|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
1-711 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 918.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 1 MKESIINYLKEHGKSSVN--DIAQALNHAGGEKFPQLIKAISAMESKGQLRFNRDGSVSLrPKKENpnqvTVEGVFRANK 78
Cdd:COG0557 4 SRETILAFLKEDAYKPLSkkELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRL-PEKLD----LVEGRVRGHR 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 79 NGFGFLHVDDSEDDMFIGRNDVGHAIDGDTVAVVIKKPADRLRgtaAETRVVEIVERSLKTVVGKFilsdEKEPYAGYIK 158
Cdd:COG0557 79 DGFGFVIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGR---PEGRVVEILERANTRVVGRF----EKEKGFGFVV 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 159 SKNQKIQQPIYIKKEPV--ALDGtEIIKVDIEKYPNRHyDYFVGSVRDIIGHQGDAGIDVLEVLESMDIVSEFPEDVMAE 236
Cdd:COG0557 152 PDDKRLLQDIFIPPDDLngAKDG-DLVVVEITRYPERR-GPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAE 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 237 AEAVPDAPSQEDLLGRVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIADVSYYVTEGSALNREAVARGTSVY 316
Cdd:COG0557 230 AEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVY 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 317 VTDRVVPMLPERLSNGICSLNPNVDRLTQSAIMEITPKGKVVNHKICQSVINTTFRMTYSDVNEMLAGNP-EKIEQFKPI 395
Cdd:COG0557 310 LPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDeELREEYADL 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 396 MDSVSAMAELHKILEDMRERRGALNFDTSEARILVNEKGMPVDIVVRERGTAERMIESFMLAANECVAEHFAKAKLPFIY 475
Cdd:COG0557 390 VPMLEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLY 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 476 RIHEEPKAEKLQRFMDYASIFGVQIKGTaNKMDQLDLQEFMARVQGKPGAEVMNMMLLRSMQQARYSEHNHGHYGLAAQY 555
Cdd:COG0557 470 RVHEEPDPEKLEALREFLANLGLKLKGG-DEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEA 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 556 YTHFTSPIRRYPDLLVHRMIREY-TNNMSQETREHFEEVIPELATSSSTLERRAIDAERVVEAMKKAEYMEEFVGQEFDG 634
Cdd:COG0557 549 YTHFTSPIRRYPDLLVHRALKAYlEGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEG 628
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 739746327 635 IVGSVVKFGMFVELPNT-IEGLVHITTLP-EFYNYNERTMTLQGEKTGKTFRVGQPIRVKLTRADKETGDIDFQYLPSE 711
Cdd:COG0557 629 VISGVTSFGLFVELDELgVEGLVHVSSLGdDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGG 707
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
1-708 |
0e+00 |
|
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA]
Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 823.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 1 MKESIINYLKEH--GKSSVNDIAQALNHAGGEKFPQLIKAISAMESKGQLRFNRDGSVSLrpkkeNPNQVTVEGVFRANK 78
Cdd:TIGR02063 3 LRELILEFLKSKkgKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYAL-----PESLKLVKGTVIAHR 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 79 NGFGFLHV-DDSEDDMFIGRNDVGHAIDGDTVAVVIKKPADRlrGTAAETRVVEIVERSLKTVVGKFilsdEKEPYAGYI 157
Cdd:TIGR02063 78 DGFGFLRPeDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPDG--GDRFEARVIKILERANDQIVGTF----YIENGIGFV 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 158 KSKNQKIQQPIYIKKEPV--ALDGTEIIkVDIEKYPNRhYDYFVGSVRDIIGHQGDAGIDVLEVLESMDIVSEFPEDVMA 235
Cdd:TIGR02063 152 IPDDKRIYLDIFIPPEQIlgAEEGDKVL-VEITKYPDR-NRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLD 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 236 EAEAVPDAPSQEDLLGRVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIADVSYYVTEGSALNREAVARGTSV 315
Cdd:TIGR02063 230 EAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSV 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 316 YVTDRVVPMLPERLSNGICSLNPNVDRLTQSAIMEITPKGKVVNHKICQSVINTTFRMTYSDVNEMLAGNPEKIEQFKPI 395
Cdd:TIGR02063 310 YLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPL 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 396 MDSVSAMAELHKILEDMRERRGALNFDTSEARILVNEKGMPVDIVVRERGTAERMIESFMLAANECVAEHFAKAKLPFIY 475
Cdd:TIGR02063 390 KEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIY 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 476 RIHEEPKAEKLQRFMDYASIFGVQIKG-TANKMDQLDLQEFMARVQGKPGAEVMNMMLLRSMQQARYSEHNHGHYGLAAQ 554
Cdd:TIGR02063 470 RVHERPSEEKLQNLREFLKTLGITLKGgTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALE 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 555 YYTHFTSPIRRYPDLLVHRMIREY----TNNMSQETREHFEEVIPELATSSSTLERRAIDAERVVEAMKKAEYMEEFVGQ 630
Cdd:TIGR02063 550 YYTHFTSPIRRYPDLIVHRLIKKAlfggENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGE 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 631 EFDGIVGSVVKFGMFVELPN-TIEGLVHITTLP-EFYNYNERTMTLQGEKTGKTFRVGQPIRVKLTRADKETGDIDFQYL 708
Cdd:TIGR02063 630 EFEGVISGVTSFGLFVELENnTIEGLVHISTLKdDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
70-705 |
0e+00 |
|
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA]
Pssm-ID: 273033 [Multi-domain] Cd Length: 654 Bit Score: 566.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 70 VEGVFRANKNGFGFLH-VDDSEDDMFIGRNDVGHAIDGDTVAVVikkPADRLRGTAAETRVVEIVERSLKTVVGKFILSD 148
Cdd:TIGR00358 17 VKGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEAC---PLSQPQRGRFEAEVERILEPALTRFVGKFLGEN 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 149 EKepyaGYIKSKNQKIQQPIYIKKEPV---ALDGTEIIkVDIEKYPNRHyDYFVGSVRDIIGHQGDAGIDVLEVLESMDI 225
Cdd:TIGR00358 94 DF----GFVVPDDPRIYLDIIVPKASVkneLAEGDKVV-VELTEYPLRR-NLFYGEITQILGNNDDPLIPWWVTLARHEI 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 226 VSEFPEDVMAEAEAVPDAPSQEDLLGRVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIADVSYYVTEGSALN 305
Cdd:TIGR00358 168 PFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLD 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 306 REAVARGTSVYVTDRVVPMLPERLSNGICSLNPNVDRLTQSAIMEITPKGKVVNHKICQSVINTTFRMTYSDVNEMLAGN 385
Cdd:TIGR00358 248 KEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLEND 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 386 PEKIEQFKPIMDSVSAMAELHKILEDMRERRGALNFDTSEARILVNEKGMPVDIVVRERGTAERMIESFMLAANECVAEH 465
Cdd:TIGR00358 328 DELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAARF 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 466 FAKAKLPFIYRIHEEPKAEKLQRFMDYASIFG-VQIKGTANKMDQLDLQEFMARVQGKPGAEVMNMMLLRSMQQARYSEH 544
Cdd:TIGR00358 408 LHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGlTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYSPE 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 545 NHGHYGLAAQYYTHFTSPIRRYPDLLVHRMIREYTNNMSQET-REHFEEVIPELATSSSTLERRAIDAERVVEAMKKAEY 623
Cdd:TIGR00358 488 PLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTeRYQPQDELLQIAEHCSDTERRARDAERDVADWLKCRY 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 624 MEEFVGQEFDGIVGSVVKFGMFVELP-NTIEGLVHITTLP-EFYNYNERTMTLQGEKTGKTFRVGQPIRVKLTRADKETG 701
Cdd:TIGR00358 568 LLDKVGTEFSGEISSVTRFGMFVRLDdNGIDGLIHISTLHnDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETR 647
|
....
gi 739746327 702 DIDF 705
Cdd:TIGR00358 648 SIIF 651
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
2-807 |
8.18e-141 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 436.10 E-value: 8.18e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 2 KESIINYLKEHGK-SSVNDIAQALNHAGGEKFPQLIKAISAMESKGQLRFNRDGSVSLrPKKENPNQVTVEGvfraNKNG 80
Cdd:PRK11642 21 REFILEHLTKREKpASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYAL-PERLDLLKGTVIG----HRDG 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 81 FGFLHVDDSEDDMFIGRNDVGHAIDGDtvaVVIKKPADRLRGTAAETRVVEIVERSLKTVVGKFILsdekEPYAGYIKSK 160
Cdd:PRK11642 96 YGFLRVEGRKDDLYLSSEQMKTCIHGD---QVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFT----DAGVGFVVPD 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 161 NQKIQQPIYIKKEPV--ALDGTEIIkVDIEKYPNRHYDYfVGSVRDIIGHQGDAGIDVLEVLESMDIVSEFPEDVMAE-- 236
Cdd:PRK11642 169 DSRLSFDILIPPEQImgARMGFVVV-VELTQRPTRRTKA-VGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQva 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 237 --AEAVPDAPSQedllGRVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIADVSYYVTEGSALNREAVARGTS 314
Cdd:PRK11642 247 glKEEVPEEAKA----GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTS 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 315 VYVTDRVVPMLPERLSNGICSLNPNVDRLTQSAIMEITPKGKVVNHKICQSVINTTFRMTYSDVNEMLAGNPEKIEQFKP 394
Cdd:PRK11642 323 VYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAP 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 395 IMDSVSAMAELHKILEDMRERRGALNFDTSEARILVNEKGMPVDIVVRERGTAERMIESFMLAANECVAEHFAKAKLPFI 474
Cdd:PRK11642 403 LVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPAL 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 475 YRIHEEPKAEKLQRFMDYASIFGVQIKGtANKMDQLDLQEFMARVQGKPGAEVMNMMLLRSMQQARYSEHNHGHYGLAAQ 554
Cdd:PRK11642 483 FRIHDKPSTEAITSFRSVLAELGLELPG-GNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQ 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 555 YYTHFTSPIRRYPDLLVHRMIReYTNNMSQETRE----------HFEEVIpELATSSSTLERRAIDAERVVEAMKKAEYM 624
Cdd:PRK11642 562 SYAHFTSPIRRYPDLSLHRAIK-YLLAKEQGHKGnttetggyhySMEEML-QLGQHCSMTERRADEATRDVADWLKCDFM 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 625 EEFVGQEFDGIVGSVVKFGMFVELPNT-IEGLVHITTLP-EFYNYNERTMTLQGEKTGKTFRVGQPIRVKLTRADKETGD 702
Cdd:PRK11642 640 LDQVGNVFKGVISSVTGFGFFVRLDDLfIDGLVHVSSLDnDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERK 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 703 IDFQYLPSEyditekvdHKARQEreekAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRKGSYDEKRKSSKKPDKR 782
Cdd:PRK11642 720 IDFSLISSE--------RAPRNV----GKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKA 787
|
810 820
....*....|....*....|....*
gi 739746327 783 KNQNRPHNDNKGRESGRRKKKGNKP 807
Cdd:PRK11642 788 KKPSAKTQKIAAATKAKRAAKKKVA 812
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
252-578 |
1.71e-137 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 409.75 E-value: 1.71e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 252 RVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIADVSYYVTEGSALNREAVARGTSVYVTDRVVPMLPERLSN 331
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 332 GICSLNPNVDRLTQSAIMEITPKGKVVNHKICQSVINTTFRMTYSDVNEMLAGNPEKIEQfKPIMDSVSAMAELHKILED 411
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 412 MRERRGALNFDTSEARILVNEKGmPVDIVVRERGTAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKLQRFMD 491
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 492 YAsifgvqikgtANKMDQLDLQEFMARVQGKpgAEVMNMMLLRSMQQARYSEHNHGHYGLAAQYYTHFTSPIRRYPDLLV 571
Cdd:pfam00773 239 LL----------QLLPDDKGLSKSLEKIKDD--ERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIV 306
|
....*..
gi 739746327 572 HRMIREY 578
Cdd:pfam00773 307 HRQLKAL 313
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
252-578 |
1.09e-129 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 388.55 E-value: 1.09e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 252 RVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIADVSYYVTEGSALNREAVARGTSVYVTDRVVPMLPERLSN 331
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 332 GICSLNPNVDRLTQSAIMEITPKG-KVVNHKICQSVINTTFRMTYSDVNEMLagnpekieqfkpimdsvsamaelhkile 410
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAIL---------------------------- 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 411 dmrerrgalnfdtseARILVNEKGMPVDIVVRERGTAERMIESFMLAANECVAEHFAKAKLPFIYRIHEEPKAEKL-QRF 489
Cdd:smart00955 133 ---------------EKIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLaELL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 490 MDYASIFGVQIKGTAnkmDQLDLQEFMARVQGKPGAEVMNMMLLRSMQQARYSEHNHGHYGLAAQYYTHFTSPIRRYPDL 569
Cdd:smart00955 198 KEFLALLGLLLLGGD---GPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDL 274
|
....*....
gi 739746327 570 LVHRMIREY 578
Cdd:smart00955 275 IVHRQLKAA 283
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
69-703 |
6.37e-52 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 192.37 E-value: 6.37e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 69 TVEGVFRANKNGFGFLHVDDSEDdMFIGRNDVGHAIDGDTVAVVIKKPADRlrgTAAETRvvEIVERSLKTVVGKfilsd 148
Cdd:COG4776 21 RVEGVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVIRTEKDK---ESAEPE--TLIEPFLTRFVGR----- 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 149 ekepyagyIKSKNQK---------IQQPIyikKEPVALDGTEIIK------VDIEKYPNRHYDYFVGSVRDIIGHQGDAG 213
Cdd:COG4776 90 --------VQKKDGRlfvvpdhplIKDAI---KARPKKGLEEGLKegdwvvAELKRHPLKGDRGFFAEITEFIADADDPF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 214 IDVLEVLESMDIVSEFPEDVmaeaeavPDAPSQEDLLGRVDLRQEVTFTIDGADAKDLDDAVHIKRLPNGNFELGVHIAD 293
Cdd:COG4776 159 APWWVTLARHNLEREAPEGD-------DEWELLDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIAD 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 294 VSYYVTEGSALNREAVARGTSVYVTDRVVPMLPERLSNGICSLNPNVDRLTQSAIMEITPKGKVVN-HKICQSVINTTFR 372
Cdd:COG4776 232 PTAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAK 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 373 MTYSDVNEMLagnpEKIEQFKPIMDSVsamAELHKILEDMRERRG------ALNF-DTSEARILVNEKGMPVDIVVRERG 445
Cdd:COG4776 312 LAYDNVSDWL----EGKGEWQPENEEI---AEQIRLLHQFALARSqwrqqhALVFkDRPDYRFELDEKGNVLDIHAEPRR 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 446 TAERMIESFMLAANECVAEHFAKaKLPF-IYRIH---EEPKAEKLQRFMDYASIfgvqikgTANKMDQLDLQEFMA---R 518
Cdd:COG4776 385 IANRIVEEAMIAANICAARVLRE-HLGFgIFNVHsgfDPEKLEQAVELLAEHGI-------EFDPEQLLTLEGFCAlrrE 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 519 VQGKPGAEVMNmmLLRSMQQ-ARYSEHNHGHYGLAAQYYTHFTSPIRRYPDLLVHRMIREYTNNmsQETREHFEEVIPEL 597
Cdd:COG4776 457 LDAQPTSYLDS--RLRRFQTfAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILG--QPAEKPDEELTERL 532
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 598 AtssstlERRAID--AERVVEAMKKAEYMEEFVG--QEFDGIVGSVVKFGMFVEL---------PntiegLVHITTLPEF 664
Cdd:COG4776 533 A------ERRRLNrmAERDVADWLYARYLKPKVGsgQVFTAEIIDINRGGLRVRLlengavafiP-----ASFIHSVRDE 601
|
650 660 670
....*....|....*....|....*....|....*....
gi 739746327 665 YNYNERTMTLQgEKTGKTFRVGQPIRVKLTRADKETGDI 703
Cdd:COG4776 602 LVCSQEEGTVY-IKGEVRYKLGDTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
70-703 |
1.01e-43 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 168.13 E-value: 1.01e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 70 VEGVFRANKNGFGFLHVDDSEDdMFIGRNDVGHAIDGDTVAVVIKKPADRlrgTAAETRvvEIVERSLKTVVGKfilsde 149
Cdd:PRK05054 22 VEGVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIAVIHTEKDR---EIAEPE--ELIEPFLTRFVGR------ 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 150 kepyagyIKSKNQKIQqpiyikkepvaldgteiIKVDiekYPnrhydyfvgSVRDIIGHQGDAGIDvlEVLESMDIV--- 226
Cdd:PRK05054 90 -------VQKKDDRLS-----------------IVPD---HP---------LLKDAIPCRAAKGLN--HEFKEGDWVvae 131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 227 ----------------SEF---PEDVMA-----------EAEAVPDAPSQEDL---LGRVDLRQEVTFTIDGADAKDLDD 273
Cdd:PRK05054 132 lrrhplkgdrgfyaeiTQFitdADDHFApwwvtlarhnlEREAPAGGVAWEMLdegLEREDLTALDFVTIDSASTEDMDD 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 274 AVHIKRLPNGNFELGVHIADVSYYVTEGSALNREAVARGTSVYVTDRVVPMLPERLSNGICSLNPNVDRLTQSAIMEITP 353
Cdd:PRK05054 212 ALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDA 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 354 KGKVVNH-KICQSVINTTFRMTYSDVNEMLagnpEKIEQFKPIMDsvsAMAELHKILEDMRERRG------ALNF-DTSE 425
Cdd:PRK05054 292 DGTIEDDiRFFAAWIESKAKLAYDNVSDWL----ENGGDWQPESE---AIAEQIRLLHQFCLARSewrkqhALVFkDRPD 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 426 ARILVNEKGMPVDIVVRERGTAERMIESFMLAANECVAeHFAKAKLPF-IYRIH---EEPKAEKLQRFMD-YASIFGVQ- 499
Cdd:PRK05054 365 YRFELGEKGEVLDIVAEPRRIANRIVEESMIAANICAA-RVLRDKLGFgIYNVHsgfDPANAEQAVALLKeHGLHFDAEe 443
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 500 ---IKGTANKMDQLDLQE----------FM--ARVQGKPGAevmnmmllrsmqqarysehnhgHYGLAAQYYTHFTSPIR 564
Cdd:PRK05054 444 lltLEGFCKLRRELDAQPtgyldsrirrFQsfAEISTEPGP----------------------HFGLGLEAYATWTSPIR 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 565 RYPDLLVHRMIREYTNNmsQETREHFEEVIPELAtssstlERRAID--AERVVEAMKKAEYMEEFVGQE--FDGIVGSVV 640
Cdd:PRK05054 502 KYGDMINHRLLKAVIKG--ETAERPQDEITVQLA------ERRRLNrmAERDVGDWLYARYLKDKAGTDtrFAAEIIDIS 573
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 641 KFGMFVELPNT-----IEG-LVH-ITTLPEFyNYNERTMTLQGEktgKTFRVGQPIRVKLTRADKETGDI 703
Cdd:PRK05054 574 RGGMRVRLLENgavafIPAsFLHaVRDELVC-NQENGTVQIKGE---TVYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
628-705 |
2.98e-32 |
|
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: 119.81 E-value: 2.98e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPN-TIEGLVHITTLP-EFYNYNERTMTLQGEKTGKTFRVGQPIRVKLTRADKETGDIDF 705
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGdDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
72-129 |
2.90e-16 |
|
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 73.34 E-value: 2.90e-16
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 739746327 72 GVFRANKNGFGFLHVDDSEDDMFIGRNDVGHAIDGDTVAVVIKKPADRLRGTAAETRV 129
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
156-230 |
4.44e-11 |
|
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.
Pssm-ID: 465546 [Multi-domain] Cd Length: 74 Bit Score: 59.33 E-value: 4.44e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 739746327 156 YIKSKNQKIQQPIYIKKEPV--ALDGtEIIKVDIEKYPNRHYdyFVGSVRDIIGHQGDAGIDVLEVLESMDIVSEFP 230
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLkgAKDG-DKVVVEITEYPDGKN--PEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
628-705 |
7.19e-11 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 58.77 E-value: 7.19e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEFYnynertmtlqGEKTGKTFRVGQPIRVKLTRADKETGDIDF 705
Cdd:smart00316 2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKR----------VKDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
627-705 |
9.88e-10 |
|
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: 55.37 E-value: 9.88e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 739746327 627 FVGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEFYNYNErtmtlqgektGKTFRVGQPIRVKLTRADKETGDIDF 705
Cdd:pfam00575 2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDP----------DEVIKVGDEVKVKVLKVDKDRRRIIL 70
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
616-698 |
8.99e-08 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 55.83 E-value: 8.99e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 616 EAMKKA-EYMEEF-----VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLpefynYNERTmtlqgEKTGKTFRVGQPI 689
Cdd:PRK11824 603 EAAEAAkERIEGItaepeVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEI-----ADERV-----EKVEDVLKEGDEV 672
|
....*....
gi 739746327 690 RVKLTRADK 698
Cdd:PRK11824 673 KVKVLEIDK 681
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
633-694 |
1.81e-07 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 52.14 E-value: 1.81e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 739746327 633 DGIVGSVVKFGMFVEL-PntIEGLVHITTLP-EFYNYNERTMTLQGEKTGKTFRVGQPIRVKLT 694
Cdd:PRK08563 86 EGEVVEVVEFGAFVRIgP--VDGLLHISQIMdDYISYDPKNGRLIGKESKRVLKVGDVVRARIV 147
|
|
| Pnp |
COG1185 |
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
616-698 |
3.79e-07 |
|
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 53.86 E-value: 3.79e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 616 EAMKKAEYM-----EEF-VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPefynyNERTmtlqgEKTGKTFRVGQPI 689
Cdd:COG1185 598 EAAEKAIERiegitAEPeVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELA-----DERV-----EKVEDVLKEGDEV 667
|
....*....
gi 739746327 690 RVKLTRADK 698
Cdd:COG1185 668 KVKVLEIDD 676
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
633-694 |
7.69e-07 |
|
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Pssm-ID: 239907 [Multi-domain] Cd Length: 99 Bit Score: 48.05 E-value: 7.69e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739746327 633 DGIVGSVVKFGMFVELpNTIEGLVHITTL-PEFYNYNERTMTLQGEKTGKTFRVGQPIRVKLT 694
Cdd:cd04460 4 EGEVVEVVDFGAFVRI-GPVDGLLHISQImDDYISYDPKNKRLIGEETKRVLKVGDVVRARIV 65
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
632-703 |
1.05e-06 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 46.60 E-value: 1.05e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 739746327 632 FDGIVGSVVKFGMFVELPNTIEGLVHITTLPEFYNynertmtlqgEKTGKTFRVGQPIRVKLTRADKETGDI 703
Cdd:cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV----------KDPSEVFKVGDEVEVKVLEVDPEKGRI 62
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
629-698 |
1.39e-05 |
|
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: 43.30 E-value: 1.39e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 629 GQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPefynyNERTmtlqgEKTGKTFRVGQPIRVKLTRADK 698
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELS-----DERV-----EKVEDVLKVGDEVKVKVIEVDD 60
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
606-703 |
1.78e-05 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 47.73 E-value: 1.78e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 606 RRAI-DAERvveAMKKAEYMEEF-VGQEFDGIVGSVVKFGMFVELPNtIEGLVHITTL-------PEfynynertmtlqg 676
Cdd:COG0539 168 RRAVlEEER---EEKREELLEKLeEGDVVEGTVKNITDFGAFVDLGG-VDGLLHISEIswgrvkhPS------------- 230
|
90 100
....*....|....*....|....*..
gi 739746327 677 ektgKTFRVGQPIRVKLTRADKETGDI 703
Cdd:COG0539 231 ----EVLKVGDEVEVKVLKIDREKERI 253
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
629-699 |
3.26e-05 |
|
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: 42.48 E-value: 3.26e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739746327 629 GQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLpefynynerTMTLQGEKTGKTFRVGQPIRVKLTRADKE 699
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDI---------SWTQRVRHPSEIYKKGQEVEAVVLNIDVE 62
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
628-749 |
8.60e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 45.93 E-value: 8.60e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLpefynynerTMTLQGEKTGKTFRVGQPIRVKLTRADKETGDID--- 704
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDI---------SWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISlgi 443
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 739746327 705 -------FQYLPSEYD--------ITEKVDHKARQEREEKAKAF-RNRGPRRDRQNGDFER 749
Cdd:PRK06299 444 kqleedpFEEFAKKHKkgsivtgtVTEVKDKGAFVELEDGVEGLiRASELSRDRVEDATEV 504
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
606-703 |
1.06e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 45.93 E-value: 1.06e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 606 RRA-IDAERvveAMKKAEYMEEF-VGQEFDGIVGSVVKFGMFVELpNTIEGLVHITTL-------PEfynynertmtlqg 676
Cdd:PRK06299 180 RRAvLEEER---AEEREELLENLeEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDIswkrvnhPS------------- 242
|
90 100
....*....|....*....|....*..
gi 739746327 677 ektgKTFRVGQPIRVKLTRADKETGDI 703
Cdd:PRK06299 243 ----EVVNVGDEVKVKVLKFDKEKKRV 265
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
628-703 |
1.08e-04 |
|
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: 41.08 E-value: 1.08e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELpNTIEGLVHITTLpefyNYNertmtlQGEKTGKTFRVGQPIRVKLTRADKETGDI 703
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDM----SWG------RVKHPSEVVNVGDEVEVKVLKIDKERKRI 65
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
628-769 |
1.22e-04 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 42.47 E-value: 1.22e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEFY--NYNErtmtlqgektgkTFRVGQPIRVKLTradketgdidf 705
Cdd:COG1098 5 VGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYvkDIND------------YLKVGDEVKVKVL----------- 61
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739746327 706 qylpseyDITEkvDHKA----RQEREEKAKAFR-NRGPRRDRQNGDFERRGKR---------GDNRNRQDGNGRKGSY 769
Cdd:COG1098 62 -------SIDE--DGKIslsiKQAEEKPKRPPRpRRNSRPKAGFESFEDKLSKflkdsderlSDLKKRTESKRGGRGR 130
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
715-800 |
1.34e-04 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 45.67 E-value: 1.34e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 715 TEKVDHKARQEREEKAKAFRNRGPRRDRQNGDfeRRGKRGDNRNRQDGNGRKGSYDEKRKSSKKPDKRKNQNRPHNDNKG 794
Cdd:PRK12678 154 TEARADAAERTEEEERDERRRRGDREDRQAEA--ERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRR 231
|
....*.
gi 739746327 795 RESGRR 800
Cdd:PRK12678 232 RRDRRD 237
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
628-710 |
1.54e-04 |
|
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 40.78 E-value: 1.54e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNT-IEGLVHITTLPEFYNYNERtmtlqgektgKTFRVGQPIRVKLTRADKETGDIDFQ 706
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTnVSGLCHKSEISDNRVADAS----------KLFRVGDKVRAKVLKIDAEKKRISLG 71
|
....
gi 739746327 707 YLPS 710
Cdd:cd05708 72 LKAS 75
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
634-699 |
2.12e-04 |
|
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: 40.35 E-value: 2.12e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 739746327 634 GIVGSVVKFGMFVELPNTIEGLVHITTLPEFYNYNERTMtlqgektgktFRVGQPIRVKLTRADKE 699
Cdd:cd05692 6 GTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDV----------LKEGDKVKVKVLSIDAR 61
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
716-806 |
2.38e-04 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 44.51 E-value: 2.38e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 716 EKVDHKARQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRKGSYDEKRKSSKK-PDKRKNQNRPHNDNKG 794
Cdd:PRK12678 177 DREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARgDDNREDRGDRDGDDGE 256
|
90
....*....|..
gi 739746327 795 RESGRRKKKGNK 806
Cdd:PRK12678 257 GRGGRRGRRFRD 268
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
603-717 |
6.53e-04 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 43.40 E-value: 6.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 603 TLERRAIDAErvVEAMKKAEYMEEF-VGQEFDGIVGSVVKFGMFVELpNTIEGLVHITTLPefYNYNertmtlqgEKTGK 681
Cdd:PRK00087 453 VLSRKAILEE--EKEKKKEETWNSLeEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEIS--WGRV--------EKPSD 519
|
90 100 110
....*....|....*....|....*....|....*....
gi 739746327 682 TFRVGQPIRVKLTRADKETGDIDF---QYLPSEYDITEK 717
Cdd:PRK00087 520 VLKVGDEIKVYILDIDKENKKLSLslkKLLPDPWENVEE 558
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
604-718 |
6.99e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 42.94 E-value: 6.99e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 604 LERRAIDAERvvEAMKKAEYMEEF-VGQEFDGIVGSVVKFGMFVELpNTIEGLVHITTLPefynyNERTmtlqgEKTGKT 682
Cdd:PRK06676 169 LSRRAVVEEE--RAAKKEELLSSLkEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELS-----HERV-----EKPSEV 235
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 739746327 683 FRVGQPIRVKLTRADKETGDIDF---QYLPSEYD-ITEKV 718
Cdd:PRK06676 236 VSVGQEVEVKVLSIDWETERISLslkDTLPGPWEgVEEKL 275
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
722-805 |
8.29e-04 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 42.97 E-value: 8.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 722 ARQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRKGSYDEKRKSSKKPDKRKNQNRPHNDNKGRESGRRK 801
Cdd:PRK12678 156 ARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDR 235
|
....
gi 739746327 802 KKGN 805
Cdd:PRK12678 236 RDAR 239
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
723-806 |
8.65e-04 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 42.97 E-value: 8.65e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 723 RQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQdGNGRKGSYDEKRKSSKKPDKRKNQNRPHNDNKGRESGRRKK 802
Cdd:PRK12678 190 RGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRR-GRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRD 268
|
....
gi 739746327 803 KGNK 806
Cdd:PRK12678 269 RDRR 272
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
715-805 |
1.33e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 42.20 E-value: 1.33e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 715 TEKVDHKARQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRKGSYDEKrksskkpDKRKNQNRPHNDNKG 794
Cdd:PRK12678 158 ADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRR-------EERGRRDGGDRRGRR 230
|
90
....*....|.
gi 739746327 795 RESGRRKKKGN 805
Cdd:PRK12678 231 RRRDRRDARGD 241
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
628-705 |
1.49e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 42.03 E-value: 1.49e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEfynynertmtLQGEKTGKTFRVGQPIRVKLTRADKETGDIDF 705
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSE----------NRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSL 513
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
628-700 |
1.97e-03 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 41.86 E-value: 1.97e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLpeFYNYNertmtlqgEKTGKTFRVGQPIRVKLTRADKET 700
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQI--SWKRI--------DKPEDVLSEGEEVKAKILEVDPEE 624
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
722-800 |
2.22e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 41.43 E-value: 2.22e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 722 ARQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRKGSYDEKRKSSKKPDKRKNQNRPHNDNKGR-ESGRR 800
Cdd:PRK12678 153 ATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRrGRRRR 232
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
628-748 |
2.96e-03 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 38.86 E-value: 2.96e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEFY--NYNErtmtlqgektgkTFRVGQPIRVKLTRADKEtGDIDF 705
Cdd:PRK08582 5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYvkDIND------------HLKVGDEVEVKVLNVEDD-GKIGL 71
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 739746327 706 QylpseydITEKVDHKARQEREEKaKAFRNRGPRRDRQNGDFE 748
Cdd:PRK08582 72 S-------IKKAKDRPKRQHDRPR-HEDNRGGGNDVAPKEDFE 106
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
628-658 |
3.48e-03 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 40.41 E-value: 3.48e-03
10 20 30
....*....|....*....|....*....|.
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHI 658
Cdd:COG0539 274 VGDVVKGKVTRLTDFGAFVELEPGVEGLVHI 304
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
723-800 |
4.43e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 40.66 E-value: 4.43e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 739746327 723 RQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRKGSYDEKRKSSKKPDKRKNQNRPHNDNKGRESGRR 800
Cdd:PRK12678 202 DRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDG 279
|
|
| PRK12678 |
PRK12678 |
transcription termination factor Rho; Provisional |
716-806 |
5.67e-03 |
|
transcription termination factor Rho; Provisional
Pssm-ID: 237171 [Multi-domain] Cd Length: 672 Bit Score: 40.27 E-value: 5.67e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 716 EKVDHKARQEREEKAKAFRNRGPRRDRQNGDFERRGKRGDNRNRQDGNGRkgsydEKRKSSKKPDKRKNQNRPHNDNKGR 795
Cdd:PRK12678 141 AARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGER-----GRREERGRDGDDRDRRDRREQGDRR 215
|
90
....*....|.
gi 739746327 796 ESGRRKKKGNK 806
Cdd:PRK12678 216 EERGRRDGGDR 226
|
|
| S1_Rrp5_repeat_hs8_sc7 |
cd04461 |
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ... |
628-699 |
5.90e-03 |
|
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: 36.41 E-value: 5.90e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEFYNynertmtlqgEKTGKTFRVGQPIRVKLTRADKE 699
Cdd:cd04461 14 PGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV----------TDPSFGFKKGQSVTAKVTSVDEE 75
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
628-707 |
6.26e-03 |
|
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: 36.43 E-value: 6.26e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEfynynertmtlqgektgkTFRVGQPIRVKLTrADKETGDIDFQY 707
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLR------------------DYEVGDEVIVQVT-DIPENGNIDLIP 76
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
628-663 |
7.48e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 39.64 E-value: 7.48e-03
10 20 30
....*....|....*....|....*....|....*.
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPE 663
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAE 328
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
628-730 |
9.37e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 39.38 E-value: 9.37e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 628 VGQEFDGIVGSVVKFGMFVELPNTIEGLVHITTLPEfynynERtmtlqGEKTGKTFRVGQPIRVKLTRADKETGDIdfqy 707
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSR-----DR-----VEDATEVLKVGDEVEAKVINIDRKNRRI---- 525
|
90 100
....*....|....*....|...
gi 739746327 708 lpseyditeKVDHKARQEREEKA 730
Cdd:PRK06299 526 ---------SLSIKALDEAEEKE 539
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
606-703 |
9.75e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 39.33 E-value: 9.75e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 739746327 606 RRAIDAERvveAMKKAEYMEEFV-GQEFDGIVGSVVKFGMFVELpNTIEGLVHITTLPEFYNYNERTMTlqgektgktfR 684
Cdd:TIGR00717 167 RAYLEEER---SQAREELLENLKeGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYV----------K 232
|
90
....*....|....*....
gi 739746327 685 VGQPIRVKLTRADKETGDI 703
Cdd:TIGR00717 233 VGQEVKVKVIKFDKEKGRI 251
|
|
| |
