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Conserved domains on  [gi|1088030732|gb|OGZ01410|]
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MAG: hypothetical protein A3A43_01130 [Candidatus Liptonbacteria bacterium RIFCSPLOWO2_01_FULL_56_20]

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 ...
 1-347 3.06e-88

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: 268.84  E-value: 3.06e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELpgNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLrDLAVGAHLPAKVIDLDGERGYTELSL 80
Cdd:COG0539     8 LLEESL--KELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGEL-EVKVGDEVEVYVEKVEDGEGEIVLSK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  81 AEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSV 160
Cdd:COG0539    85 KKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDV------------RPVRDLDEYVGKTLEF 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREIL----ATNVKELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENP 236
Cdd:COG0539   153 KIIKLDRKRNNVVVSRRAVLeeerEEKREELLEKLEEGDVVEGTVKNITDFGAF---VDLGGVDGLLHISEISWGRVKHP 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 237 KEVMKLNEPVKVKIIDI-RE-GRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFGS 314
Cdd:COG0539   230 SEVLKVGDEVEVKVLKIdREkERISLSLKQLQPDPWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSW 309

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1088030732 315 ---VEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:COG0539   310 tkrVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1-347 3.06e-88

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: 268.84  E-value: 3.06e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELpgNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLrDLAVGAHLPAKVIDLDGERGYTELSL 80
Cdd:COG0539     8 LLEESL--KELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGEL-EVKVGDEVEVYVEKVEDGEGEIVLSK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  81 AEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSV 160
Cdd:COG0539    85 KKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDV------------RPVRDLDEYVGKTLEF 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREIL----ATNVKELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENP 236
Cdd:COG0539   153 KIIKLDRKRNNVVVSRRAVLeeerEEKREELLEKLEEGDVVEGTVKNITDFGAF---VDLGGVDGLLHISEISWGRVKHP 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 237 KEVMKLNEPVKVKIIDI-RE-GRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFGS 314
Cdd:COG0539   230 SEVLKVGDEVEVKVLKIdREkERISLSLKQLQPDPWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSW 309

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1088030732 315 ---VEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:COG0539   310 tkrVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1-348 1.91e-65

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 218.28  E-value: 1.91e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELPGNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEF--LNAKDMLRDLAVGAHLPAKVIDLDGERGYTEL 78
Cdd:PRK00087  290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELtlDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  79 SLAEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNEHyskltegdrqksIDELKKFVGEEV 158
Cdd:PRK00087  370 SKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGY------------VEDLSEYKGQEL 437

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 159 SVKVINVNPRNNKLIV-SEREIL----ATNVKELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLI 233
Cdd:PRK00087  438 EVKIIEFNRKRRKKVVlSRKAILeeekEKKKEETWNSLEEGDVVEGEVKRLTDFGAF---VDIGGVDGLLHVSEISWGRV 514

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 234 ENPKEVMKLNEPVKVKIIDI-RE-GRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSE 311
Cdd:PRK00087  515 EKPSDVLKVGDEIKVYILDIdKEnKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQ 594

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 1088030732 312 F--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:PRK00087  595 IswKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKE 633
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1-348 1.59e-54

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: 186.48  E-value: 1.59e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELPGNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLRdlaVGAHLPAKVIDLDGERGYTELSL 80
Cdd:TIGR00717   6 LLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQ---VGDEVEVYLDRVEDRFGETVLSR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  81 AEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSV 160
Cdd:TIGR00717  83 EKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDV------------KPIKDLDSLIGKTLKF 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREILATNVK----ELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENP 236
Cdd:TIGR00717 151 KIIKLDQKRNNIVVSRRAYLEEERSqareELLENLKEGDVVKGVVKNITDFGAF---VDLGGVDGLLHITDMSWKRVKHP 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 237 KEVMKLNEPVKVKII--DIREGRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEF-- 312
Cdd:TIGR00717 228 SEYVKVGQEVKVKVIkfDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMsw 307

                         330       340       350
                  ....*....|....*....|....*....|....*..
gi 1088030732 313 -GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:TIGR00717 308 vKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 191-277 2.70e-19

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: 82.09  E-value: 2.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 191 YEVGQVVDGLVSGLADFGIFIRFVDNPQieGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSLKALKPN 268
Cdd:NF040579    1 YKIGDIVEGKVTGIQPYGAFVALDEHTQ--GLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEytGKISLSLRALEEA 78

                          90
                  ....*....|....*....
gi 1088030732 269 P----------WENIEEKY 277
Cdd:NF040579   79 PekhrkrrkhrWTNKRLKI 97
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 194-263 1.10e-15

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: 71.12  E-value: 1.10e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFVDNPQI-EGLVHISEIDH-RLIENPKEVMKLNEPVKVKIIDIREGRVFLSLK 263
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKGRkEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVISIQNGKISLSMK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
192-263 3.18e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 64.16  E-value: 3.18e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732  192 EVGQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSLK 263
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEekGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 191-262 5.20e-11

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.68  E-value: 5.20e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 191 YEVGQVVDGLVSGLADFGIFIRfVDNPqIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSL 262
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVD-LGNG-VEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKdrRRIILSI 72
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1-347 3.06e-88

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: 268.84  E-value: 3.06e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELpgNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLrDLAVGAHLPAKVIDLDGERGYTELSL 80
Cdd:COG0539     8 LLEESL--KELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGEL-EVKVGDEVEVYVEKVEDGEGEIVLSK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  81 AEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSV 160
Cdd:COG0539    85 KKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDV------------RPVRDLDEYVGKTLEF 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREIL----ATNVKELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENP 236
Cdd:COG0539   153 KIIKLDRKRNNVVVSRRAVLeeerEEKREELLEKLEEGDVVEGTVKNITDFGAF---VDLGGVDGLLHISEISWGRVKHP 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 237 KEVMKLNEPVKVKIIDI-RE-GRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFGS 314
Cdd:COG0539   230 SEVLKVGDEVEVKVLKIdREkERISLSLKQLQPDPWENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSW 309

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1088030732 315 ---VEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:COG0539   310 tkrVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1-348 1.91e-65

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 218.28  E-value: 1.91e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELPGNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEF--LNAKDMLRDLAVGAHLPAKVIDLDGERGYTEL 78
Cdd:PRK00087  290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELtlDEISSLKESVKVGDEIEVKVLKLEDEDGYVVL 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  79 SLAEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNEHyskltegdrqksIDELKKFVGEEV 158
Cdd:PRK00087  370 SKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGY------------VEDLSEYKGQEL 437

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 159 SVKVINVNPRNNKLIV-SEREIL----ATNVKELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLI 233
Cdd:PRK00087  438 EVKIIEFNRKRRKKVVlSRKAILeeekEKKKEETWNSLEEGDVVEGEVKRLTDFGAF---VDIGGVDGLLHVSEISWGRV 514

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 234 ENPKEVMKLNEPVKVKIIDI-RE-GRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSE 311
Cdd:PRK00087  515 EKPSDVLKVGDEIKVYILDIdKEnKKLSLSLKKLLPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQ 594

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 1088030732 312 F--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:PRK00087  595 IswKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKE 633
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1-347 2.66e-65

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 211.27  E-value: 2.66e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELPGNRLREGDVTDVALLKKTSREAFFDL-GKFGTGLVYGAEFLNAKDM-LRD-LAVGAHLPAKVIDLDGERGYTE 77
Cdd:PRK06676    5 FEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEdINDvVKVGDELEVYVLKVEDGEGNLL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  78 LSLAEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNeHYskltegdrqksIDELKKFVGEE 157
Cdd:PRK06676   85 LSKRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLIST-RF-----------VEDFSDFKGKT 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 158 VSVKVINVNPRNNKLIVSEREIL----ATNVKELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLI 233
Cdd:PRK06676  153 LEVKIIELDPEKNRVILSRRAVVeeerAAKKEELLSSLKEGDVVEGTVARLTDFGAF---VDIGGVDGLVHISELSHERV 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 234 ENPKEVMKLNEPVKVKI--IDIREGRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSE 311
Cdd:PRK06676  230 EKPSEVVSVGQEVEVKVlsIDWETERISLSLKDTLPGPWEGVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQ 309

                         330       340       350
                  ....*....|....*....|....*....|....*...
gi 1088030732 312 FGS--VEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:PRK06676  310 ISHkhIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1-347 4.44e-60

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 202.32  E-value: 4.44e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELPGNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLrDLAVGAHLPAKVIDLDGERGYTELSL 80
Cdd:PRK06299   18 LFEESLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQGEL-EVKVGDEVEVYVERIEDGFGETVLSR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  81 AEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSV 160
Cdd:PRK06299   97 EKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDV------------RPVRDTDPLEGKELEF 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREIL-ATNV---KELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENP 236
Cdd:PRK06299  165 KVIKLDKKRNNIVVSRRAVLeEERAeerEELLENLEEGQVVEGVVKNITDYGAF---VDLGGVDGLLHITDISWKRVNHP 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 237 KEVMKLNEPVKVKIIDI-RE-GRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFG- 313
Cdd:PRK06299  242 SEVVNVGDEVKVKVLKFdKEkKRVSLGLKQLGEDPWEAIEKKYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSw 321

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 1088030732 314 --SVEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:PRK06299  322 tkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1-348 1.59e-54

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: 186.48  E-value: 1.59e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   1 MLKQELPGNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLRdlaVGAHLPAKVIDLDGERGYTELSL 80
Cdd:TIGR00717   6 LLEESLKTEETRPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQ---VGDEVEVYLDRVEDRFGETVLSR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  81 AEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSV 160
Cdd:TIGR00717  83 EKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDV------------KPIKDLDSLIGKTLKF 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREILATNVK----ELLSRYEVGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENP 236
Cdd:TIGR00717 151 KIIKLDQKRNNIVVSRRAYLEEERSqareELLENLKEGDVVKGVVKNITDFGAF---VDLGGVDGLLHITDMSWKRVKHP 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 237 KEVMKLNEPVKVKII--DIREGRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEF-- 312
Cdd:TIGR00717 228 SEYVKVGQEVKVKVIkfDKEKGRISLSLKQLGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMsw 307

                         330       340       350
                  ....*....|....*....|....*....|....*..
gi 1088030732 313 -GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:TIGR00717 308 vKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQ 344
rpsA PRK13806
30S ribosomal protein S1; Provisional
 8-347 1.39e-42

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 154.11  E-value: 1.39e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   8 GNRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAKDMLrDLAVGAHLPAKVIDLDGerGYTELSLAEAGKQR 87
Cdd:PRK13806   29 KTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDRAELLDADGEL-TVAVGDEVELYVVSVNG--QEIRLSKALSGQGG 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  88 LwQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSnehyskltegdrQKSIDELKKFVGEEVSVKVINVNP 167
Cdd:PRK13806  106 A-AMLEEAYENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQID------------LRYVEDPESYVGQTFQFLITRVEE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 168 RNNKLIVSEREILATNVKELLSRY----EVGQVVDGLVSGLADFGIFIRFVdnPQIEGLVHISEIDHRLIENPKEVMKLN 243
Cdd:PRK13806  173 NGRNIVVSRRALLEREQKEALEAFmetvKEGDVVEGTVTRLAPFGAFVELA--PGVEGMVHISELSWSRVQKADEAVSVG 250

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 244 EPVKVKIIDIREG------RVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFG---S 314
Cdd:PRK13806  251 DTVRVKVLGIERAkkgkglRISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwtrR 330

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1088030732 315 VEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:PRK13806  331 VNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 56-348 3.59e-41

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 150.19  E-value: 3.59e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  56 LAVGAHLPAKVIDLDGERGYTELSLAEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLtgnILD--LKAFLPLSqlsne 133
Cdd:PRK07899   80 VEVGDEVEALVLQKEDKEGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGL---ILDigLRGFLPAS----- 151

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 134 hyskLTEGDRqksIDELKKFVGEEVSVKVINVNPRNNKLIVSEREILATNVKE----LLSRYEVGQVVDGLVSGLADFGI 209
Cdd:PRK07899  152 ----LVEMRR---VRDLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQSEvrseFLNQLQKGQVRKGVVSSIVNFGA 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 210 FirfVDNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDI---REgRVFLSLKALKPNPWENIEEKYKAAQDVSGK 286
Cdd:PRK07899  225 F---VDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVdmdRE-RVSLSLKATQEDPWQQFARTHAIGQIVPGK 300

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 287 VYKFNPFGATIDLEGGFQGMIHVSEFG--SVEEMKQQLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:PRK07899  301 VTKLVPFGAFVRVEEGIEGLVHISELAerHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 56-347 5.59e-37

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 139.91  E-value: 5.59e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  56 LAVGAHLPAKVIDLDGERGYTELSLaeagKQRL---WQQVQELADNGEIIKMKVLgsnsggltgNILDLKAFLPL----- 127
Cdd:PRK06299  245 VNVGDEVKVKVLKFDKEKKRVSLGL----KQLGedpWEAIEKKYPVGSKVKGKVT---------NITDYGAFVELeegie 311

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 128 -----SQLS----NEHYSKLTEgdrqksidelkkfVGEEVSVKVINVNPRNNKLIVSEREILATNVKELLSRYEVGQVVD 198
Cdd:PRK06299  312 glvhvSEMSwtkkNKHPSKVVS-------------VGQEVEVMVLEIDEEKRRISLGLKQCKENPWEEFAEKYPVGDVVE 378

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 199 GLVSGLADFGIFIRFVDNpqIEGLVHISEIDH-RLIENPKEVMKLNEPVKVKI--IDIREGRVFLSLKALKPNPWENIEE 275
Cdd:PRK06299  379 GKVKNITDFGAFVGLEGG--IDGLVHLSDISWdKKGEEAVELYKKGDEVEAVVlkVDVEKERISLGIKQLEEDPFEEFAK 456

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 276 KYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:PRK06299  457 KHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELsrDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 9-347 1.04e-30

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: 121.76  E-value: 1.04e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   9 NRLREGDVTDVALLKKTSREAFFDLGKFgTGLVYGAEF-----LNAKDMLRdlaVGAHLPAKVIDLDGERGYTELSLAEA 83
Cdd:TIGR00717 183 ENLKEGDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMswkrvKHPSEYVK---VGQEVKVKVIKFDKEKGRISLSLKQL 258

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  84 GkQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILD-LKAFLPLSQLS----NEHYSKLTEgdrqksidelkkfVGEEV 158
Cdd:TIGR00717 259 G-EDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEgIEGLVHVSEMSwvkkNSHPSKVVK-------------KGDEV 324

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 159 SVKVINVNPRNNKLIVSEREILATNVKELLSRYEVGQVVDGLVSGLADFGIFIRFVDNpqIEGLVHISEI----DHRLIE 234
Cdd:TIGR00717 325 EVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGG--IDGLIHLSDIswdkDGREAD 402

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 235 NPKEVMKLNEpVKVKIIDIREGRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEF-- 312
Cdd:TIGR00717 403 HLYKKGDEIE-AVVLAVDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELse 481

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 1088030732 313 GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:TIGR00717 482 NRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 72-269 1.49e-28

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 112.59  E-value: 1.49e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  72 ERGYTELSLAEAGKQRLWQQVQELADNGEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrQKSIDELk 151
Cdd:PRK07400   92 EDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHIST-----------RKPKEEL- 159

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 152 kfVGEEVSVKVINVNPRNNKLIVSEREILatnVKELLSRYEVGQVVDGLVSGLADFGIFIrfvDNPQIEGLVHISEIDHR 231
Cdd:PRK07400  160 --VGEELPLKFLEVDEERNRLVLSHRRAL---VERKMNRLEVGEVVVGTVRGIKPYGAFI---DIGGVSGLLHISEISHE 231

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 1088030732 232 LIENPKEVMKLNEPVKVKIIDI--REGRVFLSLKALKPNP 269
Cdd:PRK07400  232 HIETPHSVFNVNDEMKVMIIDLdaERGRISLSTKQLEPEP 271
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 116-348 1.42e-22

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 99.02  E-value: 1.42e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 116 GNILDLKAFLPLSqlsneHYSKLTEGDRQKSIDELKKfvGEEVSVKVINVNPRNNKLIVSEREILATNVKELLSRYEVGQ 195
Cdd:PRK12269  508 GAFIDLGGFDGLL-----HVNDMSWGHVARPREFVKK--GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFGVND 580

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 196 VVDGLVSGLADFGIFIRFVDNpqIEGLVHISEIDH-RLIENPKEVMKLNEPVKVKII--DIREGRVFLSLKALKPNPWEN 272
Cdd:PRK12269  581 VVKGRVTKIADFGAFIELAEG--IEGLAHISEFSWvKKTSKPSDMVKIGDEVECMILgyDIQAGRVSLGLKQVTANPWEE 658

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088030732 273 IEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFGSVEEMK---QQLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:PRK12269  659 IEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRpadHELEVGKEIECMVIECDPQARRIRLGVKQ 737
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 121-348 2.44e-21

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 95.16  E-value: 2.44e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 121 LKAFLPLSQlsnehySKLTEGDRQKSIDEL-KKFVGEEVSVKviNVNPRNNKLIVSEREILATNVK----ELLSRYEVGQ 195
Cdd:PRK12269  424 MMAFLPISQ------SDCQKVDAPESLIGLtSKFYIERISQS--KQHRGNDNIVINRRRYLEERARqareEFFNSVHIED 495

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 196 VVDGLVSGLADFGIFIrfvDNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKII--DIREGRVFLSLKALKPNPWENI 273
Cdd:PRK12269  496 SVSGVVKSFTSFGAFI---DLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIrlDQAEKRINLSLKHFQPDPWLEF 572

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088030732 274 EEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFGSVEEMKQ---QLTVGETYAFTIESIKLEEKRIALKLKK 348
Cdd:PRK12269  573 ENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKpsdMVKIGDEVECMILGYDIQAGRVSLGLKQ 650
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 191-277 2.70e-19

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: 82.09  E-value: 2.70e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 191 YEVGQVVDGLVSGLADFGIFIRFVDNPQieGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSLKALKPN 268
Cdd:NF040579    1 YKIGDIVEGKVTGIQPYGAFVALDEHTQ--GLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEytGKISLSLRALEEA 78

                          90
                  ....*....|....*....
gi 1088030732 269 P----------WENIEEKY 277
Cdd:NF040579   79 PekhrkrrkhrWTNKRLKI 97
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 191-269 1.05e-18

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 80.99  E-value: 1.05e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 191 YEVGQVVDGLVSGLADFGIFIRFVDNPQieGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE-GRVFLSLKALKPNP 269
Cdd:COG1098     3 IEVGDIVEGKVTGITPFGAFVELPEGTT--GLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEdGKISLSIKQAEEKP 80
PRK08059 PRK08059
general stress protein 13; Validated
 187-271 1.18e-16

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 75.08  E-value: 1.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 187 LLSRYEVGQVVDGLVSGLADFGIFIRFVDNPQieGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSLKA 264
Cdd:PRK08059    1 MMSQYEVGSVVTGKVTGIQPYGAFVALDEETQ--GLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEekGKISLSIRA 78


                  ....*..
gi 1088030732 265 LKPNPWE 271
Cdd:PRK08059   79 TEEAPEA 85
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 184-265 2.37e-16

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 80.09  E-value: 2.37e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 184 VKELLSRYEVGQVVDGLVSGLADFGIFIRFVdnPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDI-REGRVFLSL 262
Cdd:PRK11824  612 IEGITAEPEVGEIYEGKVVRIVDFGAFVEIL--PGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIdKRGRIRLSR 689


                  ...
gi 1088030732 263 KAL 265
Cdd:PRK11824  690 KAV 692
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 194-263 1.10e-15

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: 71.12  E-value: 1.10e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFVDNPQI-EGLVHISEIDH-RLIENPKEVMKLNEPVKVKIIDIREGRVFLSLK 263
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKGRkEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVISIQNGKISLSMK 72
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 99-177 8.99e-15

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: 68.25  E-value: 8.99e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088030732  99 GEIIKMKVLGSNSGGLTGNILDLKAFLPLSQLSNehyskltegdrqKSIDELKKFVGEEVSVKVINVNPRNNKLIVSER 177
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDL------------RPVEDLDEYVGKELKFKIIEIDRERNNIVLSRR 67
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 194-263 1.21e-14

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: 68.08  E-value: 1.21e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDI-REGRVFLSLK 263
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVEL--GGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIdARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
192-263 3.18e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 64.16  E-value: 3.18e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732  192 EVGQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSLK 263
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDL--GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEekGRIILSLK 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 193-263 1.60e-12

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: 61.88  E-value: 1.60e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088030732 193 VGQVVDGLVSGLADFGIFirfVDNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIREGRVFLSLK 263
Cdd:cd05688     1 EGDVVEGTVKSITDFGAF---VDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 194-261 1.93e-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: 61.79  E-value: 1.93e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFVdnPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE-GRVFLS 261
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEIL--PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDrGRISLS 67
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 25-347 1.39e-11

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 65.89  E-value: 1.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  25 TSREAFFDLGKFgTGLVYGAEF-----LNAKDMLRDlavGAHLPAKVIDLDGERGYTELSLAEAgKQRLWQQVQELADNG 99
Cdd:PRK12269  505 TSFGAFIDLGGF-DGLLHVNDMswghvARPREFVKK---GQTIELKVIRLDQAEKRINLSLKHF-QPDPWLEFENKFGVN 579

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 100 EIIKMKVLgsnsggltgNILDLKAFLPLSQLSN--EHYSKLTEGDRQKSIDELKKfVGEEVSVKVINVNPRNNKLIVSER 177
Cdd:PRK12269  580 DVVKGRVT---------KIADFGAFIELAEGIEglAHISEFSWVKKTSKPSDMVK-IGDEVECMILGYDIQAGRVSLGLK 649

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 178 EILATNVKELLSRYEVGQVVDGLVSGLADFGIFIRFVDNpqIEGLVHISEIDHRLIENPKE-VMKLNEPVKVKII--DIR 254
Cdd:PRK12269  650 QVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEG--IDGFLHVDDLSWVKRTRPADhELEVGKEIECMVIecDPQ 727

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 255 EGRVFLSLKALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMI---HVSEF--GSVEEMKQQLTVGETYA 329
Cdd:PRK12269  728 ARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVrkqHLVENrdGDPGEALRKYAVGDRVK 807

                         330
                  ....*....|....*...
gi 1088030732 330 FTIESIKLEEKRIALKLK 347
Cdd:PRK12269  808 AVIVDMNVKDRKVAFSVR 825
PRK05807 PRK05807
RNA-binding protein S1;
192-290 2.42e-11

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 60.53  E-value: 2.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIrfvdnpQIEG---LVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE-GRVFLSLK-ALK 266
Cdd:PRK05807    4 KAGSILEGTVVNITNFGAFV------EVEGktgLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDnGKISLSIKqAMK 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1088030732 267 PNP--------WENiEEKYKAAQDVSGKVYKF 290
Cdd:PRK05807   78 QKKsvkpaeidWQK-EKNKNNNGNFEDRLSKF 108
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 191-262 5.20e-11

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


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 57.68  E-value: 5.20e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 191 YEVGQVVDGLVSGLADFGIFIRfVDNPqIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSL 262
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVD-LGNG-VEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKdrRRIILSI 72
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 193-262 2.84e-10

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: 56.25  E-value: 2.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 193 VGQVVDGLVSGLADFGIFIRfVDNPQIEGLVHIS----------EIDHRLI-ENPKEVMKLNEPVKVKII--DIREGRVF 259
Cdd:cd04471     1 VGEEFDGVISGVTSFGLFVE-LDNLTVEGLVHVStlgddyyefdEENHALVgERTGKVFRLGDKVKVRVVrvDLDRRKID 79


                  ...
gi 1088030732 260 LSL 262
Cdd:cd04471    80 FEL 82
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
179-269 4.05e-10

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 61.19  E-value: 4.05e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 179 ILATNVKEL--LsryEVGQVVDGLVSGLADFGIFirfVDnpqI----EGLVHISEIDHRLIENPKEVMKLNEPVKVKI-- 250
Cdd:COG2183   628 TFREGVLKIedL---KPGMILEGTVTNVTDFGAF---VD---IgvhqDGLVHISQLSDRFVKDPREVVKVGDIVKVKVle 698

                          90
                  ....*....|....*....
gi 1088030732 251 IDIREGRVFLSLKALKPNP 269
Cdd:COG2183   699 VDLKRKRISLSMKLDDEAG 717
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 194-263 6.07e-10

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: 54.55  E-value: 6.07e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088030732 194 GQVVDGLVSGLADFGIFIRF-VDNpqiEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIREGRVFLSLK 263
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIgVKQ---DGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
VacB COG0557
Exoribonuclease R [Transcription];
175-258 6.52e-10

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 60.51  E-value: 6.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 175 SEREILATNV-KELLSRYE-------VGQVVDGLVSGLADFGIFIRfVDNPQIEGLVHISEID----------HRLI-EN 235
Cdd:COG0557   596 SETERRADEAeRDVVDLKKaeymkdrVGEEFEGVISGVTSFGLFVE-LDELGVEGLVHVSSLGddyyeyderrQALVgER 674

                          90       100
                  ....*....|....*....|....*
gi 1088030732 236 PKEVMKLNEPVKVKII--DIREGRV 258
Cdd:COG0557   675 TGKRYRLGDRVEVRVVrvDLDRRQI 699
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 192-264 1.84e-09

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: 53.49  E-value: 1.84e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRfVDNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKI--IDIREGRVFLSLKA 264
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFID-IDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVlkIDAEKKRISLGLKA 74
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 197-262 2.48e-08

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: 50.07  E-value: 2.48e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1088030732 197 VDGLVSGLADFGIFIRFVDNpqIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIREGRVFLSL 262
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDG--VEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
283-347 4.18e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.52  E-value: 4.18e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088030732  283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:smart00316   6 VEGTVTEITPGGAFVDLGNGVEGLIPISELsdKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK08582 PRK08582
RNA-binding protein S1;
192-269 4.78e-08

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 51.19  E-value: 4.78e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRFVDNPQieGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDI-REGRVFLSLKALKPNP 269
Cdd:PRK08582    4 EVGSKLQGKVTGITNFGAFVELPEGKT--GLVHISEVADNYVKDINDHLKVGDEVEVKVLNVeDDGKIGLSIKKAKDRP 80
PRK08059 PRK08059
general stress protein 13; Validated
 275-347 5.04e-08

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 50.82  E-value: 5.04e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088030732 275 EKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:PRK08059    3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEIthGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 9-263 8.03e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 53.95  E-value: 8.03e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   9 NRLREGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNAK------DMLRdlaVGAHLPAKVIDLDGERGYTELSLAE 82
Cdd:PRK12269  574 NKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKktskpsDMVK---IGDEVECMILGYDIQAGRVSLGLKQ 650

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  83 AGKQRlWQQVQELADNGEIIKMKVLG-SNSGGLTGNILDLKAFLplsqlsneHYSKLTEGDRQKSID-ELKkfVGEEVSV 160
Cdd:PRK12269  651 VTANP-WEEIEARYPVGARFTRRIVKvTNAGAFIEMEEGIDGFL--------HVDDLSWVKRTRPADhELE--VGKEIEC 719

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 161 KVINVNPRNNKLIVSEREILATNVKELLSRYEVGQVVDGLVSGLADFGIFIRFVDNpqIEGLVHISEIDHRLIENPKEVM 240
Cdd:PRK12269  720 MVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGG--VEGLVRKQHLVENRDGDPGEAL 797

                         250       260
                  ....*....|....*....|....*...
gi 1088030732 241 K---LNEPVKVKIID--IREGRVFLSLK 263
Cdd:PRK12269  798 RkyaVGDRVKAVIVDmnVKDRKVAFSVR 825
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 192-263 1.11e-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: 48.73  E-value: 1.11e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRFVDNPQIEGLVHISEIDHRLIENPKEVMKL--NEPVKVKIIDIREGRVFLSLK 263
Cdd:cd04452     2 EEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVgrKEVVKVIRVDKEKGYIDLSKK 75
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 191-262 1.33e-07

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: 48.34  E-value: 1.33e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 191 YEVGQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEID--HRLIeNPKEVMKLNEPVKVKIIDIREGRVFLSL 262
Cdd:cd05689     1 YPEGTRLFGKVTNLTDYGCFVEL--EEGVEGLVHVSEMDwtNKNI-HPSKVVSLGDEVEVMVLDIDEERRRISL 71
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 176-341 1.11e-06

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 49.66  E-value: 1.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 176 EREILATNVKELLSRYEVGQVVDGLVSGLADFGIfirFVD-NPQIEGLVHISEIDHrliENPKEVMKLNEPVKVKIIDI- 253
Cdd:COG0539     1 MSESFAELLEESLKELKEGDIVKGTVVSIDDDEV---LVDiGYKSEGIIPLSEFSD---EPGELEVKVGDEVEVYVEKVe 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 254 -REGRVFLSL-KALKPNPWENIEEKYKAAQDVSGKVYKFNPFGATIDLeGGFQGMIHVS--EFGSVEEMKQqlTVGETYA 329
Cdd:COG0539    75 dGEGEIVLSKkKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDI-GGVRAFLPASqvDVRPVRDLDE--YVGKTLE 151

                         170
                  ....*....|..
gi 1088030732 330 FTIesIKLEEKR 341
Cdd:COG0539   152 FKI--IKLDRKR 161
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
193-278 3.51e-06

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 45.46  E-value: 3.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 193 VGQVVDGLVSGLADFGIFIRFVDNpqIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GRVFLSLKALKpnpw 270
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENG--TTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEytGKASLSLRTLE---- 76


                  ....*...
gi 1088030732 271 eniEEKYK 278
Cdd:PRK07252   77 ---EEKQH 81
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 281-345 4.68e-06

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 43.77  E-value: 4.68e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088030732 281 QDVSGKVYKFNPFGATIDLeGGFQGMIHVSE--FGSVEEMKQQLTVGETYAFTIESIKLEEKRIALK 345
Cdd:cd05688     3 DVVEGTVKSITDFGAFVDL-GGVDGLLHISDmsWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 275-348 4.70e-06

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.56  E-value: 4.70e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1088030732 275 EKYKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKlEEKRIALKLKK 348
Cdd:COG1098     1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIadGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIKQ 75
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 201-269 5.90e-06

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 47.97  E-value: 5.90e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 201 VSGLADFGIFIRFVdnPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE-GRVFLSLKALKPNP 269
Cdd:PLN00207  762 IKSIAPYGAFVEIA--PGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDkGQLRLSRRALLPEA 829
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 192-263 8.16e-06

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: 43.24  E-value: 8.16e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRFVDNPQiEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE-GRVFLSLK 263
Cdd:cd05686     2 ALYQIFKGEVASVTEYGAFVKIPGCRK-QGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMkDKMKLSLS 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
9-179 8.24e-06

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 47.63  E-value: 8.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   9 NRLREGDVTDVALLKKTSREAFFDLGKFgTGLVYGAEF-----LNAKDMLRdlaVGAHLPAKVIDLDGERGYTELSLaea 83
Cdd:PRK00087  473 NSLEEGDVVEGEVKRLTDFGAFVDIGGV-DGLLHVSEIswgrvEKPSDVLK---VGDEIKVYILDIDKENKKLSLSL--- 545

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  84 gKQRL---WQQVQELADNGEIIKMKVLGSNSGGLTGNILD-LKAFLPLSQLSNEHYSKLTegdrqksiDELKkfVGEEVS 159
Cdd:PRK00087  546 -KKLLpdpWENVEEKYPVGSIVLGKVVRIAPFGAFVELEPgVDGLVHISQISWKRIDKPE--------DVLS--EGEEVK 614

                         170       180
                  ....*....|....*....|
gi 1088030732 160 VKVINVNPRNNKLIVSEREI 179
Cdd:PRK00087  615 AKILEVDPEEKRIRLSIKEV 634
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 194-262 8.51e-06

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: 43.25  E-value: 8.51e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEID-HRLIENPKEVMKLNEPVKVKIIDIREGRVFLSL 262
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGL--DGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 283-347 1.64e-05

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 42.27  E-value: 1.64e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088030732 283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEFGS--VEEMKQQLTVGETYAFTIESIKlEEKRIALKLK 347
Cdd:cd05692     4 VEGTVTRLKPFGAFVELGGGISGLVHISQIAHkrVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 48-191 3.45e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.54  E-value: 3.45e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732  48 NAKDMLRDLAVGAHLPAKVIDLDGERgyTELSLaeaGKQRL----WQQVQELADNGEIIKMKVLGSNSGGLTGNI-LDLK 122
Cdd:PRK06299  411 KGEEAVELYKKGDEVEAVVLKVDVEK--ERISL---GIKQLeedpFEEFAKKHKKGSIVTGTVTEVKDKGAFVELeDGVE 485

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088030732 123 AFLPLSQLSNEHYSKLTEgdrqksidELKkfVGEEVSVKVINVNPRNNKLIVSEREILATNVKELLSRY 191
Cdd:PRK06299  486 GLIRASELSRDRVEDATE--------VLK--VGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAIAEY 544
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
99-177 4.59e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.05  E-value: 4.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732   99 GEIIKMKVLGSNSGGLTGNILD-LKAFLPLSQLSNEHYSKLTEgdrqksidELKkfVGEEVSVKVINVNPRNNKLIVSER 177
Cdd:smart00316   3 GDVVEGTVTEITPGGAFVDLGNgVEGLIPISELSDKRVKDPEE--------VLK--VGDEVKVKVLSVDEEKGRIILSLK 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 ...
 120-175 5.20e-05

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: 40.67  E-value: 5.20e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1088030732 120 DLKAFLPLSQLSNEHYSKLTEGDRqksidelkkfVGEEVSVKVINVNPRNNKLIVS 175
Cdd:cd05698    23 NVKGFLPKSELSEAFIKDPEEHFR----------VGQVVKVKVLSCDPEQQRLLLS 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 283-344 5.27e-05

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: 40.73  E-value: 5.27e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEFGS--VEEMKQQLTVGETYAFTIESIKLEEKRIAL 344
Cdd:pfam00575   7 VEGEVTRVTKGGAFVDLGNGVEGFIPISELSDdhVEDPDEVIKVGDEVKVKVLKVDKDRRRIIL 70
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 180-262 6.96e-05

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: 41.03  E-value: 6.96e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 180 LATNVKELlsryEVGQVVDGLVSGLADFGIFIRFVDNpqIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIRE--GR 257
Cdd:cd04461     5 LPTNFSDL----KPGMVVHGYVRNITPYGVFVEFLGG--LTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEekQR 78


                  ....*
gi 1088030732 258 VFLSL 262
Cdd:cd04461    79 FLLSL 83
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 192-263 1.02e-04

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 43.27  E-value: 1.02e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRFVDNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDI--REGRVFLSLK 263
Cdd:PRK03987    7 EEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVdpRKGHIDLSLK 80
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 192-257 1.47e-04

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: 39.90  E-value: 1.47e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEIDHRLIEnpkevmklNEPVKVKIIDIREGR 257
Cdd:cd04473    15 EVGKLYKGKVNGVAKYGVFVDL--NDHVRGLIHRSNLLRDYEV--------GDEVIVQVTDIPENG 70
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 194-256 1.60e-04

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: 39.59  E-value: 1.60e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFvdNPQIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIREG 256
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTL--GRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPD 61
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 199-263 3.23e-04

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 38.75  E-value: 3.23e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088030732 199 GLVSGLADFGIFIRFVDNpqIEGLVHISEIDHRLIENPKEVMKLNEPVKVKIIDIREG--RVFLSLK 263
Cdd:cd05698     6 GTIVKVKPNGCIVSFYNN--VKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEqqRLLLSCK 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 194-262 3.80e-04

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 38.37  E-value: 3.80e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFVDNpqIEGLV---HISEIdhrLIENPKEVMKLNEPVKVKII--DIREGRVFLSL 262
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDH--IKGLVppmHLADV---RLKHPEKKFKPGLKVKCRVLsvEPERKRLVLTL 69
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 283-344 3.89e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 38.13  E-value: 3.89e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088030732 283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKRIAL 344
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELsdKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 99-175 6.14e-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: 38.04  E-value: 6.14e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088030732  99 GEIIKMKVLGSNSGGLTGNI-LDLKAFLPLSQLSNEHYskltegdrQKSIDELKkfVGEEVSVKVINVNPRNNKLIVS 175
Cdd:pfam00575   4 GDVVEGEVTRVTKGGAFVDLgNGVEGFIPISELSDDHV--------EDPDEVIK--VGDEVKVKVLKVDKDRRRIILS 71
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 283-344 8.85e-04

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: 37.47  E-value: 8.85e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088030732 283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEFG---SVEEMKQQLTVGETYAFTIESIKLEEKRIAL 344
Cdd:cd05690     4 VSGKIKSITDFGIFVGLDGGIDGLVHISDISwtqRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 278-347 1.09e-03

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


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 37.31  E-value: 1.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1088030732 278 KAAQDVSGKVYKFNPFGATIDLEG-GFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALKLK 347
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIDGtNVSGLCHKSEIsdNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
PRK11642 PRK11642
ribonuclease R;
192-250 1.14e-03

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 40.88  E-value: 1.14e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRfVDNPQIEGLVHISEIDH----------RLI-ENPKEVMKLNEPVKVKI 250
Cdd:PRK11642  642 QVGNVFKGVISSVTGFGFFVR-LDDLFIDGLVHVSSLDNdyyrfdqvgqRLIgESSGQTYRLGDRVEVRV 710
PRK08582 PRK08582
RNA-binding protein S1;
283-348 2.45e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 37.70  E-value: 2.45e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088030732 283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKrIALKLKK 348
Cdd:PRK08582    9 LQGKVTGITNFGAFVELPEGKTGLVHISEVadNYVKDINDHLKVGDEVEVKVLNVEDDGK-IGLSIKK 75
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 194-262 2.60e-03

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: 36.03  E-value: 2.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088030732 194 GQVVDGLVSGLADFGIFIRFVDNpqIEGLVHISEI--DHRLIENPKEVMKLNEPVKVKIIDIREGRVFLSL 262
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADN--VHGRIHVSEVfdEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFL 69
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
285-327 3.46e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 36.99  E-value: 3.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1088030732 285 GKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGET 327
Cdd:PRK07252    9 GTITGIKPYGAFVALENGTTGLIHISEIktGFIDNIHQLLKVGEE 53
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 277-344 4.77e-03

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: 35.25  E-value: 4.77e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088030732 277 YKAAQDVSGKVYKFNPFGATIDLEGGFQGMIHVSEFGSVEEM---KQQLTVGETYAFTIESIKLEEKRIAL 344
Cdd:cd05689     1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNihpSKVVSLGDEVEVMVLDIDEERRRISL 71
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 283-345 5.63e-03

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


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 34.90  E-value: 5.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088030732 283 VSGKVYKFNPFGATIDLEGGFQGMIHVSEF--GSVEEMKQQLTVGETYAFTIESIKLEEKRIALK 345
Cdd:cd05685     4 LEGVVTNVTDFGAFVDIGVKQDGLIHISKMadRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 192-263 6.10e-03

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 37.11  E-value: 6.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088030732 192 EVGQVVDGLVSGLADFGIFIRFvdNPqIEGLVHISEID----------HRLI-ENPKEVMKLNEPVKVKII-------DI 253
Cdd:PRK08563   80 ELQEVVEGEVVEVVEFGAFVRI--GP-VDGLLHISQIMddyisydpknGRLIgKESKRVLKVGDVVRARIVavslkerRP 156

                          90
                  ....*....|
gi 1088030732 254 REGRVFLSLK 263
Cdd:PRK08563  157 RGSKIGLTMR 166
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
12-80 6.42e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 34.89  E-value: 6.42e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088030732   12 REGDVTDVALLKKTSREAFFDLGKFGTGLVYGAEFLNA--KDMLRDLAVGAHLPAKVIDLDGERGYTELSL 80
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKrvKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
 
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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