|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
6-708 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 970.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 6 ENRKKVIMDFVESPMYVPMKEKELATFFGIEKAKRYE-LKEVLQELLLEGKLEITKRGKYKKSEK-KFLLGEFIANQRGF 83
Cdd:COG0557 2 ENSRETILAFLKEDAYKPLSKKELAKALGLKDEESREaLKRRLRALEREGQLVKTRRGRYRLPEKlDLVEGRVRGHRDGF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 84 GFVKVEGRDSDIFIPAEYTSNAMNGDTVKVVIDMESGEKKAEGHIIGIEKHANSQVVGYYQKSNRFGFVLPDDTKIFKDI 163
Cdd:COG0557 82 GFVIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDI 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 164 YIPQGKGNGAKTGDKVVVDITDFGNDKKKPEGKVVEILGKNTDIGVDILSIARSFGLPEKFGEEVENELKSIPKKVLKKD 243
Cdd:COG0557 162 FIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEAD 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 244 IKGRADFRDKVTVTIDGEDAKDLDDAITLEK--NGNvWHLGVHIADVTHYVKENTALDKEALQRATSVYLVDRVIPMLPK 321
Cdd:COG0557 242 LKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKldNGG-WRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPE 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 322 KLSNGICSLNQGEDRLALSCMMEIDEKGNIIGHNICESVINVNERMTYTAVNEVITNSNEETEKRYAEYIDLFKDFKTVS 401
Cdd:COG0557 321 RLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEELREEYADLVPMLEELYELA 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 402 DLLRGARTKRGSIDFDLPESKVILDKNGRAIDIKPYERNSATKLIEDFMLAANETVAEDFFWQDIPFLYRVHENPDPDKM 481
Cdd:COG0557 401 KILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 482 KSLAIFINNFGFTLrRKNDEVPPKEIQKLLVNIEGSDAEPIISRIALRSMKRARYDTVCIGHFGLAAKYYTHFTSPIRRY 561
Cdd:COG0557 481 EALREFLANLGLKL-KGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRY 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 562 PDLQIHRIIKENIRNGLSGRRIEHYRNILDDVALQSSKMERRAEEAERETVKYKKCEYMLSHIGEEFDGIISGVTGFGIF 641
Cdd:COG0557 560 PDLLVHRALKAYLEGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSFGLF 639
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1972712511 642 VELENT-VEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKVYDIDRLAKRIDFKLVKEK 708
Cdd:COG0557 640 VELDELgVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGG 707
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
7-705 |
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: 802.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 7 NRKKVIMDFVESPMYVPMKEKELATFFGIEKAKRYE-LKEVLQELLLEGKLEITKRGKYKKSEK-KFLLGEFIANQRGFG 84
Cdd:TIGR02063 2 PLRELILEFLKSKKGKPISLKELAKAFHLKGADEKKaLRKRLRALEDDGLVKKNRRGLYALPESlKLVKGTVIAHRDGFG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 85 FVKVEGRD-SDIFIPAEYTSNAMNGDTVKVVI-DMESGEKKAEGHIIGIEKHANSQVVGYYQKSNRFGFVLPDDTKIFKD 162
Cdd:TIGR02063 82 FLRPEDDDeDDIFIPPRQMNGAMHGDRVLVRItGKPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYLD 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 163 IYIPQGKGNGAKTGDKVVVDITDFGNDKKKPEGKVVEILGKNTDIGVDILSIARSFGLPEKFGEEVENELKSIPKKVLKK 242
Cdd:TIGR02063 162 IFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPEE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 243 DIKGRADFRDKVTVTIDGEDAKDLDDAITLEKNGN-VWHLGVHIADVTHYVKENTALDKEALQRATSVYLVDRVIPMLPK 321
Cdd:TIGR02063 242 EIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDgNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPE 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 322 KLSNGICSLNQGEDRLALSCMMEIDEKGNIIGHNICESVINVNERMTYTAVNEVITNsNEETEKRYAEYIDLFKDFKTVS 401
Cdd:TIGR02063 322 RLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEG-KDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 402 DLLRGARTKRGSIDFDLPESKVILDKNGRAIDIKPYERNSATKLIEDFMLAANETVAEDFFWQDIPFLYRVHENPDPDKM 481
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 482 KSLAIFINNFGFTLRRKN-DEVPPKEIQKLLVNIEGSDAEPIISRIALRSMKRARYDTVCIGHFGLAAKYYTHFTSPIRR 560
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGTsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 561 YPDLQIHRIIKENIR---NGLSGRRIEHYRNILDDVALQSSKMERRAEEAERETVKYKKCEYMLSHIGEEFDGIISGVTG 637
Cdd:TIGR02063 561 YPDLIVHRLIKKALFggeNTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTS 640
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1972712511 638 FGIFVELEN-TVEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKVYDIDRLAKRIDFKLV 705
Cdd:TIGR02063 641 FGLFVELENnTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
63-705 |
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 1972712511 63 KYKKSEKKFLL-GEFIANQRGFGFVK-VEGRDSDIFIPAEYTSNAMNGDTVKVVIDMESGEKKAEGHIIGIEKHANSQVV 140
Cdd:TIGR00358 7 KYALPEKDDLVkGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 141 GYYQKSNRFGFVLPDDTKIFKDIYIPQGKG-NGAKTGDKVVVDITDFGNDKKKPEGKVVEILGKNTDIGVDILSIARSFG 219
Cdd:TIGR00358 87 GKFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHE 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 220 LPEKFGEEVENELKSIPKKVLKKDIKGRADFRDKVTVTIDGEDAKDLDDAITLEK-NGNVWHLGVHIADVTHYVKENTAL 298
Cdd:TIGR00358 167 IPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKlPDGGWKLYVAIADVSYYVAENSPL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 299 DKEALQRATSVYLVDRVIPMLPKKLSNGICSLNQGEDRLALSCMMEIDEKGNIIGHNICESVINVNERMTYTAVNEVITN 378
Cdd:TIGR00358 247 DKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLEN 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 379 SnEETEKRYAEYIDLFKDFKTVSDLLRGARTKRGSIDFDLPESKVILDKNGRAIDIKPYERNSATKLIEDFMLAANETVA 458
Cdd:TIGR00358 327 D-DELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAA 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 459 EDFFWQDIPFLYRVHENPDPDKMKSLAIFINNFGFTLRRKN-DEVPPKEIQKLL-VNIEGSDAEPIISRIaLRSMKRARY 536
Cdd:TIGR00358 406 RFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNaENVTTLDGACWLrEVKDRPEYEILVTRL-LRSLSQAEY 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 537 DTVCIGHFGLAAKYYTHFTSPIRRYPDLQIHRIIKENIRNGLSGRRIEHYRNILDDVALQSSKMERRAEEAERETVKYKK 616
Cdd:TIGR00358 485 SPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVADWLK 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 617 CEYMLSHIGEEFDGIISGVTGFGIFVEL-ENTVEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKVYDIDR 695
Cdd:TIGR00358 565 CRYLLDKVGTEFSGEISSVTRFGMFVRLdDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNM 644
|
650
....*....|
gi 1972712511 696 LAKRIDFKLV 705
Cdd:TIGR00358 645 ETRSIIFELV 654
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
22-705 |
4.96e-146 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 446.11 E-value: 4.96e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 22 VPMKEKELATFFGIEKAKRYE-LKEVLQELLLEGKLEITKRGKYKKSEKKFLL-GEFIANQRGFGFVKVEGRDSDIFIPA 99
Cdd:PRK11642 33 KPASREELAVELNIEGEEQLEaLRRRLRAMERDGQLVFTRRQCYALPERLDLLkGTVIGHRDGYGFLRVEGRKDDLYLSS 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 100 EYTSNAMNGDTVKVVIDMESGEKKAEGHIIGIEKHANSQVVGYYQKSNRFGFVLPDDTKIFKDIYIPQGKGNGAKTGDKV 179
Cdd:PRK11642 113 EQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEQIMGARMGFVV 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 180 VVDITDFGNDKKKPEGKVVEILGKN--TDIGVDIlsIARSFGLPEKFGEEVENELKSIPKKVLKKDIKGRADFRDKVTVT 257
Cdd:PRK11642 193 VVELTQRPTRRTKAVGKIVEVLGDNmgTGMAVDI--ALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVT 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 258 IDGEDAKDLDDAITLE-KNGNVWHLGVHIADVTHYVKENTALDKEALQRATSVYLVDRVIPMLPKKLSNGICSLNQGEDR 336
Cdd:PRK11642 271 IDGEDARDFDDAVYCEkKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDR 350
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 337 LALSCMMEIDEKGNIIGHNICESVINVNERMTYTAVNEVItNSNEETEKRYAEYIDLFKDFKTVSDLLRGARTKRGSIDF 416
Cdd:PRK11642 351 LCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHIL-QGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISF 429
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 417 DLPESKVILDKNGRAIDIKPYERNSATKLIEDFMLAANETVAEDFFWQDIPFLYRVHENPDPDKMKSLAIFINNFGFTLR 496
Cdd:PRK11642 430 ESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELP 509
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 497 RKNdEVPPKEIQKLLVNI-EGSDAEpIISRIALRSMKRARYDTVCIGHFGLAAKYYTHFTSPIRRYPDLQIHRIIKENI- 574
Cdd:PRK11642 510 GGN-KPEPRDYAELLESVaDRPDAE-MLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLa 587
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 575 -RNGLSGRRIE----HYrNILDDVAL-QSSKMERRAEEAERETVK-YKKCEYMLSHIGEEFDGIISGVTGFGIFVELENT 647
Cdd:PRK11642 588 kEQGHKGNTTEtggyHY-SMEEMLQLgQHCSMTERRADEATRDVAdWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDL 666
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*....
gi 1972712511 648 -VEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKVYDIDRLAKRIDFKLV 705
Cdd:PRK11642 667 fIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLI 725
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
247-571 |
6.16e-131 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 389.72 E-value: 6.16e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 247 RADFRDKVTVTIDGEDAKDLDDAITLEKNGNV-WHLGVHIADVTHYVKENTALDKEALQRATSVYLVDRVIPMLPKKLSN 325
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGgYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 326 GICSLNQGEDRLALSCMMEIDEKGNIIGHNICESVINVNERMTYTAVNEVITNSNEETEKryAEYIDLFKDFKTVSDLLR 405
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK--PDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 406 GARTKRGSIDFDLPESKVILDKNGrAIDIKPYERNSATKLIEDFMLAANETVAEDFFWQDIPFLYRVHENPDPDKMKSLA 485
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 486 IFINNfgftlrrkndEVPPKEIQKLLVNIEgsDAEPIISRIALRSMKRARYDTVCIGHFGLAAKYYTHFTSPIRRYPDLQ 565
Cdd:pfam00773 238 KLLQL----------LPDDKGLSKSLEKIK--DDERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305
|
....*.
gi 1972712511 566 IHRIIK 571
Cdd:pfam00773 306 VHRQLK 311
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
247-576 |
5.05e-126 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 375.84 E-value: 5.05e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 247 RADFRDKVTVTIDGEDAKDLDDAITLEKNGN-VWHLGVHIADVTHYVKENTALDKEALQRATSVYLVDRVIPMLPKKLSN 325
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNgGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 326 GICSLNQGEDRLALSCMMEIDEKG-NIIGHNICESVINVNERMTYTAVNEVITnsneetekryaeyidlfkdfktvsdll 404
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 405 rgartkrgsidfdlpesKVILDKNGRAIDIKPYERNSATKLIEDFMLAANETVAEDFFWQDIPFLYRVHENPDPDKM-KS 483
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLaEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 484 LAIFINNFGFTLRRKNDevpPKEIQKLLVNIEGSDAEPIISRIALRSMKRARYDTVCIGHFGLAAKYYTHFTSPIRRYPD 563
Cdd:smart00955 197 LKEFLALLGLLLLGGDG---PKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273
|
330
....*....|...
gi 1972712511 564 LQIHRIIKENIRN 576
Cdd:smart00955 274 LIVHRQLKAALRG 286
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
78-655 |
1.07e-56 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 204.32 E-value: 1.07e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 78 ANQRGFGFVKVEGRDSdIFIPAEYTSNAMNGDTVKVVIDMESGEKKAEghiigIEK--HANSQV-VGYYQ-KSNRFgFVL 153
Cdd:COG4776 28 ATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVIRTEKDKESAE-----PETliEPFLTRfVGRVQkKDGRL-FVV 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 154 PDDTKIFKDIYIPQGKG--NGAKTGDKVVVDITDFG-NDKKKPEGKVVEILGKNTDIGVDIL-SIARsFGLPEK---FGE 226
Cdd:COG4776 101 PDHPLIKDAIKARPKKGleEGLKEGDWVVAELKRHPlKGDRGFFAEITEFIADADDPFAPWWvTLAR-HNLEREapeGDD 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 227 EVEnelksipkkvLKKDIKGRADFRDKVTVTIDGEDAKDLDDAITLEKNGN-VWHLGVHIADVTHYVKENTALDKEALQR 305
Cdd:COG4776 180 EWE----------LLDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENgGWKLTVAIADPTAYIPEGSELDKEARQR 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 306 ATSVYLVDRVIPMLPKKLSNGICSLNQGEDRLALSCMMEIDEKGNIIG-HNICESVINVNERMTYTAVNEVITNSNEET- 383
Cdd:COG4776 250 AFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKGEWQp 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 384 -EKRYAEYIDLFKDFKtvsdLLRGA-RTKRGSIDFDLPESKVILDKNGRAIDIKPYERNSATKLIEDFMLAANETVAEdF 461
Cdd:COG4776 330 eNEEIAEQIRLLHQFA----LARSQwRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAAR-V 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 462 FWQDIPF-LYRVHENPDPDKMKSLAIFINNF-------------GF-TLRRKNDEVPPK----EIQKLLVNIEGSdAEPi 522
Cdd:COG4776 405 LREHLGFgIFNVHSGFDPEKLEQAVELLAEHgiefdpeqlltleGFcALRRELDAQPTSyldsRLRRFQTFAEIS-TEP- 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 523 isrialrsmkrarydtvciG-HFGLAAKYYTHFTSPIRRYPDLQIHRIIKENIRNG------------LSGRRiEHYRNI 589
Cdd:COG4776 483 -------------------GpHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQpaekpdeelterLAERR-RLNRMA 542
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972712511 590 LDDVA--LqsskmerraeeaeretvkYkkCEYMLSHIGEE--FDGIISGVTGFGIFVEL-ENTVEGFIRMS 655
Cdd:COG4776 543 ERDVAdwL------------------Y--ARYLKPKVGSGqvFTAEIIDINRGGLRVRLlENGAVAFIPAS 593
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
78-576 |
6.38e-47 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 176.61 E-value: 6.38e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 78 ANQRGFGFVKVEGRDSdIFIPAEYTSNAMNGDTVKVVIDMESGEKKAEGHIIgIEKHANsQVVGYYQKSNRFGFVLPDDT 157
Cdd:PRK05054 28 ATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIAVIHTEKDREIAEPEEL-IEPFLT-RFVGRVQKKDDRLSIVPDHP 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 158 KIFKDIYIPQGKG--NGAKTGDKVVVDItdfgndKKKP----EGKVVEILGKNTDiGVDIL-----SIARsFGLPEkfgE 226
Cdd:PRK05054 105 LLKDAIPCRAAKGlnHEFKEGDWVVAEL------RRHPlkgdRGFYAEITQFITD-ADDHFapwwvTLAR-HNLER---E 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 227 EVENElksIPKKVLKKDIKgRADFRDKVTVTIDGEDAKDLDDAITLEKNGNV-WHLGVHIADVTHYVKENTALDKEALQR 305
Cdd:PRK05054 174 APAGG---VAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGgLQLTVAIADPTAYIAEGSKLDKAARQR 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 306 ATSVYLVDRVIPMLPKKLSNGICSLNQGEDRLALSCMMEIDEKGNiIGHNICESVINVNE--RMTYTAVNEVITNS---- 379
Cdd:PRK05054 250 AFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGT-IEDDIRFFAAWIESkaKLAYDNVSDWLENGgdwq 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 380 --NEETekryAEYIDLFKDFKtvsdLLRGA-RTKRGSIDFDLPESKVILDKNGRAIDIKPYERNSATKLIEDFMLAANeT 456
Cdd:PRK05054 329 peSEAI----AEQIRLLHQFC----LARSEwRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAAN-I 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 457 VAEDFFWQDIPF-LYRVHENPDPDKMKSLAIFINNFGFtlrrkndEVPPKEIQKLlvniEG-------SDAEP---IISR 525
Cdd:PRK05054 400 CAARVLRDKLGFgIYNVHSGFDPANAEQAVALLKEHGL-------HFDAEELLTL----EGfcklrreLDAQPtgyLDSR 468
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|.
gi 1972712511 526 IAlRSMKRARYDTVCIGHFGLAAKYYTHFTSPIRRYPDLQIHRIIKENIRN 576
Cdd:PRK05054 469 IR-RFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKG 518
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
624-705 |
7.54e-33 |
|
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: 121.35 E-value: 7.54e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELEN-TVEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKVYDIDRLAKRIDF 702
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 1972712511 703 KLV 705
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
151-224 |
6.10e-28 |
|
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: 107.09 E-value: 6.10e-28
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972712511 151 FVLPDDTKIFKDIYIPQGKGNGAKTGDKVVVDITDFGnDKKKPEGKVVEILGKNTDIGVDILSIARSFGLPEKF 224
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYP-DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEF 73
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
74-131 |
3.42e-14 |
|
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: 67.56 E-value: 3.42e-14
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1972712511 74 GEFIANQRGFGFVKVEGRDSDIFIPAEYTSNAMNGDTVKVVIDMESGEKKAEGHIIGI 131
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
624-704 |
1.90e-10 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 57.23 E-value: 1.90e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYfeyneagyelvGEFTKKKFVLGQKVRVKVYDIDRLAKRIDFK 703
Cdd:smart00316 2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
|
.
gi 1972712511 704 L 704
Cdd:smart00316 71 L 71
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
149-200 |
1.97e-08 |
|
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: 51.00 E-value: 1.97e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 1972712511 149 FGFVLPDDTKifKDIYIPQGKGNGAKTGDKVVVDITDfGNDKKKPEGKVVEI 200
Cdd:pfam08206 10 FGFLIPDDEE--DDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
624-702 |
2.41e-07 |
|
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: 48.44 E-value: 2.41e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYFEyneagyelVGEFTKKKfvlGQKVRVKVYDIDRLAKRIDF 702
Cdd:pfam00575 3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--------DPDEVIKV---GDEVKVKVLKVDKDRRRIIL 70
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
628-700 |
5.06e-07 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 47.38 E-value: 5.06e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1972712511 628 FDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYFeyneagyelvgEFTKKKFVLGQKVRVKVYDIDRLAKRI 700
Cdd:cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRI 62
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
630-700 |
1.13e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 51.70 E-value: 1.13e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972712511 630 GIISGVTGFGIFVELENTVEGFIRMSDLEGDYfeyneagyelvGEFTKKKFVLGQKVRVKVYDIDRLAKRI 700
Cdd:PRK06299 466 GTVTEVKDKGAFVELEDGVEGLIRASELSRDR-----------VEDATEVLKVGDEVEAKVINIDRKNRRI 525
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
624-700 |
1.50e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 51.32 E-value: 1.50e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEgdyfeyneagYELVGEFTKKKFVLGQKVRVKVYDIDRLAKRI 700
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDIS----------WDKKGEEAVELYKKGDEVEAVVLKVDVEKERI 439
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
625-700 |
2.91e-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: 45.18 E-value: 2.91e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1972712511 625 GEEFDGIISGVTGFGIFVELENTVEGFIRMSDLegdyfEYNEAGYELVGEFTKkkfvlGQKVRVKVYDIDRLAKRI 700
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDI-----SWTQRVRHPSEIYKK-----GQEVEAVVLNIDVERERI 66
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
623-704 |
4.08e-05 |
|
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: 42.32 E-value: 4.08e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 623 HIGEEFDGIISGVTGFGIFVELENT-VEGFIRMSDLEGDyfeyneagyelVGEFTKKKFVLGQKVRVKVYDIDRLAKRID 701
Cdd:cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTnVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRIS 69
|
...
gi 1972712511 702 FKL 704
Cdd:cd05708 70 LGL 72
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
149-201 |
1.08e-04 |
|
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 40.66 E-value: 1.08e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1972712511 149 FGFVLPDDTKifKDIYIP----QGKGNGAKTGDKVVVDITDfGNDKKKPEGKVVEIL 201
Cdd:smart00357 11 FGFIRPDDGG--KDVFVHpsqiQGGLKSLREGDEVEFKVVS-PEGGEKPEAENVVKL 64
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
80-129 |
1.81e-04 |
|
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 39.89 E-value: 1.81e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1972712511 80 QRGFGFVKVEGRDSDIFIPAE----YTSNAMNGDTVKVVIDMESGEKKAEGHII 129
Cdd:smart00357 8 NKGFGFIRPDDGGKDVFVHPSqiqgGLKSLREGDEVEFKVVSPEGGEKPEAENV 61
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
630-702 |
2.11e-04 |
|
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: 44.34 E-value: 2.11e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1972712511 630 GIISGVTGFGIFVELENTVEGFIRMSDLEGDYFEYneagyelvgefTKKKFVLGQKVRVKVYDIDRLAKRIDF 702
Cdd:TIGR00717 452 GKVTEIKDFGAFVELPGGVEGLIRNSELSENRDED-----------KTDEIKVGDEVEAKVVDIDKKNRKVSL 513
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
629-690 |
2.97e-04 |
|
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: 40.35 E-value: 2.97e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1972712511 629 DGIISGVTGFGIFVELeNTVEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKV 690
Cdd:cd04460 4 EGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARI 64
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
624-700 |
3.48e-04 |
|
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: 43.95 E-value: 3.48e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLegdyfEYNEAGYELVGEFTKkkfvlGQKVRVKVYDIDRLAKRI 700
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDI-----SWDKDGREADHLYKK-----GDEIEAVVLAVDKEKKRI 425
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
624-691 |
3.75e-04 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 42.12 E-value: 3.75e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELeNTVEGFIRMSDLEGDYFEYNEAGYELVGEFTKKKFVLGQKVRVKVY 691
Cdd:PRK08563 81 LQEVVEGEVVEVVEFGAFVRI-GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV 147
|
|
| PRK07252 |
PRK07252 |
S1 RNA-binding domain-containing protein; |
624-699 |
4.29e-04 |
|
S1 RNA-binding domain-containing protein;
Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 40.46 E-value: 4.29e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYFeynEAGYELVGeftkkkfvLGQKVRVKVYDIDRLAKR 699
Cdd:PRK07252 3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFI---DNIHQLLK--------VGEEVLVQVVDFDEYTGK 67
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
624-695 |
5.91e-04 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 43.11 E-value: 5.91e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYFEYneagyelVGEFTKkkfvLGQKVRVKVYDIDR 695
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEK-------VEDVLK----EGDEVKVKVLEIDK 681
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
623-700 |
6.17e-04 |
|
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: 42.72 E-value: 6.17e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 623 HIGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLegdyfeyneagyelvgEFTKK-----KFV-LGQKVRVKVYDIDRL 696
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEM----------------SWTKRvahpsDVVkVGDEVEVKVLDIDPE 336
|
....
gi 1972712511 697 AKRI 700
Cdd:COG0539 337 ERRI 340
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
623-700 |
6.80e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.84 E-value: 6.80e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 623 HIGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLegdyfeyneagyelvgEFTKK-----KFV-LGQKVRVKVYDIDRL 696
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEM----------------SWTKKnkhpsKVVsVGQEVEVMVLEIDEE 348
|
....
gi 1972712511 697 AKRI 700
Cdd:PRK06299 349 KRRI 352
|
|
| S1_RPS1_repeat_ec4 |
cd05689 |
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
625-700 |
8.79e-04 |
|
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: 38.33 E-value: 8.79e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1972712511 625 GEEFDGIISGVTGFGIFVELENTVEGFIRMSDLegDYFEYNEAGYELVGeftkkkfvLGQKVRVKVYDIDRLAKRI 700
Cdd:cd05689 4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEM--DWTNKNIHPSKVVS--------LGDEVEVMVLDIDEERRRI 69
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
624-700 |
1.26e-03 |
|
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: 37.61 E-value: 1.26e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELeNTVEGFIRMSDLEGdyfeyneagyelvGEFTKKKFVL--GQKVRVKVYDIDRLAKRI 700
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSW-------------GRVKHPSEVVnvGDEVEVKVLKIDKERKRI 65
|
|
| S1_Rrp5_repeat_sc11 |
cd05707 |
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
625-701 |
2.00e-03 |
|
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: 37.27 E-value: 2.00e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1972712511 625 GEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYfeyneagyelVGEFtKKKFVLGQKVRVKVYDIDRLAKRID 701
Cdd:cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSY----------LKDW-KKRFKVGQLVKGKIVSIDPDNGRIE 66
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
630-698 |
2.44e-03 |
|
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: 36.88 E-value: 2.44e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1972712511 630 GIISGVTGFGIFVELENTVEGFIRMSDLEGDYFEYneagyelVGEFTKKkfvlGQKVRVKVYDIDRLAK 698
Cdd:cd05692 6 GTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKD-------VKDVLKE----GDKVKVKVLSIDARGR 63
|
|
| S1_RPS1_repeat_ec6 |
cd05691 |
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
630-700 |
2.54e-03 |
|
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240196 [Multi-domain] Cd Length: 73 Bit Score: 37.25 E-value: 2.54e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972712511 630 GIISGVTGFGIFVELENTVEGFIRMSDLegdyfeyneaGYELVGEFTkKKFVLGQKVRVKVYDIDRLAKRI 700
Cdd:cd05691 6 GKVTEVDAKGATVKLGDGVEGFLRAAEL----------SRDRVEDAT-ERFKVGDEVEAKITNVDRKNRKI 65
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
624-661 |
4.13e-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: 4.13e-03
10 20 30
....*....|....*....|....*....|....*...
gi 1972712511 624 IGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDY 661
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY 53
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
623-700 |
5.85e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 39.47 E-value: 5.85e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 623 HIGEEFDGIISGVTGFGIFVELENTVEGFIRMSDLEGDYFEyneagyelvgeftKKKFVL--GQKVRVKVYDIDRLAKRI 700
Cdd:PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIA-------------TPSEVLeeGQEVKVKVLEVNEEEKRI 342
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
623-700 |
9.59e-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: 38.87 E-value: 9.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972712511 623 HIGEEFDGIISGVTGFGIFVELENtVEGFIRMSDLE-------GDYFEyneagyelvgeftkkkfvLGQKVRVKVYDIDR 695
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG-VDGLLHISEISwgrvkhpSEVLK------------------VGDEVEVKVLKIDR 248
|
....*
gi 1972712511 696 LAKRI 700
Cdd:COG0539 249 EKERI 253
|
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