 125
Cdd:cd05899    72 SSLTIKSAEPEDSAVYLCAS 91
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 38-123 2.74e-07

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


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 48.04  E-value: 2.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  38 SPARLVVPEGANATFTCSFSSKPEHFVLnWYRMSPSNQtdklaafPE------DRSQPGRDQRFRVTPLPDGQHFLMSVV 111
Cdd:cd04983     4 SPQSLSVQEGENVTLNCNYSTSTFYYLF-WYRQYPGQG-------PQfliyisSDSGNKKKGRFSATLDKSRKSSSLHIS 75

                          90
                  ....*....|..
gi 1187631538 112 AAQRNDSGVYFC 123
Cdd:cd04983    76 AAQLSDSAVYFC 87
IGv smart00406
Immunoglobulin V-Type;
49-123 6.10e-06

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 43.52  E-value: 6.10e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1187631538   49 NATFTCSFS-SKPEHFVLNWYRMSPSNQTDKLAAFPEDRSQPGRDQ---RFRVTPLPDGQHFLMSVVAAQRNDSGVYFC 123
Cdd:smart00406   1 SVTLSCKFSgSTFSSYYVSWVRQPPGKGLEWLGYIGSNGSSYYQESykgRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 35-132 6.12e-06

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


Pssm-ID: 409369  Cd Length: 106  Bit Score: 44.30  E-value: 6.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  35 LTFSPARLVVPEGANATFTCSFSSKPEHFVLNWYRMSPsNQTDKLAAFPEDRSQPGRDQRFRVTplPDGQHFLMSVVAAQ 114
Cdd:cd04980     3 MTQSPASLSVSPGERVTISCKASQSISSNYLAWYQQKP-GQAPKLLIYYASTLHSGVPSRFSGS--GSGTDFTLTISSVE 79

                          90
                  ....*....|....*...
gi 1187631538 115 RNDSGVYFCGAIYLPPRT 132
Cdd:cd04980    80 PEDAAVYYCQQGYTFPYT 97
IgC_1_Robo cd07693
First immunoglobulin (Ig)-like constant domain in Robo (roundabout) receptors, and similar ...
 39-125 1.40e-05

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


Pssm-ID: 409490 [Multi-domain]  Cd Length: 99  Bit Score: 42.92  E-value: 1.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  39 PARLVVPEGANATFTCSFSSKPEHfVLNWYRMSPSNQTDKLAAfpedRSQPgrdqrfrvTPLPDGQHFLMSVVAAQRN-- 116
Cdd:cd07693     7 PSDLIVSKGDPATLNCKAEGRPTP-TIQWLKNGQPLETDKDDP----RSHR--------IVLPSGSLFFLRVVHGRKGrs 73


                  ....*....
gi 1187631538 117 DSGVYFCGA 125
Cdd:cd07693    74 DEGVYVCVA 82
IgC2_3_Dscam cd20957
Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; ...
 31-123 6.92e-04

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


Pssm-ID: 409549 [Multi-domain]  Cd Length: 88  Bit Score: 37.90  E-value: 6.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  31 PWSAlTFSPARLVVPEGANATFTCSFSSKPEHFVLnWYRmspsnqtdklaafpeDRSQPGRDQRFRVTPLPdgqhfLMSV 110
Cdd:cd20957     1 PLSA-TIDPPVQTVDFGRTAVFNCSVTGNPIHTVL-WMK---------------DGKPLGHSSRVQILSED-----VLVI 58

                          90
                  ....*....|...
gi 1187631538 111 VAAQRNDSGVYFC 123
Cdd:cd20957    59 PSVKREDKGMYQC 71
I-set pfam07679
Immunoglobulin I-set domain;
39-125 1.08e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 37.24  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  39 PARLVVPEGANATFTCSFSSKPEhFVLNWYRmspsnqtdklaafpeDRSQPGRDQRFRVTPLPDGQHFLMSvvAAQRNDS 118
Cdd:pfam07679   7 PKDVEVQEGESARFTCTVTGTPD-PEVSWFK---------------DGQPLRSSDRFKVTYEGGTYTLTIS--NVQPDDS 68


                  ....*..
gi 1187631538 119 GVYFCGA 125
Cdd:pfam07679  69 GKYTCVA 75
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 35-125 2.78e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.00  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  35 LTFSPARLVVPEGANATFTCSFSSKPEHFVLnWYRMSpsnqtdklaafpedrsQPGRDQRFRVTPLPDGQHFLmSVVAAQ 114
Cdd:pfam13927   4 ITVSPSSVTVREGETVTLTCEATGSPPPTIT-WYKNG----------------EPISSGSTRSRSLSGSNSTL-TISNVT 65

                          90
                  ....*....|.
gi 1187631538 115 RNDSGVYFCGA 125
Cdd:pfam13927  66 RSDAGTYTCVA 76
IgI_4_Robo cd05726
Fourth immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
 39-126 4.19e-03

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


Pssm-ID: 409391 [Multi-domain]  Cd Length: 98  Bit Score: 36.09  E-value: 4.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  39 PARLVVPEGANATFTCSFSSKPEHFVLnWYRMSPSNqtdklAAFPEDRSQPgrDQRFRVTPLPDgqhflMSVVAAQRNDS 118
Cdd:cd05726     6 PRDQVVALGRTVTFQCETKGNPQPAIF-WQKEGSQN-----LLFPYQPPQP--SSRFSVSPTGD-----LTITNVQRSDV 72


                  ....*...
gi 1187631538 119 GVYFCGAI 126
Cdd:cd05726    73 GYYICQAL 80
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 39-125 5.33e-03

Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins. pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their C-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into mucosal secretions. Human pIgR is a glycosylated type I transmembrane protein, comprised of a 620-residue extracellular region, a 23-residue transmembrane region, and a 103-residue cytoplasmic tail. The extracellular region contains five domains that share sequence similarity with Ig variable (v) regions. This group also contains the Ig-like extracellular domains of other receptors such as NK cell receptor Nkp44 and myeloid receptors, among others.


Pssm-ID: 409381  Cd Length: 100  Bit Score: 35.84  E-value: 5.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  39 PARLVVPEGANATFTCSFSSKPEHFVLNWYRMSPSNQTDKLaafpeDRSQPGRDQRFRVTPLPDGQHFLMSVVAAQRNDS 118
Cdd:cd05716     4 PEVVTGVEGGSVTIQCPYPPKYASSRKYWCKWGSEGCQTLV-----SSEGVVPGGRISLTDDPDNGVFTVTLNQLRKEDA 78


                  ....*..
gi 1187631538 119 GVYFCGA 125
Cdd:cd05716    79 GWYWCGV 85
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 42-123 6.29e-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: 35.25  E-value: 6.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1187631538  42 LVVPEGANATFTCSFSSKPEHFVLNWYRMSPSNQTdklaafpEDRSQPGRDQRFrvtplpdgqHFLMSVVAAQRNDSGVY 121
Cdd:pfam00047   6 VTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIE-------SLKVKHDNGRTT---------QSSLLISNVTKEDAGTY 69


                  ..
gi 1187631538 122 FC 123
Cdd:pfam00047  70 TC 71
 
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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