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Conserved domains on  [gi|4758256|ref|NP_004085|]
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eukaryotic translation initiation factor 2 subunit 1 [Homo sapiens]

Protein Classification

eukaryotic translation initiation factor 2 subunit alpha( domain architecture ID 1000628)

eukaryotic translation initiation factor 2 subunit alpha is part of the eIF-2 complex that functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA

CATH:  1.10.150.190|2.40.50.140
Gene Ontology:  GO:0003723|GO:0003743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00248 super family cl36533
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-315 2.70e-130

eukaryotic translation initiation factor 2 subunit 1; Provisional


The actual alignment was detected with superfamily member PTZ00248:

Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 373.61  E-value: 2.70e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256     4 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYI 83
Cdd:PTZ00248   5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    84 DLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEvleyTKDEQLESLFQRTAWVFDDKYKRpgygAYDAFKHAVSDPS-I 162
Cdd:PTZ00248  85 DLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQ----KHGMSVEELYTKIIWPLYKKYGH----ALDALKEALTNPDnV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   163 LDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTL 242
Cdd:PTZ00248 157 FEGLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCS 236

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4758256   243 ERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDtDETELARQMERLERENAEV------DGDDDAEEMEAKAED 315
Cdd:PTZ00248 237 DKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEEEEEEDdyseseDEDEEDEDEEEEEDD 314
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-315 2.70e-130

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 373.61  E-value: 2.70e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256     4 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYI 83
Cdd:PTZ00248   5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    84 DLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEvleyTKDEQLESLFQRTAWVFDDKYKRpgygAYDAFKHAVSDPS-I 162
Cdd:PTZ00248  85 DLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQ----KHGMSVEELYTKIIWPLYKKYGH----ALDALKEALTNPDnV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   163 LDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTL 242
Cdd:PTZ00248 157 FEGLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCS 236

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4758256   243 ERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDtDETELARQMERLERENAEV------DGDDDAEEMEAKAED 315
Cdd:PTZ00248 237 DKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEEEEEEDdyseseDEDEEDEDEEEEEDD 314
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 12-271 3.48e-43

Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440710 [Multi-domain]  Cd Length: 259  Bit Score: 148.81  E-value: 3.48e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   12 KFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVS 91
Cdd:COG1093   6 ELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLSLKRVN 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   92 PEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLfqrtAWVFDDKYKRPgygaYDAFKHAVSD-PSILDSLDLNE 170
Cdd:COG1093  86 EHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEV----GWKLEDEYGSL----YDAFEEAAIEgPEALEDAGLPE 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256  171 DEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGL-NCSTENMPIKINLIAPPRYVMTTTTLERTEGLS 249
Cdd:COG1093 158 EWIDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEeNIEPEDVDVEITYVGAPRYRIEVTAPDYKTAEK 237

                       250       260
                ....*....|....*....|..
gi 4758256  250 VLSQAMAVIKEKIEEKRGVFNV 271
Cdd:COG1093 238 ALKKAAEKAIKAIKKLGGEGEF 259
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 14-89 3.68e-42

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 140.41  E-value: 3.68e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4758256   14 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR 89
Cdd:cd04452   1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 132-241 2.64e-39

Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of similarity that falls towards the C terminus from pfam00575.


Pssm-ID: 462200  Cd Length: 112  Bit Score: 134.21  E-value: 2.64e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    132 QRTAWVFDDKYKrpgyGAYDAF-KHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKE 210
Cdd:pfam07541   2 EEIGWPLEEKYG----SLYDAFeKAAIEGPEVLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKK 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 4758256    211 ALRAGLN----CSTENMPIKINLIAPPRYVMTTTT 241
Cdd:pfam07541  78 ALKAGAEsteeIKGEDVPIKIKLVGAPRYRITVTA 112
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
15-88 5.70e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 57.61  E-value: 5.70e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4758256      15 EVEDVVMVNVRSIAEMGAYVSLleYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKR 88
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 15-102 8.40e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 43.95  E-value: 8.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256     15 EVEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEE 94
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDP 262


                  ....*...
gi 4758256     95 AIKCEDKF 102
Cdd:TIGR00717 263 WEAIEKKF 270
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-315 2.70e-130

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 373.61  E-value: 2.70e-130
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256     4 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYI 83
Cdd:PTZ00248   5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    84 DLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEvleyTKDEQLESLFQRTAWVFDDKYKRpgygAYDAFKHAVSDPS-I 162
Cdd:PTZ00248  85 DLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQ----KHGMSVEELYTKIIWPLYKKYGH----ALDALKEALTNPDnV 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   163 LDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTL 242
Cdd:PTZ00248 157 FEGLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCS 236

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4758256   243 ERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDtDETELARQMERLERENAEV------DGDDDAEEMEAKAED 315
Cdd:PTZ00248 237 DKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEEEEEEDdyseseDEDEEDEDEEEEEDD 314
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 12-271 3.48e-43

Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440710 [Multi-domain]  Cd Length: 259  Bit Score: 148.81  E-value: 3.48e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   12 KFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVS 91
Cdd:COG1093   6 ELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLSLKRVN 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   92 PEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLfqrtAWVFDDKYKRPgygaYDAFKHAVSD-PSILDSLDLNE 170
Cdd:COG1093  86 EHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEV----GWKLEDEYGSL----YDAFEEAAIEgPEALEDAGLPE 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256  171 DEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGL-NCSTENMPIKINLIAPPRYVMTTTTLERTEGLS 249
Cdd:COG1093 158 EWIDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEeNIEPEDVDVEITYVGAPRYRIEVTAPDYKTAEK 237

                       250       260
                ....*....|....*....|..
gi 4758256  250 VLSQAMAVIKEKIEEKRGVFNV 271
Cdd:COG1093 238 ALKKAAEKAIKAIKKLGGEGEF 259
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 14-89 3.68e-42

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 140.41  E-value: 3.68e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4758256   14 PEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR 89
Cdd:cd04452   1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 132-241 2.64e-39

Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of similarity that falls towards the C terminus from pfam00575.


Pssm-ID: 462200  Cd Length: 112  Bit Score: 134.21  E-value: 2.64e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    132 QRTAWVFDDKYKrpgyGAYDAF-KHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKE 210
Cdd:pfam07541   2 EEIGWPLEEKYG----SLYDAFeKAAIEGPEVLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKK 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 4758256    211 ALRAGLN----CSTENMPIKINLIAPPRYVMTTTT 241
Cdd:pfam07541  78 ALKAGAEsteeIKGEDVPIKIKLVGAPRYRITVTA 112
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 13-276 1.41e-34

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 126.48  E-value: 1.41e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    13 FPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSP 92
Cdd:PRK03987   5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    93 ---EEAI---KCEDKFTKsktvysILRHVAEVLEYTKDEQLESLfqrtAWVFDDKYKRPgygaYDAFKHAVSD-PSILDS 165
Cdd:PRK03987  85 hqrREKIqewKNEQKADK------WLELAAEKLGKSLEEAWEEV----GYKLEDEFGDL----YDAFEEAAIEgEEALDD 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   166 LDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCST-ENMPIKINLIAPPRYVMTTTTLER 244
Cdd:PRK03987 151 LGVPEEWADALVEIARENIEVPKVKISGYVDLTSPEPDGVEIIKKALKAAEKANKyEDVEVEIYYVGAPRYRIDVTAPDY 230

                        250       260       270
                 ....*....|....*....|....*....|..
gi 4758256   245 TEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPK 276
Cdd:PRK03987 231 KTAEKALKKIAERAIKVIKKLGGEGSFVREEK 262
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 14-87 2.17e-12

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 61.53  E-value: 2.17e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4758256     14 PEVEDVVMVNVRSIAEMGAYVSLLeyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSK 87
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLG--NGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
15-88 5.70e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 57.61  E-value: 5.70e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4758256      15 EVEDVVMVNVRSIAEMGAYVSLleYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKR 88
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
43-108 8.65e-07

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 50.33  E-value: 8.65e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4758256    43 EGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKC-EDKFTKSKTV 108
Cdd:PRK00087 327 EGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKElEEAFENGEPV 393
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 20-86 1.82e-06

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 44.68  E-value: 1.82e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4758256   20 VMVNVRSIAEMGAYVSLLEynNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLS 86
Cdd:cd00164   1 VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 16-86 1.82e-06

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 44.93  E-value: 1.82e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4758256   16 VEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLS 86
Cdd:cd05688   1 EGDVVEGTVKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 14-90 5.98e-06

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 47.74  E-value: 5.98e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4758256    14 PEVEDVVMVNVRSIAEMGAYVSLLeyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKeKGYIDLSKRRV 90
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK-RGRIRLSRKAV 692
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
12-95 2.40e-05

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 45.71  E-value: 2.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    12 KFPeVEDVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVS 91
Cdd:PRK00087 559 KYP-VGSIVLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVE 635


                 ....
gi 4758256    92 PEEA 95
Cdd:PRK00087 636 EEPG 639
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
15-102 2.89e-05

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 45.71  E-value: 2.89e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    15 EVEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEE 94
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDP 552


                 ....*...
gi 4758256    95 AIKCEDKF 102
Cdd:PRK00087 553 WENVEEKY 560
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 15-102 8.40e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 43.95  E-value: 8.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256     15 EVEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEE 94
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDP 262


                  ....*...
gi 4758256     95 AIKCEDKF 102
Cdd:TIGR00717 263 WEAIEKKF 270
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 15-102 8.45e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.71  E-value: 8.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    15 EVEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEE 94
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFVDI---GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGP 267


                 ....*...
gi 4758256    95 AIKCEDKF 102
Cdd:PRK06676 268 WEGVEEKL 275
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 15-92 1.45e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 43.23  E-value: 1.45e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4758256    15 EVEDVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELS-RRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSP 92
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKE 361
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 15-92 1.60e-04

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 42.72  E-value: 1.60e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4758256   15 EVEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSP 92
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDL---GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQP 262
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 24-87 1.79e-04

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 39.06  E-value: 1.79e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4758256   24 VRSIAEMGAYVSLLEynNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKeKGYIDLSK 87
Cdd:cd04472   8 VVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 12-91 2.55e-04

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 42.34  E-value: 2.55e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256   12 KFPeVEDVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELSR-RRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRV 90
Cdd:COG0539 271 KYP-VGDVVKGKVTRLTDFGAFVELEP--GVEGLVHISEMSWtKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347


                .
gi 4758256   91 S 91
Cdd:COG0539 348 A 348
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 15-108 3.10e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.17  E-value: 3.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    15 EVEDVVMVNVRSIAEMGAYVSLLEYNnIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEE 94
Cdd:PRK06676  16 EVGDVVTGEVLKVEDKQVFVNIEGYK-VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEK 94

                         90
                 ....*....|....*
gi 4758256    95 AI-KCEDKFTKSKTV 108
Cdd:PRK06676  95 AWdKLEEKFEEGEVV 109
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 15-86 5.03e-04

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 38.08  E-value: 5.03e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4758256   15 EVEDVVMVNVRSIAEMGAYVSLlEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLS 86
Cdd:cd05708   1 KVGQKIDGTVRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 12-92 5.07e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 41.69  E-value: 5.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    12 KFPeVEDVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELS-RRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRV 90
Cdd:PRK06299 370 KYP-VGDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQL 446


                 ..
gi 4758256    91 SP 92
Cdd:PRK06299 447 EE 448
PRK08059 PRK08059
general stress protein 13; Validated
 15-92 5.46e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 39.26  E-value: 5.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4758256    15 EVEDVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSP 92
Cdd:PRK08059   6 EVGSVVTGKVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEE 81
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 15-93 8.30e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 40.55  E-value: 8.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4758256    15 EVEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPE 93
Cdd:PRK07400 195 EVGEVVVGTVRGIKPYGAFIDI---GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPE 270
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 10-101 8.99e-04

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 40.87  E-value: 8.99e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256     10 QHKFPeVEDVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELS-RRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKR 88
Cdd:TIGR00717 267 EKKFP-VGDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343

                          90
                  ....*....|...
gi 4758256     89 RVSPEEAIKCEDK 101
Cdd:TIGR00717 344 QCKANPWEQFEEK 356
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 18-85 1.19e-03

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 36.70  E-value: 1.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4758256   18 DVVMVNVRSIAEMGAYVSLLEynNIEGMILLSELS-RRRIRSINKLIRIGRNECVVVIRVDKEKGYIDL 85
Cdd:cd05690   2 TVVSGKIKSITDFGIFVGLDG--GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 16-145 1.34e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 40.47  E-value: 1.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4758256    16 VEDVVMVNVRSIAEMGAYVSLleyNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEA 95
Cdd:PRK12269 493 IEDSVSGVVKSFTSFGAFIDL---GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPW 569

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 4758256    96 IKCEDKFTKSKTVYSILRHVAEVLEYTK-DEQLESLFQRTAWVFDDKYKRP 145
Cdd:PRK12269 570 LEFENKFGVNDVVKGRVTKIADFGAFIElAEGIEGLAHISEFSWVKKTSKP 620
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 43-88 1.52e-03

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 36.74  E-value: 1.52e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 4758256   43 EGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKR 88
Cdd:cd05687  25 EGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 16-89 1.68e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 39.76  E-value: 1.68e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4758256    16 VEDVVMVNVRSIAEMGAYVSLleYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRR 89
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVEL--EDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 24-86 2.72e-03

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 35.67  E-value: 2.72e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4758256   24 VRSIAEMGAYVSLLEYNNieGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLS 86
Cdd:cd05685   8 VTNVTDFGAFVDIGVKQD--GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 16-88 5.93e-03

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 38.18  E-value: 5.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4758256     16 VEDVVMVNVRSIAEMGAYVSLleYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKR 88
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVEL--PGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
 
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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