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Conserved domains on  [gi|818893441|gb|KKW28198|]
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RNA binding S1 domain protein [Candidatus Kaiserbacteria bacterium GW2011_GWB1_52_6]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpsA super family cl33936
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 29-371 2.62e-80

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


The actual alignment was detected with superfamily member COG0539:

Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 249.58  E-value: 2.62e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  29 MAELLKSAPKPPTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKnVNVGDTVTAKIIGTDNADGYIELS 108
Cdd:COG0539    5 FAELLEESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELE-VKVGDEVEVYVEKVEDGEGEIVLS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 109 LREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLAPahyPRVPDgdkekifaeLKRMVGQKLD 188
Cdd:COG0539   84 KKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDV---RPVRD---------LDEYVGKTLE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 189 VQIITANPKEQKLIFSEKGAGVSE----RTSLVEKYHVGDVVGGIVTGATEFGVFIKLeEGLEGLVHISEMDWALVENPK 264
Cdd:COG0539  152 FKIIKLDRKRNNVVVSRRAVLEEEreekREELLEKLEEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPS 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 265 SRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFASE 342
Cdd:COG0539  231 EVLKVGDEVEVKVLKIdrEKERISLSLKQLQPDPWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWT 310

                        330       340       350
                 ....*....|....*....|....*....|..
gi 818893441 343 EELRS---RLELGKVYPFIITFFEPKERRMTL 371
Cdd:COG0539  311 KRVAHpsdVVKVGDEVEVKVLDIDPEERRISL 342
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 29-371 2.62e-80

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: 249.58  E-value: 2.62e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  29 MAELLKSAPKPPTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKnVNVGDTVTAKIIGTDNADGYIELS 108
Cdd:COG0539    5 FAELLEESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELE-VKVGDEVEVYVEKVEDGEGEIVLS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 109 LREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLAPahyPRVPDgdkekifaeLKRMVGQKLD 188
Cdd:COG0539   84 KKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDV---RPVRD---------LDEYVGKTLE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 189 VQIITANPKEQKLIFSEKGAGVSE----RTSLVEKYHVGDVVGGIVTGATEFGVFIKLeEGLEGLVHISEMDWALVENPK 264
Cdd:COG0539  152 FKIIKLDRKRNNVVVSRRAVLEEEreekREELLEKLEEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPS 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 265 SRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFASE 342
Cdd:COG0539  231 EVLKVGDEVEVKVLKIdrEKERISLSLKQLQPDPWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWT 310

                        330       340       350
                 ....*....|....*....|....*....|..
gi 818893441 343 EELRS---RLELGKVYPFIITFFEPKERRMTL 371
Cdd:COG0539  311 KRVAHpsdVVKVGDEVEVKVLDIDPEERRISL 342
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
6-371 3.99e-61

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 207.49  E-value: 3.99e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   6 EGVKRLHDEEEEGAVVVAEKEGPMAELLKsapkPPTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARET--LK 83
Cdd:PRK00087 270 EVIKKMSELDNMEEVEENEQLEYMNELEK----QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISslKE 345

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  84 NVNVGDTVTAKIIGTDNADGYIELSLREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQlapah 163
Cdd:PRK00087 346 SVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASH----- 420

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 164 yprVPDGDKEkifaELKRMVGQKLDVQIITANPKE-------QKLIFSEKGAGVSERTslVEKYHVGDVVGGIVTGATEF 236
Cdd:PRK00087 421 ---VELGYVE----DLSEYKGQELEVKIIEFNRKRrkkvvlsRKAILEEEKEKKKEET--WNSLEEGDVVEGEVKRLTDF 491

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 237 GVFIKLeEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVV 314
Cdd:PRK00087 492 GAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKV 570

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 315 IKHNKHGALASIEEGVAGLVHISEFASE--EELRSRLELGKVYPFIITFFEPKERRMTL 371
Cdd:PRK00087 571 VRIAPFGAFVELEPGVDGLVHISQISWKriDKPEDVLSEGEEVKAKILEVDPEEKRIRL 629
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 31-371 1.05e-44

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: 161.06  E-value: 1.05e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   31 ELLKSAPKPPTtddVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKnvnVGDTVTAKIIGTDNADGYIELSLR 110
Cdd:TIGR00717  10 SLKTEETRPGS---IVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQ---VGDEVEVYLDRVEDRFGETVLSRE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  111 EARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLapahyprvpdgDKEKIfAELKRMVGQKLDVQ 190
Cdd:TIGR00717  84 KAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQV-----------DVKPI-KDLDSLIGKTLKFK 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  191 IITANPKEQKLIFSEKGAGVSERTS----LVEKYHVGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDWALVENPKSR 266
Cdd:TIGR00717 152 IIKLDQKRNNIVVSRRAYLEEERSQareeLLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEY 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  267 YKVGEAVKVKVIEIKDDK--ISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFA---S 341
Cdd:TIGR00717 231 VKVGQEVKVKVIKFDKEKgrISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwvkK 310

                         330       340       350
                  ....*....|....*....|....*....|
gi 818893441  342 EEELRSRLELGKVYPFIITFFEPKERRMTL 371
Cdd:TIGR00717 311 NSHPSKVVKKGDEVEVMILDIDPERRRLSL 340
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 220-306 2.04e-22

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 90.95  E-value: 2.04e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 220 YHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPW 297
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIdeYTGKISLSLRALEEAPE 80


                 ....*....
gi 818893441 298 KVAGTKYHK 306
Cdd:NF040579  81 KHRKRRKHR 89
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
222-290 9.20e-18

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 76.87  E-value: 9.20e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818893441   222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSIK 290
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 223-290 1.31e-17

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: 76.17  E-value: 1.31e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD-KISLSIK 290
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 222-289 1.73e-14

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: 67.70  E-value: 1.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSI 289
Cdd:pfam00575   3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRrrIILSI 72
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 29-371 2.62e-80

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: 249.58  E-value: 2.62e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  29 MAELLKSAPKPPTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKnVNVGDTVTAKIIGTDNADGYIELS 108
Cdd:COG0539    5 FAELLEESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELE-VKVGDEVEVYVEKVEDGEGEIVLS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 109 LREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLAPahyPRVPDgdkekifaeLKRMVGQKLD 188
Cdd:COG0539   84 KKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDV---RPVRD---------LDEYVGKTLE 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 189 VQIITANPKEQKLIFSEKGAGVSE----RTSLVEKYHVGDVVGGIVTGATEFGVFIKLeEGLEGLVHISEMDWALVENPK 264
Cdd:COG0539  152 FKIIKLDRKRNNVVVSRRAVLEEEreekREELLEKLEEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPS 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 265 SRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFASE 342
Cdd:COG0539  231 EVLKVGDEVEVKVLKIdrEKERISLSLKQLQPDPWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWT 310

                        330       340       350
                 ....*....|....*....|....*....|..
gi 818893441 343 EELRS---RLELGKVYPFIITFFEPKERRMTL 371
Cdd:COG0539  311 KRVAHpsdVVKVGDEVEVKVLDIDPEERRISL 342
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
6-371 3.99e-61

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 207.49  E-value: 3.99e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   6 EGVKRLHDEEEEGAVVVAEKEGPMAELLKsapkPPTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARET--LK 83
Cdd:PRK00087 270 EVIKKMSELDNMEEVEENEQLEYMNELEK----QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISslKE 345

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  84 NVNVGDTVTAKIIGTDNADGYIELSLREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQlapah 163
Cdd:PRK00087 346 SVKVGDEIEVKVLKLEDEDGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASH----- 420

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 164 yprVPDGDKEkifaELKRMVGQKLDVQIITANPKE-------QKLIFSEKGAGVSERTslVEKYHVGDVVGGIVTGATEF 236
Cdd:PRK00087 421 ---VELGYVE----DLSEYKGQELEVKIIEFNRKRrkkvvlsRKAILEEEKEKKKEET--WNSLEEGDVVEGEVKRLTDF 491

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 237 GVFIKLeEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVV 314
Cdd:PRK00087 492 GAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKV 570

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 315 IKHNKHGALASIEEGVAGLVHISEFASE--EELRSRLELGKVYPFIITFFEPKERRMTL 371
Cdd:PRK00087 571 VRIAPFGAFVELEPGVDGLVHISQISWKriDKPEDVLSEGEEVKAKILEVDPEEKRIRL 629
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 29-342 5.20e-53

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 180.07  E-value: 5.20e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  29 MAELLKSApKPPTTDDVVEGPVIAIGRACVFVDLHPFGT-GIIFGREYLSARETLKN--VNVGDTVTAKIIGTDNADGYI 105
Cdd:PRK06676   5 FEESLNSV-KEVEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIEDINdvVKVGDELEVYVLKVEDGEGNL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 106 ELSLREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLAPAhypRVPDgdkekifaeLKRMVGQ 185
Cdd:PRK06676  84 LLSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTR---FVED---------FSDFKGK 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 186 KLDVQIITANPKEQKLIFSEKgAGVSE-----RTSLVEKYHVGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDWALV 260
Cdd:PRK06676 152 TLEVKIIELDPEKNRVILSRR-AVVEEeraakKEELLSSLKEGDVVEGTVARLTDFGAFVDIG-GVDGLVHISELSHERV 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 261 ENPKSRYKVGEAVKVKVIEIKDD--KISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISE 338
Cdd:PRK06676 230 EKPSEVVSVGQEVEVKVLSIDWEteRISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQ 309


                 ....
gi 818893441 339 FASE 342
Cdd:PRK06676 310 ISHK 313
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 29-339 6.34e-52

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 181.52  E-value: 6.34e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  29 MAELLKSAPKPPTT--DDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKnVNVGDTVTAKIIGTDNADGYIE 106
Cdd:PRK06299  15 FAELFEESLKESETreGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQGELE-VKVGDEVEVYVERIEDGFGETV 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 107 LSLREARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLApahYPRVPDGDKekifaelkrMVGQK 186
Cdd:PRK06299  94 LSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVD---VRPVRDTDP---------LEGKE 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 187 LDVQIITANPKEQKLIFS-------EKGAgvsERTSLVEKYHVGDVVGGIVTGATEFGVFIKLeEGLEGLVHISEMDWAL 259
Cdd:PRK06299 162 LEFKVIKLDKKRNNIVVSrravleeERAE---EREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKR 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 260 VENPKSRYKVGEAVKVKVIEIKDDK--ISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHIS 337
Cdd:PRK06299 238 VNHPSEVVNVGDEVKVKVLKFDKEKkrVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVS 317


                 ..
gi 818893441 338 EF 339
Cdd:PRK06299 318 EM 319
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 31-371 1.05e-44

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: 161.06  E-value: 1.05e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   31 ELLKSAPKPPTtddVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKnvnVGDTVTAKIIGTDNADGYIELSLR 110
Cdd:TIGR00717  10 SLKTEETRPGS---IVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQ---VGDEVEVYLDRVEDRFGETVLSRE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  111 EARQALIWGEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLapahyprvpdgDKEKIfAELKRMVGQKLDVQ 190
Cdd:TIGR00717  84 KAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQV-----------DVKPI-KDLDSLIGKTLKFK 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  191 IITANPKEQKLIFSEKGAGVSERTS----LVEKYHVGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDWALVENPKSR 266
Cdd:TIGR00717 152 IIKLDQKRNNIVVSRRAYLEEERSQareeLLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEY 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  267 YKVGEAVKVKVIEIKDDK--ISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFA---S 341
Cdd:TIGR00717 231 VKVGQEVKVKVIKFDKEKgrISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwvkK 310

                         330       340       350
                  ....*....|....*....|....*....|
gi 818893441  342 EEELRSRLELGKVYPFIITFFEPKERRMTL 371
Cdd:TIGR00717 311 NSHPSKVVKKGDEVEVMILDIDPERRRLSL 340
rpsA PRK13806
30S ribosomal protein S1; Provisional
 9-338 2.13e-39

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 146.41  E-value: 2.13e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   9 KRLHDEEEEGavvvaekEGPMAELLKS----APKPPTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLkN 84
Cdd:PRK13806   4 EKFDTPELDE-------SESFAELLEAyegeRKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADGEL-T 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  85 VNVGDTVTAKIIGTDnaDGYIELS-----------LREARQALIwgeaemAVQKKslfelaITDANKGGLIINWNGIQGF 153
Cdd:PRK13806  76 VAVGDEVELYVVSVN--GQEIRLSkalsgqggaamLEEAYENGV------PVEGK------VTGTCKGGFNVEVLGRRAF 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 154 LPASQLApAHYPRVPDGdkekifaelkrMVGQKLDVQIITANPKEQKLIFSEKG----AGVSERTSLVEKYHVGDVVGGI 229
Cdd:PRK13806 142 CPVSQID-LRYVEDPES-----------YVGQTFQFLITRVEENGRNIVVSRRAllerEQKEALEAFMETVKEGDVVEGT 209

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 230 VTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI------KDDKISLSIKALAEDPWKVAGTK 303
Cdd:PRK13806 210 VTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIerakkgKGLRISLSIKQAGGDPWDTVGDR 289

                        330       340       350
                 ....*....|....*....|....*....|....*
gi 818893441 304 YHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISE 338
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSE 324
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 44-340 2.84e-35

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 134.79  E-value: 2.84e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  44 DVVEGPVIAIGRACVFVDLHPFGTGIIFGREyLSARETL---KNVNVGDTVTAKIIGTDNADGYIELSLREARQALIWGE 120
Cdd:PRK07899  37 DIVEGTVVKVDRDEVLLDIGYKTEGVIPSRE-LSIKHDVdpnEVVEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGT 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 121 AEMAVQKKSLFELAITDANKGGLIINWnGIQGFLPASQLapaHYPRVPDgdkekifaeLKRMVGQKLDVQIITANPKEQK 200
Cdd:PRK07899 116 IEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLV---EMRRVRD---------LQPYIGQEIEAKIIELDKNRNN 182

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 201 LIFSEKG---AGVSE-RTSLVEKYHVGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDWALVENPKSRYKVGEAVKVK 276
Cdd:PRK07899 183 VVLSRRAwleQTQSEvRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLG-GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVE 261

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818893441 277 VIEIKDD--KISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFA 340
Cdd:PRK07899 262 VLDVDMDreRVSLSLKATQEDPWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELA 327
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 44-371 1.44e-33

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: 130.62  E-value: 1.44e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   44 DVVEGPVIAIGRACVFVDLHPFG-----TGIIFGReylsARETLKNVNVGDTVTAKIIGTDNADGYIELSLREARQAlIW 118
Cdd:TIGR00717 189 DVVKGVVKNITDFGAFVDLGGVDgllhiTDMSWKR----VKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLGED-PW 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  119 GEAEMAVQKKSLFELAITD-ANKGGLIINWNGIQGFLPASQLapahyprvpDGDKEKIFAELKRMVGQKLDVQIITANPK 197
Cdd:TIGR00717 264 EAIEKKFPVGDKITGRVTNlTDYGVFVEIEEGIEGLVHVSEM---------SWVKKNSHPSKVVKKGDEVEVMILDIDPE 334

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  198 EQKLIFSEKGAGVSERTSLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSR-YKVGEAVKVK 276
Cdd:TIGR00717 335 RRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHlYKKGDEIEAV 414

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  277 VIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFASE--EELRSRLELG 352
Cdd:TIGR00717 415 VLAVdkEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENrdEDKTDEIKVG 494

                         330
                  ....*....|....*....
gi 818893441  353 KVYPFIITFFEPKERRMTL 371
Cdd:TIGR00717 495 DEVEAKVVDIDKKNRKVSL 513
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 100-371 1.13e-23

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 102.87  E-value: 1.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 100 NADGYIELSLREARQaliwgEAEMAVQKKSLFELAITDANKGGLIINWNGIQGFLPASQLAPAHYPRVPDGDKEkifael 179
Cdd:PRK12269 471 NRRRYLEERARQARE-----EFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKK------ 539

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 180 krmvGQKLDVQIITANPKEQKLIFSEKGAGVSERTSLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWA- 258
Cdd:PRK12269 540 ----GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVk 615

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 259 LVENPKSRYKVGEAVKVKVI--EIKDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLVHI 336
Cdd:PRK12269 616 KTSKPSDMVKIGDEVECMILgyDIQAGRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHV 695

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 818893441 337 SEFASEEELRS---RLELGKVYPFIITFFEPKERRMTL 371
Cdd:PRK12269 696 DDLSWVKRTRPadhELEVGKEIECMVIECDPQARRIRL 733
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 220-306 2.04e-22

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 90.95  E-value: 2.04e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 220 YHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPW 297
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIdeYTGKISLSLRALEEAPE 80


                 ....*....
gi 818893441 298 KVAGTKYHK 306
Cdd:NF040579  81 KHRKRRKHR 89
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 218-296 3.87e-22

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 90.62  E-value: 3.87e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 218 EKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD-KISLSIKALAEDP 296
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQAEEKP 80
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 8-290 2.29e-20

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: 92.49  E-value: 2.29e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441    8 VKRLHDEEEEGAVVVAEK---EGPMAELLKSAPkpptTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETL-- 82
Cdd:TIGR00717 239 VKVIKFDKEKGRISLSLKqlgEDPWEAIEKKFP----VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNShp 314

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441   83 -KNVNVGDTVTAKIIGTDNADGYIELSLREArQALIWGEAEMAVQKKSLFELAITDANKGGLIINW-NGIQGFLPASQLA 160
Cdd:TIGR00717 315 sKVVKKGDEVEVMILDIDPERRRLSLGLKQC-KANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELeGGIDGLIHLSDIS 393

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  161 PAHYPRVPDGDKEKifaelkrmvGQKLDVQIITANPKEQKLIFSEKGAGVSERTSLVEKYHVGDVVGGIVTGATEFGVFI 240
Cdd:TIGR00717 394 WDKDGREADHLYKK---------GDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFV 464

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 818893441  241 KLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIK 290
Cdd:TIGR00717 465 ELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIdkKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 183-308 1.93e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 89.84  E-value: 1.93e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 183 VGQKLDVQIITANPKEQKLIFSEKGAGVSERTSLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVEN 262
Cdd:PRK06299 421 KGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVED 500

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 818893441 263 PKSRYKVGEAVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQ 308
Cdd:PRK06299 501 ATEVLKVGDEVEAKVINIdrKNRRISLSIKALDEAEEKEAIAEYNSAS 548
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
222-290 9.20e-18

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 76.87  E-value: 9.20e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818893441   222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSIK 290
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 223-290 1.31e-17

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: 76.17  E-value: 1.31e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD-KISLSIK 290
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 215-292 1.57e-17

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 83.95  E-value: 1.57e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 215 SLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI-KDDKISLSIKAL 292
Cdd:PRK11824 614 GITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIdKRGRIRLSRKAV 692
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 43-290 2.97e-17

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 83.61  E-value: 2.97e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  43 DDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKN---VNVGDTVTAKIIGTDNADGYIELSLREArQALIWG 119
Cdd:PRK12269 579 NDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPsdmVKIGDEVECMILGYDIQAGRVSLGLKQV-TANPWE 657

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 120 EAEMAVQKKSLFELAITD-ANKGGLIINWNGIQGFLPASQLAPAHYPRVPDGDKEkifaelkrmVGQKLDVQIITANPKE 198
Cdd:PRK12269 658 EIEARYPVGARFTRRIVKvTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADHELE---------VGKEIECMVIECDPQA 728

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 199 QKLIFSEKGAGVSERTSLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEmdwaLVENPKS-------RYKVGE 271
Cdd:PRK12269 729 RRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQH----LVENRDGdpgealrKYAVGD 804

                        250       260
                 ....*....|....*....|.
gi 818893441 272 AVKVKVIE--IKDDKISLSIK 290
Cdd:PRK12269 805 RVKAVIVDmnVKDRKVAFSVR 825
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 95-296 4.86e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 81.00  E-value: 4.86e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  95 IIGTDNADGYIELSLREARQALIWG-----EAEMAVQKKSLFElaitdANKGGLIINWNGIQGFLPASQLAPahypRVPD 169
Cdd:PRK07400  86 ILSDENEDGQLTLSIRRIEYMRAWErvrqlQKEDATVRSEVFA-----TNRGGALVRIEGLRGFIPGSHIST----RKPK 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 170 GDkekifaelkrMVGQKLDVQIITANPKEQKLIFSEKGAGVSERTSLVEkyhVGDVVGGIVTGATEFGVFIKLEeGLEGL 249
Cdd:PRK07400 157 EE----------LVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLE---VGEVVVGTVRGIKPYGAFIDIG-GVSGL 222

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 818893441 250 VHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD--KISLSIKALAEDP 296
Cdd:PRK07400 223 LHISEISHEHIETPHSVFNVNDEMKVMIIDLDAErgRISLSTKQLEPEP 271
PRK08059 PRK08059
general stress protein 13; Validated
 218-296 5.70e-17

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 76.24  E-value: 5.70e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 218 EKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIKALAED 295
Cdd:PRK08059   3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVdeEKGKISLSIRATEEA 82


                 .
gi 818893441 296 P 296
Cdd:PRK08059  83 P 83
PRK08582 PRK08582
RNA-binding protein S1;
222-296 1.22e-16

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 75.84  E-value: 1.22e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD-KISLSIKALAEDP 296
Cdd:PRK08582   5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDgKIGLSIKKAKDRP 80
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 215-291 1.77e-16

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 80.82  E-value: 1.77e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441 215 SLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI-KDDKISLSIKA 291
Cdd:COG1185  609 GITAEPEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIdDQGRIKLSRKA 686
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 43-334 1.34e-14

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 75.52  E-value: 1.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  43 DDVVEGPVIAIGRACVFVDLHPF-GTGIIFGREYLSARETLKNVNVGDTVTAKIIGTDNADGYIELSLREArQALIWGEA 121
Cdd:PRK12269 494 EDSVSGVVKSFTSFGAFIDLGGFdGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHF-QPDPWLEF 572

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 122 EMAVQKKSLFELAITD-ANKGGLIINWNGIQGFLPASQLAPAHYPRVPDgDKEKIFAELKRMV-------GQ-KLDVQII 192
Cdd:PRK12269 573 ENKFGVNDVVKGRVTKiADFGAFIELAEGIEGLAHISEFSWVKKTSKPS-DMVKIGDEVECMIlgydiqaGRvSLGLKQV 651

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 193 TANPKEQklifsekgagvsertsLVEKYHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKS-RYKVGE 271
Cdd:PRK12269 652 TANPWEE----------------IEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADhELEVGK 715

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818893441 272 AVKVKVIEI--KDDKISLSIKALAEDPWKVAGTKYHKDQKVDAVVIKHNKHGALASIEEGVAGLV 334
Cdd:PRK12269 716 EIECMVIECdpQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLV 780
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 223-290 1.55e-14

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 68.03  E-value: 1.55e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818893441 223 GDVVGGIVTGATEFGVFIKLE---EGLEGLVHISEMDW-ALVENPKSRYKVGEAVKVKVIEIKDDKISLSIK 290
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEglkGRKEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVISIQNGKISLSMK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 222-289 1.73e-14

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: 67.70  E-value: 1.73e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSI 289
Cdd:pfam00575   3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRrrIILSI 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 222-288 2.75e-14

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: 66.88  E-value: 2.75e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLS 288
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLG-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERkrISLG 68
PRK05807 PRK05807
RNA-binding protein S1;
222-290 8.10e-14

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 67.85  E-value: 8.10e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD-KISLSIK 290
Cdd:PRK05807   5 AGSILEGTVVNITNFGAFVEVE-GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNgKISLSIK 73
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 221-291 1.30e-13

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: 65.43  E-value: 1.30e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818893441 221 HVGDVVGGIVTGATEFGVFIKLE-EGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSIKA 291
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDgTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKkrISLGLKA 74
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 226-288 2.10e-13

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: 64.32  E-value: 2.10e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818893441 226 VGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDKISLS 288
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRIS 63
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 223-287 7.81e-13

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: 62.90  E-value: 7.81e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWAL-VENPKSRYKVGEAVKVKV--IEIKDDKISL 287
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQrVRHPSEIYKKGQEVEAVVlnIDVERERISL 68
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 223-289 2.95e-12

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: 61.40  E-value: 2.95e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI-KDDKISLSI 289
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVdDRGRISLSR 68
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 220-289 3.81e-12

S1_RPS1_repeat_ec4: 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 (ec4) 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: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 61.05  E-value: 3.81e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818893441 220 YHVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVE-NPKSRYKVGEAVKVKVIEIKDDKISLSI 289
Cdd:cd05689    1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNiHPSKVVSLGDEVEVMVLDIDEERRRISL 71
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 222-280 4.06e-12

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 61.26  E-value: 4.06e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEE-GLEGLVHISEM--DW--------ALV-ENPKSRYKVGEAVKVKVIEI 280
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLgdDYyefdeenhALVgERTGKVFRLGDKVKVRVVRV 71
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 223-288 6.93e-12

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: 60.32  E-value: 6.93e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLS 288
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIdeERGRISLS 68
VacB COG0557
Exoribonuclease R [Transcription];
221-280 7.15e-12

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 66.67  E-value: 7.15e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818893441 221 HVGDVVGGIVTGATEFGVFIKLEE-GLEGLVHISEM--DW--------ALV-ENPKSRYKVGEAVKVKVIEI 280
Cdd:COG0557  621 RVGEEFEGVISGVTSFGLFVELDElGVEGLVHVSSLgdDYyeyderrqALVgERTGKRYRLGDRVEVRVVRV 692
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
222-295 1.08e-11

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 61.26  E-value: 1.08e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKD--DKISLSIKALAED 295
Cdd:PRK07252   3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEytGKASLSLRTLEEE 78
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 135-206 2.60e-11

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: 58.62  E-value: 2.60e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818893441 135 ITDANKGGLIINWNGIQGFLPASQLAPAHyprVPDgdkekifaeLKRMVGQKLDVQIITANPKEQKLIFSEK 206
Cdd:cd04465    8 VTEKVKGGLIVDIEGVRAFLPASQVDLRP---VED---------LDEYVGKELKFKIIEIDRERNNIVLSRR 67
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 234-296 1.36e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 56.83  E-value: 1.36e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818893441 234 TEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD-KISLSIKALAEDP 296
Cdd:PLN00207 766 APYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKgQLRLSRRALLPEA 829
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 223-284 1.55e-08

S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 51.05  E-value: 1.55e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEM--DWALVENPKSRYKVGEAVKVKVIEIKDDK 284
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVfdEWPDGKNPLSKFKIGQKIKARVIGGHDAK 64
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 223-292 2.81e-08

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: 50.35  E-value: 2.81e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIKAL 292
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVdrKNRKISLSIKAK 72
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 222-284 8.30e-08

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 49.14  E-value: 8.30e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDwalvenpkSRYKVGEAVKVKVIEIKDDK 284
Cdd:cd04473   16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENG 70
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
221-296 8.77e-08

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 53.88  E-value: 8.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 221 HVGDVVGGIVTGATEFGVFIKLeeGL--EGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIkdDK----ISLSIKALAE 294
Cdd:COG2183  640 KPGMILEGTVTNVTDFGAFVDI--GVhqDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEV--DLkrkrISLSMKLDDE 715


                 ..
gi 818893441 295 DP 296
Cdd:COG2183  716 AG 717
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 228-294 2.24e-07

Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, recombination and repair];


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 52.53  E-value: 2.24e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441 228 GIVTGATEFGVFIKLEEGLEGLVHISEMDwalvenpkSRYKVGEAVKVKVIEIKDD-KISLSIKALAE 294
Cdd:COG1107   45 GTVDGVADFGVFVDLNDHVTGLLHRSELD--------QDWEVGDEVFVQVKEVRDNgNVDLGWVSIDS 104
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 223-288 3.34e-07

S1_Rrp5_repeat_sc11: 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 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 46.90  E-value: 3.34e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLS 288
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNgrIEMT 68
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 222-290 3.75e-07

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: 47.19  E-value: 3.75e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEE--GLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSIK 290
Cdd:cd04452    3 EGELVVVTVKSIADMGAYVSLLEygNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKgyIDLSKK 75
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 228-290 3.96e-07

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 47.09  E-value: 3.96e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818893441 228 GIVTGATEFGVFIKLEeGL--EGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIK-DDKISLSIK 290
Cdd:cd05686    9 GEVASVTEYGAFVKIP-GCrkQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREmKDKMKLSLS 73
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 223-290 6.56e-07

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: 46.45  E-value: 6.56e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEI--KDDKISLSIK 290
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCdpEQQRLLLSCK 70
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 221-284 6.76e-07

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. 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 S. cerevisiae Rrp5 and 14 S1 repeats in H. 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 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 46.81  E-value: 6.76e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818893441 221 HVGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK 284
Cdd:cd04461   13 KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEK 76
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 222-311 6.43e-06

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 47.13  E-value: 6.43e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEE--GLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK--ISLSIKALAEDPW 297
Cdd:PRK03987   8 EGELVVGTVKEVKDFGAFVTLDEypGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKghIDLSLKRVNEHQR 87

                         90
                 ....*....|....
gi 818893441 298 KVAGTKYHKDQKVD 311
Cdd:PRK03987  88 REKIQEWKNEQKAD 101
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
306-371 8.51e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.36  E-value: 8.51e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818893441   306 KDQKVDAVVIKHNKHGALASIEEGVAGLVHISEFASE--EELRSRLELGKVYPFIITFFEPKERRMTL 371
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKrvKDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69
rpsA PRK13806
30S ribosomal protein S1; Provisional
 178-340 1.10e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 47.03  E-value: 1.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 178 ELKRMVGQKLDVQIITANPKEQKLifSEKGAGVSERTSLVEKYHVGDVVGGIVTGATEFGVFIKLEeGLEGLVHISEMDW 257
Cdd:PRK13806  73 ELTVAVGDEVELYVVSVNGQEIRL--SKALSGQGGAAMLEEAYENGVPVEGKVTGTCKGGFNVEVL-GRRAFCPVSQIDL 149

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 258 ALVENPKSRykVGEAVKVKVIEIKDD--KISLSIKALAEDPWKVAGTKYHKDQK----VDAVVIKHNKHGALASIEEGVA 331
Cdd:PRK13806 150 RYVEDPESY--VGQTFQFLITRVEENgrNIVVSRRALLEREQKEALEAFMETVKegdvVEGTVTRLAPFGAFVELAPGVE 227


                 ....*....
gi 818893441 332 GLVHISEFA 340
Cdd:PRK13806 228 GMVHISELS 236
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 44-110 1.28e-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: 1.28e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441  44 DVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKN--VNVGDTVTAKIIGTDNADGYIELSLR 110
Cdd:cd05687    2 DIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEdeVKVGDEVEVYVLRVEDEEGNVVLSKR 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
44-110 1.53e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.59  E-value: 1.53e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441    44 DVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSAR--ETLKNVNVGDTVTAKIIGTDNADGYIELSLR 110
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRvkDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 223-284 2.93e-05

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: 41.45  E-value: 2.93e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDK 284
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPER 62
rpsA PRK13806
30S ribosomal protein S1; Provisional
 43-208 8.37e-05

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 44.33  E-value: 8.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441  43 DDVVEGPVIAIGRACVFVDLHPFGTGIIFGREYLSARETLKN---VNVGDTVTAKIIGTDNADGYIELSLREA------- 112
Cdd:PRK13806 293 GDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPedvVAPGDAVAVKIKDIDPAKRRISLSLRDAegdpwad 372

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 113 --RQALIWGEAEMAVQKKSLFelaitdankgGLIINWN-GIQGFLPASQLAPAhyprvpdgDKEKIFAELKrmVGQKLDV 189
Cdd:PRK13806 373 vaERFAPGTTVTGTVEKRAQF----------GLFVNLApGVTGLLPASVISRA--------GKPATYEKLK--PGDSVTL 432

                        170
                 ....*....|....*....
gi 818893441 190 QIITANPKEQKLIFSEKGA 208
Cdd:PRK13806 433 VVEEIDTAKRKISLAPAGA 451
PRK11642 PRK11642
ribonuclease R;
221-312 2.57e-04

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 43.19  E-value: 2.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 221 HVGDVVGGIVTGATEFGVFIKLEE-GLEGLVHISEMD----------WALV-ENPKSRYKVGEAVKVKV--IEIKDDKIS 286
Cdd:PRK11642 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDndyyrfdqvgQRLIgESSGQTYRLGDRVEVRVeaVNMDERKID 721

                         90       100
                 ....*....|....*....|....*.
gi 818893441 287 LSIKALAEDPWKVAGTKYHKDQKVDA 312
Cdd:PRK11642 722 FSLISSERAPRNVGKTAREKAKKGDA 747
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 222-288 3.72e-04

S1_Rrp5_repeat_sc10: 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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 38.77  E-value: 3.72e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 222 VGDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDD--KISLS 288
Cdd:cd05706    3 VGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPnkKIALS 71
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 223-290 6.24e-04

S1_Rrp5_repeat_hs13: 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 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 38.10  E-value: 6.24e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 223 GDVVGGIVTGATEF-GVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKVIEIKDDKISLSIK 290
Cdd:cd05704    4 GAVTLGMVTKVIPHsGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 223-290 7.15e-04

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 37.89  E-value: 7.15e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 223 GDVVGGIVTGATEFGVFIKLEEGLEGLVHISEMDWALVENPKSRYKVGEAVKVKV--IEIKDDKISLSIK 290
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVlrVEDEEGNVVLSKR 70
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 40-109 9.76e-04

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: 37.27  E-value: 9.76e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818893441   40 PTTDDVVEGPVIAIGRACVFVDLHPFGTGIIFGREyLSARETLKN---VNVGDTVTAKIIGTDNADGYIELSL 109
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISE-LSDDHVEDPdevIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 135-206 1.10e-03

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: 37.21  E-value: 1.10e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818893441 135 ITDANKGGLIIN-WNGIQGFLPASQLAPAhyprvPDGDKEKIFaelkrMVGQKLDVQIITANPKEQKLIFSEK 206
Cdd:cd05698    8 IVKVKPNGCIVSfYNNVKGFLPKSELSEA-----FIKDPEEHF-----RVGQVVKVKVLSCDPEQQRLLLSCK 70
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 44-112 1.34e-03

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 38.62  E-value: 1.34e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818893441  44 DVVEGPVIAIGRACVFVDLHPFGTGII----FGREYLsaretlKNVN----VGDTVTAKIIGTDNaDGYIELSLREA 112
Cdd:COG1098    7 DIVEGKVTGITPFGAFVELPEGTTGLVhiseIADGYV------KDINdylkVGDEVKVKVLSIDE-DGKISLSIKQA 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
135-206 1.88e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 36.43  E-value: 1.88e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 818893441   135 ITDANKGGLIIN-WNGIQGFLPASQLapahyprvPDGDKEKIFAELKrmVGQKLDVQIITANPKEQKLIFSEK 206
Cdd:smart00316  10 VTEITPGGAFVDlGNGVEGLIPISEL--------SDKRVKDPEEVLK--VGDEVKVKVLSVDEEKGRIILSLK 72
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 225-282 1.90e-03

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 37.27  E-value: 1.90e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 818893441 225 VVGGIVTGATEFGVFIKLEEgLEGLVHISE-MDWALVENPKSRYKVGEAVKvKVIEIKD 282
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRIGP-VDGLLHISQiMDDYISYDPKNKRLIGEETK-RVLKVGD 58
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 225-290 4.74e-03

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 37.88  E-value: 4.74e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818893441 225 VVGGIVTGATEFGVFIKLeeG-LEGLVHISE-MDWALVENPKSR----------YKVGEAVKVKVI-------EIKDDKI 285
Cdd:PRK08563  84 VVEGEVVEVVEFGAFVRI--GpVDGLLHISQiMDDYISYDPKNGrligkeskrvLKVGDVVRARIVavslkerRPRGSKI 161


                 ....*
gi 818893441 286 SLSIK 290
Cdd:PRK08563 162 GLTMR 166
 
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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