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Conserved domains on  [gi|398364767|ref|NP_012540|]
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translation initiation factor eIF2 subunit alpha [Saccharomyces cerevisiae S288C]

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
 5-290 3.50e-131

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: 375.54  E-value: 3.50e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   5 HCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYID 84
Cdd:PTZ00248   6 DCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYID 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  85 LSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDET-VWEGIEPPSk 163
Cdd:PTZ00248  86 LSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDnVFEGLDIPE- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767 164 DVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALDKQKGIEQ 243
Cdd:PTZ00248 165 EVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDKGMEI 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 398364767 244 LESAIEKITEVITKYGGVCNITMPPKAVTATEDAELQALLESKELDN 290
Cdd:PTZ00248 245 IGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEE 291
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 5-290 3.50e-131

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 375.54  E-value: 3.50e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   5 HCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYID 84
Cdd:PTZ00248   6 DCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYID 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  85 LSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDET-VWEGIEPPSk 163
Cdd:PTZ00248  86 LSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDnVFEGLDIPE- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767 164 DVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALDKQKGIEQ 243
Cdd:PTZ00248 165 EVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDKGMEI 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 398364767 244 LESAIEKITEVITKYGGVCNITMPPKAVTATEDAELQALLESKELDN 290
Cdd:PTZ00248 245 IGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEE 291
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 7-260 4.78e-51

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: 168.84  E-value: 4.78e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   7 RFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:COG1093    1 VMKRKELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  87 KRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIID-ETVWEGIEPPsKDV 165
Cdd:COG1093   81 LKRVNEHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEVGWKLEDEYGSLYDAFEEAAIEgPEALEDAGLP-EEW 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767 166 LDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMST-EQMQVKVKLVAAPLYVLTTQALDKQKGIEQL 244
Cdd:COG1093  160 IDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEENIEpEDVDVEITYVGAPRYRIEVTAPDYKTAEKAL 239

                        250
                 ....*....|....*.
gi 398364767 245 ESAIEKITEVITKYGG 260
Cdd:COG1093  240 KKAAEKAIKAIKKLGG 255
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 14-89 2.70e-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: 2.70e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398364767  14 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR 89
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 127-234 2.65e-41

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: 138.84  E-value: 2.65e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  127 YKTIAWPLSRKFGHAYEAF-KLSIIDETVWEGIEPPsKDVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDAL 205
Cdd:pfam07541   1 YEEIGWPLEEKYGSLYDAFeKAAIEGPEVLDDLGIP-EEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKKAL 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 398364767  206 KSAE----DMSTEQMQVKVKLVAAPLYVLTTQA 234
Cdd:pfam07541  80 KAGAesteEIKGEDVPIKIKLVGAPRYRITVTA 112
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
15-88 2.81e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 55.69  E-value: 2.81e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398364767    15 EIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 9-108 1.14e-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: 43.57  E-value: 1.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767    9 YENKYPeIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELS-RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSK 87
Cdd:TIGR00717 353 FEEKHP-VGDRVTGKIKKITDFGAFVEL--EGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429

                          90       100
                  ....*....|....*....|.
gi 398364767   88 RRVSSEDIIKCEEKYQKSKTV 108
Cdd:TIGR00717 430 KQLTENPWEKFAAKYKVGSVV 450
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 5-290 3.50e-131

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 375.54  E-value: 3.50e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   5 HCRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYID 84
Cdd:PTZ00248   6 DCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYID 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  85 LSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIIDET-VWEGIEPPSk 163
Cdd:PTZ00248  86 LSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDnVFEGLDIPE- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767 164 DVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMSTEQMQVKVKLVAAPLYVLTTQALDKQKGIEQ 243
Cdd:PTZ00248 165 EVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDKGMEI 244

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 398364767 244 LESAIEKITEVITKYGGVCNITMPPKAVTATEDAELQALLESKELDN 290
Cdd:PTZ00248 245 IGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEE 291
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 7-260 4.78e-51

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: 168.84  E-value: 4.78e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   7 RFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:COG1093    1 VMKRKELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  87 KRRVSSEDIIKCEEKYQKSKTVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAFKLSIID-ETVWEGIEPPsKDV 165
Cdd:COG1093   81 LKRVNEHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEVGWKLEDEYGSLYDAFEEAAIEgPEALEDAGLP-EEW 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767 166 LDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMST-EQMQVKVKLVAAPLYVLTTQALDKQKGIEQL 244
Cdd:COG1093  160 IDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEENIEpEDVDVEITYVGAPRYRIEVTAPDYKTAEKAL 239

                        250
                 ....*....|....*.
gi 398364767 245 ESAIEKITEVITKYGG 260
Cdd:COG1093  240 KKAAEKAIKAIKKLGG 255
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 10-260 7.06e-46

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 155.75  E-value: 7.06e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  10 ENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR 89
Cdd:PRK03987   2 RKEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  90 VS---SEDIIKCEEKYQKsktVHSILRYCAEKFQIPLEELYKTIAWPLSRKFGHAYEAF-KLSIIDETVWEGIEPPsKDV 165
Cdd:PRK03987  82 VNehqRREKIQEWKNEQK---ADKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFeEAAIEGEEALDDLGVP-EEW 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767 166 LDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDALKSAEDMST-EQMQVKVKLVAAPLYVLTTQALDKQKGIEQL 244
Cdd:PRK03987 158 ADALVEIARENIEVPKVKISGYVDLTSPEPDGVEIIKKALKAAEKANKyEDVEVEIYYVGAPRYRIDVTAPDYKTAEKAL 237

                        250
                 ....*....|....*.
gi 398364767 245 ESAIEKITEVITKYGG 260
Cdd:PRK03987 238 KKIAERAIKVIKKLGG 253
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 14-89 2.70e-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: 2.70e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398364767  14 PEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR 89
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 127-234 2.65e-41

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: 138.84  E-value: 2.65e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  127 YKTIAWPLSRKFGHAYEAF-KLSIIDETVWEGIEPPsKDVLDELKNYISKRLTPQAVKIRADVEVSCFSYEGIDAIKDAL 205
Cdd:pfam07541   1 YEEIGWPLEEKYGSLYDAFeKAAIEGPEVLDDLGIP-EEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKKAL 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 398364767  206 KSAE----DMSTEQMQVKVKLVAAPLYVLTTQA 234
Cdd:pfam07541  80 KAGAesteEIKGEDVPIKIKLVGAPRYRITVTA 112
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 14-87 7.76e-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: 59.99  E-value: 7.76e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398364767   14 PEIDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSK 87
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGN--GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
15-88 2.81e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 55.69  E-value: 2.81e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 398364767    15 EIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 20-86 6.74e-09

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: 51.61  E-value: 6.74e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398364767  20 VMVNVQQIAEMGAYVKLLeyDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:cd00164    1 VTGKVVSITKFGVFVELE--DGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
10-103 5.04e-08

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 53.80  E-value: 5.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  10 ENKYPeIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRR 89
Cdd:PRK00087 557 EEKYP-VGSIVLGKVVRIAPFGAFVEL--EPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKE 633

                         90
                 ....*....|....
gi 398364767  90 VSSEDIIKCEEKYQ 103
Cdd:PRK00087 634 VEEEPGDIEKVELE 647
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
9-108 1.09e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.95  E-value: 1.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   9 YENKYPEIDDIVMVNVQQIAEMGAYVklleydNI----EGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYID 84
Cdd:PRK00087 295 ELEKQIRRGDIVKGTVVSVNENEVFV------DVgyksEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVV 368

                         90       100
                 ....*....|....*....|....
gi 398364767  85 LSKRRVSSEDIIKCEEKYQKSKTV 108
Cdd:PRK00087 369 LSKKEADREKAWKELEEAFENGEP 392
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 10-91 6.97e-06

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: 46.96  E-value: 6.97e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  10 ENKYPEiDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELSR-RRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:COG0539  269 AEKYPV-GDVVKGKVTRLTDFGAFVELEP--GVEGLVHISEMSWtKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345


                 ...
gi 398364767  89 RVS 91
Cdd:COG0539  346 QLA 348
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 18-86 1.35e-05

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: 42.23  E-value: 1.35e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398364767  18 DIVMVNVQQIAEMGAYVKLleyDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:cd05688    3 DVVEGTVKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 10-108 1.77e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.93  E-value: 1.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  10 ENKYPeIDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELS-RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:PRK06299 281 EKKYP-VGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357

                         90       100
                 ....*....|....*....|
gi 398364767  89 RVSSEDIIKCEEKYQKSKTV 108
Cdd:PRK06299 358 QCKENPWEEFAEKYPVGDVV 377
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 18-86 1.95e-05

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: 41.93  E-value: 1.95e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398364767  18 DIVMVNVQQIAEMGAYVKLlEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:cd05708    4 QKIDGTVRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
15-103 2.44e-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: 2.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  15 EIDDIVMVNVQQIAEMGAYVKLleyDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSED 94
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDP 552


                 ....*....
gi 398364767  95 IIKCEEKYQ 103
Cdd:PRK00087 553 WENVEEKYP 561
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 9-108 1.14e-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: 43.57  E-value: 1.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767    9 YENKYPeIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELS-RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSK 87
Cdd:TIGR00717 353 FEEKHP-VGDRVTGKIKKITDFGAFVEL--EGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429

                          90       100
                  ....*....|....*....|.
gi 398364767   88 RRVSSEDIIKCEEKYQKSKTV 108
Cdd:TIGR00717 430 KQLTENPWEKFAAKYKVGSVV 450
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 10-104 1.96e-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: 42.80  E-value: 1.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   10 ENKYPEiDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELS-RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:TIGR00717 267 EKKFPV-GDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343

                          90
                  ....*....|....*.
gi 398364767   89 RVSSEDIIKCEEKYQK 104
Cdd:TIGR00717 344 QCKANPWEQFEEKHPV 359
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 9-102 2.08e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.78  E-value: 2.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   9 YENKYpEIDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELS-RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSK 87
Cdd:PRK12269 572 FENKF-GVNDVVKGRVTKIADFGAFIELAE--GIEGLAHISEFSwVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGL 648

                         90
                 ....*....|....*
gi 398364767  88 RRVSSEDIIKCEEKY 102
Cdd:PRK12269 649 KQVTANPWEEIEARY 663
rpsA PRK13806
30S ribosomal protein S1; Provisional
 15-91 3.91e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 41.63  E-value: 3.91e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398364767  15 EIDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELS-RRRIRSIQKLIRVGkNDVAVVLrvdKEkgyIDLSKRRVS 91
Cdd:PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILP--GIEGLVHVSEMSwTRRVNKPEDVVAPG-DAVAVKI---KD---IDPAKRRIS 359
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 9-89 4.73e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 41.69  E-value: 4.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   9 YENKYPeIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:PRK06299 454 FAKKHK-KGSIVTGTVTEVKDKGAFVEL--EDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530


                 .
gi 398364767  89 R 89
Cdd:PRK06299 531 A 531
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 15-108 5.79e-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: 41.26  E-value: 5.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   15 EIDDIVMVNVQQIAEMGAYVKLleyDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSED 94
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDP 262

                          90
                  ....*....|....
gi 398364767   95 IIKCEEKYQKSKTV 108
Cdd:TIGR00717 263 WEAIEKKFPVGDKI 276
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 14-90 6.30e-04

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 41.19  E-value: 6.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398364767  14 PEIDDIVMVNVQQIAEMGAYVKLLeyDNIEGMILLSELSRRRIRSIQKLIRVGkNDVAV-VLRVDKeKGYIDLSKRRV 90
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEG-DEVKVkVLEIDK-RGRIRLSRKAV 692
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 18-108 6.94e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 41.01  E-value: 6.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  18 DIVMVNVQQIAEMGAYVKLLEYdNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSSE-DII 96
Cdd:PRK06676  19 DVVTGEVLKVEDKQVFVNIEGY-KVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEkAWD 97

                         90
                 ....*....|..
gi 398364767  97 KCEEKYQKSKTV 108
Cdd:PRK06676  98 KLEEKFEEGEVV 109
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 10-108 8.63e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 40.92  E-value: 8.63e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  10 ENKYPEiDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELSRrrIRSIQKLIR-VGKNDV--AVVLRVDKEKGYIDLS 86
Cdd:PRK06299 368 AEKYPV-GDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISW--DKKGEEAVElYKKGDEveAVVLKVDVEKERISLG 442

                         90       100
                 ....*....|....*....|..
gi 398364767  87 KRRVSSEDIIKCEEKYQKSKTV 108
Cdd:PRK06299 443 IKQLEEDPFEEFAKKHKKGSIV 464
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 17-86 1.07e-03

S1_RPS1_repeat_ec6: 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 6 (ec6) 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: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 36.86  E-value: 1.07e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  17 DDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKL--GDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLS 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 18-86 1.40e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 39.86  E-value: 1.40e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398364767  18 DIVMVNVQQIAEMGAYVKLleyDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLS 86
Cdd:PRK06676 194 DVVEGTVARLTDFGAFVDI---GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLS 259
rpsA PRK13806
30S ribosomal protein S1; Provisional
 7-91 2.42e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 39.32  E-value: 2.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767   7 RFYENKYPeiDDIVMVNVQQIAEMGAYVKLLEydNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDK-EKGY--- 82
Cdd:PRK13806 195 AFMETVKE--GDVVEGTVTRLAPFGAFVELAP--GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERaKKGKglr 270


                 ....*....
gi 398364767  83 IDLSKRRVS 91
Cdd:PRK13806 271 ISLSIKQAG 279
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 2.78e-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: 35.58  E-value: 2.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 398364767  43 EGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:cd05687   25 EGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 24-108 2.86e-03

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: 38.87  E-value: 2.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767  24 VQQIAEMGAYVKLleyDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKRRVSS---EDIikcEE 100
Cdd:COG0539  197 VKNITDFGAFVDL---GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQPdpwENI---AE 270


                 ....*...
gi 398364767 101 KYQKSKTV 108
Cdd:COG0539  271 KYPVGDVV 278
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 18-85 3.80e-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: 35.55  E-value: 3.80e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 398364767  18 DIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELS-RRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDL 85
Cdd:cd05690    2 TVVSGKIKSITDFGIFVGL--DGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 16-91 4.37e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 38.49  E-value: 4.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398364767  16 IDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGknDVAVVLRVDkekgyIDLSKRRVS 91
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRV--EEGIEGLVHISELAERHVEVPEQVVQVG--DEVFVKVID-----IDLERRRIS 359
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 9-88 4.96e-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: 4.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398364767    9 YENKYPeIDDIVMVNVQQIAEMGAYVKLleYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVLRVDKEKGYIDLSKR 88
Cdd:TIGR00717 440 FAAKYK-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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