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Conserved domains on  [gi|18860087|ref|NP_573130|]
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eukaryotic translation initiation factor 2 subunit alpha, isoform A [Drosophila melanogaster]

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
 3-295 6.60e-118

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: 343.18  E-value: 6.60e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    3 LTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYI 82
Cdd:PTZ00248   5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   83 DLSKRRVSPEDVEKCTERFAKAKAINSLLRHVADILGFegneKLEDLYQKTAWHFEKKYNNktvAYDIFKQSVTDPT-VF 161
Cdd:PTZ00248  85 DLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGM----SVEELYTKIIWPLYKKYGH---ALDALKEALTNPDnVF 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  162 DECNLEPETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKASLTKGLELSTEELPIRINLIAPPLYVMTTSTTK 241
Cdd:PTZ00248 158 EGLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSD 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 18860087  242 KTDGLKALEVAIEHIRAKTSEYDGEFKVIMAPKLVTAiDEADLARRLERAEAEN 295
Cdd:PTZ00248 238 KDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEEEE 290
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 3-295 6.60e-118

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 343.18  E-value: 6.60e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    3 LTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYI 82
Cdd:PTZ00248   5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   83 DLSKRRVSPEDVEKCTERFAKAKAINSLLRHVADILGFegneKLEDLYQKTAWHFEKKYNNktvAYDIFKQSVTDPT-VF 161
Cdd:PTZ00248  85 DLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGM----SVEELYTKIIWPLYKKYGH---ALDALKEALTNPDnVF 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  162 DECNLEPETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKASLTKGLELSTEELPIRINLIAPPLYVMTTSTTK 241
Cdd:PTZ00248 158 EGLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSD 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 18860087  242 KTDGLKALEVAIEHIRAKTSEYDGEFKVIMAPKLVTAiDEADLARRLERAEAEN 295
Cdd:PTZ00248 238 KDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEEEE 290
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 13-88 9.87e-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: 140.03  E-value: 9.87e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18860087  13 PEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:cd04452   1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 10-269 1.81e-39

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: 139.95  E-value: 1.81e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  10 ERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRV 89
Cdd:COG1093   5 KELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLSLKRV 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  90 SPEDVEKCTERFAKAKAINSLLRHVADILGfegnEKLEDLYQKTAWHFEKKYNNktvAYDIFKQSVTD-PTVFDECNLEP 168
Cdd:COG1093  85 NEHQRREKIQEWKNEQKAEKLLEIAAEKLG----KSLDEAYEEVGWKLEDEYGS---LYDAFEEAAIEgPEALEDAGLPE 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087 169 ETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKASLTKGLELST-EELPIRINLIAPPLY-VMTTSTTKKTdGL 246
Cdd:COG1093 158 EWIDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEENIEpEDVDVEITYVGAPRYrIEVTAPDYKT-AE 236

                       250       260
                ....*....|....*....|...
gi 18860087 247 KALEVAIEHIRAKTSEYDGEFKV 269
Cdd:COG1093 237 KALKKAAEKAIKAIKKLGGEGEF 259
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 130-239 1.57e-35

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: 124.97  E-value: 1.57e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   130 YQKTAWHFEKKYNNktvAYDIF-KQSVTDPTVFDECNLEPETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKA 208
Cdd:pfam07541   1 YEEIGWPLEEKYGS---LYDAFeKAAIEGPEVLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKK 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 18860087   209 SLTKGLE----LSTEELPIRINLIAPPLYVMTTST 239
Cdd:pfam07541  78 ALKAGAEsteeIKGEDVPIKIKLVGAPRYRITVTA 112
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
14-87 4.04e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 63.78  E-value: 4.04e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18860087     14 EIEDVVMVNVLSIAEMGAYVHLleYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKR 87
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 14-116 5.09e-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: 48.19  E-value: 5.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    14 EIEDVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPED 93
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDP 262

                          90       100
                  ....*....|....*....|...
gi 18860087    94 VEKCTERFAKAKAINSLLRHVAD 116
Cdd:TIGR00717 263 WEAIEKKFPVGDKITGRVTNLTD 285
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 3-295 6.60e-118

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 343.18  E-value: 6.60e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    3 LTSRFYNERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYI 82
Cdd:PTZ00248   5 LDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   83 DLSKRRVSPEDVEKCTERFAKAKAINSLLRHVADILGFegneKLEDLYQKTAWHFEKKYNNktvAYDIFKQSVTDPT-VF 161
Cdd:PTZ00248  85 DLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGM----SVEELYTKIIWPLYKKYGH---ALDALKEALTNPDnVF 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  162 DECNLEPETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKASLTKGLELSTEELPIRINLIAPPLYVMTTSTTK 241
Cdd:PTZ00248 158 EGLDIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSD 237

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 18860087  242 KTDGLKALEVAIEHIRAKTSEYDGEFKVIMAPKLVTAiDEADLARRLERAEAEN 295
Cdd:PTZ00248 238 KDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGG-DEEDLEELLEKAEEEE 290
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 13-88 9.87e-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: 140.03  E-value: 9.87e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18860087  13 PEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:cd04452   1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 10-269 1.81e-39

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: 139.95  E-value: 1.81e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  10 ERYPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRV 89
Cdd:COG1093   5 KELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLSLKRV 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  90 SPEDVEKCTERFAKAKAINSLLRHVADILGfegnEKLEDLYQKTAWHFEKKYNNktvAYDIFKQSVTD-PTVFDECNLEP 168
Cdd:COG1093  85 NEHQRREKIQEWKNEQKAEKLLEIAAEKLG----KSLDEAYEEVGWKLEDEYGS---LYDAFEEAAIEgPEALEDAGLPE 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087 169 ETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKASLTKGLELST-EELPIRINLIAPPLY-VMTTSTTKKTdGL 246
Cdd:COG1093 158 EWIDAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEENIEpEDVDVEITYVGAPRYrIEVTAPDYKT-AE 236

                       250       260
                ....*....|....*....|...
gi 18860087 247 KALEVAIEHIRAKTSEYDGEFKV 269
Cdd:COG1093 237 KALKKAAEKAIKAIKKLGGEGEF 259
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 130-239 1.57e-35

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: 124.97  E-value: 1.57e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   130 YQKTAWHFEKKYNNktvAYDIF-KQSVTDPTVFDECNLEPETKEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKA 208
Cdd:pfam07541   1 YEEIGWPLEEKYGS---LYDAFeKAAIEGPEVLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKK 77

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 18860087   209 SLTKGLE----LSTEELPIRINLIAPPLYVMTTST 239
Cdd:pfam07541  78 ALKAGAEsteeIKGEDVPIKIKLVGAPRYRITVTA 112
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 12-270 1.43e-31

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 119.16  E-value: 1.43e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   12 YPEIEDVVMVNVLSIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSP 91
Cdd:PRK03987   5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRVNE 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   92 EDVEKCTERFAKAKAINSLLRHVADILGfegnEKLEDLYQKTAWHFEKKYNNktvAYDIFKQSVTD-PTVFDECNLEPET 170
Cdd:PRK03987  85 HQRREKIQEWKNEQKADKWLELAAEKLG----KSLEEAWEEVGYKLEDEFGD---LYDAFEEAAIEgEEALDDLGVPEEW 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  171 KEVLLSNIKRKLVSPTVKIRADIECSCYGYEGIDAVKASLTKGLELST-EELPIRINLIAPPLY-VMTTSTTKKTdGLKA 248
Cdd:PRK03987 158 ADALVEIARENIEVPKVKISGYVDLTSPEPDGVEIIKKALKAAEKANKyEDVEVEIYYVGAPRYrIDVTAPDYKT-AEKA 236

                        250       260
                 ....*....|....*....|..
gi 18860087  249 LEVAIEHIRAKTSEYDGEFKVI 270
Cdd:PRK03987 237 LKKIAERAIKVIKKLGGEGSFV 258
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 13-86 7.46e-16

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: 71.16  E-value: 7.46e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18860087    13 PEIEDVVMVNVLSIAEMGAYVHLLeyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSK 86
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLG--NGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
14-87 4.04e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 63.78  E-value: 4.04e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18860087     14 EIEDVVMVNVLSIAEMGAYVHLleYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKR 87
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 19-85 2.97e-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: 52.77  E-value: 2.97e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18860087  19 VMVNVLSIAEMGAYVHLLEynNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLS 85
Cdd:cd00164   1 VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
8-104 2.36e-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: 2.36e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    8 YNERYPEIEDVVMVNVLSIAEMGAYVhlleynNI----EGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYID 83
Cdd:PRK00087 295 ELEKQIRRGDIVKGTVVSVNENEVFV------DVgyksEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVV 368

                         90       100
                 ....*....|....*....|.
gi 18860087   84 LSKRRVspeDVEKCTERFAKA 104
Cdd:PRK00087 369 LSKKEA---DREKAWKELEEA 386
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
10-96 3.61e-07

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 51.87  E-value: 3.61e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   10 ERYPeIEDVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRV 89
Cdd:PRK00087 558 EKYP-VGSIVLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634


                 ....*..
gi 18860087   90 SPEDVEK 96
Cdd:PRK00087 635 EEEPGDI 641
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 15-85 5.14e-07

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: 46.47  E-value: 5.14e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18860087  15 IEDVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLS 85
Cdd:cd05688   1 EGDVVEGTVKSITDFGAFVDL---GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 17-107 4.73e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 47.95  E-value: 4.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   17 DVVMVNVLSIAEMGAYVHLLEYNnIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDV-E 95
Cdd:PRK06676  19 DVVTGEVLKVEDKQVFVNIEGYK-VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEKAwD 97

                         90
                 ....*....|..
gi 18860087   96 KCTERFAKAKAI 107
Cdd:PRK06676  98 KLEEKFEEGEVV 109
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 10-91 4.92e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 48.24  E-value: 4.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   10 ERYPeIEDVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:PRK06299 282 KKYP-VGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQ 358


                 ...
gi 18860087   89 VSP 91
Cdd:PRK06299 359 CKE 361
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 14-116 5.09e-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: 48.19  E-value: 5.09e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    14 EIEDVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPED 93
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDL---GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDP 262

                          90       100
                  ....*....|....*....|...
gi 18860087    94 VEKCTERFAKAKAINSLLRHVAD 116
Cdd:TIGR00717 263 WEAIEKKFPVGDKITGRVTNLTD 285
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 10-90 5.33e-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: 47.73  E-value: 5.33e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087  10 ERYPEiEDVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:COG0539 270 EKYPV-GDVVKGKVTRLTDFGAFVELEP--GVEGLVHISEMSWtKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQ 346


                ..
gi 18860087  89 VS 90
Cdd:COG0539 347 LA 348
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 13-89 6.84e-06

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 47.74  E-value: 6.84e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18860087   13 PEIEDVVMVNVLSIAEMGAYVHLLeyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKeKGYIDLSKRRV 89
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDK-RGRIRLSRKAV 692
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 23-86 9.86e-06

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: 42.91  E-value: 9.86e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18860087  23 VLSIAEMGAYVHLLEynNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKeKGYIDLSK 86
Cdd:cd04472   8 VVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLSR 68
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 17-87 1.36e-05

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: 42.52  E-value: 1.36e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18860087  17 DVVMVNVLSIAEMGAYVhlleynNI----EGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKR 87
Cdd:cd05687   2 DIVKGTVVSVDDDEVLV------DIgyksEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-101 6.25e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.55  E-value: 6.25e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    2 ALTSRFYNERypEIEDVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGY 81
Cdd:PRK00087 466 KKKEETWNSL--EEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKK 540

                         90       100
                 ....*....|....*....|
gi 18860087   82 IDLSKRRVSPEDVEKCTERF 101
Cdd:PRK00087 541 LSLSLKKLLPDPWENVEEKY 560
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 23-96 9.22e-05

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: 43.88  E-value: 9.22e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18860087  23 VLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSP---EDVEK 96
Cdd:COG0539 197 VKNITDFGAFVDL---GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQPdpwENIAE 270
PRK08059 PRK08059
general stress protein 13; Validated
 14-105 9.81e-05

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 41.57  E-value: 9.81e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   14 EIEDVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPED 93
Cdd:PRK08059   6 EVGSVVTGKVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAP 83

                         90
                 ....*....|..
gi 18860087   94 VEKCTERFAKAK 105
Cdd:PRK08059  84 EAKRKKGKILIP 95
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 17-102 1.24e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.33  E-value: 1.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   17 DVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDVEK 96
Cdd:PRK06676 194 DVVEGTVARLTDFGAFVDI---GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEG 270


                 ....*.
gi 18860087   97 CTERFA 102
Cdd:PRK06676 271 VEEKLP 276
rpsA PRK13806
30S ribosomal protein S1; Provisional
 17-102 1.76e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.17  E-value: 1.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   17 DVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKG----YIDLSKRRVSPE 92
Cdd:PRK13806 204 DVVEGTVTRLAPFGAFVELAP--GVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQAGGD 281

                         90
                 ....*....|
gi 18860087   93 DVEKCTERFA 102
Cdd:PRK13806 282 PWDTVGDRLK 291
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-88 2.30e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.84  E-value: 2.30e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18860087   17 DVVMVNVLSIAEMGAYVHLleYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:PRK06299 462 SIVTGTVTEVKDKGAFVEL--EDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531
rpsA PRK13806
30S ribosomal protein S1; Provisional
 17-102 2.71e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.40  E-value: 2.71e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   17 DVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPEDVE 95
Cdd:PRK13806 294 DKVTGKVVRLAPFGAFVEILP--GIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWA 371


                 ....*..
gi 18860087   96 KCTERFA 102
Cdd:PRK13806 372 DVAERFA 378
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 10-123 3.77e-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: 42.03  E-value: 3.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    10 ERYPEiEDVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:TIGR00717 268 KKFPV-GDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 18860087    89 VSPEDVEKCTERFAKAKAINSLLRHVAD---ILGFEGN 123
Cdd:TIGR00717 345 CKANPWEQFEEKHPVGDRVTGKIKKITDfgaFVELEGG 382
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 10-103 5.25e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 41.69  E-value: 5.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   10 ERYPEiEDVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELS-RRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRR 88
Cdd:PRK06299 369 EKYPV-GDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQ 445

                         90
                 ....*....|....*
gi 18860087   89 VSPEDVEKCTERFAK 103
Cdd:PRK06299 446 LEEDPFEEFAKKHKK 460
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 7-140 1.12e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 40.85  E-value: 1.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087    7 FYNERYpeIEDVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSK 86
Cdd:PRK12269 487 FFNSVH--IEDSVSGVVKSFTSFGAFIDL---GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 18860087   87 RRVSPEDVEKCTERFAKAKAINSLLRHVADILGF-EGNEKLEDLYQKTAWHFEKK 140
Cdd:PRK12269 562 KHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFiELAEGIEGLAHISEFSWVKK 616
PHA02945 PHA02945
interferon resistance protein; Provisional
 32-89 1.35e-03

interferon resistance protein; Provisional


Pssm-ID: 165255 [Multi-domain]  Cd Length: 88  Bit Score: 37.29  E-value: 1.35e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   32 YVHLLEYNNIEGMILLSELSR--RRIRSINKLirVGKTEPVVVIRVDKEKGYIDLSKRRV 89
Cdd:PHA02945  27 YIDLFDYPHSEAILAESVQMHmnRYFKYRDKL--VGKTVKVKVIRVDYTKGYIDVNYKRM 84
PHA02858 PHA02858
EIF2a-like PKR inhibitor; Provisional
 12-86 1.48e-03

EIF2a-like PKR inhibitor; Provisional


Pssm-ID: 165194  Cd Length: 86  Bit Score: 37.00  E-value: 1.48e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18860087   12 YPEIEDVVMvNVLSIAEMGAYVHLLEYNnIEGMIL-LSELSRRRIRSINKLIrVGKTEPVVVIRVDKEKGYIDLSK 86
Cdd:PHA02858  13 FPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVnYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRH 85
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 17-85 2.23e-03

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: 36.54  E-value: 2.23e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18860087  17 DVVMVNVLSIAEMGAYVHLlEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLS 85
Cdd:cd05708   4 QKIDGTVRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 8-104 3.15e-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: 3.15e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18860087   8 YNERYPEIE--DVVMVNVLSIAEMGAYVhlleynNI----EGMILLSELSRRRIrsiNKLIRVGKTEPVVVIRVDKEKGY 81
Cdd:COG0539   9 LEESLKELKegDIVKGTVVSIDDDEVLV------DIgyksEGIIPLSEFSDEPG---ELEVKVGDEVEVYVEKVEDGEGE 79

                        90       100
                ....*....|....*....|...
gi 18860087  82 IDLSKRRVspeDVEKCTERFAKA 104
Cdd:COG0539  80 IVLSKKKA---DREKAWEELEEA 99
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 23-85 3.17e-03

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


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 35.67  E-value: 3.17e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18860087  23 VLSIAEMGAYVHLLEYNNieGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLS 85
Cdd:cd05685   8 VTNVTDFGAFVDIGVKQD--GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 14-92 5.15e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 38.24  E-value: 5.15e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18860087   14 EIEDVVMVNVLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKRRVSPE 92
Cdd:PRK07400 195 EVGEVVVGTVRGIKPYGAFIDI---GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTKQLEPE 270
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 17-87 6.66e-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: 6.66e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18860087    17 DVVMVNVLSIAEMGAYVHLleYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLSKR 87
Cdd:TIGR00717 448 SVVKGKVTEIKDFGAFVEL--PGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 17-85 7.62e-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: 7.62e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18860087  17 DVVMVNVLSIAEMGAYVHLLEynNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLS 85
Cdd:cd05691   2 SIVTGKVTEVDAKGATVKLGD--GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLS 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 23-85 8.60e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 37.84  E-value: 8.60e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18860087   23 VLSIAEMGAYVHLleyNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKGYIDLS 85
Cdd:PRK06299 209 VKNITDYGAFVDL---GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLG 268
 
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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