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Conserved domains on  [gi|1534506063|gb|AZL87758|]
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L7Ae (TCS_S)-ins3-scFv35 [Cloning vector p146]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 2-125 1.03e-69

ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the pfam01248 model which also recognizes the L30 protein.


:

Pssm-ID: 188367 [Multi-domain]  Cd Length: 117  Bit Score: 215.39  E-value: 1.03e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063   2 YVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenly 81
Cdd:TIGR03677   1 YVKFEVPEELADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVK---- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1534506063  82 fqsSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQ 125
Cdd:TIGR03677  77 ---SKEDLGAAAGLEVGAASAAIVDAGKAEELLKEIIEKVEALK 117
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 141-254 8.95e-66

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), 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. 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 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 can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


:

Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 205.24  E-value: 8.95e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 141 QLQQSGAELVRSGASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPENGDTEYTQKFKGKATLTADKSPSTAYMQ 220
Cdd:cd04981     1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1534506063 221 LSSLTSEDSAVYYCARITTDY---YFDYWGQGTTLTV 254
Cdd:cd04981    81 LNSLTSEDTAVYYCARGLGGYgysYFDYWGQGTTVTV 117
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 273-382 5.18e-59

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: 187.21  E-value: 5.18e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 273 VVMTQTPLSLPVSLGDQASISCRSSQSLvhsnGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKIS 352
Cdd:cd04980     1 IVMTQSPASLSVSPGERVTISCKASQSI----SSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTIS 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 1534506063 353 RVEAEDLGVYFCSQSTHVPLTFGAGTKLEI 382
Cdd:cd04980    77 SVEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106
 
Name Accession Description Interval E-value
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 2-125 1.03e-69

ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the pfam01248 model which also recognizes the L30 protein.


Pssm-ID: 188367 [Multi-domain]  Cd Length: 117  Bit Score: 215.39  E-value: 1.03e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063   2 YVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenly 81
Cdd:TIGR03677   1 YVKFEVPEELADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVK---- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1534506063  82 fqsSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQ 125
Cdd:TIGR03677  77 ---SKEDLGAAAGLEVGAASAAIVDAGKAEELLKEIIEKVEALK 117
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 141-254 8.95e-66

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), 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. 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 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 can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 205.24  E-value: 8.95e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 141 QLQQSGAELVRSGASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPENGDTEYTQKFKGKATLTADKSPSTAYMQ 220
Cdd:cd04981     1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1534506063 221 LSSLTSEDSAVYYCARITTDY---YFDYWGQGTTLTV 254
Cdd:cd04981    81 LNSLTSEDTAVYYCARGLGGYgysYFDYWGQGTTVTV 117
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 273-382 5.18e-59

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: 187.21  E-value: 5.18e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 273 VVMTQTPLSLPVSLGDQASISCRSSQSLvhsnGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKIS 352
Cdd:cd04980     1 IVMTQSPASLSVSPGERVTISCKASQSI----SSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTIS 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 1534506063 353 RVEAEDLGVYFCSQSTHVPLTFGAGTKLEI 382
Cdd:cd04980    77 SVEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 14-109 5.30e-33

Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.


Pssm-ID: 426153 [Multi-domain]  Cd Length: 95  Bit Score: 119.24  E-value: 5.30e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  14 EALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenlyfqsSKNDLGRAV 93
Cdd:pfam01248   2 AIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVP-------SKKELGEAC 74

                          90
                  ....*....|....*.
gi 1534506063  94 GIEVPCASAAIINEGE 109
Cdd:pfam01248  75 GKKRPVSALAIKDEGD 90
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 13-114 1.40e-32

Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein L7Ae or related RNA K-turn-binding protein is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 440969 [Multi-domain]  Cd Length: 98  Bit Score: 117.95  E-value: 1.40e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  13 NEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDpPEIVAHLPLLCEEKNVPYIYVkenlyfqSSKNDLGRA 92
Cdd:COG1358     1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDAS-ENTKKKLLDLCEEYGVPVVEV-------GTKEELGKA 72

                          90       100
                  ....*....|....*....|....*
gi 1534506063  93 VGiEVPCASAAIINEG---ELRKEL 114
Cdd:COG1358    73 IG-KVGRAVVAITDEGfakKLLELL 96
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 8-124 3.34e-28

U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, also known as NHP2-like protein 1 or U4/U6.U5 tri-snRNP 15.5 kDa protein, is a component of the spliceosome B complex, involved in pre-mRNA splicing. It binds to the 5'-stem-loop of U4 snRNA.


Pssm-ID: 411046  Cd Length: 122  Bit Score: 107.41  E-value: 3.34e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063   8 PEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenlyfqsSKN 87
Cdd:cd21104     9 DAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVP-------SKQ 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1534506063  88 DLGRAVGIEVPCASAAII-NEG-ELRKELGSLVEKIKGL 124
Cdd:cd21104    82 ALGRACGVSRPVIACSVTtNEGsQLKSQIQSLKDAIEKL 120
IGv smart00406
Immunoglobulin V-Type;
155-236 3.50e-28

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 105.93  E-value: 3.50e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  155 SVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPeNGDTEYTQKFKGKATLTADKSPSTAYMQLSSLTSEDSAVYYC 234
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGS-NGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 1534506063  235 AR 236
Cdd:smart00406  80 AV 81
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 277-382 5.21e-18

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: 79.04  E-value: 5.21e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 277 QTPLSLPVSLGDQASISCrsSQSLVHSNGNTYLEWYLQKPGQSPKLLI--YKVSNRFSGVPDRFSGSG--SGTDFTLKIS 352
Cdd:pfam07686   1 QTPREVTVALGGSVTLPC--TYSSSMSEASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSGRGdpSNGDGSLTIQ 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 1534506063 353 RVEAEDLGVYFCSQSTHVPLTFGAGTKLEI 382
Cdd:pfam07686  79 NLTLSDSGTYTCAVIPSGEGVFGKGTRLTV 108
IGv smart00406
Immunoglobulin V-Type;
290-366 1.11e-16

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 74.34  E-value: 1.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  290 ASISCRSSQSlvhSNGNTYLEWYLQKPGQSPKLLIYKVSNR----FSGVPDRFSGSG--SGTDFTLKISRVEAEDLGVYF 363
Cdd:smart00406   2 VTLSCKFSGS---TFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYY 78


                   ...
gi 1534506063  364 CSQ 366
Cdd:smart00406  79 CAV 81
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
20-105 2.46e-16

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 73.28  E-value: 2.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  20 EKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPeIVAHLPLLCEEKNVPYIYVkenlyfqSSKNDLGRAVGIEVPC 99
Cdd:PRK13602    4 EKVSQAKSIVIGTKQTVKALKRGSVKEVVVAEDADPR-LTEKVEALANEKGVPVSKV-------DSMKKLGKACGIEVGA 75


                  ....*.
gi 1534506063 100 ASAAII 105
Cdd:PRK13602   76 AAVAII 81
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 153-254 1.91e-11

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: 60.55  E-value: 1.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 153 GASVKLSCTASGF-NIKDYYMHWVKQRPEQGLEWIgwIDPENGDTEyTQKFKGKATLTADKSPSTAYMQLSSLTSEDSAV 231
Cdd:pfam07686  11 GGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFL--IAYYSNGSE-EGVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGT 87

                          90       100
                  ....*....|....*....|...
gi 1534506063 232 YYCARITTDYyfDYWGQGTTLTV 254
Cdd:pfam07686  88 YTCAVIPSGE--GVFGKGTRLTV 108
 
Name Accession Description Interval E-value
eL8_ribo TIGR03677
ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version ...
 2-125 1.03e-69

ribosomal protein eL8, archaeal form; This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the pfam01248 model which also recognizes the L30 protein.


Pssm-ID: 188367 [Multi-domain]  Cd Length: 117  Bit Score: 215.39  E-value: 1.03e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063   2 YVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenly 81
Cdd:TIGR03677   1 YVKFEVPEELADKALEAVEKARETGKIKKGTNEVTKAVERGIAKLVVIAEDVEPPEIVAHLPALCEEKGIPYIYVK---- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1534506063  82 fqsSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQ 125
Cdd:TIGR03677  77 ---SKEDLGAAAGLEVGAASAAIVDAGKAEELLKEIIEKVEALK 117
IgV_H cd04981
Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the ...
 141-254 8.95e-66

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), 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. 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 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 can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.


Pssm-ID: 409370 [Multi-domain]  Cd Length: 118  Bit Score: 205.24  E-value: 8.95e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 141 QLQQSGAELVRSGASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPENGDTEYTQKFKGKATLTADKSPSTAYMQ 220
Cdd:cd04981     1 QLQESGPGLVKPGQSLKLSCKASGFTFTSYGMGWVRQAPGKGLEWIGLIYPGGGDTYYADSFKGRFTITRDTSKSTAYLQ 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1534506063 221 LSSLTSEDSAVYYCARITTDY---YFDYWGQGTTLTV 254
Cdd:cd04981    81 LNSLTSEDTAVYYCARGLGGYgysYFDYWGQGTTVTV 117
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 273-382 5.18e-59

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: 187.21  E-value: 5.18e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 273 VVMTQTPLSLPVSLGDQASISCRSSQSLvhsnGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKIS 352
Cdd:cd04980     1 IVMTQSPASLSVSPGERVTISCKASQSI----SSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTIS 76

                          90       100       110
                  ....*....|....*....|....*....|
gi 1534506063 353 RVEAEDLGVYFCSQSTHVPLTFGAGTKLEI 382
Cdd:cd04980    77 SVEPEDAAVYYCQQGYTFPYTFGGGTKLEI 106
Ribosomal_L7Ae pfam01248
Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from ...
 14-109 5.30e-33

Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.


Pssm-ID: 426153 [Multi-domain]  Cd Length: 95  Bit Score: 119.24  E-value: 5.30e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  14 EALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenlyfqsSKNDLGRAV 93
Cdd:pfam01248   2 AIYEVLKKALKTGKLVLGLKEVTKALERGEAKLVIIAEDCDPEEKVKLIPALCKEKNVPYVKVP-------SKKELGEAC 74

                          90
                  ....*....|....*.
gi 1534506063  94 GIEVPCASAAIINEGE 109
Cdd:pfam01248  75 GKKRPVSALAIKDEGD 90
Rpl7Ae COG1358
Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure ...
 13-114 1.40e-32

Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure and biogenesis]; Ribosomal protein L7Ae or related RNA K-turn-binding protein is part of the Pathway/BioSystem: Ribosome 50S subunit


Pssm-ID: 440969 [Multi-domain]  Cd Length: 98  Bit Score: 117.95  E-value: 1.40e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  13 NEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDpPEIVAHLPLLCEEKNVPYIYVkenlyfqSSKNDLGRA 92
Cdd:COG1358     1 DKILNLLGLARRAGKLVSGEEQVLKAIRKGKAKLVIIAEDAS-ENTKKKLLDLCEEYGVPVVEV-------GTKEELGKA 72

                          90       100
                  ....*....|....*....|....*
gi 1534506063  93 VGiEVPCASAAIINEG---ELRKEL 114
Cdd:COG1358    73 IG-KVGRAVVAITDEGfakKLLELL 96
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 274-380 3.78e-31

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 114.48  E-value: 3.78e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 274 VMTQtPLSLPVSLGDQASISCRSSQSLVHSNgntYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISR 353
Cdd:cd04984     1 VLTQ-PSSLSVSPGETVTITCTGSSGNISGN---YVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISG 76

                          90       100
                  ....*....|....*....|....*..
gi 1534506063 354 VEAEDLGVYFCSQSTHVPLTFGAGTKL 380
Cdd:cd04984    77 AQTEDEADYYCQVWDSNSYVFGGGTKL 103
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 275-382 1.05e-30

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: 113.58  E-value: 1.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 275 MTQTPLSLPVSLGDQASISCRSSQSlvhsNGNTYLEWYLQKPGQSPKLLIYKVSNRFS---GVPDRFSGSGSG-TDFTLK 350
Cdd:cd00099     1 VTQSPRSLSVQEGESVTLSCEVSSS----FSSTYIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGtSSFSLT 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1534506063 351 ISRVEAEDLGVYFCSQS---THVPLTFGAGTKLEI 382
Cdd:cd00099    77 ISNLQPEDSGTYYCAVSesgGTDKLTFGSGTRLTV 111
SNU13 cd21104
U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, ...
 8-124 3.34e-28

U4/U6.U5 small nuclear ribonucleoprotein SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13, also known as NHP2-like protein 1 or U4/U6.U5 tri-snRNP 15.5 kDa protein, is a component of the spliceosome B complex, involved in pre-mRNA splicing. It binds to the 5'-stem-loop of U4 snRNA.


Pssm-ID: 411046  Cd Length: 122  Bit Score: 107.41  E-value: 3.34e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063   8 PEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenlyfqsSKN 87
Cdd:cd21104     9 DAQLTQTILDLVQQAANYKQLKKGANEATKTLNRGIAEFIVMAADAEPLEILLHLPLLCEDKNVPYVFVP-------SKQ 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1534506063  88 DLGRAVGIEVPCASAAII-NEG-ELRKELGSLVEKIKGL 124
Cdd:cd21104    82 ALGRACGVSRPVIACSVTtNEGsQLKSQIQSLKDAIEKL 120
IGv smart00406
Immunoglobulin V-Type;
155-236 3.50e-28

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 105.93  E-value: 3.50e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  155 SVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPeNGDTEYTQKFKGKATLTADKSPSTAYMQLSSLTSEDSAVYYC 234
Cdd:smart00406   1 SVTLSCKFSGSTFSSYYVSWVRQPPGKGLEWLGYIGS-NGSSYYQESYKGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79


                   ..
gi 1534506063  235 AR 236
Cdd:smart00406  80 AV 81
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 142-254 2.40e-24

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: 96.63  E-value: 2.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 142 LQQSGAELVRS-GASVKLSCTASGFnIKDYYMHWVKQRPEQGLEWIGWIDPenGDTEYTQKFKGKATLTADKSpSTAYMQ 220
Cdd:cd00099     1 VTQSPRSLSVQeGESVTLSCEVSSS-FSSTYIYWYRQKPGQGPEFLIYLSS--SKGKTKGGVPGRFSGSRDGT-SSFSLT 76

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1534506063 221 LSSLTSEDSAVYYCARITT-DYYFDYWGQGTTLTV 254
Cdd:cd00099    77 ISNLQPEDSGTYYCAVSESgGTDKLTFGSGTRLTV 111
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 276-380 5.06e-20

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: 84.64  E-value: 5.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 276 TQTPLSLPVSLGDQASISCRssqslvHSNGNTYLEWYLQKPGQSPKLLIY---KVSNRFSGVP-DRFSGSG-SGTDFTLK 350
Cdd:cd05899     2 TQSPRYLIKRRGQSVTLRCS------QKSGHDNMYWYRQDPGKGLQLLFYsygGGLNEEGDLPgDRFSASRpSLTRSSLT 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1534506063 351 ISRVEAEDLGVYFC---SQSTHVPLTFGAGTKL 380
Cdd:cd05899    76 IKSAEPEDSAVYLCassLGGGADEAYFGPGTRL 108
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 277-382 5.21e-18

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: 79.04  E-value: 5.21e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 277 QTPLSLPVSLGDQASISCrsSQSLVHSNGNTYLEWYLQKPGQSPKLLI--YKVSNRFSGVPDRFSGSG--SGTDFTLKIS 352
Cdd:pfam07686   1 QTPREVTVALGGSVTLPC--TYSSSMSEASTSVYWYRQPPGKGPTFLIayYSNGSEEGVKKGRFSGRGdpSNGDGSLTIQ 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 1534506063 353 RVEAEDLGVYFCSQSTHVPLTFGAGTKLEI 382
Cdd:pfam07686  79 NLTLSDSGTYTCAVIPSGEGVFGKGTRLTV 108
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 276-383 1.09e-17

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: 78.08  E-value: 1.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 276 TQTPLSLPVSLGDQASISCRSSQSlvhsnGNTYLEWYLQKPGQSPKLLIYKVSN-------RFSGVPDRFSGSgsgtdFT 348
Cdd:cd04983     2 TQSPQSLSVQEGENVTLNCNYSTS-----TFYYLFWYRQYPGQGPQFLIYISSDsgnkkkgRFSATLDKSRKS-----SS 71

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1534506063 349 LKISRVEAEDLGVYFCSQSTHVP---LTFGAGTKLEIK 383
Cdd:cd04983    72 LHISAAQLSDSAVYFCALSESGGtgkLTFGKGTRLTVE 109
IGv smart00406
Immunoglobulin V-Type;
290-366 1.11e-16

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 74.34  E-value: 1.11e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  290 ASISCRSSQSlvhSNGNTYLEWYLQKPGQSPKLLIYKVSNR----FSGVPDRFSGSG--SGTDFTLKISRVEAEDLGVYF 363
Cdd:smart00406   2 VTLSCKFSGS---TFSSYYVSWVRQPPGKGLEWLGYIGSNGssyyQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYY 78


                   ...
gi 1534506063  364 CSQ 366
Cdd:smart00406  79 CAV 81
PRK13602 PRK13602
50S ribosomal protein L7ae-like protein;
20-105 2.46e-16

50S ribosomal protein L7ae-like protein;


Pssm-ID: 184174 [Multi-domain]  Cd Length: 82  Bit Score: 73.28  E-value: 2.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  20 EKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPeIVAHLPLLCEEKNVPYIYVkenlyfqSSKNDLGRAVGIEVPC 99
Cdd:PRK13602    4 EKVSQAKSIVIGTKQTVKALKRGSVKEVVVAEDADPR-LTEKVEALANEKGVPVSKV-------DSMKKLGKACGIEVGA 75


                  ....*.
gi 1534506063 100 ASAAII 105
Cdd:PRK13602   76 AAVAII 81
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 143-254 1.17e-15

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: 72.30  E-value: 1.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 143 QQSGAEL-VRSGASVKLSCT--ASGFnikdYYMHWVKQRPEQGLEWIgwidpENGDTEYTQKFKGKATLTADKSPSTAYM 219
Cdd:cd04983     2 TQSPQSLsVQEGENVTLNCNysTSTF----YYLFWYRQYPGQGPQFL-----IYISSDSGNKKKGRFSATLDKSRKSSSL 72

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1534506063 220 QLSSLTSEDSAVYYCA-RITTDYYFDYWGQGTTLTV 254
Cdd:cd04983    73 HISAAQLSDSAVYFCAlSESGGTGKLTFGKGTRLTV 108
IgV_L_lambda cd04984
Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of ...
 142-254 8.57e-15

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409373  Cd Length: 105  Bit Score: 69.80  E-value: 8.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 142 LQQSGAELVRSGASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPENGDTeYTQKFKGKatltadKSPSTAYMQL 221
Cdd:cd04984     2 LTQPSSLSVSPGETVTITCTGSSGNISGNYVNWYQQKPGSAPRYLIYEDKHRPSG-IPDRFSGS------KSGNTASLTI 74

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1534506063 222 SSLTSEDSAVYYCAritTDYYFDY-WGQGTTLTV 254
Cdd:cd04984    75 SGAQTEDEADYYCQ---VWDSNSYvFGGGTKLTV 105
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 149-254 3.13e-14

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: 68.46  E-value: 3.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 149 LVRSGASVKLSCTasgfNIKDYY-MHWVKQRPEQGLEWIGW----IDPENGDTeYTQKFKGKATltaDKSPSTayMQLSS 223
Cdd:cd05899     9 IKRRGQSVTLRCS----QKSGHDnMYWYRQDPGKGLQLLFYsyggGLNEEGDL-PGDRFSASRP---SLTRSS--LTIKS 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1534506063 224 LTSEDSAVYYCA----RITTDYYFdywGQGTTLTV 254
Cdd:cd05899    79 AEPEDSAVYLCAsslgGGADEAYF---GPGTRLTV 110
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 142-254 1.76e-13

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


Pssm-ID: 409371  Cd Length: 117  Bit Score: 66.62  E-value: 1.76e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 142 LQQSGAELVRS-GASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPENGDTEYTQKFKGKATLTADKSPSTAYMQ 220
Cdd:cd04982     1 LEQPQLSITREeSKSVTISCKVSGIDFSTTYIHWYRQKPGQALERLLYVSSTSAVRKDSGKTKNKFEARKDVGKSTSTLT 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1534506063 221 LSSLTSEDSAVYYCA--RITTDYYFDYWGQGTTLTV 254
Cdd:cd04982    81 ITNLEKEDSATYYCAywESGSGYYIKVFGSGTKLIV 116
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 149-254 2.96e-13

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: 64.83  E-value: 2.96e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  149 LVRSGASVKLSCTASGFniKDYYMHWVKQrpeqGLEWIGwidpengdteYTQKFKGkatltaDKSPSTAYMQLSSLTSED 228
Cdd:smart00410   5 TVKEGESVTLSCEASGS--PPPEVTWYKQ----GGKLLA----------ESGRFSV------SRSGSTSTLTISNVTPED 62

                           90       100
                   ....*....|....*....|....*.
gi 1534506063  229 SAVYYCARitTDYYFDYWGqGTTLTV 254
Cdd:smart00410  63 SGTYTCAA--TNSSGSASS-GTTLTV 85
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 279-382 4.21e-13

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: 64.45  E-value: 4.21e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  279 PLSLPVSLGDQASISCRssqslVHSNGNTYLEWYLQKPgqspKLLIYkvsnrfsgvPDRFSGSGSGTDFTLKISRVEAED 358
Cdd:smart00410   1 PPSVTVKEGESVTLSCE-----ASGSPPPEVTWYKQGG----KLLAE---------SGRFSVSRSGSTSTLTISNVTPED 62

                           90       100
                   ....*....|....*....|....
gi 1534506063  359 LGVYFCSQSTHVPLTFGaGTKLEI 382
Cdd:smart00410  63 SGTYTCAATNSSGSASS-GTTLTV 85
IgV_TCR_gamma cd04982
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain; The members here ...
 275-380 1.42e-12

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


Pssm-ID: 409371  Cd Length: 117  Bit Score: 63.92  E-value: 1.42e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 275 MTQTPLSLPVSLGDQASISCRSSqslVHSNGNTYLEWYLQKPGQSPKLLIY------------KVSNRFSgvPDRFSGSG 342
Cdd:cd04982     1 LEQPQLSITREESKSVTISCKVS---GIDFSTTYIHWYRQKPGQALERLLYvsstsavrkdsgKTKNKFE--ARKDVGKS 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1534506063 343 SgtdFTLKISRVEAEDLGVYFCS-----QSTHVPLtFGAGTKL 380
Cdd:cd04982    76 T---STLTITNLEKEDSATYYCAywesgSGYYIKV-FGSGTKL 114
PTZ00365 PTZ00365
60S ribosomal protein L7Ae-like; Provisional
 28-113 8.46e-12

60S ribosomal protein L7Ae-like; Provisional


Pssm-ID: 240382  Cd Length: 266  Bit Score: 64.87  E-value: 8.46e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  28 VKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKenlyfqsSKNDLGRAVGiEVPCASAAIINe 107
Cdd:PTZ00365  133 LKYGLNHVTDLVEYKKAKLVVIAHDVDPIELVCFLPALCRKKEVPYCIIK-------GKSRLGKLVH-QKTAAVVAIDN- 203


                  ....*.
gi 1534506063 108 geLRKE 113
Cdd:PTZ00365  204 --VRKE 207
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 153-254 1.91e-11

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: 60.55  E-value: 1.91e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 153 GASVKLSCTASGF-NIKDYYMHWVKQRPEQGLEWIgwIDPENGDTEyTQKFKGKATLTADKSPSTAYMQLSSLTSEDSAV 231
Cdd:pfam07686  11 GGSVTLPCTYSSSmSEASTSVYWYRQPPGKGPTFL--IAYYSNGSE-EGVKKGRFSGRGDPSNGDGSLTIQNLTLSDSGT 87

                          90       100
                  ....*....|....*....|...
gi 1534506063 232 YYCARITTDYyfDYWGQGTTLTV 254
Cdd:pfam07686  88 YTCAVIPSGE--GVFGKGTRLTV 108
RPL30E COG1911
Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]; Ribosomal protein ...
 19-109 7.82e-10

Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]; Ribosomal protein L30E is part of the Pathway/BioSystem: Archaeal ribosomal proteins


Pssm-ID: 441515 [Multi-domain]  Cd Length: 97  Bit Score: 55.60  E-value: 7.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  19 LEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVdPPEIVAHLPLLCEEKNVPyIYVkenlyFQSSKNDLGRAVGIEVP 98
Cdd:COG1911     8 LRDAVKTGKVVLGSKQTIKAIKLGKAKLVILAANC-PPEIREDIEYYAKLSNVP-VYV-----YPGTSVELGALCGKPFR 80

                          90
                  ....*....|.
gi 1534506063  99 CASAAIINEGE 109
Cdd:COG1911    81 VSALAIIDPGE 91
PTZ00222 PTZ00222
60S ribosomal protein L7a; Provisional
 28-94 2.11e-09

60S ribosomal protein L7a; Provisional


Pssm-ID: 140249  Cd Length: 263  Bit Score: 57.79  E-value: 2.11e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1534506063  28 VKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKEnlyfqssKNDLGRAVG 94
Cdd:PTZ00222  133 VVTGLQEVTRAIEKKQARMVVIANNVDPVELVLWMPNLCRANKIPYAIVKD-------MARLGDAIG 192
PRK01018 PRK01018
50S ribosomal protein L30e; Reviewed
 19-109 4.51e-08

50S ribosomal protein L30e; Reviewed


Pssm-ID: 179205 [Multi-domain]  Cd Length: 99  Bit Score: 50.73  E-value: 4.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  19 LEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVdPPEIVAHLPLLCEEKNVPyIYVkenlyFQSSKNDLGRAVGIEVP 98
Cdd:PRK01018    8 LRVAVDTGKVILGSKRTIKAIKLGKAKLVIVASNC-PKDIKEDIEYYAKLSGIP-VYE-----YEGSSVELGTLCGKPFT 80

                          90
                  ....*....|.
gi 1534506063  99 CASAAIINEGE 109
Cdd:PRK01018   81 VSALAIVDPGE 91
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 142-254 7.76e-08

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409497  Cd Length: 116  Bit Score: 50.52  E-value: 7.76e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 142 LQQSGAELVRSGASVKLSCTASGFnIKDYYMHWVKQR----PEQGLEWIGWIDPENGDTEYTQKFKGKATLTADKSPSTA 217
Cdd:cd07700     2 LQTPGSLLVQTNQTVKMSCEAKTS-PKNTRIYWLRQRqapsKDSHFEFLASWDPSKGIVYGEGVDQEKLIILSDSDSSRY 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1534506063 218 YMQLSSLTSEDSAVYYCARI-TTDYYFdywGQGTTLTV 254
Cdd:cd07700    81 ILSLMSVKPEDSGTYFCMTVgSPELIF---GTGTKLSV 115
IgV_H_TCR_mu cd16095
T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the ...
 139-254 1.38e-07

T-cell receptor Mu, Heavy chain, variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. 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 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 can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409514  Cd Length: 115  Bit Score: 49.87  E-value: 1.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 139 EVQLQQSGAELVRSGASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIGWIDPENGDTEytqkfKGKATLTADKSPSTAY 218
Cdd:cd16095     1 ETQLEESGGGSHPAGKTLSLKCQTSGFQFNTSQLSWYLWVPGHAPLWLTSLDHISTKVS-----EDRITSSREDTNSQIF 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1534506063 219 MQLSSLTSEDSAVYYCARIT-----TDYYFdyWGQGTTLTV 254
Cdd:cd16095    76 LQIKGLGLRDSGQYHCARRVgygddTDKLI--FGPGTDVIV 114
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 276-382 2.41e-07

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta 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. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409503  Cd Length: 112  Bit Score: 49.05  E-value: 2.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 276 TQTPLSLPVSLGDQASISCRSSQSlvhsNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTD--FTLKISR 353
Cdd:cd07706     3 TQAQPDVSVQVGEEVTLNCRYETS----WTNYYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQksISLTISA 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1534506063 354 VEAEDLGVYFCSQSTHVP---LTFGAGTKLEI 382
Cdd:cd07706    79 LQLEDSAKYFCALSLPYDtdkLIFGKGTRLTV 110
IgV_CD8_beta cd07700
Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The ...
 277-382 7.58e-07

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409497  Cd Length: 116  Bit Score: 47.44  E-value: 7.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 277 QTPLSLPVSLGDQASISCRSSQSLvhsnGNTYLEWYLQKPGQSP----KLLIYKVSNRFS----GV-PDRFS--GSGSGT 345
Cdd:cd07700     3 QTPGSLLVQTNQTVKMSCEAKTSP----KNTRIYWLRQRQAPSKdshfEFLASWDPSKGIvygeGVdQEKLIilSDSDSS 78

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1534506063 346 DFTLKISRVEAEDLGVYFCSQSTHVPLTFGAGTKLEI 382
Cdd:cd07700    79 RYILSLMSVKPEDSGTYFCMTVGSPELIFGTGTKLSV 115
IgV_TCR_delta cd07706
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here ...
 150-254 4.15e-06

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta 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. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409503  Cd Length: 112  Bit Score: 45.20  E-value: 4.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 150 VRSGASVKLSCTasgFNIKD--YYMHWVKQRPEQGLEWIgwidpENGDTEYTQKFKGKATLTADKSPSTAYMQLSSLTSE 227
Cdd:cd07706    11 VQVGEEVTLNCR---YETSWtnYYLFWYKQLPSGEMTFL-----IRQDSSEQNAKSGRYSVNFQKAQKSISLTISALQLE 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 1534506063 228 DSAVYYCA---RITTDYYFdyWGQGTTLTV 254
Cdd:cd07706    83 DSAKYFCAlslPYDTDKLI--FGKGTRLTV 110
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 281-383 1.38e-05

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the 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. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409580  Cd Length: 114  Bit Score: 44.09  E-value: 1.38e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 281 SLPVSLGDQASISCRSSQSLVhsnGNTYLEWYLQKPGqSPKLLIYKVSNRFS-GVPDRFSGS--GSGTDFTLKISRVEAE 357
Cdd:cd20988     7 TVTVSVGKPVTLKCSMKGEAI---SNYYINWYRKTQG-NTMTFIYREGGIYGpGFKDNFRGDidSSNNLAVLKILEASER 82

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1534506063 358 DLGVYFCSQST------HVPLTFGAGTKLEIK 383
Cdd:cd20988    83 DEGSYYCASDTpgggreYDPLIFGKGTYLTVE 114
IgV_CD79b_beta cd16096
Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are ...
 302-382 1.45e-05

Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B; The members here are composed of the immunoglobulin variable domain (IgV) of the Cluster of Differentiation (CD) 79B (also known as CD79b molecule, immunoglobulin-associated beta (Ig-beta), and B29). The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. Members of the IgV family 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409515  Cd Length: 96  Bit Score: 43.40  E-value: 1.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 302 HSNGNTYLEWYLQKPGQSPKLLIYKvsnrfsgvPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQ---STHVPLTFGAGT 378
Cdd:cd16096    21 YTNYSGVMTWFRKKGNQRPQELFPE--------DGRISQTQNGSVYTLTIQNIQYEDNGIYFCQQkcnSTEPDVTDGCGT 92


                  ....
gi 1534506063 379 KLEI 382
Cdd:cd16096    93 ELLV 96
PRK13601 PRK13601
putative L7Ae-like ribosomal protein; Provisional
 31-107 3.11e-05

putative L7Ae-like ribosomal protein; Provisional


Pssm-ID: 184173  Cd Length: 82  Bit Score: 41.89  E-value: 3.11e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1534506063  31 GTNETTKAVERGLAKLVYIAEDVDpPEIVAHLPLLCEEKNVPYIYVkenlyfqSSKNDLGRAVGIEVPCASAA-IINE 107
Cdd:PRK13601   12 GAKQTLKAITNCNVLQVYIAKDAE-EHVTKKIKELCEEKSIKIVYI-------DTMKELGVMCGIDVGAAAAAdIIGE 81
IgV_CD8_alpha cd05720
Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; ...
 311-377 1.15e-04

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409385  Cd Length: 110  Bit Score: 41.32  E-value: 1.15e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1534506063 311 WYLQKPGQSPK---LLIYKVSNRFSGVPD----RFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPLTFGAG 377
Cdd:cd05720    32 WLFQPRGSAPQptfLLYLSSSNKTKWAEGldskRFSGSRSGSSYVLTLKDFRKEDEGYYFCSVISNSVLYFSSF 105
IgV_TCR_gammadelta cd20988
Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the ...
 150-254 2.77e-04

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the 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. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.


Pssm-ID: 409580  Cd Length: 114  Bit Score: 40.23  E-value: 2.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 150 VRSGASVKLSCTASGFNIKDYYMHWVKQRPEQGLEWIgwidPENGDTeYTQKFKGKATLTADKSPSTAYMQLSSLTSEDS 229
Cdd:cd20988    10 VSVGKPVTLKCSMKGEAISNYYINWYRKTQGNTMTFI----YREGGI-YGPGFKDNFRGDIDSSNNLAVLKILEASERDE 84

                          90       100
                  ....*....|....*....|....*....
gi 1534506063 230 AVYYCARITT--DYYFD--YWGQGTTLTV 254
Cdd:cd20988    85 GSYYCASDTPggGREYDplIFGKGTYLTV 113
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 276-364 4.71e-04

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: 39.41  E-value: 4.71e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063 276 TQTPLSLPVSLGDQASISCrssqSLVHSNGNTYLEWYLQKPG-QSPKLLIYKVSNRFSGVPDRFSGSG--SGTDFTLKIS 352
Cdd:cd16088     3 TFSPALLVVTEGANATFTC----SFSNTSESFVLNWYRLSPSnQTDKLAAFPEDRSQPGQDWRFRVTQlpNGRDFHMSVV 78

                          90
                  ....*....|..
gi 1534506063 353 RVEAEDLGVYFC 364
Cdd:cd16088    79 RARRNDSGTYLC 90
PTZ00106 PTZ00106
60S ribosomal protein L30; Provisional
 19-109 8.08e-04

60S ribosomal protein L30; Provisional


Pssm-ID: 185450  Cd Length: 108  Bit Score: 38.90  E-value: 8.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  19 LEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVdPPEIVAHLPLLCEEKNVPyIYVkenlyFQSSKNDLGRAVGIEVP 98
Cdd:PTZ00106   17 LQLVMKSGKYTLGTKSTLKALRNGKAKLVIISNNC-PPIRRSEIEYYAMLSKTG-VHH-----YAGNNNDLGTACGRHFR 89

                          90
                  ....*....|.
gi 1534506063  99 CASAAIINEGE 109
Cdd:PTZ00106   90 VSVMSITDAGD 100
PRK06683 PRK06683
hypothetical protein; Provisional
 20-106 1.07e-03

hypothetical protein; Provisional


Pssm-ID: 136002  Cd Length: 82  Bit Score: 37.75  E-value: 1.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  20 EKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDP--PEIVAHLPLlceEKNVPYIYVKenlyfqsSKNDLGRAVGIEV 97
Cdd:PRK06683    4 QKVSNAENVVVGHKRTLEAIKNGIVKEVVIAEDADMrlTHVIIRTAL---QHNIPITKVE-------SVRKLGKVAGIQV 73


                  ....*....
gi 1534506063  98 PCASAAIIN 106
Cdd:PRK06683   74 GASAIGIIS 82
PRK07714 PRK07714
YlxQ family RNA-binding protein;
12-112 1.52e-03

YlxQ family RNA-binding protein;


Pssm-ID: 236077  Cd Length: 100  Bit Score: 37.84  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  12 QNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDpPEIVAHLPLLCEEKNVPYIYVkenlyfqSSKNDLGR 91
Cdd:PRK07714    3 MSDWKSFLGLANRARKVISGEELVLKEVRSGKAKLVLLSEDAS-VNTTKKITDKCTYYNVPMRKV-------ENRQQLGH 74

                          90       100
                  ....*....|....*....|.
gi 1534506063  92 AVGIEVPCAsAAIINEGELRK 112
Cdd:PRK07714   75 AIGKDERVV-VAVLDEGFAKK 94
PRK05583 PRK05583
ribosomal protein L7Ae family protein; Provisional
 11-94 6.32e-03

ribosomal protein L7Ae family protein; Provisional


Pssm-ID: 235517  Cd Length: 104  Bit Score: 36.18  E-value: 6.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1534506063  11 MQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDP---PEIVAHlpllCEEKNVPYIyvkeNLYfqsSKN 87
Cdd:PRK05583    1 MMNKFLNFLGLTKKAGKLLEGYNKCEEAIKKKKVYLIIISNDISEnskNKFKNY----CNKYNIPYI----EGY---SKE 69


                  ....*..
gi 1534506063  88 DLGRAVG 94
Cdd:PRK05583   70 ELGNAIG 76
PELOTA_1 pfam15608
PELOTA RNA binding domain; This RNA binding Pelota domain is at the C-terminus of a PRTase ...
 28-72 7.84e-03

PELOTA RNA binding domain; This RNA binding Pelota domain is at the C-terminus of a PRTase family. These PRTase+Pelota genes are found in the biosynthetic operon associated with the Ter stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response.


Pssm-ID: 434808  Cd Length: 79  Bit Score: 35.19  E-value: 7.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1534506063  28 VKKGTNETTKAVERGLAKLVYIAEDVDPPeiVAHLPLLCEEKNVP 72
Cdd:pfam15608  20 IKPGIGEATRVLLRRVPWKVLVRDPDDPD--LAHLLLLAKEKGVP 62
 
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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