|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
3-713 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1097.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 3 EMTKERLLTFMKEEAVKPLAIKDIEEALGLSDSSQFKEFVKLLNELEEEGELVRTRSNRYGIPDKMNLLRGEVIMHPKGF 82
Cdd:COG0557 2 ENSRETILAFLKEDAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 83 AFVKTEVEHDDVYIASAEMNGAMNKDKVLVRLHTGSTGEKPEGAIIRILERGTTRTVGTYVDDKHYGFVVPDDKRIPNDI 162
Cdd:COG0557 82 GFVIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDI 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 163 FIPKGSEGGAVDGHKVLVEIVKYPEGRMSAEGHVLEVLGHKNDPGVDILSVIYKHGLPGEFDQETLDHANSVPNEIDPSE 242
Cdd:COG0557 162 FIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEAD 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 243 LENRRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAERATSCYLVDRVIPMIPHR 322
Cdd:COG0557 242 LKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPER 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 323 LSNGICSLNPQVDRLTLSCNMEFSPNGELVNHEIFQSVINTTERMTYTDVRKILQEEDEEVSKRYESLIPFFKGMEELAE 402
Cdd:COG0557 322 LSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEELREEYADLVPMLEELYELAK 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 403 ILRNKRMARGAIDFDFKEAKVLVDEDGTPTDVVMRERSVAERLIEEFMLAANETIAEHFHWMKVPFMYRIHEDPDEEKLN 482
Cdd:COG0557 402 ILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLE 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 483 KFLEFITNFGYVVKGaANTVHPRALQELLDQVKGEPEEAVISTVMLRSMRQAKYDPENVGHFGLSADFYTHFTSPIRRYP 562
Cdd:COG0557 482 ALREFLANLGLKLKG-GDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYP 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 563 DLIVHRLIRTYLiEGKTDDKTIEKWNEKLYEIAKHSSEMERRAEDASRETDELKKVQYMADKIGEEYDGMISGVTNFGIF 642
Cdd:COG0557 561 DLLVHRALKAYL-EGKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSFGLF 639
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503255424 643 VELPNT-IEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNVDERIIDFEVVGMKPRKE 713
Cdd:COG0557 640 VELDELgVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEAP 711
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
5-706 |
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: 947.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 5 TKERLLTFMKEEAVKPLAIKDIEEALGLSDSSQFKEFVKLLNELEEEGELVRTRSNRYGIPDKMNLLRGEVIMHPKGFAF 84
Cdd:TIGR02063 3 LRELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGFGF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 85 VKTEVE-HDDVYIASAEMNGAMNKDKVLVRLHTGST-GEKPEGAIIRILERGTTRTVGTYVDDKHYGFVVPDDKRIPNDI 162
Cdd:TIGR02063 83 LRPEDDdEDDIFIPPRQMNGAMHGDRVLVRITGKPDgGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYLDI 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 163 FIPKGSEGGAVDGHKVLVEIVKYPEGRMSAEGHVLEVLGHKNDPGVDILSVIYKHGLPGEFDQETLDHANSVPNEIDPSE 242
Cdd:TIGR02063 163 FIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPEEE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 243 LENRRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAERATSCYLVDRVIPMIPHR 322
Cdd:TIGR02063 243 IKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPER 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 323 LSNGICSLNPQVDRLTLSCNMEFSPNGELVNHEIFQSVINTTERMTYTDVRKILQEEDEEvSKRYESLIPFFKGMEELAE 402
Cdd:TIGR02063 323 LSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDAL-DKKEPPLKEMLKNLFELYK 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 403 ILRNKRMARGAIDFDFKEAKVLVDEDGTPTDVVMRERSVAERLIEEFMLAANETIAEHFHWMKVPFMYRIHEDPDEEKLN 482
Cdd:TIGR02063 402 ILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKLQ 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 483 KFLEFITNFGYVVKG-AANTVHPRALQELLDQVKGEPEEAVISTVMLRSMRQAKYDPENVGHFGLSADFYTHFTSPIRRY 561
Cdd:TIGR02063 482 NLREFLKTLGITLKGgTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRRY 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 562 PDLIVHRLIRTYLIEGK--TDDKTIEKWNEKLYEIAKHSSEMERRAEDASRETDELKKVQYMADKIGEEYDGMISGVTNF 639
Cdd:TIGR02063 562 PDLIVHRLIKKALFGGEntTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTSF 641
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503255424 640 GIFVELPN-TIEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNVDERIIDFEVV 706
Cdd:TIGR02063 642 GLFVELENnTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
61-706 |
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: 757.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 61 RYGIPDKMNLLRGEVIMHPKGFAFVKT-EVEHDDVYIASAEMNGAMNKDKVLVRLHTGSTGEKPEGAIIRILERGTTRTV 139
Cdd:TIGR00358 7 KYALPEKDDLVKGVVKAHNKGFGFLRPdDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFV 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 140 GTYVDDKHYGFVVPDDKRIPNDIFIPKGS-EGGAVDGHKVLVEIVKYPEGRMSAEGHVLEVLGHKNDPGVDILSVIYKHG 218
Cdd:TIGR00358 87 GKFLGENDFGFVVPDDPRIYLDIIVPKASvKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHE 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 219 LPGEFDQETLDHANSVPNEIDPSELENRRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPI 298
Cdd:TIGR00358 167 IPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 299 DKEAAERATSCYLVDRVIPMIPHRLSNGICSLNPQVDRLTLSCNMEFSPNGELVNHEIFQSVINTTERMTYTDVRKILqE 378
Cdd:TIGR00358 247 DKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWL-E 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 379 EDEEVSKRYESLIPFFKGMEELAEILRNKRMARGAIDFDFKEAKVLVDEDGTPTDVVMRERSVAERLIEEFMLAANETIA 458
Cdd:TIGR00358 326 NDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAA 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 459 EHFHWMKVPFMYRIHEDPDEEKLNKFLEFITNFGYV-VKGAANTVHPRALQELLDQVKGEPEEAVISTVMLRSMRQAKYD 537
Cdd:TIGR00358 406 RFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTlPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYS 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 538 PENVGHFGLSADFYTHFTSPIRRYPDLIVHRLIRTYLIEGKTDDKTiEKWNEKLYEIAKHSSEMERRAEDASRETDELKK 617
Cdd:TIGR00358 486 PEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTER-YQPQDELLQIAEHCSDTERRARDAERDVADWLK 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 618 VQYMADKIGEEYDGMISGVTNFGIFVELP-NTIEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNV 696
Cdd:TIGR00358 565 CRYLLDKVGTEFSGEISSVTRFGMFVRLDdNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNM 644
|
650
....*....|
gi 503255424 697 DERIIDFEVV 706
Cdd:TIGR00358 645 ETRSIIFELV 654
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
19-750 |
2.14e-174 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 522.00 E-value: 2.14e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 19 KPLAIKDIEEALGLSDSSQFKEFVKLLNELEEEGELVRTRSNRYGIPDKMNLLRGEVIMHPKGFAFVKTEVEHDDVYIAS 98
Cdd:PRK11642 33 KPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSS 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 99 AEMNGAMNKDKVLVRLHTGSTGEKPEGAIIRILERGTTRTVGTYVDDKHYGFVVPDDKRIPNDIFIPKGSEGGAVDGHKV 178
Cdd:PRK11642 113 EQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEQIMGARMGFVV 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 179 LVEIVKYPEGRMSAEGHVLEVLGHKNDPGVDILSVIYKHGLPGEFDQETLDHANSVPNEIDPSELENRRDLRDETIVTID 258
Cdd:PRK11642 193 VVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTID 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 259 GADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAERATSCYLVDRVIPMIPHRLSNGICSLNPQVDRLT 338
Cdd:PRK11642 273 GEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLC 352
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 339 LSCNMEFSPNGELVNHEIFQSVINTTERMTYTDVRKILQeEDEEVSKRYESLIPFFKGMEELAEILRNKRMARGAIDFDF 418
Cdd:PRK11642 353 MVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQ-GDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFES 431
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 419 KEAKVLVDEDGTPTDVVMRERSVAERLIEEFMLAANETIAEHFHWMKVPFMYRIHEDPDEEKLNKFLEFITNFGYVVKGa 498
Cdd:PRK11642 432 EEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPG- 510
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 499 ANTVHPRALQELLDQVKGEPEEAVISTVMLRSMRQAKYDPENVGHFGLSADFYTHFTSPIRRYPDLIVHRLIRtYLIEGK 578
Cdd:PRK11642 511 GNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIK-YLLAKE 589
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 579 TDDKtiEKWN---------EKLYEIAKHSSEMERRAEDASRETDELKKVQYMADKIGEEYDGMISGVTNFGIFVELPNT- 648
Cdd:PRK11642 590 QGHK--GNTTetggyhysmEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLf 667
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 649 IEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNVDERIIDFEVVGM--KPRKERRQDRPRVIEGGI 726
Cdd:PRK11642 668 IDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLISSerAPRNVGKTAREKAKKGDA 747
|
730 740
....*....|....*....|....*....
gi 503255424 727 -RPTRKKKGPGS----EKDGDAKKGRRKK 750
Cdd:PRK11642 748 gKKGGKRRQVGKkvnfEPDSAFRGEKKAK 776
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
246-574 |
1.73e-137 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 408.98 E-value: 1.73e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 246 RRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAERATSCYLVDRVIPMIPHRLSN 325
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 326 GICSLNPQVDRLTLSCNMEFSPNGELVNHEIFQSVINTTERMTYTDVRKILqeEDEEVSKRYESLIPFFKGMEELAEILR 405
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLL--EGKDAEKDKPDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 406 NKRMARGAIDFDFKEAKVLVDEDGtPTDVVMRERSVAERLIEEFMLAANETIAEHFHWMKVPFMYRIHEDPDEEKLNKFL 485
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEEG-VIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 486 EFitnfgyvvkgAANTVHPRALQELLDQVKGepEEAVISTVMLRSMRQAKYDPENVGHFGLSADFYTHFTSPIRRYPDLI 565
Cdd:pfam00773 238 KL----------LQLLPDDKGLSKSLEKIKD--DERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLI 305
|
....*....
gi 503255424 566 VHRLIRTYL 574
Cdd:pfam00773 306 VHRQLKALL 314
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
246-576 |
8.60e-136 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 403.57 E-value: 8.60e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 246 RRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAERATSCYLVDRVIPMIPHRLSN 325
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 326 GICSLNPQVDRLTLSCNMEFSPNG-ELVNHEIFQSVINTTERMTYTDVRKILQeedeevskryeslipffkgmeelaeil 404
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 405 rnkrmargaidfdfkeaKVLVDEDGTPTDVVMRERSVAERLIEEFMLAANETIAEHFHWMKVPFMYRIHEDPDEEKLNKF 484
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 485 L-EFITNFGYVVKGAANtvhPRALQELLDQVKGEPEEAVISTVMLRSMRQAKYDPENVGHFGLSADFYTHFTSPIRRYPD 563
Cdd:smart00955 197 LkEFLALLGLLLLGGDG---PKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273
|
330
....*....|...
gi 503255424 564 LIVHRLIRTYLIE 576
Cdd:smart00955 274 LIVHRQLKAALRG 286
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
80-701 |
5.99e-66 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 231.28 E-value: 5.99e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 80 KGFAFVktEVEHDDVY-IASAEMNGAMNKDKVLVRLHTgsTGEKPEGAIIRILERGTTRTVGTYVDDKHYGFVVPDDKRI 158
Cdd:COG4776 31 KGFGFL--EVDDQKSYfIPPPQMKKVMHGDRIKAVIRT--EKDKESAEPETLIEPFLTRFVGRVQKKDGRLFVVPDHPLI 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 159 PNDIFIP--KGSEGGAVDGHKVLVEIVKYP-EGRMSAEGHVLEVLGHKNDPGVDILSVIYKHGLPgefdqetldhaNSVP 235
Cdd:COG4776 107 KDAIKARpkKGLEEGLKEGDWVVAELKRHPlKGDRGFFAEITEFIADADDPFAPWWVTLARHNLE-----------REAP 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 236 NEIDPSELE----NRRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAERATSCYL 311
Cdd:COG4776 176 EGDDEWELLdeglEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKEARQRAFTNYL 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 312 VDRVIPMIPHRLSNGICSLNPQVDRLTLSCNMEFSPNGELVN-HEIFQSVINTTERMTYTDVRKILQEEDEEVskryesl 390
Cdd:COG4776 256 PGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKGEWQ------- 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 391 iPFFKGMEELAEILRNKRMARGA------------IDFDFKeakvlVDEDGTPTDVVMRERSVAERLIEEFMLAAN---- 454
Cdd:COG4776 329 -PENEEIAEQIRLLHQFALARSQwrqqhalvfkdrPDYRFE-----LDEKGNVLDIHAEPRRIANRIVEEAMIAANicaa 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 455 ETIAEHFHWMkvpfMYRIHEDPDEEKLNKFLEFITNFGYVV-KGAANTVHP-RALQELLDQVKGEPEEAvistvMLRSMR 532
Cdd:COG4776 403 RVLREHLGFG----IFNVHSGFDPEKLEQAVELLAEHGIEFdPEQLLTLEGfCALRRELDAQPTSYLDS-----RLRRFQ 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 533 Q-AKYDPENVGHFGLSADFYTHFTSPIRRYPDLIVHRLIRTYLIEGKTddktiEKWNEklyEIAKHSSEMERRAEDASRE 611
Cdd:COG4776 474 TfAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPA-----EKPDE---ELTERLAERRRLNRMAERD 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 612 TDELKKVQYMADKIGEE--YDGMISGVTNFGIFVELP-NTIEGLVHVSYLTDDyyhydeKQYAMIGERTG-------NVF 681
Cdd:COG4776 546 VADWLYARYLKPKVGSGqvFTAEIIDINRGGLRVRLLeNGAVAFIPASFIHSV------RDELVCSQEEGtvyikgeVRY 619
|
650 660
....*....|....*....|
gi 503255424 682 RIGDEIEVRLINVNVDERII 701
Cdd:COG4776 620 KLGDTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
80-701 |
9.72e-49 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 182.77 E-value: 9.72e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 80 KGFAFVktEVEHDDVY-IASAEMNGAMNKDKVLVRLHTgsTGEK----PEGAIirilERGTTRTVGTYV--DDKHygFVV 152
Cdd:PRK05054 31 KGFGFL--EVDAQKSYfIPPPQMKKVMHGDRIIAVIHT--EKDReiaePEELI----EPFLTRFVGRVQkkDDRL--SIV 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 153 PDDKRIPNDIFI--PKGSEGGAVDGHKVLVEIVKYP-EGRMSAEGHVLEVLGHKNDPGVDILSVIYKHGLPgefdqetld 229
Cdd:PRK05054 101 PDHPLLKDAIPCraAKGLNHEFKEGDWVVAELRRHPlKGDRGFYAEITQFITDADDHFAPWWVTLARHNLE--------- 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 230 haNSVPNEIDPSELEN----RRDLRDETIVTIDGADAKDLDDAVQVKKLENGNYLLGVHIADVSYYVKENSPIDKEAAER 305
Cdd:PRK05054 172 --REAPAGGVAWEMLDegleREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQR 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 306 ATSCYLVDRVIPMIPHRLSNGICSLNPQVDRLTLSCNMEFSPNGELVNH-EIFQSVINTTERMTYTDVRKIL------QE 378
Cdd:PRK05054 250 AFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDiRFFAAWIESKAKLAYDNVSDWLenggdwQP 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 379 EDEEVSKRYESLipffkgmEELAEILRNKRMARGAI-----DFDFKeakvlVDEDGTPTDVVMRERSVAERLIEEFMLAA 453
Cdd:PRK05054 330 ESEAIAEQIRLL-------HQFCLARSEWRKQHALVfkdrpDYRFE-----LGEKGEVLDIVAEPRRIANRIVEESMIAA 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 454 N----ETIAEHFHwmkvpF-MYRIHEDPDEEKLNKFLEFITNFG--YVVKGAANTVHPRALQELLDQvkgepeeavISTV 526
Cdd:PRK05054 398 NicaaRVLRDKLG-----FgIYNVHSGFDPANAEQAVALLKEHGlhFDAEELLTLEGFCKLRRELDA---------QPTG 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 527 MLRS-MRQ----AKYDPENVGHFGLSADFYTHFTSPIRRYPDLIVHRLIRTYLIEgktddKTIEKWNEklyEIAKHSSEM 601
Cdd:PRK05054 464 YLDSrIRRfqsfAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKG-----ETAERPQD---EITVQLAER 535
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 602 ERRAEDASRETDELKKVQYMADKIGEE--YDGMISGVTNFGIFVEL-PNTIEGLVHVSYLTDD----YYHYDEKQYAMIG 674
Cdd:PRK05054 536 RRLNRMAERDVGDWLYARYLKDKAGTDtrFAAEIIDISRGGMRVRLlENGAVAFIPASFLHAVrdelVCNQENGTVQIKG 615
|
650 660
....*....|....*....|....*..
gi 503255424 675 ERtgnVFRIGDEIEVRLINVNVDERII 701
Cdd:PRK05054 616 ET---VYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
625-706 |
5.82e-40 |
|
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: 141.77 E-value: 5.82e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 625 IGEEYDGMISGVTNFGIFVELPN-TIEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNVDERIIDF 703
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNlTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 503255424 704 EVV 706
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
150-223 |
1.60e-34 |
|
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: 125.97 E-value: 1.60e-34
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503255424 150 FVVPDDKRIPNDIFIPKGSEGGAVDGHKVLVEIVKYPEGRmSAEGHVLEVLGHKNDPGVDILSVIYKHGLPGEF 223
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYPDGK-NPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEF 73
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
73-130 |
6.57e-17 |
|
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: 75.27 E-value: 6.57e-17
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 503255424 73 GEVIMHPKGFAFVKTEVEHDDVYIASAEMNGAMNKDKVLVRLHTGSTGEKPEGAIIRI 130
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
624-703 |
6.67e-14 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 67.24 E-value: 6.67e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYyhydekqyamiGERTGNVFRIGDEIEVRLINVNVDERIIDF 703
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
624-701 |
5.04e-13 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 68.31 E-value: 5.04e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503255424 624 KIGEEYDGMISGVTNFGIFVEL-PntIEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNVDERII 701
Cdd:PRK08563 80 ELQEVVEGEVVEVVEFGAFVRIgP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
630-699 |
7.54e-13 |
|
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: 65.00 E-value: 7.54e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 630 DGMISGVTNFGIFVELpNTIEGLVHVSYLTDDYYHYDEKQYAMIGERTGNVFRIGDEIEVRLINVNVDER 699
Cdd:cd04460 4 EGEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKER 72
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
621-739 |
1.21e-12 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 65.82 E-value: 1.21e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 621 MADKIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERi 700
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYV-----------KDINDHLKVGDEVEVKVLNVEDDGK- 68
|
90 100 110
....*....|....*....|....*....|....*....
gi 503255424 701 IDFEVVGMKPRKERRQDRPRVIEGGIRPTRKKKGPGSEK 739
Cdd:PRK08582 69 IGLSIKKAKDRPKRQHDRPRHEDNRGGGNDVAPKEDFEQ 107
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
623-705 |
5.38e-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: 56.14 E-value: 5.38e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 623 DKIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERIID 702
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRII 69
|
...
gi 503255424 703 FEV 705
Cdd:pfam00575 70 LSI 72
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
621-700 |
8.75e-10 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 57.11 E-value: 8.75e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 621 MADKIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERI 700
Cdd:COG1098 1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYV-----------KDINDYLKVGDEVKVKVLSIDEDGKI 69
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
624-700 |
1.04e-09 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 61.72 E-value: 1.04e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTddyyhYDEKqyamiGERTGNVFRIGDEIEVRLINVNVD-ERI 700
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDIS-----WDKK-----GEEAVELYKKGDEVEAVVLKVDVEkERI 439
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
631-700 |
2.92e-09 |
|
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: 53.83 E-value: 2.92e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 631 GMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERI 700
Cdd:cd05692 6 GTVTRLKPFGAFVELGGGISGLVHISQIAHKRV-----------KDVKDVLKEGDKVKVKVLSIDARGRI 64
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
626-700 |
8.34e-09 |
|
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: 52.54 E-value: 8.34e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503255424 626 GEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERI 700
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERV-----------EKVEDVLKVGDEVKVKVIEVDDRGRI 64
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
624-700 |
1.17e-08 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 58.52 E-value: 1.17e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDdyyhydekqyamigERTGNV---FRIGDEIEVRLINVNVDERI 700
Cdd:PRK11824 620 EVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIAD--------------ERVEKVedvLKEGDEVKVKVLEIDKRGRI 685
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
626-700 |
2.44e-08 |
|
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: 51.34 E-value: 2.44e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503255424 626 GEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTddyyhydekqYAMIGERTGNVFRIGDEIEVRLINVNVD-ERI 700
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVVLNIDVErERI 66
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
624-714 |
2.95e-08 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 57.10 E-value: 2.95e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYyhydekqyamiGERTGNVFRIGDEIEVRLINVNVDERIIDF 703
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDR-----------VEDATEVLKVGDEVEAKVINIDRKNRRISL 527
|
90
....*....|.
gi 503255424 704 EVVGMKPRKER 714
Cdd:PRK06299 528 SIKALDEAEEK 538
|
|
| Pnp |
COG1185 |
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ... |
624-699 |
4.41e-08 |
|
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440798 [Multi-domain] Cd Length: 686 Bit Score: 56.55 E-value: 4.41e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDdyyhydekqyamigERTGNV---FRIGDEIEVRLInvNVDER 699
Cdd:COG1185 615 EVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELAD--------------ERVEKVedvLKEGDEVKVKVL--EIDDQ 677
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
624-699 |
1.96e-07 |
|
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: 53.89 E-value: 1.96e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDyyhydekqyamigERTGN---VFRIGDEIEVRLINVNVDER 699
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWT-------------KRVAHpsdVVKVGDEVEVKVLDIDPEER 338
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
629-699 |
2.09e-07 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 48.53 E-value: 2.09e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503255424 629 YDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDER 699
Cdd:cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKG 60
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
624-705 |
3.83e-07 |
|
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: 53.58 E-value: 3.83e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERIIDF 703
Cdd:TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRD-----------EDKTDEIKVGDEVEAKVVDIDKKNRKVSL 513
|
..
gi 503255424 704 EV 705
Cdd:TIGR00717 514 SV 515
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
72-131 |
8.11e-07 |
|
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: 46.82 E-value: 8.11e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 503255424 72 RGEVIMHPKGFAFVKTEVEHDDVYIASAE----MNGAMNKDKVLVRLHTGSTGEKPEGAIIRIL 131
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQiqggLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
148-199 |
5.10e-06 |
|
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: 44.45 E-value: 5.10e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 503255424 148 YGFVVPDDKRipNDIFIPKGSEGGAVDGHKVLVEIVKyPEGRMSAEGHVLEV 199
Cdd:pfam08206 10 FGFLIPDDEE--DDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
626-701 |
6.24e-06 |
|
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 44.53 E-value: 6.24e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503255424 626 GEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYHydekqyamigeRTGNVFRIGDEIEVRLINVNVDERII 701
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS-----------HPSDVVSVGDIVEVKVISIDEERGRI 65
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
624-710 |
6.54e-06 |
|
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 44.63 E-value: 6.54e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNT-IEGLVHVSYLTDDyyhydekqyamigeRTGNV---FRIGDEIEVRLINVNVDER 699
Cdd:cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTnVSGLCHKSEISDN--------------RVADAsklFRVGDKVRAKVLKIDAEKK 66
|
90
....*....|.
gi 503255424 700 IIDFevvGMKP 710
Cdd:cd05708 67 RISL---GLKA 74
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
625-704 |
8.17e-06 |
|
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: 44.52 E-value: 8.17e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 625 IGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYyhydekqyamigertgnvfRIGDEIEVRLINVNvDERIIDFE 704
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY-------------------EVGDEVIVQVTDIP-ENGNIDLI 75
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
625-700 |
1.84e-05 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 43.00 E-value: 1.84e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503255424 625 IGEEYDGMISGVTNFGIFVELpNTIEGLVHVSyltddyyhydEKQYAMIgERTGNVFRIGDEIEVRLINVNVD-ERI 700
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHIS----------DMSWGRV-KHPSEVVNVGDEVEVKVLKIDKErKRI 65
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
625-720 |
2.34e-05 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 48.17 E-value: 2.34e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 625 IGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTddyyhydEKQYAMIGERTGNvFRIGDEIEVRLINVNVDERIIDFE 704
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLV-------ENRDGDPGEALRK-YAVGDRVKAVIVDMNVKDRKVAFS 823
|
90
....*....|....*.
gi 503255424 705 VVGMKpRKERRQDRPR 720
Cdd:PRK12269 824 VRDYQ-RKVQRDELSR 838
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
623-701 |
2.36e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 47.56 E-value: 2.36e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 623 DKIGEEY------DGMISGVTNFGIFVELPNTIEGLVHVSYLTddyyhydekqyamiGERTGN---VFRIGDEIEVRLIN 693
Cdd:PRK06676 269 EGVEEKLpegdviEGTVKRLTDFGAFVEVLPGVEGLVHISQIS--------------HKHIATpseVLEEGQEVKVKVLE 334
|
....*...
gi 503255424 694 VNVDERII 701
Cdd:PRK06676 335 VNEEEKRI 342
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
624-714 |
2.64e-05 |
|
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: 47.42 E-value: 2.64e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTddyyhYDEKQyamigERTGNVFRIGDEIEVRLINVNVDERIIdf 703
Cdd:TIGR00717 271 PVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMS-----WVKKN-----SHPSKVVKKGDEVEVMILDIDPERRRL-- 338
|
90
....*....|.
gi 503255424 704 eVVGMKPRKER 714
Cdd:TIGR00717 339 -SLGLKQCKAN 348
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
624-709 |
5.02e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 46.70 E-value: 5.02e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYL--TDDYYHydekqyamigerTGNVFRIGDEIEVRLINVNVDERII 701
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMswTKKNKH------------PSKVVSVGQEVEVMVLEIDEEKRRI 352
|
....*...
gi 503255424 702 DfevVGMK 709
Cdd:PRK06299 353 S---LGLK 357
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
625-701 |
6.10e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 46.19 E-value: 6.10e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503255424 625 IGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERII 701
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHV-----------EVPEQVVQVGDEVFVKVIDIDLERRRI 358
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
624-721 |
8.08e-05 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 42.73 E-value: 8.08e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERIIDF 703
Cdd:PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFV-----------KDIHDFLSVGDEVKVKVLSVDEEKGKISL 74
|
90 100
....*....|....*....|
gi 503255424 704 EV--VGMKPRKERRQDRPRV 721
Cdd:PRK08059 75 SIraTEEAPEAKRKKGKILI 94
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
624-700 |
8.53e-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: 45.42 E-value: 8.53e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNtIEGLVHVSYLTddYYHYDekqyamigeRTGNVFRIGDEIEVRLINVNVD-ERI 700
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG-VDGLLHISEIS--WGRVK---------HPSEVLKVGDEVEVKVLKIDREkERI 253
|
|
| PLN00207 |
PLN00207 |
polyribonucleotide nucleotidyltransferase; Provisional |
621-695 |
2.06e-04 |
|
polyribonucleotide nucleotidyltransferase; Provisional
Pssm-ID: 215104 [Multi-domain] Cd Length: 891 Bit Score: 44.88 E-value: 2.06e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503255424 621 MADKIGEEYDGM-ISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVN 695
Cdd:PLN00207 749 MVPTVGDIYRNCeIKSIAPYGAFVEIAPGREGLCHISELSSNWL-----------AKPEDAFKVGDRIDVKLIEVN 813
|
|
| S1_RPS1_repeat_ec4 |
cd05689 |
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
626-701 |
4.47e-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: 39.48 E-value: 4.47e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503255424 626 GEEYDGMISGVTNFGIFVELPNTIEGLVHVSyltddyyhydEKQYAMIGERTGNVFRIGDEIEVRLINVNVDERII 701
Cdd:cd05689 4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVS----------EMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRI 69
|
|
| OB_Dis3 |
pfam17849 |
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ... |
150-218 |
5.68e-04 |
|
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA.
Pssm-ID: 436091 [Multi-domain] Cd Length: 77 Bit Score: 39.13 E-value: 5.68e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503255424 150 FVVPDDKRIPNdIFIPKGSEG-------GAVDGHKVLVEIVKYPEGRMSAEGHVLEVLGHKNDPGVDILSVIYKHG 218
Cdd:pfam17849 3 LFVPRDKRIPR-IRIPTKSAPeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
|
|
| PRK07252 |
PRK07252 |
S1 RNA-binding domain-containing protein; |
624-698 |
6.37e-04 |
|
S1 RNA-binding domain-containing protein;
Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 40.07 E-value: 6.37e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLinVNVDE 698
Cdd:PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFI-----------DNIHQLLKVGEEVLVQV--VDFDE 63
|
|
| S1_Rrp5_repeat_hs5 |
cd05697 |
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ... |
626-701 |
8.91e-04 |
|
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240202 [Multi-domain] Cd Length: 69 Bit Score: 38.37 E-value: 8.91e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 503255424 626 GEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYHYDEKQyamigertgnvFRIGDEIEVRLINVNVDERII 701
Cdd:cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKK-----------FKPGLKVKCRVLSVEPERKRL 65
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
631-700 |
1.45e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 41.95 E-value: 1.45e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 503255424 631 GMISGVTNFGIFVELpNTIEGLVHVSYLTddYYHYDEKqyamigertGNVFRIGDEIEVRLINVNVD-ERI 700
Cdd:PRK07899 214 GVVSSIVNFGAFVDL-GGVDGLVHVSELS--WKHIDHP---------SEVVEVGQEVTVEVLDVDMDrERV 272
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
626-661 |
1.84e-03 |
|
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Pssm-ID: 240189 [Multi-domain] Cd Length: 79 Bit Score: 37.60 E-value: 1.84e-03
10 20 30
....*....|....*....|....*....|....*....
gi 503255424 626 GEEYDGMISGVTNFGIFVELPNT---IEGLVHVSYLTDD 661
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgrKEGLVHISQLSFE 39
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
624-701 |
1.96e-03 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 41.47 E-value: 1.96e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVDERII 701
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRI-----------DKPEDVLSEGEEVKAKILEVDPEEKRI 627
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
625-700 |
2.09e-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: 41.64 E-value: 2.09e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 503255424 625 IGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYHYDEKQYamigertgnvFRIGDEIEVRLINVN-VDERI 700
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHL----------YKKGDEIEAVVLAVDkEKKRI 425
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| S1_Rrp5_repeat_hs8_sc7 |
cd04461 |
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ... |
624-701 |
2.51e-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: 37.57 E-value: 2.51e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELPNTIEGLVHVSYLTDDYYhydekqyamigERTGNVFRIGDEIEVRLINVNVD-ERII 701
Cdd:cd04461 13 KPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV-----------TDPSFGFKKGQSVTAKVTSVDEEkQRFL 80
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|
| PRK05807 |
PRK05807 |
RNA-binding protein S1; |
621-715 |
3.59e-03 |
|
RNA-binding protein S1;
Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 38.57 E-value: 3.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503255424 621 MADKIGEEYDGMISGVTNFGIFVELPNTIeGLVHVSYLTDDYYHyDEKQYamIGERtgnvfrigDEIEVRLINVNVDERI 700
Cdd:PRK05807 1 MTLKAGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVK-DIREH--LKEQ--------DKVKVKVISIDDNGKI 68
|
90
....*....|....*
gi 503255424 701 IDFEVVGMKPRKERR 715
Cdd:PRK05807 69 SLSIKQAMKQKKSVK 83
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|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
624-695 |
4.94e-03 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 40.32 E-value: 4.94e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELpNTIEGLVHVSYLTddyYHYDEKqyamigerTGNVFRIGDEIEVRLINVN 695
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEIS---WGRVEK--------PSDVLKVGDEIKVYILDID 535
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|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
624-700 |
7.64e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 39.47 E-value: 7.64e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 503255424 624 KIGEEYDGMISGVTNFGIFVELpNTIEGLVHVSYLTddYYHYdekqyamigERTGNVFRIGDEIEVRLINVNVD-ERI 700
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELS--HERV---------EKPSEVVSVGQEVEVKVLSIDWEtERI 256
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