NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|332823708|ref|XP_003339166|]
View 

PREDICTED: HLA class II histocompatibility antigen, DQ beta 1 chain isoform X3 [Pan troglodytes]

Protein Classification

class II histocompatibility antigen beta chain (domain architecture ID 10469854)

class II histocompatibility antigen beta chain forms a heterodimer with the alpha chain to form the MHC class II molecule, which plays a critical role in immune recognition

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
IgC_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; ...
129-222 1.22e-53

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


:

Pssm-ID: 143243  Cd Length: 94  Bit Score: 171.82  E-value: 1.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCHVE 208
Cdd:cd05766    1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEGVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                         90
                 ....*....|....
gi 332823708 209 HPSLQNPITVEWRA 222
Cdd:cd05766   81 HSSLQEPLTVDWRP 94
MHC_II_beta pfam00969
Class II histocompatibility antigen, beta domain;
45-117 3.93e-42

Class II histocompatibility antigen, beta domain;


:

Pssm-ID: 307218  Cd Length: 75  Bit Score: 141.29  E-value: 3.93e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332823708   45 GMCYFTNGTERVRLVTRYIYNREEYVRFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQL 117
Cdd:pfam00969   1 SECYFTNGTERVRFLYRYIYNKEEYARFDSDVGEFVAVTELGRPDAEYWNSQKDLLERLRAGVDTVCRHNYPF 73
 
Name Accession Description Interval E-value
IgC_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; ...
129-222 1.22e-53

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 143243  Cd Length: 94  Bit Score: 171.82  E-value: 1.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCHVE 208
Cdd:cd05766    1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEGVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                         90
                 ....*....|....
gi 332823708 209 HPSLQNPITVEWRA 222
Cdd:cd05766   81 HSSLQEPLTVDWRP 94
MHC_II_beta pfam00969
Class II histocompatibility antigen, beta domain;
45-117 3.93e-42

Class II histocompatibility antigen, beta domain;


Pssm-ID: 307218  Cd Length: 75  Bit Score: 141.29  E-value: 3.93e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332823708   45 GMCYFTNGTERVRLVTRYIYNREEYVRFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQL 117
Cdd:pfam00969   1 SECYFTNGTERVRFLYRYIYNKEEYARFDSDVGEFVAVTELGRPDAEYWNSQKDLLERLRAGVDTVCRHNYPF 73
MHC_II_beta smart00921
Class II histocompatibility antigen, beta domain; Class II MHC glycoproteins are expressed on ...
45-116 1.04e-41

Class II histocompatibility antigen, beta domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 197989  Cd Length: 72  Bit Score: 140.43  E-value: 1.04e-41
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332823708    45 GMCYFTNGTERVRLVTRYIYNREEYVRFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQ 116
Cdd:smart00921   1 SECYFSNGTEDVRYVVRYIYNKEELVRFDSDVGKFVAFTELGRPAAEYWNSQKDLLERLRAEVDTVCRHNYQ 72
C1-set pfam07654
Immunoglobulin C1-set domain;
129-212 1.49e-35

Immunoglobulin C1-set domain;


Pssm-ID: 311543  Cd Length: 89  Bit Score: 124.69  E-value: 1.49e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708  129 PTVTI--SPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQ---HGDVY 203
Cdd:pfam07654   1 PSVYVfpPSKEPLELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVTSTTLPQNGDWTYQLSSYLTVTPSdweSGDEY 80

                  ....*....
gi 332823708  204 TCHVEHPSL 212
Cdd:pfam07654  81 TCRVEHEGL 89
IGc1 smart00407
Immunoglobulin C-Type;
144-215 5.91e-25

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 96.23  E-value: 5.91e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 332823708   144 HNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEM---TPQHGDVYTCHVEHPSLQNP 215
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHEGLKEP 75
 
Name Accession Description Interval E-value
IgC_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; ...
129-222 1.22e-53

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; IgC_MHC_II_beta: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 143243  Cd Length: 94  Bit Score: 171.82  E-value: 1.22e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCHVE 208
Cdd:cd05766    1 PSVKISPSQTGSLSHPHLLVCHVWGFYPPEITVKWFKNGQEETEGVVSTELIPNGDWTYQILVMLETTPSRGDTYTCVVE 80
                         90
                 ....*....|....
gi 332823708 209 HPSLQNPITVEWRA 222
Cdd:cd05766   81 HSSLQEPLTVDWRP 94
MHC_II_beta pfam00969
Class II histocompatibility antigen, beta domain;
45-117 3.93e-42

Class II histocompatibility antigen, beta domain;


Pssm-ID: 307218  Cd Length: 75  Bit Score: 141.29  E-value: 3.93e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332823708   45 GMCYFTNGTERVRLVTRYIYNREEYVRFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQL 117
Cdd:pfam00969   1 SECYFTNGTERVRFLYRYIYNKEEYARFDSDVGEFVAVTELGRPDAEYWNSQKDLLERLRAGVDTVCRHNYPF 73
MHC_II_beta smart00921
Class II histocompatibility antigen, beta domain; Class II MHC glycoproteins are expressed on ...
45-116 1.04e-41

Class II histocompatibility antigen, beta domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 197989  Cd Length: 72  Bit Score: 140.43  E-value: 1.04e-41
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332823708    45 GMCYFTNGTERVRLVTRYIYNREEYVRFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQ 116
Cdd:smart00921   1 SECYFSNGTEDVRYVVRYIYNKEELVRFDSDVGKFVAFTELGRPAAEYWNSQKDLLERLRAEVDTVCRHNYQ 72
C1-set pfam07654
Immunoglobulin C1-set domain;
129-212 1.49e-35

Immunoglobulin C1-set domain;


Pssm-ID: 311543  Cd Length: 89  Bit Score: 124.69  E-value: 1.49e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708  129 PTVTI--SPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQ---HGDVY 203
Cdd:pfam07654   1 PSVYVfpPSKEPLELGKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVTSTTLPQNGDWTYQLSSYLTVTPSdweSGDEY 80

                  ....*....
gi 332823708  204 TCHVEHPSL 212
Cdd:pfam07654  81 TCRVEHEGL 89
IgC cd00098
Immunoglobulin Constant (IgC) domain; Members of the IgC family are components of ...
133-221 4.51e-25

Immunoglobulin Constant (IgC) domain; Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 319274  Cd Length: 95  Bit Score: 97.13  E-value: 4.51e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 133 ISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQ---HGDVYTCHVEH 209
Cdd:cd00098    4 LPPSPEEKLGGTVTLVCLVSGFYPKDITVTWLKNGKEVTSGVSTTPPTKNSDGTFSVTSYLTVPPSdwdEGTTYTCEVSH 83
                         90
                 ....*....|..
gi 332823708 210 PSLQNPITVEWR 221
Cdd:cd00098   84 ESLSQPVSKSLN 95
IGc1 smart00407
Immunoglobulin C-Type;
144-215 5.91e-25

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 96.23  E-value: 5.91e-25
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 332823708   144 HNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEM---TPQHGDVYTCHVEHPSLQNP 215
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHEGLKEP 75
IgC_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain; ...
127-220 3.96e-20

Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain; IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta2 microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 143322  Cd Length: 93  Bit Score: 83.49  E-value: 3.96e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 127 VEPTVTISPSRteALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCH 206
Cdd:cd07698    1 VPPEVRVTRKR--APDGSLTLSCHATGFYPRDIEVTWLRDGEDSVDDVESGEILPNGDGTYQLWVTLEVPPEDKARYSCR 78
                         90
                 ....*....|....
gi 332823708 207 VEHPSLQNPITVEW 220
Cdd:cd07698   79 VEHSGLKEPLIVPW 92
IgC_beta2m cd05770
Class I major histocompatibility complex (MHC) beta2-microglobulin; IgC_beta2m: ...
145-221 1.96e-17

Class I major histocompatibility complex (MHC) beta2-microglobulin; IgC_beta2m: Immunoglobulin-like domain in beta2-Microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta -sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded and then excreted.


Pssm-ID: 143247  Cd Length: 93  Bit Score: 75.98  E-value: 1.96e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 332823708 145 NLLVCSVTDFYPGQIKVRWFRNDQEeTTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCHVEHPSLQNPITVEWR 221
Cdd:cd05770   18 NVLNCYVTGFHPPDIEIRLLKNGVK-IPKVEQSDLSFSKDWTFYLLKSTEFTPTKGDEYACRVRHNSMSEPKKYKWD 93
IgC_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; ...
129-220 8.24e-17

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from protelytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 143244  Cd Length: 94  Bit Score: 73.91  E-value: 8.24e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCHVE 208
Cdd:cd05767    2 PEVTVFSLKPVELGEPNTLICFVDNFFPPVLNVTWLKNGVPVTDGVSETRYYPRQDLSFQKFSYLNFTPEEGDIYSCIVE 81
                         90
                 ....*....|..
gi 332823708 209 HPSLQNPITVEW 220
Cdd:cd05767   82 HWGLETPATRYW 93
IgC_L cd07699
Immunoglobulin Constant domain; IgC_L: Immunoglobulin (Ig) light chain constant (C) domain. ...
128-217 2.76e-13

Immunoglobulin Constant domain; IgC_L: Immunoglobulin (Ig) light chain constant (C) domain. 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. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: 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: 319325  Cd Length: 99  Bit Score: 64.40  E-value: 2.76e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 128 EPTVTISPSRTEALNHHNL-LVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGD---VY 203
Cdd:cd07699    1 APSVTIFPPSSEELSSGKAtLVCLINKFYPGFATVTWKVDGSTVSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNkhkVY 80
                         90
                 ....*....|....
gi 332823708 204 TCHVEHPSLQNPIT 217
Cdd:cd07699   81 TCEVTHEGLSSTIT 94
IgC_CH3_IgAGD_CH4_IgAEM cd05768
CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin; ...
129-218 1.76e-09

CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH3_IgAGD_CH4_IgAEM: Contains the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. 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 and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 319312  Cd Length: 100  Bit Score: 54.24  E-value: 1.76e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTI-SPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRNDQE--ETTGVVSTPLIRNGDWTFQILVMLEMTP---QHGDV 202
Cdd:cd05768    1 PSVYLlPPPEEELSLNTVTLTCLVKGFSPEDIFVRWLQNGQPlpEEDYKTTTPVKEESDGSFFVYSKLTVTAsdwKSGDV 80
                         90
                 ....*....|....*.
gi 332823708 203 YTCHVEHPSLQNPITV 218
Cdd:cd05768   81 FSCVVGHEALPLQFTQ 96
IgC_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; IgC_Tapasin_R: Immunoglobulin-like domain on Tapasin-R. ...
109-218 1.92e-09

Tapasin-R immunoglobulin-like domain; IgC_Tapasin_R: 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: 319313  Cd Length: 138  Bit Score: 54.84  E-value: 1.92e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 109 TVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPGQIKVRWFRndqEETTGVVSTPLIRNG----- 183
Cdd:cd05771   19 SVSTPPFQAQQIIQLSVSEPPRVRLSLEKTVSIEEPQTLICHIAGYYPLDVQVEWTR---EPPGDSPPRVSVSNVsfssh 95
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 332823708 184 ----DWTFQILVMLEM---TPQHGDVYTCHVEHPSLQNPITV 218
Cdd:cd05771   96 rqhaDGTYSLSSALTLepgTPHPGATYTCRVTHVALETPVSV 137
IgC_CH2_IgE cd05847
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); ...
147-210 1.02e-08

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); IgC_CH2_IgE: The second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (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 and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) and three (in alpha, delta, and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.


Pssm-ID: 143255  Cd Length: 94  Bit Score: 52.02  E-value: 1.02e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 332823708 147 LVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQH---GDVYTCHVEHP 210
Cdd:cd05847   19 LLCLISGYTPGTIEVEWLVDGQVATLVAASTAPQKEEGSTFSTTSELNVTQEDwksGKTYTCKVTHQ 85
IgC_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; IgC_TCR_beta: Constant domain ...
128-189 2.23e-08

T cell receptor (TCR) beta chain constant immunoglobulin domain; IgC_TCR_beta: Constant 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 beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 143246  Cd Length: 115  Bit Score: 51.22  E-value: 2.23e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 332823708 128 EPTVTI-SPSRTEALNHHNL-LVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPL-IRNGDWTFQI 189
Cdd:cd05769    2 PPTVAIfPPSEAEIRNKRKAtLVCLATGFYPDHVSLSWKVNGKEVTDGVATDPQaLRENTSTYSI 66
IgC_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; IgC: immunoglobulin (Ig)-like ...
129-217 4.06e-06

Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; IgC: immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 2 (C1 repeat 1). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity.


Pssm-ID: 319314  Cd Length: 103  Bit Score: 44.61  E-value: 4.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTISPSRTeALNHHNLLVCSVTDFYPGQIKVRWFRNDQEETTGVVS-TPLirNGDWTFQILVMLEMTPQHGDV---YT 204
Cdd:cd05772    5 PVVSGPAARA-TPGQTVSFTCKSHGFSPRDITLKWFKNGNELSALQTTvLPE--GDSVSYSVSSTVQVVLTKDDVhsqLT 81
                         90
                 ....*....|...
gi 332823708 205 CHVEHPSLQNPIT 217
Cdd:cd05772   82 CEVAHVTLQAPLR 94
IgC_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The ...
147-212 6.87e-06

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. 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 and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 319342  Cd Length: 100  Bit Score: 43.84  E-value: 6.87e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332823708 147 LVCSVTDFYPGQIKVRWFRNDQEETTGVVSTPL----IRNGDWTFQILVMLEMTPQH---GDVYTCHVEHPSL 212
Cdd:cd16093   21 LICQATGFSPRQISVSWLREGKQVGSGVTTDAVeaeaKESGPTTFRVTSTLTITESEwlsQSMFTCRVDHRGL 93
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
129-208 1.19e-05

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 316449  Cd Length: 76  Bit Score: 42.87  E-value: 1.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708  129 PTVTISPSRTEALNHHNL-LVCSVTDFYPGQIkvRWFRNDQEETTGVVSTPLIRNGdwtfqILVMLEMTPQHGDVYTCHV 207
Cdd:pfam13927   2 PVITVSPSSVVVLEGESVtLTCEATGGPPPTI--TWYKNGKPGPTSSRISLSGSNS-----TLTISNVTREDSGTYTCVA 74

                  .
gi 332823708  208 E 208
Cdd:pfam13927  75 S 75
IgC_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; Immunoglobulin (Ig)-like domain ...
127-217 3.48e-05

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; Immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity.


Pssm-ID: 319334  Cd Length: 104  Bit Score: 42.02  E-value: 3.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 127 VEPTVTISPSRTEALNHHNLlVCSVTDFYPGQIKVRWFRNDQEETTGVVSTpLIRNGDWTFQI--LVMLEMTPQHGDV-Y 203
Cdd:cd16085    1 VPPTLEVTQQPTMVWNQVNV-TCQVQKFYPQKLQLTWLENGNVSRTEEPST-LTVNKDGTYNWtsWLLVNVSAHREDVvL 78
                         90
                 ....*....|....
gi 332823708 204 TCHVEHPSlQNPIT 217
Cdd:cd16085   79 TCQVEHDG-QPAVT 91
IgC_TCR_gamma cd07697
T cell receptor (TCR) gamma chain constant immunoglobulin domain; IgC_TCR_gamma; ...
129-209 8.78e-05

T cell receptor (TCR) gamma chain constant immunoglobulin domain; IgC_TCR_gamma; immunoglobulin (Ig) constant (C) domain of the gamma chain of gamma-delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha-beta TCRs but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 319324  Cd Length: 97  Bit Score: 40.66  E-value: 8.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 129 PTVTI-SPSRTE-ALNHHNLLVCSVTDFYPGQIKVRWfRNDQEETTGVVS----TPLIRNGDWTFQILVMLEMTPqhGDV 202
Cdd:cd07697    1 PKPTIfPPSTAElEKQSKGFYLCLLEDFFPDVIEVHW-KEDGKEQKELGSqdsvTKKGNNTYSLISWLTVTKLSL--GKP 77

                 ....*..
gi 332823708 203 YTCHVEH 209
Cdd:cd07697   78 IRCHYKH 84
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
129-216 1.16e-03

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


Pssm-ID: 311910  Cd Length: 89  Bit Score: 37.39  E-value: 1.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708  129 PTVTISPSRTEALNHHNLLVCSVTDFYPgQIKVRWFRNDQEETTGVVSTpLIRNGDWTFQILVMLEMTPQ---HGDVYTC 205
Cdd:pfam08205   1 PEIEPPASLLEGEGPEVVATCSSAGGKP-APRITWYLNGKPLEAAETSS-EQDPESGLYTVTSTLKLVPSrsdHGQSLTC 78
                          90
                  ....*....|.
gi 332823708  206 HVEHPSLQNPI 216
Cdd:pfam08205  79 QVSYPALRGPQ 89
Ig cd00096
Immunoglobulin domain; Immunoglobulin (Ig) domain found in the Ig superfamily. The Ig ...
147-219 1.83e-03

Immunoglobulin domain; 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, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.


Pssm-ID: 319273  Cd Length: 70  Bit Score: 36.45  E-value: 1.83e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 332823708 147 LVCSVTDfYPgQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQIlvmLEMTPQHGDVYTCHVEHPSLQNPITVE 219
Cdd:cd00096    3 LTCSASG-NP-PPTITWLKNGKPLPSSSRFRRRSSGGNGTLTI---SNVTPEDSGTYTCVASNSAGSASASVT 70
IgC_CH1_IgAEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The first ...
149-214 3.32e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin; IgC_CH2: The first immunoglobulin constant domain of alpha, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. 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 and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 319288  Cd Length: 96  Bit Score: 36.11  E-value: 3.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 332823708 149 CSVTDFYPGQIKVRWFrNDQEETTGVVSTP--LIRNGDWTF--QILVMlEMTPQHGDVYTCHVEHPSLQN 214
Cdd:cd04985   23 CLATGFFPEPVTFTWN-SGSNSTSGVKTFPavLQSGGLYTAssQLTVP-ASEWKSKKSFYCKVEHPPTTS 90
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
147-218 8.52e-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: 278476  Cd Length: 86  Bit Score: 34.48  E-value: 8.52e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 332823708  147 LVCSVTDFYPgQIKVRWFRNDQEETTGVVSTPlIRNGDWTFQILVmLEMTPQHGDVYTCHVEHPSLQNPITV 218
Cdd:pfam00047  16 LTCSASTGSP-GPDVTWSKEGGTLIESLKVKH-DNGRTTQSSLLI-SNVTKEDAGTYTCVVNNPGGPATLST 84
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.16
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH