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Conserved domains on  [gi|1002242327|ref|XP_015625394|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rpsA super family cl35504
30S ribosomal protein S1; Reviewed
 567-689 1.39e-23

30S ribosomal protein S1; Reviewed


The actual alignment was detected with superfamily member PRK06676:

Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 103.80  E-value: 1.39e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 567 LSSFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEV 646
Cdd:PRK06676  145 FSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISEL 224

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 647 SWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK06676  225 SHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGP 267
rpsA super family cl36730
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 391-689 2.35e-12

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]


The actual alignment was detected with superfamily member TIGR00717:

Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 70.15  E-value: 2.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 391 MQAFLQGkpkmkdlavetfpSQVDAEKMNASENNMNYV---------DDGGNVLSSKLEDITESDWTRLENYAST---GE 458
Cdd:TIGR00717 123 VEAFLPG-------------SQVDVKPIKDLDSLIGKTlkfkiikldQKRNNIVVSRRAYLEEERSQAREELLENlkeGD 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 459 KVEVELINCSSKGFVVSLDSLIGFLPYRNLA----------------TKWKFLAFET-------WLRQKGGDPSLfkqsv 515
Cdd:TIGR00717 190 VVKGVVKNITDFGAFVDLGGVDGLLHITDMSwkrvkhpseyvkvgqeVKVKVIKFDKekgrislSLKQLGEDPWE----- 264

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 516 GIEESFEVNDRNIESVSssdselAVQDQGS-MPSKEKFEDLLR------TYNTEK-SKFLSsfIGQRLRVSVVLADRKSK 587
Cdd:TIGR00717 265 AIEKKFPVGDKITGRVT------NLTDYGVfVEIEEGIEGLVHvsemswVKKNSHpSKVVK--KGDEVEVMILDIDPERR 336

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 588 KIFFSMKPKESEELIQkkksLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDE-TLDPSVSYKIGQVVD 665
Cdd:TIGR00717 337 RLSLGLKQCKANPWEQ----FEEKHPVGDRVTGKIKKITDFGAFVELEgGIDGLIHLSDISWDKdGREADHLYKKGDEIE 412

                         330       340
                  ....*....|....*....|....
gi 1002242327 666 AKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:TIGR00717 413 AVVLAVDKEKKRISLGVKQLTENP 436
 
Name Accession Description Interval E-value
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 567-689 1.39e-23

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 103.80  E-value: 1.39e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 567 LSSFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEV 646
Cdd:PRK06676  145 FSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISEL 224

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 647 SWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK06676  225 SHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGP 267
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 429-689 2.18e-22

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: 99.35  E-value: 2.18e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 429 DDGGNVLSSKLEDITESDWTRLENYASTGEKVEVELINCSSKGFVVSLDSLIGFLPYrnlatkwkflafetwlrqkggdp 508
Cdd:COG0539    75 DGEGEIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPA----------------------- 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 509 SLfkqsvgieesfeVNDRNIESvsssdselavqdqgsmpskekfedllrtyntekskfLSSFIGQRLRVSVVLADRKSKK 588
Cdd:COG0539   132 SQ------------VDVRPVRD------------------------------------LDEYVGKTLEFKIIKLDRKRNN 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 589 IFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKV 668
Cdd:COG0539   164 VVVSRRAVLEEEREEKREELLEKLEEGDVVEGTVKNITDFGAFVDLGGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKV 243

                         250       260
                  ....*....|....*....|.
gi 1002242327 669 IQLDYNNNRIFLSLKDVKPNP 689
Cdd:COG0539   244 LKIDREKERISLSLKQLQPDP 264
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 571-689 5.72e-14

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: 75.16  E-value: 5.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMKPKESE--ELIQKKkslmakLNVGDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVS 647
Cdd:TIGR00717 233 VGQEVKVKVIKFDKEKGRISLSLKQLGEDpwEAIEKK------FPVGDKITGRVTNLTDYGVFVEIeEGIEGLVHVSEMS 306

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 648 WD-ETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:TIGR00717 307 WVkKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANP 349
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
613-683 8.93e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 66.86  E-value: 8.93e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002242327  613 NVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGnGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 391-689 2.35e-12

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: 70.15  E-value: 2.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 391 MQAFLQGkpkmkdlavetfpSQVDAEKMNASENNMNYV---------DDGGNVLSSKLEDITESDWTRLENYAST---GE 458
Cdd:TIGR00717 123 VEAFLPG-------------SQVDVKPIKDLDSLIGKTlkfkiikldQKRNNIVVSRRAYLEEERSQAREELLENlkeGD 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 459 KVEVELINCSSKGFVVSLDSLIGFLPYRNLA----------------TKWKFLAFET-------WLRQKGGDPSLfkqsv 515
Cdd:TIGR00717 190 VVKGVVKNITDFGAFVDLGGVDGLLHITDMSwkrvkhpseyvkvgqeVKVKVIKFDKekgrislSLKQLGEDPWE----- 264

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 516 GIEESFEVNDRNIESVSssdselAVQDQGS-MPSKEKFEDLLR------TYNTEK-SKFLSsfIGQRLRVSVVLADRKSK 587
Cdd:TIGR00717 265 AIEKKFPVGDKITGRVT------NLTDYGVfVEIEEGIEGLVHvsemswVKKNSHpSKVVK--KGDEVEVMILDIDPERR 336

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 588 KIFFSMKPKESEELIQkkksLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDE-TLDPSVSYKIGQVVD 665
Cdd:TIGR00717 337 RLSLGLKQCKANPWEQ----FEEKHPVGDRVTGKIKKITDFGAFVELEgGIDGLIHLSDISWDKdGREADHLYKKGDEIE 412

                         330       340
                  ....*....|....*....|....
gi 1002242327 666 AKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:TIGR00717 413 AVVLAVDKEKKRISLGVKQLTENP 436
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 612-682 4.76e-11

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 59.22  E-value: 4.76e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002242327 612 LNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSL 682
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGnGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 614-681 7.69e-11

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: 58.41  E-value: 7.69e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002242327 614 VGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLS 681
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
 
Name Accession Description Interval E-value
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 567-689 1.39e-23

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 103.80  E-value: 1.39e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 567 LSSFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEV 646
Cdd:PRK06676  145 FSDFKGKTLEVKIIELDPEKNRVILSRRAVVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISEL 224

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 647 SWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK06676  225 SHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLPGP 267
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 429-689 2.18e-22

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: 99.35  E-value: 2.18e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 429 DDGGNVLSSKLEDITESDWTRLENYASTGEKVEVELINCSSKGFVVSLDSLIGFLPYrnlatkwkflafetwlrqkggdp 508
Cdd:COG0539    75 DGEGEIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPA----------------------- 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 509 SLfkqsvgieesfeVNDRNIESvsssdselavqdqgsmpskekfedllrtyntekskfLSSFIGQRLRVSVVLADRKSKK 588
Cdd:COG0539   132 SQ------------VDVRPVRD------------------------------------LDEYVGKTLEFKIIKLDRKRNN 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 589 IFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKV 668
Cdd:COG0539   164 VVVSRRAVLEEEREEKREELLEKLEEGDVVEGTVKNITDFGAFVDLGGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKV 243

                         250       260
                  ....*....|....*....|.
gi 1002242327 669 IQLDYNNNRIFLSLKDVKPNP 689
Cdd:COG0539   244 LKIDREKERISLSLKQLQPDP 264
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
567-689 1.36e-21

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 100.02  E-value: 1.36e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 567 LSSFIGQRLRVSVV-LADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWE 645
Cdd:PRK00087  429 LSEYKGQELEVKIIeFNRKRRKKVVLSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSE 508

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1002242327 646 VSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK00087  509 ISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDP 552
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 571-686 3.19e-16

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: 80.86  E-value: 3.19e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMKpkeseeliQKK----KSLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWE 645
Cdd:COG0539   235 VGDEVEVKVLKIDREKERISLSLK--------QLQpdpwENIAEKYPVGDVVKGKVTRLTDFGAFVELEpGVEGLVHISE 306

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1002242327 646 VSWDETL-DPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVK 686
Cdd:COG0539   307 MSWTKRVaHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQLA 348
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
571-689 4.13e-16

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 82.69  E-value: 4.13e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMKpkeseELIQKK-KSLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSW 648
Cdd:PRK00087  523 VGDEIKVYILDIDKENKKLSLSLK-----KLLPDPwENVEEKYPVGSIVLGKVVRIAPFGAFVELEpGVDGLVHISQISW 597

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1002242327 649 DETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK00087  598 KRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEP 638
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 567-689 7.70e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 78.28  E-value: 7.70e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 567 LSSFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEV 646
Cdd:PRK06299  154 TDPLEGKELEFKVIKLDKKRNNIVVSRRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDI 233

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 647 SWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK06299  234 SWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGEDP 276
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 564-689 3.84e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 75.97  E-value: 3.84e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 564 SKFLSsfIGQRLRVSVVLADRKSKKIFFSMK---PKESEELIQKKKslmaklnVGDIVECTIKRFVYFGIFVEVE-GVPA 639
Cdd:PRK06299  329 SKVVS--VGQEVEVMVLEIDEEKRRISLGLKqckENPWEEFAEKYP-------VGDVVEGKVKNITDFGAFVGLEgGIDG 399

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1002242327 640 LIQQWEVSWDETL-DPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK06299  400 LVHLSDISWDKKGeEAVELYKKGDEVEAVVLKVDVEKERISLGIKQLEEDP 450
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 571-689 5.72e-14

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: 75.16  E-value: 5.72e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMKPKESE--ELIQKKkslmakLNVGDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVS 647
Cdd:TIGR00717 233 VGQEVKVKVIKFDKEKGRISLSLKQLGEDpwEAIEKK------FPVGDKITGRVTNLTDYGVFVEIeEGIEGLVHVSEMS 306

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 648 WD-ETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:TIGR00717 307 WVkKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANP 349
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
613-683 8.93e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 66.86  E-value: 8.93e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002242327  613 NVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGnGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 561-689 1.14e-13

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: 74.39  E-value: 1.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 561 TEKSKFLSSFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPAL 640
Cdd:TIGR00717 134 VKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGL 213

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1002242327 641 IQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:TIGR00717 214 LHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGEDP 262
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 391-689 2.35e-12

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: 70.15  E-value: 2.35e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 391 MQAFLQGkpkmkdlavetfpSQVDAEKMNASENNMNYV---------DDGGNVLSSKLEDITESDWTRLENYAST---GE 458
Cdd:TIGR00717 123 VEAFLPG-------------SQVDVKPIKDLDSLIGKTlkfkiikldQKRNNIVVSRRAYLEEERSQAREELLENlkeGD 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 459 KVEVELINCSSKGFVVSLDSLIGFLPYRNLA----------------TKWKFLAFET-------WLRQKGGDPSLfkqsv 515
Cdd:TIGR00717 190 VVKGVVKNITDFGAFVDLGGVDGLLHITDMSwkrvkhpseyvkvgqeVKVKVIKFDKekgrislSLKQLGEDPWE----- 264

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 516 GIEESFEVNDRNIESVSssdselAVQDQGS-MPSKEKFEDLLR------TYNTEK-SKFLSsfIGQRLRVSVVLADRKSK 587
Cdd:TIGR00717 265 AIEKKFPVGDKITGRVT------NLTDYGVfVEIEEGIEGLVHvsemswVKKNSHpSKVVK--KGDEVEVMILDIDPERR 336

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 588 KIFFSMKPKESEELIQkkksLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDE-TLDPSVSYKIGQVVD 665
Cdd:TIGR00717 337 RLSLGLKQCKANPWEQ----FEEKHPVGDRVTGKIKKITDFGAFVELEgGIDGLIHLSDISWDKdGREADHLYKKGDEIE 412

                         330       340
                  ....*....|....*....|....
gi 1002242327 666 AKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:TIGR00717 413 AVVLAVDKEKKRISLGVKQLTENP 436
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 571-691 5.79e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 68.36  E-value: 5.79e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMK-----PKESEEliqkkkslmAKLNVGDIVECTIKRFVYFGIFVEV-EGVPALIQQW 644
Cdd:PRK06676  238 VGQEVEVKVLSIDWETERISLSLKdtlpgPWEGVE---------EKLPEGDVIEGTVKRLTDFGAFVEVlPGVEGLVHIS 308

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1002242327 645 EVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNPSV 691
Cdd:PRK06676  309 QISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEEAPAE 355
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 571-683 6.64e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 69.04  E-value: 6.64e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMKPKES---EELIQKKKslmaklnVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEV 646
Cdd:PRK06299  421 KGDEVEAVVLKVDVEKERISLGIKQLEEdpfEEFAKKHK-------KGSIVTGTVTEVKDKGAFVELEdGVEGLIRASEL 493

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1002242327 647 SWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:PRK06299  494 SRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 612-682 4.76e-11

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 59.22  E-value: 4.76e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002242327 612 LNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSL 682
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGnGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 614-681 7.69e-11

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: 58.41  E-value: 7.69e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002242327 614 VGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLS 681
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 569-689 7.05e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 62.05  E-value: 7.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 569 SFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVS 647
Cdd:PRK13806  157 SYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELApGVEGMVHISELS 236

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1002242327 648 WDETLDPSVSYKIGQVVDAKVIQLDYNNN----RIFLSLKDVKPNP 689
Cdd:PRK13806  237 WSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQAGGDP 282
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 576-689 2.54e-09

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.88  E-value: 2.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 576 RVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPS 655
Cdd:PRK12269  455 RISQSKQHRGNDNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPR 534

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1002242327 656 VSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK12269  535 EFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDP 568
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 572-689 3.97e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 57.03  E-value: 3.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 572 GQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKslmaKLNVGDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSW-D 649
Cdd:PRK12269  540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFEN----KFGVNDVVKGRVTKIADFGAFIELaEGIEGLAHISEFSWvK 615

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1002242327 650 ETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK12269  616 KTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANP 655
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 572-683 4.40e-08

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: 56.67  E-value: 4.40e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 572 GQRLRVSVVLADRKSKKIFFSMK---PKESEELIQKKKslmaklnVGDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVS 647
Cdd:TIGR00717 408 GDEIEAVVLAVDKEKKRISLGVKqltENPWEKFAAKYK-------VGSVVKGKVTEIKDFGAFVELpGGVEGLIRNSELS 480

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1002242327 648 WDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:TIGR00717 481 ENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK13806
30S ribosomal protein S1; Provisional
 572-695 7.04e-08

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 55.89  E-value: 7.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 572 GQRLRVSVVLADRKSK----KIFFSMKPKESEELiqkkKSLMAKLNVGDIVECTIKRFVYFGIFVEVE-GVPALIQQWEV 646
Cdd:PRK13806  250 GDTVRVKVLGIERAKKgkglRISLSIKQAGGDPW----DTVGDRLKAGDKVTGKVVRLAPFGAFVEILpGIEGLVHVSEM 325

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002242327 647 SWDE-TLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNPSVGALE 695
Cdd:PRK13806  326 SWTRrVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAE 375
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 615-680 2.10e-07

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


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 48.64  E-value: 2.10e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002242327 615 GDIVECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDETL-DPSVSYKIGQVVDAKVIQLDYNNNRIFL 680
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDgGIDGLVHISDISWTQRVrHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 618-681 8.09e-07

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: 46.99  E-value: 8.09e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002242327 618 VECTIKRFVYFGIFVEVE-GVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLS 681
Cdd:cd00164     1 VTGKVVSITKFGVFVELEdGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 611-716 1.56e-06

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 47.87  E-value: 1.56e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 611 KLNVGDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSWD------ETLdpsvsyKIGQVVDAKVIQLDyNNNRIFLSLK 683
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELpEGTTGLVHISEIADGyvkdinDYL------KVGDEVKVKVLSID-EDGKISLSIK 74

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1002242327 684 DVKPNPSVGALEAVIGEElslggalEPAEADFE 716
Cdd:COG1098    75 QAEEKPKRPPRPRRNSRP-------KAGFESFE 100
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 614-683 2.84e-06

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: 45.78  E-value: 2.84e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002242327 614 VGDIVECTIKRFVYFGIFVEVEG--VPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:cd05708     2 VGQKIDGTVRRVEDYGVFIDIDGtnVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 599-685 3.55e-06

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 50.43  E-value: 3.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 599 EELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEV----EGvpaLIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDyN 674
Cdd:PRK11824  606 EAAKERIEGITAEPEVGEIYEGKVVRIVDFGAFVEIlpgkDG---LVHISEIADERVEKVEDVLKEGDEVKVKVLEID-K 681

                          90
                  ....*....|.
gi 1002242327 675 NNRIFLSLKDV 685
Cdd:PRK11824  682 RGRIRLSRKAV 692
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 567-689 4.29e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 50.04  E-value: 4.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 567 LSSFIGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEV 646
Cdd:PRK07899  161 LQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSEL 240

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1002242327 647 SWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVKPNP 689
Cdd:PRK07899  241 SWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDP 283
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
592-685 9.10e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.17  E-value: 9.10e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 592 SMKPKESEELIQKKKSLMAKLNVGDIVECTIKRFVYFGIFVEV----EGVpalIQQWEVSWDETLDPSVSYKIGQVVDAK 667
Cdd:PRK00087  280 NMEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVgyksEGV---IPLRELTLDEISSLKESVKVGDEIEVK 356

                          90
                  ....*....|....*...
gi 1002242327 668 VIQLDYNNNRIFLSLKDV 685
Cdd:PRK00087  357 VLKLEDEDGYVVLSKKEA 374
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 601-689 2.16e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 47.49  E-value: 2.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 601 LIQKKkslMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFL 680
Cdd:PRK07400  186 LVERK---MNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISL 262


                  ....*....
gi 1002242327 681 SLKDVKPNP 689
Cdd:PRK07400  263 STKQLEPEP 271
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 615-683 3.81e-05

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: 42.26  E-value: 3.81e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 615 GDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLgDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
PRK05807 PRK05807
RNA-binding protein S1;
612-695 4.64e-05

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 43.97  E-value: 4.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 612 LNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDyNNNRIFLSLKD-VKPNPS 690
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQaMKQKKS 81


                  ....*
gi 1002242327 691 VGALE 695
Cdd:PRK05807   82 VKPAE 86
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 615-683 6.32e-05

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: 41.50  E-value: 6.32e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 615 GDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDyNNNRIFLSLK 683
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELgGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 613-685 7.59e-05

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: 45.19  E-value: 7.59e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 613 NVGDIVECTIKRFVYFGIFV---EVEGVPALIQQWEVS--WdetldpsVSY-----KIGQVVDAKVIQLDYNNNRIFLSL 682
Cdd:COG1093     9 EEGELVVGTVKEVKDFGAYVtldEYEGKEGFIHISEVAsgW-------IKNirdyvREGQKVVCKVLRVDPKRGHIDLSL 81


                  ...
gi 1002242327 683 KDV 685
Cdd:COG1093    82 KRV 84
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 615-681 9.33e-05

S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 40.91  E-value: 9.33e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002242327 615 GDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDETLDPSVsyKIGQVVDAKVIQLDYNNNRIFLS 681
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLS 65
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 613-685 9.89e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 44.81  E-value: 9.89e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 613 NVGDIVECTIKRFVYFGIFV---EVEGVPALIQQWEVS--WdetldpsVSY-----KIGQVVDAKVIQLDYNNNRIFLSL 682
Cdd:PRK03987    7 EEGELVVGTVKEVKDFGAFVtldEYPGKEGFIHISEVAsgW-------VKNirdhvKEGQKVVCKVIRVDPRKGHIDLSL 79


                  ...
gi 1002242327 683 KDV 685
Cdd:PRK03987   80 KRV 82
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 615-681 2.90e-04

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: 39.91  E-value: 2.90e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002242327 615 GDIVECTIKRFVYFGIFVEVeGV--PALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLS 681
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDI-GVkqDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 615-683 3.38e-04

S1_Rrp5_repeat_hs6_sc5: 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 H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 39.52  E-value: 3.38e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 615 GDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLK 683
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFyNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 615-682 4.39e-04

S1_Rrp5_repeat_hs5: 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 H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 39.14  E-value: 4.39e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 615 GDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSwDETL-DPSVSYKIGQVVDAKVIQLDYNNNRIFLSL 682
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLsDHIKGLVPPMHLA-DVRLkHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
PRK08059 PRK08059
general stress protein 13; Validated
 608-689 4.86e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.80  E-value: 4.86e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 608 LMAKLNVGDIVECTIKRFVYFGIFVEV-EGVPALIQQWEVSWDETLDPSVSYKIGQVVDAKVIQLDYNNNRIFLSLKDVK 686
Cdd:PRK08059    1 MMSQYEVGSVVTGKVTGIQPYGAFVALdEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATE 80


                  ...
gi 1002242327 687 PNP 689
Cdd:PRK08059   81 EAP 83
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 571-685 1.04e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.17  E-value: 1.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002242327 571 IGQRLRVSVVLADRKSKKIFFSMKPKESEELIQKkksLMAKLNVGDIVECTIKRFVYFGIFVEVEGVPALIQQWEVSWDE 650
Cdd:PRK06676   65 VGDELEVYVLKVEDGEGNLLLSKRRLEAEKAWDK---LEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRF 141

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1002242327 651 TLDPSvSYKiGQVVDAKVIQLDYNNNRIFLSLKDV 685
Cdd:PRK06676  142 VEDFS-DFK-GKTLEVKIIELDPEKNRVILSRRAV 174
 
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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