NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|294887089|ref|XP_002771974|]
View 

eukaryotic initiation factor-2 alpha subunit, putative [Perkinsus marinus ATCC 50983]

Protein Classification

eukaryotic translation initiation factor 2 subunit alpha( domain architecture ID 11488290)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-294 5.19e-161

eukaryotic translation initiation factor 2 subunit 1; Provisional


:

Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 451.81  E-value: 5.19e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   4 EAAHLHCRFYREQFPEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKE 83
Cdd:PTZ00248   1 EADLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  84 KGYIDLSKKRVSREDAEALDQKYSKAKTVQSIMRHIASTHGMSLEEVCSKIAWPLYDTFGHAYDGLSKLVGDNADlsILE 163
Cdd:PTZ00248  81 KGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDN--VFE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089 164 GLDITPEMRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALIAGRTVANDNSKVndddslkattTVKLIAPPQ 243
Cdd:PTZ00248 159 GLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKI----------TIKLIAPPQ 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 294887089 244 YYIVTTCSLRDVGFERIGACIEAIKESIEKEGGTFALKQAPELVGLDEEEL 294
Cdd:PTZ00248 229 YVIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDL 279
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-294 5.19e-161

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 451.81  E-value: 5.19e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   4 EAAHLHCRFYREQFPEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKE 83
Cdd:PTZ00248   1 EADLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  84 KGYIDLSKKRVSREDAEALDQKYSKAKTVQSIMRHIASTHGMSLEEVCSKIAWPLYDTFGHAYDGLSKLVGDNADlsILE 163
Cdd:PTZ00248  81 KGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDN--VFE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089 164 GLDITPEMRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALIAGRTVANDNSKVndddslkattTVKLIAPPQ 243
Cdd:PTZ00248 159 GLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKI----------TIKLIAPPQ 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 294887089 244 YYIVTTCSLRDVGFERIGACIEAIKESIEKEGGTFALKQAPELVGLDEEEL 294
Cdd:PTZ00248 229 YVIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDL 279
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 11-280 1.10e-41

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: 145.34  E-value: 1.10e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  11 RFYREQFPEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:COG1093    1 VMKRKELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  91 KKRVSREDAEALDQKYSKAKTVQSIMRHIASTHGMSLEEVCSKIAWPLYDTFGHAYDGLSKLVGDNADlsILEGLDITPE 170
Cdd:COG1093   81 LKRVNEHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEVGWKLEDEYGSLYDAFEEAAIEGPE--ALEDAGLPEE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089 171 MRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALIAgrtvANDNSKVNDddslkATTTVKLIAPPQYYIVTTC 250
Cdd:COG1093  159 WIDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKA----AEENIEPED-----VDVEITYVGAPRYRIEVTA 229

                        250       260       270
                 ....*....|....*....|....*....|
gi 294887089 251 SLRDVGFERIGACIEAIKESIEKEGGTFAL 280
Cdd:COG1093  230 PDYKTAEKALKKAAEKAIKAIKKLGGEGEF 259
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 18-93 5.00e-32

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: 114.22  E-value: 5.00e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 294887089  18 PEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKR 93
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 133-250 8.19e-30

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: 109.56  E-value: 8.19e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  133 KIAWPLYDTFGHAYDGLSKLVGDNADlsILEGLDITPEMRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALI 212
Cdd:pfam07541   3 EIGWPLEEKYGSLYDAFEKAAIEGPE--VLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKKALK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 294887089  213 AGrtVANDNSKVNDDDSLKatttVKLIAPPQYYIVTTC 250
Cdd:pfam07541  81 AG--AESTEEIKGEDVPIK----IKLVGAPRYRITVTA 112
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
24-92 1.44e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 1.44e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089    24 VVALVKQVTDVAAYVSLceYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKK 92
Cdd:smart00316   6 VEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 14-112 3.02e-06

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: 48.58  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   14 REQFPE---IDQCVVALVKQVTDVAAYVSLceyDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:TIGR00717 178 REELLEnlkEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLS 254

                          90       100
                  ....*....|....*....|..
gi 294887089   91 KKRVSREDAEALDQKYSKAKTV 112
Cdd:TIGR00717 255 LKQLGEDPWEAIEKKFPVGDKI 276
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 4-294 5.19e-161

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 451.81  E-value: 5.19e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   4 EAAHLHCRFYREQFPEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKE 83
Cdd:PTZ00248   1 EADLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  84 KGYIDLSKKRVSREDAEALDQKYSKAKTVQSIMRHIASTHGMSLEEVCSKIAWPLYDTFGHAYDGLSKLVGDNADlsILE 163
Cdd:PTZ00248  81 KGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDN--VFE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089 164 GLDITPEMRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALIAGRTVANDNSKVndddslkattTVKLIAPPQ 243
Cdd:PTZ00248 159 GLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKI----------TIKLIAPPQ 228

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 294887089 244 YYIVTTCSLRDVGFERIGACIEAIKESIEKEGGTFALKQAPELVGLDEEEL 294
Cdd:PTZ00248 229 YVIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDL 279
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 11-280 1.10e-41

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: 145.34  E-value: 1.10e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  11 RFYREQFPEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:COG1093    1 VMKRKELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  91 KKRVSREDAEALDQKYSKAKTVQSIMRHIASTHGMSLEEVCSKIAWPLYDTFGHAYDGLSKLVGDNADlsILEGLDITPE 170
Cdd:COG1093   81 LKRVNEHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEVGWKLEDEYGSLYDAFEEAAIEGPE--ALEDAGLPEE 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089 171 MRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALIAgrtvANDNSKVNDddslkATTTVKLIAPPQYYIVTTC 250
Cdd:COG1093  159 WIDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKA----AEENIEPED-----VDVEITYVGAPRYRIEVTA 229

                        250       260       270
                 ....*....|....*....|....*....|
gi 294887089 251 SLRDVGFERIGACIEAIKESIEKEGGTFAL 280
Cdd:COG1093  230 PDYKTAEKALKKAAEKAIKAIKKLGGEGEF 259
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 14-280 4.37e-36

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 130.71  E-value: 4.37e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  14 REQFPEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKR 93
Cdd:PRK03987   2 RKEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  94 VSREDAEALDQKYSKAKTVQSIMRHIASTHGMSLEEVCSKIAWPLYDTFGHAYDGLSKLVGDNADlsILEGLDITPEMRD 173
Cdd:PRK03987  82 VNEHQRREKIQEWKNEQKADKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEE--ALDDLGVPEEWAD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089 174 TLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALIAgrtvANDNSKVnDDDSLKATTtvklIAPPQYYIVTTCSLR 253
Cdd:PRK03987 160 ALVEIARENIEVPKVKISGYVDLTSPEPDGVEIIKKALKA----AEKANKY-EDVEVEIYY----VGAPRYRIDVTAPDY 230

                        250       260
                 ....*....|....*....|....*..
gi 294887089 254 DVGFERIGACIEAIKESIEKEGGTFAL 280
Cdd:PRK03987 231 KTAEKALKKIAERAIKVIKKLGGEGSF 257
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 18-93 5.00e-32

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: 114.22  E-value: 5.00e-32
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 294887089  18 PEIDQCVVALVKQVTDVAAYVSLCEYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKR 93
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 133-250 8.19e-30

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: 109.56  E-value: 8.19e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  133 KIAWPLYDTFGHAYDGLSKLVGDNADlsILEGLDITPEMRDTLLNVVTRRMAPHQLRVKAKVEVSCFDYEGIEAIQRALI 212
Cdd:pfam07541   3 EIGWPLEEKYGSLYDAFEKAAIEGPE--VLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKKALK 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 294887089  213 AGrtVANDNSKVNDDDSLKatttVKLIAPPQYYIVTTC 250
Cdd:pfam07541  81 AG--AESTEEIKGEDVPIK----IKLVGAPRYRITVTA 112
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
24-92 1.44e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 1.44e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089    24 VVALVKQVTDVAAYVSLceYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKK 92
Cdd:smart00316   6 VEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 18-91 2.34e-08

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: 50.36  E-value: 2.34e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 294887089   18 PEIDQCVVALVKQVTDVAAYVSLCEydDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSK 91
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGN--GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
46-117 2.27e-07

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 52.26  E-value: 2.27e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 294887089  46 MEGMVQLSELSKRRIRSIPKLIKVGryDTF--MVLRVDKEKGYIDLSKKRVSREDA-EALDQKYSKAKTVQSIMR 117
Cdd:PRK00087 326 SEGVIPLRELTLDEISSLKESVKVG--DEIevKVLKLEDEDGYVVLSKKEADREKAwKELEEAFENGEPVKGKVK 398
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 14-112 3.02e-06

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: 48.58  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   14 REQFPE---IDQCVVALVKQVTDVAAYVSLceyDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:TIGR00717 178 REELLEnlkEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLS 254

                          90       100
                  ....*....|....*....|..
gi 294887089   91 KKRVSREDAEALDQKYSKAKTV 112
Cdd:TIGR00717 255 LKQLGEDPWEAIEKKFPVGDKI 276
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 22-90 5.90e-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: 43.39  E-value: 5.90e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089  22 QCVVALVKQVTDVAAYVSLCEYDdmeGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:cd05688    3 DVVEGTVKSITDFGAFVDLGGVD---GLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
15-106 7.91e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 47.25  E-value: 7.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  15 EQFPeIDQCVVALVKQVTDVAAYVSLceYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRV 94
Cdd:PRK00087 558 EKYP-VGSIVLGKVVRIAPFGAFVEL--EPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634

                         90
                 ....*....|..
gi 294887089  95 SREDAEALDQKY 106
Cdd:PRK00087 635 EEEPGDIEKVEL 646
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
19-106 1.21e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 46.86  E-value: 1.21e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  19 EIDQCVVALVKQVTDVAAYVSLCEYDdmeGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVSRED 98
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGGVD---GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDP 552


                 ....*...
gi 294887089  99 AEALDQKY 106
Cdd:PRK00087 553 WENVEEKY 560
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 24-90 1.59e-05

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: 41.98  E-value: 1.59e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 294887089  24 VVALVKQVTDVAAYVSLceYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:cd00164    1 VTGKVVSITKFGVFVEL--EDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 28-109 1.23e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 43.61  E-value: 1.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  28 VKQVTDVAAYVSLceYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVSREDAEALDQKYS 107
Cdd:PRK06299 468 VTEVKDKGAFVEL--EDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAIAEYN 545


                 ..
gi 294887089 108 KA 109
Cdd:PRK06299 546 SA 547
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 47-92 1.38e-04

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: 39.43  E-value: 1.38e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 294887089  47 EGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKK 92
Cdd:cd05687   25 EGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 24-120 1.91e-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: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   24 VVALVKQVTDVAAYVSLceYDDMEGMVQLSELS-KRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVSREDAEAL 102
Cdd:TIGR00717 363 VTGKIKKITDFGAFVEL--EGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKF 440

                          90
                  ....*....|....*...
gi 294887089  103 DQKYSKAKTVQSIMRHIA 120
Cdd:TIGR00717 441 AAKYKVGSVVKGKVTEIK 458
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 28-106 2.79e-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: 41.95  E-value: 2.79e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089  28 VKQVTDVAAYVSLceyDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVSREDAEALDQKY 106
Cdd:COG0539  197 VKNITDFGAFVDL---GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQPDPWENIAEKY 272
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 24-92 2.98e-04

S1_RPS1_repeat_hs4: 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 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 38.42  E-value: 2.98e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089  24 VVALVKQVTDVAAYVSLCEydDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDkEKGYIDLSKK 92
Cdd:cd05692    4 VEGTVTRLKPFGAFVELGG--GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 28-91 7.71e-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: 37.52  E-value: 7.71e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 294887089  28 VKQVTDVAAYVSLCEydDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKeKGYIDLSK 91
Cdd:cd04472    8 VVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 15-119 8.27e-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: 8.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089   15 EQFPEIDQCVVALVKqVTDVAAYVSLCEydDMEGMVQLSELSKRRIRSIP-KLIKVGRYDTFMVLRVDKEKGYIDLSKKR 93
Cdd:TIGR00717 268 KKFPVGDKITGRVTN-LTDYGVFVEIEE--GIEGLVHVSEMSWVKKNSHPsKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344

                          90       100
                  ....*....|....*....|....*.
gi 294887089   94 VSREDAEALDQKYSKAKTVQSIMRHI 119
Cdd:TIGR00717 345 CKANPWEQFEEKHPVGDRVTGKIKKI 370
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 28-92 1.15e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 40.24  E-value: 1.15e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 294887089  28 VKQVTDVAAYVSLCEyddMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKK 92
Cdd:PRK06676 200 VARLTDFGAFVDIGG---VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 28-130 1.18e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 40.24  E-value: 1.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  28 VKQVTDVAAYVSLceYDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVSREDAEALDQKYS 107
Cdd:PRK06676 285 VKRLTDFGAFVEV--LPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAEEEDRREE 362

                         90       100
                 ....*....|....*....|...
gi 294887089 108 KAKTVQSimrhiASTHGMSLEEV 130
Cdd:PRK06676 363 YRQYELP-----EEETGFSLGDL 380
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 28-90 1.20e-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: 36.83  E-value: 1.20e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 294887089  28 VKQVTDVAAYVSLCEYDDmeGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLS 90
Cdd:cd05685    8 VTNVTDFGAFVDIGVKQD--GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 28-113 1.33e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 40.15  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  28 VKQVTDVAAYVSLcEyDDMEGMVQLSELS-KRRIRSIPKLIKVGryDTF--MVLRVDKEKGYIDLSKKRVSREDAEALDQ 104
Cdd:PRK06299 381 VKNITDFGAFVGL-E-GGIDGLVHLSDISwDKKGEEAVELYKKG--DEVeaVVLKVDVEKERISLGIKQLEEDPFEEFAK 456


                 ....*....
gi 294887089 105 KYSKAKTVQ 113
Cdd:PRK06299 457 KHKKGSIVT 465
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 22-112 1.37e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 40.24  E-value: 1.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  22 QCVVALVKQVTDVAAYVSLCEYDdMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRV-SREDAE 100
Cdd:PRK06676  19 DVVTGEVLKVEDKQVFVNIEGYK-VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLeAEKAWD 97

                         90
                 ....*....|..
gi 294887089 101 ALDQKYSKAKTV 112
Cdd:PRK06676  98 KLEEKFEEGEVV 109
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 31-113 1.71e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 40.15  E-value: 1.71e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  31 VTDVAAYVSLCEydDMEGMVQLSELS-KRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVSREDAEALDQKYSKA 109
Cdd:PRK06299 297 ITDYGAFVELEE--GIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVG 374


                 ....
gi 294887089 110 KTVQ 113
Cdd:PRK06299 375 DVVE 378
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 47-113 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  47 EGMVQLSELSKRRIRSIpklIKVGryDTF--MVLRVDKEKGYIDLSKKRVSREDA-EALDQKYSKAKTVQ 113
Cdd:COG0539   43 EGIIPLSEFSDEPGELE---VKVG--DEVevYVEKVEDGEGEIVLSKKKADREKAwEELEEAFENGEPVE 107
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 20-106 3.23e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 39.31  E-value: 3.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  20 IDQCVVALVKQVTDVAAYVSLCEydDMEGMVQLSELSKRRIRSIPK-LIKVGRYDTFMVLRVDKEKGYIDLSKKRVSRED 98
Cdd:PRK12269 578 VNDVVKGRVTKIADFGAFIELAE--GIEGLAHISEFSWVKKTSKPSdMVKIGDEVECMILGYDIQAGRVSLGLKQVTANP 655


                 ....*...
gi 294887089  99 AEALDQKY 106
Cdd:PRK12269 656 WEEIEARY 663
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 28-95 3.73e-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: 38.49  E-value: 3.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089  28 VKQVTDVAAYVSLceYDDMEGMVQLSELSK-RRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKKRVS 95
Cdd:COG0539  282 VTRLTDFGAFVEL--EPGVEGLVHISEMSWtKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQLA 348
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 19-92 4.33e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 38.61  E-value: 4.33e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 294887089  19 EIDQCVVALVKQVTDVAAYVSLceyDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKK 92
Cdd:PRK06299 200 EEGQVVEGVVKNITDYGAFVDL---GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 21-92 5.83e-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: 34.94  E-value: 5.83e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 294887089  21 DQCVVALVKQVTDVAAYVSLCeyDDMEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSKK 92
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLG--DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
PRK08059 PRK08059
general stress protein 13; Validated
 30-114 7.14e-03

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 36.18  E-value: 7.14e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294887089  30 QVTDVAAYVSLCEYDD-MEGMVQLSELSKRRIRSIPKLIKVGRYDTFMVLRVDKEKGYIDLSkkrvSREDAEALDQKYSK 108
Cdd:PRK08059  14 KVTGIQPYGAFVALDEeTQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLS----IRATEEAPEAKRKK 89


                 ....*.
gi 294887089 109 AKTVQS 114
Cdd:PRK08059  90 GKILIP 95
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 18-94 7.59e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 38.11  E-value: 7.59e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 294887089  18 PEIDQCVVALVKQVTDVAAYVSLCEYDDmeGMVQLSELSKRRIRSIPKLIKVGryDTFMV--LRVDKeKGYIDLSKKRV 94
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILPGKD--GLVHISEIADERVEKVEDVLKEG--DEVKVkvLEIDK-RGRIRLSRKAV 692
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH