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Conserved domains on  [gi|914578359|gb|KOB84786|]
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eukaryotic translation initiation factor 2 subunit 1 [Plasmodium falciparum Dd2]

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

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List of domain hits

 Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 7-314 0e+00

eukaryotic translation initiation factor 2 subunit 1; Provisional


:

Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 506.89  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359   7 KADLGDCRFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQ 86
Cdd:PTZ00248   1 EADLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  87 KGYIDLSKRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVEELNEKAIWPLYERYGHALDALKEATMNPENVFKGL 166
Cdd:PTZ00248  81 KGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359 167 DISEEIKNSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKKGKEISNDKVSINIKLIAPPQYVIVTSCHDKDL 246
Cdd:PTZ00248 161 DIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDK 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914578359 247 GMAKIQEAMKVISDKIKEYkGGDFKQQGEILVIGGDEEKRlEELLDKHDGISSDDDDYNTSDEDDENS 314
Cdd:PTZ00248 241 GMEIIGAALEAIKEVIKKK-GGDFKVKGEPEVVGGDEEDL-EELLEKAEEEEEEDDYSESEDEDEEDE 306
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 7-314 0e+00

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 506.89  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359   7 KADLGDCRFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQ 86
Cdd:PTZ00248   1 EADLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  87 KGYIDLSKRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVEELNEKAIWPLYERYGHALDALKEATMNPENVFKGL 166
Cdd:PTZ00248  81 KGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359 167 DISEEIKNSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKKGKEISNDKVSINIKLIAPPQYVIVTSCHDKDL 246
Cdd:PTZ00248 161 DIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDK 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914578359 247 GMAKIQEAMKVISDKIKEYkGGDFKQQGEILVIGGDEEKRlEELLDKHDGISSDDDDYNTSDEDDENS 314
Cdd:PTZ00248 241 GMEIIGAALEAIKEVIKKK-GGDFKVKGEPEVVGGDEEDL-EELLEKAEEEEEEDDYSESEDEDEEDE 306
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 14-267 2.14e-46

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: 157.67  E-value: 2.14e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  14 RFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLS 93
Cdd:COG1093    1 VMKRKELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  94 KRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVEELNEKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIK 173
Cdd:COG1093   81 LKRVNEHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEVGWKLEDEYGSLYDAFEEAAIEGPEALEDAGLPEEWI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359 174 NSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKKGKEISN-DKVSINIKLIAPPQYVIVTSCHDKDLGMAKIQ 252
Cdd:COG1093  161 DAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEENIEpEDVDVEITYVGAPRYRIEVTAPDYKTAEKALK 240

                        250
                 ....*....|....*
gi 914578359 253 EAMKVISDKIKEYKG 267
Cdd:COG1093  241 KAAEKAIKAIKKLGG 255
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 135-241 1.43e-38

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: 132.67  E-value: 1.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  135 EKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIKNSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKK 214
Cdd:pfam07541   2 EEIGWPLEEKYGSLYDAFEKAAIEGPEVLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKKALKA 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 914578359  215 GKEISNDK----VSINIKLIAPPQYVIVTSC 241
Cdd:pfam07541  82 GAESTEEIkgedVPIKIKLVGAPRYRITVTA 112
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 21-96 1.41e-37

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: 128.86  E-value: 1.41e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914578359  21 PEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRR 96
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
22-95 5.52e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.14  E-value: 5.52e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 914578359    22 EVDDLIMVKVNRIEDMGAYVSIleYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKR 95
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 17-122 4.60e-05

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 45.11  E-value: 4.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359   17 KKKFPeVDDLIMVKVNRIEDMGAYVSILEynDMEGMILMSELS-KRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKR 95
Cdd:TIGR00717 267 EKKFP-VGDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343

                          90       100
                  ....*....|....*....|....*..
gi 914578359   96 RVSPKDIIKCEEKFSKSKKVHQTVRHV 122
Cdd:TIGR00717 344 QCKANPWEQFEEKHPVGDRVTGKIKKI 370
 
Name Accession Description Interval E-value
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 7-314 0e+00

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 506.89  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359   7 KADLGDCRFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQ 86
Cdd:PTZ00248   1 EADLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  87 KGYIDLSKRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVEELNEKAIWPLYERYGHALDALKEATMNPENVFKGL 166
Cdd:PTZ00248  81 KGYIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359 167 DISEEIKNSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKKGKEISNDKVSINIKLIAPPQYVIVTSCHDKDL 246
Cdd:PTZ00248 161 DIPEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDK 240

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914578359 247 GMAKIQEAMKVISDKIKEYkGGDFKQQGEILVIGGDEEKRlEELLDKHDGISSDDDDYNTSDEDDENS 314
Cdd:PTZ00248 241 GMEIIGAALEAIKEVIKKK-GGDFKVKGEPEVVGGDEEDL-EELLEKAEEEEEEDDYSESEDEDEEDE 306
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 14-267 2.14e-46

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: 157.67  E-value: 2.14e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  14 RFYKKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLS 93
Cdd:COG1093    1 VMKRKELPEEGELVVGTVKEVKDFGAYVTLDEYEGKEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  94 KRRVSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVEELNEKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIK 173
Cdd:COG1093   81 LKRVNEHQRREKIQEWKNEQKAEKLLEIAAEKLGKSLDEAYEEVGWKLEDEYGSLYDAFEEAAIEGPEALEDAGLPEEWI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359 174 NSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKKGKEISN-DKVSINIKLIAPPQYVIVTSCHDKDLGMAKIQ 252
Cdd:COG1093  161 DAIVEIAKENIKVPKVKISGYVELTSLAPDGVERIKKALKAAEENIEpEDVDVEITYVGAPRYRIEVTAPDYKTAEKALK 240

                        250
                 ....*....|....*
gi 914578359 253 EAMKVISDKIKEYKG 267
Cdd:COG1093  241 KAAEKAIKAIKKLGG 255
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 17-267 5.12e-40

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 141.11  E-value: 5.12e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  17 KKKFPEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRR 96
Cdd:PRK03987   2 RKEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  97 VSPKDIIKCEEKFSKSKKVHQTVRHVAKEHGITVEELNEKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIKNSL 176
Cdd:PRK03987  82 VNEHQRREKIQEWKNEQKADKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEEALDDLGVPEEWADAL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359 177 LKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKKGKEISNDK-VSINIKLIAPPQYVIVTSCHDKDLGMAKIQEAM 255
Cdd:PRK03987 162 VEIARENIEVPKVKISGYVDLTSPEPDGVEIIKKALKAAEKANKYEdVEVEIYYVGAPRYRIDVTAPDYKTAEKALKKIA 241

                        250
                 ....*....|..
gi 914578359 256 KVISDKIKEYKG 267
Cdd:PRK03987 242 ERAIKVIKKLGG 253
EIF_2_alpha pfam07541
Eukaryotic translation initiation factor 2 alpha subunit; These proteins share a region of ...
 135-241 1.43e-38

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: 132.67  E-value: 1.43e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  135 EKAIWPLYERYGHALDALKEATMNPENVFKGLDISEEIKNSLLKDIKLRLTPQALKLRGRIDVWCFGYEGIDAVKEALKK 214
Cdd:pfam07541   2 EEIGWPLEEKYGSLYDAFEKAAIEGPEVLDDLGIPEEWIEALLEIAKERLTPPPVKIRADIELTCFAPDGIEAIKKALKA 81

                          90       100       110
                  ....*....|....*....|....*....|.
gi 914578359  215 GKEISNDK----VSINIKLIAPPQYVIVTSC 241
Cdd:pfam07541  82 GAESTEEIkgedVPIKIKLVGAPRYRITVTA 112
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 21-96 1.41e-37

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: 128.86  E-value: 1.41e-37
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 914578359  21 PEVDDLIMVKVNRIEDMGAYVSILEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRR 96
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 21-94 1.50e-09

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: 53.83  E-value: 1.50e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 914578359   21 PEVDDLIMVKVNRIEDMGAYVSILeyNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSK 94
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLG--NGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
22-95 5.52e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.14  E-value: 5.52e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 914578359    22 EVDDLIMVKVNRIEDMGAYVSIleYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKR 95
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 21-97 9.26e-07

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 50.43  E-value: 9.26e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914578359  21 PEVDDLIMVKVNRIEDMGAYVSILEYNDmeGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQkGYIDLSKRRV 97
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILPGKD--GLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRKAV 692
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
49-124 4.91e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 48.02  E-value: 4.91e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 914578359  49 MEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRRVSPKDIIKC-EEKFSKSKKVHQTVRHVAK 124
Cdd:PRK00087 326 SEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKElEEAFENGEPVKGKVKEVVK 402
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 17-122 4.60e-05

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 45.11  E-value: 4.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359   17 KKKFPeVDDLIMVKVNRIEDMGAYVSILEynDMEGMILMSELS-KRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKR 95
Cdd:TIGR00717 267 EKKFP-VGDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343

                          90       100
                  ....*....|....*....|....*..
gi 914578359   96 RVSPKDIIKCEEKFSKSKKVHQTVRHV 122
Cdd:TIGR00717 344 QCKANPWEQFEEKHPVGDRVTGKIKKI 370
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-120 6.03e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 44.77  E-value: 6.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  17 KKKFPeVDDLIMVKVNRIEDMGAYVSILEynDMEGMILMSELS-KRRFRSVNKLIRVGRhEV-VLVLRVDSQKGYIDLSK 94
Cdd:PRK06299 281 EKKYP-VGSKVKGKVTNITDYGAFVELEE--GIEGLVHVSEMSwTKKNKHPSKVVSVGQ-EVeVMVLEIDEEKRRISLGL 356

                         90       100
                 ....*....|....*....|....*.
gi 914578359  95 RRVSPKDIIKCEEKFSKSKKVHQTVR 120
Cdd:PRK06299 357 KQCKENPWEEFAEKYPVGDVVEGKVK 382
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 27-93 2.03e-04

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: 38.90  E-value: 2.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 914578359  27 IMVKVNRIEDMGAYVSILEYndMEGMILMSELSKRRFRSVNKLIRVG-RHEVVlVLRVDSQKGYIDLS 93
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDG--VEGLVHISELSDKFVKDPSEVFKVGdEVEVK-VLEVDPEKGRISLS 65
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 30-94 2.98e-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: 38.68  E-value: 2.98e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 914578359  30 KVNRIEDMGAYVSILEynDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQkGYIDLSK 94
Cdd:cd04472    7 KVVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDR-GRISLSR 68
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 22-93 3.60e-04

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


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 38.46  E-value: 3.60e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 914578359  22 EVDDLIMVKVNRIEDMGAYVSIlEYNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLS 93
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDI-DGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
22-109 5.02e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 41.86  E-value: 5.02e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  22 EVDDLIMVKVNRIEDMGAYVSIleyNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRRVSPKD 101
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDI---GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDP 552


                 ....*...
gi 914578359 102 IIKCEEKF 109
Cdd:PRK00087 553 WENVEEKY 560
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 22-124 1.40e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 40.24  E-value: 1.40e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  22 EVDDLIMVKVNRIEDMGAYVSILEYNdMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRRV-SPK 100
Cdd:PRK06676  16 EVGDVVTGEVLKVEDKQVFVNIEGYK-VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLeAEK 94

                         90       100
                 ....*....|....*....|....
gi 914578359 101 DIIKCEEKFSKSKKVHQTVRHVAK 124
Cdd:PRK06676  95 AWDKLEEKFEEGEVVEVKVTEVVK 118
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 17-98 2.55e-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: 39.26  E-value: 2.55e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  17 KKKFPeVDDLIMVKVNRIEDMGAYVSILEynDMEGMILMSELSK-RRFRSVNKLIRVG-RHEVVlVLRVDSQKGYIDLSK 94
Cdd:COG0539  269 AEKYP-VGDVVKGKVTRLTDFGAFVELEP--GVEGLVHISEMSWtKRVAHPSDVVKVGdEVEVK-VLDIDPEERRISLSI 344


                 ....
gi 914578359  95 RRVS 98
Cdd:COG0539  345 KQLA 348
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 30-93 6.21e-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: 34.90  E-value: 6.21e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 914578359  30 KVNRIEDMGAYVSILEYNDmeGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLS 93
Cdd:cd05685    7 VVTNVTDFGAFVDIGVKQD--GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 30-119 7.87e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 37.55  E-value: 7.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  30 KVNRIEDMGAYVSIleyNDMEGMILMSELSKRRFRSVNKLIRVGRHEVVLVLRVDSQKGYIDLSKRRVSPKDIIKCEEKF 109
Cdd:PRK06676 199 TVARLTDFGAFVDI---GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGPWEGVEEKL 275

                         90
                 ....*....|
gi 914578359 110 SKSKKVHQTV 119
Cdd:PRK06676 276 PEGDVIEGTV 285
PHA02945 PHA02945
interferon resistance protein; Provisional
 20-97 9.26e-03

interferon resistance protein; Provisional


Pssm-ID: 165255 [Multi-domain]  Cd Length: 88  Bit Score: 34.98  E-value: 9.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 914578359  20 FPEVDDLIMVKVNRiEDMGAYVSILEYNDMEGMILMSELS--KRRFRSVNKLirVGRHEVVLVLRVDSQKGYIDLSKRRV 97
Cdd:PHA02945   8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMhmNRYFKYRDKL--VGKTVKVKVIRVDYTKGYIDVNYKRM 84
 
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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