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Conserved domains on  [gi|7304953|ref|NP_038516|]
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T-cell surface glycoprotein CD4 precursor [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CD4-extracel pfam09191
CD4, extracellular; Members of this family adopt an immunoglobulin-like beta-sandwich, with ...
 211-316 2.42e-60

CD4, extracellular; Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens.


:

Pssm-ID: 462712  Cd Length: 106  Bit Score: 192.13  E-value: 2.42e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953    211 TAITAYKSEGESAEFSFPLNFAEENGWGELMWKAEKDSFFQPWISFSIKNKEVSVQKSTKDLKLQLKETLPLTLKIPQVS 290
Cdd:pfam09191   1 VSNTVYKKEGEQVEFSFPLTFEDENLSGELRWQAEGASSSQSWITFSLKNRKVSVQKVTQDPKLQMKEKLPLTLTLPQAL 80

                          90       100
                  ....*....|....*....|....*.
gi 7304953    291 LQFAGSGNLTLTLDKGTLHQEVNLVV 316
Cdd:pfam09191  81 LQYAGSGNLTLTLDKGKLHQEVNLVV 106
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 27-125 9.55e-43

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 cd07690:

Pssm-ID: 472250  Cd Length: 97  Bit Score: 146.15  E-value: 9.55e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   27 KTLVLGKEGESAELPCESSQKKITVFTWKFSDQRKILGQHGKgvLIRGGSPSQFDRFDSKKGAWEKGSFPLIINKLKMED 106
Cdd:cd07690   1 KKVVLGKKGDTAELPCTASQKKSIQFHWKNSNQIKILGNQGS--FLTKGPSKLNDRADSRRNLWDQGSFPLIIKNLKIED 78

                        90
                ....*....|....*....
gi 7304953  107 SQTYICELENRKEEVELWV 125
Cdd:cd07690  79 SDTYICEVEDKKEEVELLV 97
CD4_CD cd22570
cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins; CD4, also called ...
 400-443 6.25e-21

cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins; CD4, also called T-cell surface antigen T4/Leu-3, is an integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, CD4 functions primarily as a coreceptor for MHC class II molecule:peptide complex. In other cells such as macrophages or NK cells, it plays a role in differentiation/activation, cytokine expression and cell migration in a TCR/LCK-independent pathway. CD4 participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages. The model corresponds to cytoplasmic domain of CD4, which is responsible for the interaction with HIV-1 Nef protein that suppresses multiple immune surveillance mechanisms to promote viral pathogenesis.


:

Pssm-ID: 439337  Cd Length: 44  Bit Score: 85.64  E-value: 6.25e-21
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 7304953  400 VLGGSFGFLGFLGLCILCCVRCRHQQRQAARMSQIKRLLSEKKT 443
Cdd:cd22570   1 VLGGAAGLLLFIGLCIFCCVRCRHRRRQAERMSQIKRLLSEKKT 44
C2-set pfam05790
Immunoglobulin C2-set domain;
128-207 1.50e-17

Immunoglobulin C2-set domain;


:

Pssm-ID: 399065  Cd Length: 80  Bit Score: 77.00  E-value: 1.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953    128 VTFSPGTSLLQGQSLTLTLDSNSKvSNPLTECKHKKGKVVSGSKVLSMSNLRVQDSDFWNCTVT-LDQKKNWFGMTLSVL 206
Cdd:pfam05790   1 VTVSCSNNLLTCEVLELTLPKGSK-MDPSLKLKGQEAKSLETKKLESTFQPTTEDSGTWVCLASdNDQKKLESVIEVLVL 79


                  .
gi 7304953    207 G 207
Cdd:pfam05790  80 E 80
C2-set pfam05790
Immunoglobulin C2-set domain;
317-387 1.42e-16

Immunoglobulin C2-set domain;


:

Pssm-ID: 399065  Cd Length: 80  Bit Score: 74.30  E-value: 1.42e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7304953    317 MKVAQLNNTLTCEVMGPTSPK---MRLTLKQENQEARVSEEQKVVQVVAP---ETGLWQCLLSEGDKVKMDSRIQVL 387
Cdd:pfam05790   1 VTVSCSNNLLTCEVLELTLPKgskMDPSLKLKGQEAKSLETKKLESTFQPtteDSGTWVCLASDNDQKKLESVIEVL 77
 
Name Accession Description Interval E-value
CD4-extracel pfam09191
CD4, extracellular; Members of this family adopt an immunoglobulin-like beta-sandwich, with ...
 211-316 2.42e-60

CD4, extracellular; Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens.


Pssm-ID: 462712  Cd Length: 106  Bit Score: 192.13  E-value: 2.42e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953    211 TAITAYKSEGESAEFSFPLNFAEENGWGELMWKAEKDSFFQPWISFSIKNKEVSVQKSTKDLKLQLKETLPLTLKIPQVS 290
Cdd:pfam09191   1 VSNTVYKKEGEQVEFSFPLTFEDENLSGELRWQAEGASSSQSWITFSLKNRKVSVQKVTQDPKLQMKEKLPLTLTLPQAL 80

                          90       100
                  ....*....|....*....|....*.
gi 7304953    291 LQFAGSGNLTLTLDKGTLHQEVNLVV 316
Cdd:pfam09191  81 LQYAGSGNLTLTLDKGKLHQEVNLVV 106
IgV_1_CD4 cd07690
First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of ...
 27-125 9.55e-43

First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains; The members here are composed of the first immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.


Pssm-ID: 409487  Cd Length: 97  Bit Score: 146.15  E-value: 9.55e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   27 KTLVLGKEGESAELPCESSQKKITVFTWKFSDQRKILGQHGKgvLIRGGSPSQFDRFDSKKGAWEKGSFPLIINKLKMED 106
Cdd:cd07690   1 KKVVLGKKGDTAELPCTASQKKSIQFHWKNSNQIKILGNQGS--FLTKGPSKLNDRADSRRNLWDQGSFPLIIKNLKIED 78

                        90
                ....*....|....*....
gi 7304953  107 SQTYICELENRKEEVELWV 125
Cdd:cd07690  79 SDTYICEVEDKKEEVELLV 97
IgV_3_CD4 cd07695
Third immunoglobulin (Ig) Variable (V) domain of Cluster of Differentiation (CD) 4; member of ...
 214-314 2.39e-28

Third immunoglobulin (Ig) Variable (V) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains; The members here are composed of the third immunoglobulin variable (IgV) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.


Pssm-ID: 409492  Cd Length: 107  Bit Score: 108.14  E-value: 2.39e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953  214 TAYKSEGESAEFSFPLNF----AEENGWGELMWKAEKDSFFQPWISFSIKNKEVSVQKSTKDLKLQLKETLPLTLKIPQV 289
Cdd:cd07695   3 IVYTKVGEQVEFSFPLNFtkekWKEGGSGELWWQAEGASSSKSWITFSLKNKEVSVKRVTQDPKLQMGKKLPLDLTLPQV 82

                        90       100
                ....*....|....*....|....*
gi 7304953  290 SLQFAGSGNLTLTLDKGTLHQEVNL 314
Cdd:cd07695  83 LPQHAGSGNLTLALETGKLEQEVNL 107
CD4_CD cd22570
cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins; CD4, also called ...
 400-443 6.25e-21

cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins; CD4, also called T-cell surface antigen T4/Leu-3, is an integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, CD4 functions primarily as a coreceptor for MHC class II molecule:peptide complex. In other cells such as macrophages or NK cells, it plays a role in differentiation/activation, cytokine expression and cell migration in a TCR/LCK-independent pathway. CD4 participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages. The model corresponds to cytoplasmic domain of CD4, which is responsible for the interaction with HIV-1 Nef protein that suppresses multiple immune surveillance mechanisms to promote viral pathogenesis.


Pssm-ID: 439337  Cd Length: 44  Bit Score: 85.64  E-value: 6.25e-21
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 7304953  400 VLGGSFGFLGFLGLCILCCVRCRHQQRQAARMSQIKRLLSEKKT 443
Cdd:cd22570   1 VLGGAAGLLLFIGLCIFCCVRCRHRRRQAERMSQIKRLLSEKKT 44
C2-set pfam05790
Immunoglobulin C2-set domain;
128-207 1.50e-17

Immunoglobulin C2-set domain;


Pssm-ID: 399065  Cd Length: 80  Bit Score: 77.00  E-value: 1.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953    128 VTFSPGTSLLQGQSLTLTLDSNSKvSNPLTECKHKKGKVVSGSKVLSMSNLRVQDSDFWNCTVT-LDQKKNWFGMTLSVL 206
Cdd:pfam05790   1 VTVSCSNNLLTCEVLELTLPKGSK-MDPSLKLKGQEAKSLETKKLESTFQPTTEDSGTWVCLASdNDQKKLESVIEVLVL 79


                  .
gi 7304953    207 G 207
Cdd:pfam05790  80 E 80
C2-set pfam05790
Immunoglobulin C2-set domain;
317-387 1.42e-16

Immunoglobulin C2-set domain;


Pssm-ID: 399065  Cd Length: 80  Bit Score: 74.30  E-value: 1.42e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7304953    317 MKVAQLNNTLTCEVMGPTSPK---MRLTLKQENQEARVSEEQKVVQVVAP---ETGLWQCLLSEGDKVKMDSRIQVL 387
Cdd:pfam05790   1 VTVSCSNNLLTCEVLELTLPKgskMDPSLKLKGQEAKSLETKKLESTFQPtteDSGTWVCLASDNDQKKLESVIEVL 77
IgC2_2_CD4 cd07694
Second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the C2-set ...
 126-208 2.57e-12

Second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the C2-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig) Constant 2 (C2)-set domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy. 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: 409491  Cd Length: 88  Bit Score: 62.70  E-value: 2.57e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953  126 FKVTFSPGTSLLQGQSLTLTLDSNSKvSNPLTECKHKKGKVVSGS------KVLSMSNLRVQDSDFWNCTVTLDQKKNWF 199
Cdd:cd07694   1 FKLTATSSDHVLSGTNLTLTLHGSSN-SLPAFKVEWRGPGNKSKQilnqdkKTLNLVQLGPNDSGTWDCIVSVNSSEKTL 79


                ....*....
gi 7304953  200 GMTLSVLGF 208
Cdd:cd07694  80 KLDIKVLAF 88
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 25-125 5.10e-10

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: 56.05  E-value: 5.10e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953     25 QGKTLVLGKEGESAELPCESS-QKKITVFTWKFSDQRKILGQHgkgvlirggspsqfdrfdSKKGAWEKGSFPLIINKLK 103
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSAStGSPGPDVTWSKEGGTLIESLK------------------VKHDNGRTTQSSLLISNVT 62

                          90       100
                  ....*....|....*....|..
gi 7304953    104 MEDSQTYICELENRKEEVELWV 125
Cdd:pfam00047  63 KEDAGTYTCVVNNPGGSATLST 84
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 30-122 5.29e-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: 52.89  E-value: 5.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953      30 VLGKEGESAELPCESSQKKITVFTWKFSDQRKILGQhgkgvlirggspsqfDRFdskKGAWEKGSFPLIINKLKMEDSQT 109
Cdd:smart00410   4 VTVKEGESVTLSCEASGSPPPEVTWYKQGGKLLAES---------------GRF---SVSRSGSTSTLTISNVTPEDSGT 65

                           90
                   ....*....|...
gi 7304953     110 YICELENRKEEVE 122
Cdd:smart00410  66 YTCAATNSSGSAS 78
Tcell_CD4_C pfam12104
T cell CD4 receptor C terminal region; This domain is the C terminal domain of the CD4 T cell ...
 425-452 7.80e-03

T cell CD4 receptor C terminal region; This domain is the C terminal domain of the CD4 T cell receptor. The C terminal domain is the cytoplasmic domain which relays the signal for T cell activation. This process involves co-receptor internalization. This domain is involved in binding to the N terminal of Lck co-receptor in a Zn2+ clasp structure.


Pssm-ID: 403359  Cd Length: 28  Bit Score: 34.02  E-value: 7.80e-03
                          10        20
                  ....*....|....*....|....*...
gi 7304953    425 QRQAARMSQIKRLLSEKKTCQCPHRMQK 452
Cdd:pfam12104   1 RKRARRMAQAKQYLLEKKTCQCQRRMYK 28
 
Name Accession Description Interval E-value
CD4-extracel pfam09191
CD4, extracellular; Members of this family adopt an immunoglobulin-like beta-sandwich, with ...
 211-316 2.42e-60

CD4, extracellular; Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens.


Pssm-ID: 462712  Cd Length: 106  Bit Score: 192.13  E-value: 2.42e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953    211 TAITAYKSEGESAEFSFPLNFAEENGWGELMWKAEKDSFFQPWISFSIKNKEVSVQKSTKDLKLQLKETLPLTLKIPQVS 290
Cdd:pfam09191   1 VSNTVYKKEGEQVEFSFPLTFEDENLSGELRWQAEGASSSQSWITFSLKNRKVSVQKVTQDPKLQMKEKLPLTLTLPQAL 80

                          90       100
                  ....*....|....*....|....*.
gi 7304953    291 LQFAGSGNLTLTLDKGTLHQEVNLVV 316
Cdd:pfam09191  81 LQYAGSGNLTLTLDKGKLHQEVNLVV 106
IgV_1_CD4 cd07690
First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of ...
 27-125 9.55e-43

First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains; The members here are composed of the first immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.


Pssm-ID: 409487  Cd Length: 97  Bit Score: 146.15  E-value: 9.55e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   27 KTLVLGKEGESAELPCESSQKKITVFTWKFSDQRKILGQHGKgvLIRGGSPSQFDRFDSKKGAWEKGSFPLIINKLKMED 106
Cdd:cd07690   1 KKVVLGKKGDTAELPCTASQKKSIQFHWKNSNQIKILGNQGS--FLTKGPSKLNDRADSRRNLWDQGSFPLIIKNLKIED 78

                        90
                ....*....|....*....
gi 7304953  107 SQTYICELENRKEEVELWV 125
Cdd:cd07690  79 SDTYICEVEDKKEEVELLV 97
IgV_3_CD4 cd07695
Third immunoglobulin (Ig) Variable (V) domain of Cluster of Differentiation (CD) 4; member of ...
 214-314 2.39e-28

Third immunoglobulin (Ig) Variable (V) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains; The members here are composed of the third immunoglobulin variable (IgV) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.


Pssm-ID: 409492  Cd Length: 107  Bit Score: 108.14  E-value: 2.39e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953  214 TAYKSEGESAEFSFPLNF----AEENGWGELMWKAEKDSFFQPWISFSIKNKEVSVQKSTKDLKLQLKETLPLTLKIPQV 289
Cdd:cd07695   3 IVYTKVGEQVEFSFPLNFtkekWKEGGSGELWWQAEGASSSKSWITFSLKNKEVSVKRVTQDPKLQMGKKLPLDLTLPQV 82

                        90       100
                ....*....|....*....|....*
gi 7304953  290 SLQFAGSGNLTLTLDKGTLHQEVNL 314
Cdd:cd07695  83 LPQHAGSGNLTLALETGKLEQEVNL 107
CD4_CD cd22570
cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins; CD4, also called ...
 400-443 6.25e-21

cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins; CD4, also called T-cell surface antigen T4/Leu-3, is an integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, CD4 functions primarily as a coreceptor for MHC class II molecule:peptide complex. In other cells such as macrophages or NK cells, it plays a role in differentiation/activation, cytokine expression and cell migration in a TCR/LCK-independent pathway. CD4 participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages. The model corresponds to cytoplasmic domain of CD4, which is responsible for the interaction with HIV-1 Nef protein that suppresses multiple immune surveillance mechanisms to promote viral pathogenesis.


Pssm-ID: 439337  Cd Length: 44  Bit Score: 85.64  E-value: 6.25e-21
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 7304953  400 VLGGSFGFLGFLGLCILCCVRCRHQQRQAARMSQIKRLLSEKKT 443
Cdd:cd22570   1 VLGGAAGLLLFIGLCIFCCVRCRHRRRQAERMSQIKRLLSEKKT 44
C2-set pfam05790
Immunoglobulin C2-set domain;
128-207 1.50e-17

Immunoglobulin C2-set domain;


Pssm-ID: 399065  Cd Length: 80  Bit Score: 77.00  E-value: 1.50e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953    128 VTFSPGTSLLQGQSLTLTLDSNSKvSNPLTECKHKKGKVVSGSKVLSMSNLRVQDSDFWNCTVT-LDQKKNWFGMTLSVL 206
Cdd:pfam05790   1 VTVSCSNNLLTCEVLELTLPKGSK-MDPSLKLKGQEAKSLETKKLESTFQPTTEDSGTWVCLASdNDQKKLESVIEVLVL 79


                  .
gi 7304953    207 G 207
Cdd:pfam05790  80 E 80
C2-set pfam05790
Immunoglobulin C2-set domain;
317-387 1.42e-16

Immunoglobulin C2-set domain;


Pssm-ID: 399065  Cd Length: 80  Bit Score: 74.30  E-value: 1.42e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7304953    317 MKVAQLNNTLTCEVMGPTSPK---MRLTLKQENQEARVSEEQKVVQVVAP---ETGLWQCLLSEGDKVKMDSRIQVL 387
Cdd:pfam05790   1 VTVSCSNNLLTCEVLELTLPKgskMDPSLKLKGQEAKSLETKKLESTFQPtteDSGTWVCLASDNDQKKLESVIEVL 77
IgC2_2_CD4 cd07694
Second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the C2-set ...
 126-208 2.57e-12

Second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the C2-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig) Constant 2 (C2)-set domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy. 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: 409491  Cd Length: 88  Bit Score: 62.70  E-value: 2.57e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953  126 FKVTFSPGTSLLQGQSLTLTLDSNSKvSNPLTECKHKKGKVVSGS------KVLSMSNLRVQDSDFWNCTVTLDQKKNWF 199
Cdd:cd07694   1 FKLTATSSDHVLSGTNLTLTLHGSSN-SLPAFKVEWRGPGNKSKQilnqdkKTLNLVQLGPNDSGTWDCIVSVNSSEKTL 79


                ....*....
gi 7304953  200 GMTLSVLGF 208
Cdd:cd07694  80 KLDIKVLAF 88
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 25-125 5.10e-10

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: 56.05  E-value: 5.10e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953     25 QGKTLVLGKEGESAELPCESS-QKKITVFTWKFSDQRKILGQHgkgvlirggspsqfdrfdSKKGAWEKGSFPLIINKLK 103
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSAStGSPGPDVTWSKEGGTLIESLK------------------VKHDNGRTTQSSLLISNVT 62

                          90       100
                  ....*....|....*....|..
gi 7304953    104 MEDSQTYICELENRKEEVELWV 125
Cdd:pfam00047  63 KEDAGTYTCVVNNPGGSATLST 84
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 30-122 5.29e-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: 52.89  E-value: 5.29e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953      30 VLGKEGESAELPCESSQKKITVFTWKFSDQRKILGQhgkgvlirggspsqfDRFdskKGAWEKGSFPLIINKLKMEDSQT 109
Cdd:smart00410   4 VTVKEGESVTLSCEASGSPPPEVTWYKQGGKLLAES---------------GRF---SVSRSGSTSTLTISNVTPEDSGT 65

                           90
                   ....*....|...
gi 7304953     110 YICELENRKEEVE 122
Cdd:smart00410  66 YTCAATNSSGSAS 78
IGv smart00406
Immunoglobulin V-Type;
37-113 1.06e-06

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 46.22  E-value: 1.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953      37 SAELPCESSQKKITVFTWKFSDQRkilgqHGKGV--LIRGGSPSQF-------DRFD-SKKGAweKGSFPLIINKLKMED 106
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQP-----PGKGLewLGYIGSNGSSyyqesykGRFTiSKDTS--KNDVSLTISNLRVED 73


                   ....*..
gi 7304953     107 SQTYICE 113
Cdd:smart00406  74 TGTYYCA 80
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 23-136 6.46e-05

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: 41.94  E-value: 6.46e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   23 VTQGKTLVLGKEGESAELPCE-SSQKKITVFTWKFSDQRK----ILGQHGKGVLIRGGSPSQFD-RFDSKKgawekgSFP 96
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEvSSSFSSTYIYWYRQKPGQgpefLIYLSSSKGKTKGGVPGRFSgSRDGTS------SFS 74

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 7304953   97 LIINKLKMEDSQTYICELENRkeeveLWVFKVTFSPGTSL 136
Cdd:cd00099  75 LTISNLQPEDSGTYYCAVSES-----GGTDKLTFGSGTRL 109
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 25-112 9.06e-05

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 41.67  E-value: 9.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953     25 QGKTLVLGKEGESAELPCE---SSQKKITVFTWKFSDQrkilgQHGKGVLIRGGSPSQFDRFDSKKGAWEK----GSFPL 97
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTyssSMSEASTSVYWYRQPP-----GKGPTFLIAYYSNGSEEGVKKGRFSGRGdpsnGDGSL 75

                          90
                  ....*....|....*
gi 7304953     98 IINKLKMEDSQTYIC 112
Cdd:pfam07686  76 TIQNLTLSDSGTYTC 90
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 23-136 2.20e-04

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: 40.33  E-value: 2.20e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   23 VTQGKTLVLGKEGESAELPCESSQKKITVFTWkfsdQRKILGQhGKGVLIRGGSPS---QFDRFDSKKGAWEKgSFPLII 99
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTSTFYYLFW----YRQYPGQ-GPQFLIYISSDSgnkKKGRFSATLDKSRK-SSSLHI 74

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 7304953  100 NKLKMEDSQTYICELENRkeeveLWVFKVTFSPGTSL 136
Cdd:cd04983  75 SAAQLSDSAVYFCALSES-----GGTGKLTFGKGTRL 106
IgV_CD2_like_N cd05775
N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains; ...
 30-129 6.78e-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: 38.87  E-value: 6.78e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   30 VLGKEGESAELPCESSQKKITVFTWKFSDQrKILGqhgkgvLIRGGSPSQFDRFDSKKGaWEKGSFPLIINKLKMEDSQT 109
Cdd:cd05775   5 VYGALGGNVTLTISSLQDDIDEIKWKKTKD-KIVE------WENNIGPTYFGSFKDRVL-LDKESGSLTIKNLTKEDSGT 76

                        90       100
                ....*....|....*....|
gi 7304953  110 YICELENRKEEVELWVFKVT 129
Cdd:cd05775  77 YELEITSTNGKVLSSKFTLE 96
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 23-116 6.81e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 38.32  E-value: 6.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953     23 VTQGKTLVLGKEGESAELPCESSQKKITVFTWKFSDQRKILGQHGKGVLIRGGSpsqfdrfdskkgawekgsfPLIINKL 102
Cdd:pfam13927   4 ITVSPSSVTVREGETVTLTCEATGSPPPTITWYKNGEPISSGSTRSRSLSGSNS-------------------TLTISNV 64

                          90
                  ....*....|....
gi 7304953    103 KMEDSQTYICELEN 116
Cdd:pfam13927  65 TRSDAGTYTCVASN 78
Ig_SLAM-like_N cd16842
N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule ...
 30-110 6.98e-03

N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family and similar proteins. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. Members of this group include proteins such as CD84, SLAM (CD150), Ly-9 (CD229), NTB-A (ly-108, SLAM6), 19A (CRACC), and SLAMF9. The genes coding for the SLAM family are nested on chromosome 1, in humans at 1q23, and in mice at 1H2. The SLAM family is a subset of the CD2 family, which also includes CD2 and CD58 located on chromosome 1 at 1p13 in humans. In mice, CD2 is located on chromosome 3, and there is no CD58 homolog. The SLAM family proteins are organized as an extracellular domain with either 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: 409517  Cd Length: 102  Bit Score: 36.14  E-value: 6.98e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7304953   30 VLGKEGESAELPCE-SSQKKITVFTWKF-SDQRKI-LGQHGKGVLIrggspsQFDRFDSKKGAWEKGSFPLIINKLKMED 106
Cdd:cd16842   3 VNGILGGSVTFPLNiSDGQEIENITWSFkTSLAVIaPGEGGAPEII------ITDKSYKERLNISQNDYSLQISNLTMED 76


                ....
gi 7304953  107 SQTY 110
Cdd:cd16842  77 AGSY 80
Tcell_CD4_C pfam12104
T cell CD4 receptor C terminal region; This domain is the C terminal domain of the CD4 T cell ...
 425-452 7.80e-03

T cell CD4 receptor C terminal region; This domain is the C terminal domain of the CD4 T cell receptor. The C terminal domain is the cytoplasmic domain which relays the signal for T cell activation. This process involves co-receptor internalization. This domain is involved in binding to the N terminal of Lck co-receptor in a Zn2+ clasp structure.


Pssm-ID: 403359  Cd Length: 28  Bit Score: 34.02  E-value: 7.80e-03
                          10        20
                  ....*....|....*....|....*...
gi 7304953    425 QRQAARMSQIKRLLSEKKTCQCPHRMQK 452
Cdd:pfam12104   1 RKRARRMAQAKQYLLEKKTCQCQRRMYK 28
 
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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