|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
18-749 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1141.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 18 YDNpipSRELILAHLAD-RGAPATRPQLAEEFGLVTEDQLEALRRRMRAMERDGQVIYTRRGAYAPIDKLDLVRGRIAGH 96
Cdd:COG0557 1 YEN---SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGH 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 97 RDGFGFLIPDDGSDDLFLSPAQMRLVFDGDIALARVAGHDRRGRREGGLVEVVTRAHESLVGRFFQESGLAYVVPDNPKI 176
Cdd:COG0557 78 RDGFGFVIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 177 GQQVLVPEGKHGGAAHGQFVQVRIDEWPTTFRQAQGEVVEILGDYMAPGMEIEVALRSYDIPNEWPKAVEKEAAKLKPEV 256
Cdd:COG0557 158 LQDIFIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEV 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 257 EEKDKQKRIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSHYVKVGSALDAEAEKRGNSVYFPERVIPM 336
Cdd:COG0557 238 PEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPM 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 337 LPEALSNGLCSLNPQVDRLAMVCEMTIAGSGRMTGYQFYEAVIHSHARLTYNKVSTVLEQPKSAegkqLRKQLGEVVPHL 416
Cdd:COG0557 318 LPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDEE----LREEYADLVPML 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 417 EQLYSLYKVLLAARHVRGAIDFETQDTRIVFGADRKISEIRPTQRNDAHKLIEECMLCANVATAKFLEKHKVPALYRVHD 496
Cdd:COG0557 394 EELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHE 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 497 APPLEKQTNLRQFLGEMGLSLTKGKaNPVPSDYQALLQQIRERPDFRLIQTVMLRSLSQAVYSPDNNGHFGLNYEAYTHF 576
Cdd:COG0557 474 EPDPEKLEALREFLANLGLKLKGGD-EPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHF 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 577 TSPIRRYPDLLVHRAIRSVIRSKLETKhvkragatsmakarIYPYDELRLDQLGEQCSMTERRADEATRDVSNWLKCEFM 656
Cdd:COG0557 553 TSPIRRYPDLLVHRALKAYLEGKRSPG--------------LQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYM 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 657 KDRVGETYAGVITAVTGFGLFVELSEVFVEGLVHVTALPDDYYHFDSVHHRLSGERSGRSYRLGDPLEVVVARVDLDERK 736
Cdd:COG0557 619 KDRVGEEFEGVISGVTSFGLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQ 698
|
730
....*....|...
gi 516238951 737 IDFVLPASAGAPR 749
Cdd:COG0557 699 IDFELVEGGSEAP 711
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
22-741 |
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: 960.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 22 IPSRELILAHL-ADRGAPATRPQLAEEFGLVTEDQLEALRRRMRAMERDGQVIYTRRGAYAPIDKLDLVRGRIAGHRDGF 100
Cdd:TIGR02063 1 SPLRELILEFLkSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 101 GFLIP-DDGSDDLFLSPAQMRLVFDGDIALARVAGH-DRRGRREGGLVEVVTRAHESLVGRFFQESGLAYVVPDNPKIGQ 178
Cdd:TIGR02063 81 GFLRPeDDDEDDIFIPPRQMNGAMHGDRVLVRITGKpDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 179 QVLVPEGKHGGAAHGQFVQVRIDEWPTTFRQAQGEVVEILGDYMAPGMEIEVALRSYDIPNEWPKAVEKEAAKLKPEVEE 258
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 259 KDKQKRIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSHYVKVGSALDAEAEKRGNSVYFPERVIPMLP 338
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 339 EALSNGLCSLNPQVDRLAMVCEMTIAGSGRMTGYQFYEAVIHSHARLTYNKVSTVLEQPKSAEGKQlrkqlGEVVPHLEQ 418
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKE-----PPLKEMLKN 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 419 LYSLYKVLLAARHVRGAIDFETQDTRIVFGADRKISEIRPTQRNDAHKLIEECMLCANVATAKFLEKHKVPALYRVHDAP 498
Cdd:TIGR02063 396 LFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERP 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 499 PLEKQTNLRQFLGEMGLSLTKGKAN-PVPSDYQALLQQIRERPDFRLIQTVMLRSLSQAVYSPDNNGHFGLNYEAYTHFT 577
Cdd:TIGR02063 476 SEEKLQNLREFLKTLGITLKGGTSDkPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFT 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 578 SPIRRYPDLLVHRAIRSVIRskletkhvkraGATSMAKARIYPYDELRLDQLGEQCSMTERRADEATRDVSNWLKCEFMK 657
Cdd:TIGR02063 556 SPIRRYPDLIVHRLIKKALF-----------GGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMS 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 658 DRVGETYAGVITAVTGFGLFVELSEVFVEGLVHVTALPDDYYHFDSVHHRLSGERSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:TIGR02063 625 EKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKI 704
|
....
gi 516238951 738 DFVL 741
Cdd:TIGR02063 705 DFEL 708
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
6-772 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 958.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 6 SLDPEAAREAEKYDNPIPSRELILAHLADRGAPATRPQLAEEFGLVTEDQLEALRRRMRAMERDGQVIYTRRGAYAPIDK 85
Cdd:PRK11642 2 SQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 86 LDLVRGRIAGHRDGFGFLIPDDGSDDLFLSPAQMRLVFDGDIALARVAGHDRRGRREGGLVEVVTRAHESLVGRFFQESG 165
Cdd:PRK11642 82 LDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAG 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 166 LAYVVPDNPKIGQQVLVPEGKHGGAAHGQFVQVRIDEWPTTFRQAQGEVVEILGDYMAPGMEIEVALRSYDIPNEWPKAV 245
Cdd:PRK11642 162 VGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 246 EKEAAKLKPEVEEKDKQKRIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSHYVKVGSALDAEAEKRGN 325
Cdd:PRK11642 242 EQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGT 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 326 SVYFPERVIPMLPEALSNGLCSLNPQVDRLAMVCEMTIAGSGRMTGYQFYEAVIHSHARLTYNKVSTVLeqpksaEGKQ- 404
Cdd:PRK11642 322 SVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHIL------QGDQd 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 405 LRKQLGEVVPHLEQLYSLYKVLLAARHVRGAIDFETQDTRIVFGADRKISEIRPTQRNDAHKLIEECMLCANVATAKFLE 484
Cdd:PRK11642 396 LREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVE 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 485 KHKVPALYRVHDAPPLEKQTNLRQFLGEMGLSLtKGKANPVPSDYQALLQQIRERPDFRLIQTVMLRSLSQAVYSPDNNG 564
Cdd:PRK11642 476 KAKEPALFRIHDKPSTEAITSFRSVLAELGLEL-PGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRG 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 565 HFGLNYEAYTHFTSPIRRYPDLLVHRAIRSVIRSklETKHVKRAGATSMakariYPYDELRLDQLGEQCSMTERRADEAT 644
Cdd:PRK11642 555 HFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAK--EQGHKGNTTETGG-----YHYSMEEMLQLGQHCSMTERRADEAT 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 645 RDVSNWLKCEFMKDRVGETYAGVITAVTGFGLFVELSEVFVEGLVHVTALPDDYYHFDSVHHRLSGERSGRSYRLGDPLE 724
Cdd:PRK11642 628 RDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVE 707
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|
gi 516238951 725 VVVARVDLDERKIDFVLPASAGAPRV--REEREpRQKRGNRRRGAPAPAQ 772
Cdd:PRK11642 708 VRVEAVNMDERKIDFSLISSERAPRNvgKTARE-KAKKGDAGKKGGKRRQ 756
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
80-741 |
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: 772.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 80 YAPIDKLDLVRGRIAGHRDGFGFLIPDDGS-DDLFLSPAQMRLVFDGDIALARVAGHDRRGRREGGLVEVVTRAHESLVG 158
Cdd:TIGR00358 8 YALPEKDDLVKGVVKAHNKGFGFLRPDDDDkKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFVG 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 159 RFFQESGLAYVVPDNPKIGQQVLVPEGKH-GGAAHGQFVQVRIDEWPTTFRQAQGEVVEILGDYMAPGMEIEVALRSYDI 237
Cdd:TIGR00358 88 KFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEI 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 238 PNEWPKAVEKEAAKLKPEVEEKDKQKRIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSHYVKVGSALD 317
Cdd:TIGR00358 168 PFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLD 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 318 AEAEKRGNSVYFPERVIPMLPEALSNGLCSLNPQVDRLAMVCEMTIAGSGRMTGYQFYEAVIHSHARLTYNKVSTVLEQp 397
Cdd:TIGR00358 248 KEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLEN- 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 398 ksaeGKQLRKQLGEVVPHLEQLYSLYKVLLAARHVRGAIDFETQDTRIVFGADRKISEIRPTQRNDAHKLIEECMLCANV 477
Cdd:TIGR00358 327 ----DDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANI 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 478 ATAKFLEKHKVPALYRVHDAPPLEKQTNLRQFLGEMGLSLTKGKANPV-PSDYQALLQQIRERPDFRLIQTVMLRSLSQA 556
Cdd:TIGR00358 403 CAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVtTLDGACWLREVKDRPEYEILVTRLLRSLSQA 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 557 VYSPDNNGHFGLNYEAYTHFTSPIRRYPDLLVHRAIRSVIrSKLETkhvkragatsmAKARIYPYDElrLDQLGEQCSMT 636
Cdd:TIGR00358 483 EYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVL-AKEQT-----------DTERYQPQDE--LLQIAEHCSDT 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 637 ERRADEATRDVSNWLKCEFMKDRVGETYAGVITAVTGFGLFVELSEVFVEGLVHVTALPDDYYHFDSVHHRLSGERSGRS 716
Cdd:TIGR00358 549 ERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKV 628
|
650 660
....*....|....*....|....*
gi 516238951 717 YRLGDPLEVVVARVDLDERKIDFVL 741
Cdd:TIGR00358 629 YRIGDRVTVKLTEVNMETRSIIFEL 653
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
264-597 |
1.35e-137 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 415.13 E-value: 1.35e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 264 RIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSHYVKVGSALDAEAEKRGNSVYFPERVIPMLPEALSN 343
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 344 GLCSLNPQVDRLAMVCEMTI-AGSGRMTGYQFYEAVIHSHARLTYNKVSTVLEqpksaegkqlrkqlgevvphleqlysl 422
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLdADGGEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 423 ykvllaarhvrgaidfetqdtRIVFGADRKISEIRPTQRNDAHKLIEECMLCANVATAKFLEKHKVPALYRVHDAPPLEK 502
Cdd:smart00955 134 ---------------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEK 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 503 QTN-LRQFLGEMGLSLTKGkanPVPSDYQALLQQIRERPDFRLIQTVMLRSLSQAVYSPDNNGHFGLNYEAYTHFTSPIR 581
Cdd:smart00955 193 LAElLKEFLALLGLLLLGG---DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIR 269
|
330
....*....|....*.
gi 516238951 582 RYPDLLVHRAIRSVIR 597
Cdd:smart00955 270 RYPDLIVHRQLKAALR 285
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
264-596 |
4.57e-131 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 399.35 E-value: 4.57e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 264 RIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSHYVKVGSALDAEAEKRGNSVYFPERVIPMLPEALSN 343
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 344 GLCSLNPQVDRLAMVCEMTIAGSGRMTGYQFYEAVIHSHARLTYNKVSTVLEQPKSAEGKqlrkqlGEVVPHLEQLYSLY 423
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK------PDLAEDLRLLYELA 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 424 KVLLAARHVRGAIDFETQDTRIVFGADRKIsEIRPTQRNDAHKLIEECMLCANVATAKFLEKHKVPALYRVHDAPPLEKQ 503
Cdd:pfam00773 155 KILRAKRLQRGALDLDTPENKLILDEEGVI-DILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 504 TNLRQFLGEmglsltkgkanpvPSDYQALLQQIRERPD-FRLIQTVMLRSLSQAVYSPDNNGHFGLNYEAYTHFTSPIRR 582
Cdd:pfam00773 234 NSLIKLLQL-------------LPDDKGLSKSLEKIKDdERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRR 300
|
330
....*....|....
gi 516238951 583 YPDLLVHRAIRSVI 596
Cdd:pfam00773 301 YPDLIVHRQLKALL 314
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
84-737 |
4.79e-96 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 318.34 E-value: 4.79e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 84 DKLDLVRGRIAGHRDGFGFLIPDDGSDdLFLSPAQMRLVFDGDIALARVaghdrrgRREGG--------LVE-VVTRahe 154
Cdd:COG4776 17 EQTPRVEGVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVI-------RTEKDkesaepetLIEpFLTR--- 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 155 sLVGRFFQESGLAYVVPDNPKIGQQVL------VPEG-KHGGAAHGQFVQ--VRIDewpttfRQAQGEVVEILGDYMAPG 225
Cdd:COG4776 86 -FVGRVQKKDGRLFVVPDHPLIKDAIKarpkkgLEEGlKEGDWVVAELKRhpLKGD------RGFFAEITEFIADADDPF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 226 MEIEVALRSYDIPNEWPKAVEkeaaklkpEVEEKDKQ-KRIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIA 304
Cdd:COG4776 159 APWWVTLARHNLEREAPEGDD--------EWELLDEGlEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIA 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 305 DVSHYVKVGSALDAEAEKRGNSVYFPERVIPMLPEALSNGLCSLNPQVDRLAMVCEMTIAGSGRMTG-YQFYEAVIHSHA 383
Cdd:COG4776 231 DPTAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKA 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 384 RLTYNKVSTVLEQPKS--AEGKQLRKQlgevvphLEQLYSLYKVLLAARHvRGAIDFETQ-DTRIVFGADRKISEIRPTQ 460
Cdd:COG4776 311 KLAYDNVSDWLEGKGEwqPENEEIAEQ-------IRLLHQFALARSQWRQ-QHALVFKDRpDYRFELDEKGNVLDIHAEP 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 461 RNDAHKLIEECMLCANVATAKFLEKHKVPALYRVHDAPPLEKQTNLRQFLGEMGLSLTKGKANPVPsDYQALLQQIRERP 540
Cdd:COG4776 383 RRIANRIVEEAMIAANICAARVLREHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLE-GFCALRRELDAQP 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 541 ----DFRLiqtvmLRSLSQAVYSPDNNGHFGLNYEAYTHFTSPIRRYPDLLVHRAIRSVIRsklETKHVKragatsmaka 616
Cdd:COG4776 462 tsylDSRL-----RRFQTFAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVIL---GQPAEK---------- 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 617 riyPYDELrLDQLGEQcsmteRRADE-ATRDVSNWLKCEFMKDRVGE--TYAGVITAVTGFGLFVELSE----VFVEG-L 688
Cdd:COG4776 524 ---PDEEL-TERLAER-----RRLNRmAERDVADWLYARYLKPKVGSgqVFTAEIIDINRGGLRVRLLEngavAFIPAsF 594
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....
gi 516238951 689 VH-----VTALPDDyyhfDSVhhRLSGErsgRSYRLGDPLEVVVARVDLDERKI 737
Cdd:COG4776 595 IHsvrdeLVCSQEE----GTV--YIKGE---VRYKLGDTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
84-737 |
2.54e-84 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 286.39 E-value: 2.54e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 84 DKLDLVRGRIAGHRDGFGFLIPDDGSDdLFLSPAQMRLVFDGD--IALARVAGhDRRGRREGGLVE-VVTRahesLVGRF 160
Cdd:PRK05054 17 SQTPRVEGVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDriIAVIHTEK-DREIAEPEELIEpFLTR----FVGRV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 161 FQESGLAYVVPDNPKIGQQV-------LVPEGKHGGAAHGQFVQ--VRIDewpttfRQAQGEVVEIL---GDYMAPGMei 228
Cdd:PRK05054 91 QKKDDRLSIVPDHPLLKDAIpcraakgLNHEFKEGDWVVAELRRhpLKGD------RGFYAEITQFItdaDDHFAPWW-- 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 229 eVALRSYDIPNEWPkAVEKEAAKLKPEVEekdkqkRIDLRQLPFVTIDGEDARDFDDAVYAEAKKSGGWRLYVAIADVSH 308
Cdd:PRK05054 163 -VTLARHNLEREAP-AGGVAWEMLDEGLE------REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTA 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 309 YVKVGSALDAEAEKRGNSVYFPERVIPMLPEALSNGLCSLNPQVDRLAMVCEMTIAGSGRMTG-YQFYEAVIHSHARLTY 387
Cdd:PRK05054 235 YIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAY 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 388 NKVSTVLE-----QPKSAEGKQlrkqlgevvphleQLYSLYKVLLAARHVR--GAIDFETQ-DTRIVFGADRKISEIRPT 459
Cdd:PRK05054 315 DNVSDWLEnggdwQPESEAIAE-------------QIRLLHQFCLARSEWRkqHALVFKDRpDYRFELGEKGEVLDIVAE 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 460 QRNDAHKLIEECMLCANVATAKFLEKHKVPALYRVHDAPPLEKQTNLRQFLGEMGLSLTKGKANPVPSdYQALLQQIRER 539
Cdd:PRK05054 382 PRRIANRIVEESMIAANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEG-FCKLRRELDAQ 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 540 P----DFRLiqtvmLRSLSQAVYSPDNNGHFGLNYEAYTHFTSPIRRYPDLLVHRAIRSVIRSKLETKhvkragatsmak 615
Cdd:PRK05054 461 PtgylDSRI-----RRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAER------------ 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 616 ariyPYDELrLDQLGEQcsmteRRADE-ATRDVSNWLKCEFMKDRVGE--TYAGVITAVTGFGLFVELSE----VFVEG- 687
Cdd:PRK05054 524 ----PQDEI-TVQLAER-----RRLNRmAERDVGDWLYARYLKDKAGTdtRFAAEIIDISRGGMRVRLLEngavAFIPAs 593
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*....
gi 516238951 688 LVHvtalpddyyhfdSVHHRL--SGErSGR-------SYRLGDPLEVVVARVDLDERKI 737
Cdd:PRK05054 594 FLH------------AVRDELvcNQE-NGTvqikgetVYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
660-741 |
2.99e-43 |
|
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: 151.40 E-value: 2.99e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 660 VGETYAGVITAVTGFGLFVELSEVFVEGLVHVTALPDDYYHFDSVHHRLSGERSGRSYRLGDPLEVVVARVDLDERKIDF 739
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
..
gi 516238951 740 VL 741
Cdd:cd04471 81 EL 82
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
168-242 |
1.13e-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: 109.40 E-value: 1.13e-28
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516238951 168 YVVPDNPKIGQQVLVPEGKHGGAAHGQFVQVRIDEWPTTfRQAQGEVVEILGDYMAPGMEIEVALRSYDIPNEWP 242
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYPDG-KNPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
91-148 |
1.75e-22 |
|
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: 91.45 E-value: 1.75e-22
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 516238951 91 GRIAGHRDGFGFLIPDDGSDDLFLSPAQMRLVFDGDIALARVAGHDRRGRREGGLVEV 148
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
659-739 |
4.38e-11 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 59.54 E-value: 4.38e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 659 RVGETYAGVITAVTGFGLFVELSEvFVEGLVHVTALPDDYyhfdsvhhrlsGERSGRSYRLGDPLEVVVARVDLDERKID 738
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
.
gi 516238951 739 F 739
Cdd:smart00316 69 L 69
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
658-739 |
2.78e-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: 57.30 E-value: 2.78e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 658 DRVGETYAGVITAVTGFGLFVELsEVFVEGLVHVTALPDDYYhfdsvhhrlsgERSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRI 68
|
..
gi 516238951 738 DF 739
Cdd:pfam00575 69 IL 70
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
90-149 |
6.53e-10 |
|
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: 56.07 E-value: 6.53e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516238951 90 RGRIAGHRDGFGFLIPDDGSDDLFLSPAQ----MRLVFDGDIALARVAGHDRRGRREGGLVEVV 149
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQiqggLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
666-737 |
1.11e-08 |
|
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: 53.45 E-value: 1.11e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516238951 666 GVITAVTGFGLFVELSEVfvEGLVHVTALPDDYYHFDSVHHRLSGERSGRSYRLGDpleVVVAR---VDLDERKI 737
Cdd:cd04460 5 GEVVEVVDFGAFVRIGPV--DGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGD---VVRARivaVSLKERRP 74
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
666-737 |
1.32e-08 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 55.60 E-value: 1.32e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516238951 666 GVITAVTGFGLFVELSEVfvEGLVHVTALPDDYYHFDSVHHRLSGERSGRSYRLGDpleVVVAR---VDLDERKI 737
Cdd:PRK08563 87 GEVVEVVEFGAFVRIGPV--DGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGD---VVRARivaVSLKERRP 156
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
660-744 |
1.71e-07 |
|
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: 49.64 E-value: 1.71e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 660 VGETYAGVITAVTGFGLFVELSEVFVEGLVHVTALPDDyyhfdsvhhrlSGERSGRSYRLGDPLEVVVARVDLDERKIDF 739
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRISL 70
|
....*
gi 516238951 740 VLPAS 744
Cdd:cd05708 71 GLKAS 75
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
654-737 |
5.37e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 53.63 E-value: 5.37e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 654 EFM-KDRVGETYAGVITAVTGFGLFVELsEVFVEGLVHVtalpddyyhFDSVHHRlSGERSGRSYRLGDPLEVVVARVDL 732
Cdd:PRK06299 366 EFAeKYPVGDVVEGKVKNITDFGAFVGL-EGGIDGLVHL---------SDISWDK-KGEEAVELYKKGDEVEAVVLKVDV 434
|
....*
gi 516238951 733 DERKI 737
Cdd:PRK06299 435 EKERI 439
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
661-737 |
1.38e-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: 46.72 E-value: 1.38e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516238951 661 GETYAGVITAVTGFGLFVELSEvFVEGLVHVTALPddyyhfdsvhHRLSGERSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
664-737 |
3.50e-06 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 45.45 E-value: 3.50e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 516238951 664 YAGVITAVTGFGLFVELsEVFVEGLVHVTALPDDYYHFDSVHhrlsgersgrsYRLGDPLEVVVARVDLDERKI 737
Cdd:cd00164 1 VTGKVVSITKFGVFVEL-EDGVEGLVHISELSDKFVKDPSEV-----------FKVGDEVEVKVLEVDPEKGRI 62
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
660-737 |
5.47e-06 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 49.66 E-value: 5.47e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 516238951 660 VGETYAGVITAVTGFGLFVELSEVfVEGLVHVTALpddyyhfdSVHHRLsgERSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:COG0539 274 VGDVVKGKVTRLTDFGAFVELEPG-VEGLVHISEM--------SWTKRV--AHPSDVVKVGDEVEVKVLDIDPEERRI 340
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
26-81 |
6.38e-06 |
|
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.
Pssm-ID: 285637 [Multi-domain] Cd Length: 66 Bit Score: 44.70 E-value: 6.38e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 516238951 26 ELILAHLADRGAPATRPQLAEEFGLVTED-QLEALRRRMRAMERDGqviYTRRGAYA 81
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYA 54
|
|
| PRK07764 |
PRK07764 |
DNA polymerase III subunits gamma and tau; Validated |
702-936 |
1.27e-05 |
|
DNA polymerase III subunits gamma and tau; Validated
Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 49.21 E-value: 1.27e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 702 DSVHHRLSGERSGRSYRLgdPLEVVVARVdlderkidfVLPASAGAPRVREEREPRQKRGNRRRGAPAPAQEPSALPVAE 781
Cdd:PRK07764 336 DVVNDGLTEMRGATSPRL--LLELLCARM---------LLPSASDDERGLLARLERLERRLGVAGGAGAPAAAAPSAAAA 404
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 782 TATETVSPE-PERESRRSRNGRRRGTPAPAQEPSALPDAETATETVSPEPEREPRRSRNGRRrdAPTQEQGVAATVEAAP 860
Cdd:PRK07764 405 APAAAPAPAaAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQP--APAPAAAPEPTAAPAP 482
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 861 ASvspepeseprrsrserrratSSAQQQNASTPMPASVEATPSKSSRQD-----DQLLGnTDVRRSRAVKQALLAEAKVE 935
Cdd:PRK07764 483 AP--------------------PAAPAPAAAPAAPAAPAAPAGADDAATlrerwPEILA-AVPKRSRKTWAILLPEATVL 541
|
.
gi 516238951 936 G 936
Cdd:PRK07764 542 G 542
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
659-737 |
2.54e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 48.24 E-value: 2.54e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516238951 659 RVGETYAGVITAVTGFGLFVELSEvFVEGLVHVTALPDDyyhfdsvhhrlSGERSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRD-----------RVEDATEVLKVGDEVEAKVINIDRKNRRI 525
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
585-739 |
2.89e-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: 47.81 E-value: 2.89e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 585 DLLVHRAIRSVIRSKLETKHVKRAGATSMAKAriypydeLRLDQLGEQCSMTERR-ADEATRDVSNwlkcefmKDRVGET 663
Cdd:TIGR00717 384 DGLIHLSDISWDKDGREADHLYKKGDEIEAVV-------LAVDKEKKRISLGVKQlTENPWEKFAA-------KYKVGSV 449
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516238951 664 YAGVITAVTGFGLFVELSEVfVEGLVHVTALPDDYYhfdsvhhrlsgERSGRSYRLGDPLEVVVARVDLDERKIDF 739
Cdd:TIGR00717 450 VKGKVTEIKDFGAFVELPGG-VEGLIRNSELSENRD-----------EDKTDEIKVGDEVEAKVVDIDKKNRKVSL 513
|
|
| PRK12323 |
PRK12323 |
DNA polymerase III subunit gamma/tau; |
742-862 |
9.34e-05 |
|
DNA polymerase III subunit gamma/tau;
Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 46.41 E-value: 9.34e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 742 PASAGAPRVRE-----EREPRQKRGNRRRGAPAPAQEPSALPVAETATETVSPEPERESRRSRNGRRRGTPAPAQEPSAL 816
Cdd:PRK12323 417 RAVAAAPARRSpapeaLAAARQASARGPGGAPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDP 496
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 516238951 817 PDAETATETVsPEPEREPRRSRNGRRRDAPTQEQGVAATVEAAPAS 862
Cdd:PRK12323 497 PPWEELPPEF-ASPAPAQPDAAPAGWVAESIPDPATADPDDAFETL 541
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
661-737 |
2.23e-04 |
|
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: 40.29 E-value: 2.23e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516238951 661 GETYAGVITAVTGFGLFVELSeVFVEGLVHVTALPDDYyhfdsVHHRLsgERSGrsyrLGDPLEVVVARVDLDERKI 737
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMADRF-----VSHPS--DVVS----VGDIVEVKVISIDEERGRI 65
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
660-741 |
2.29e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 44.87 E-value: 2.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 660 VGETYAGVITAVTGFGLFVELSEvfVEGLVHVTALpdDYYHFDSVHHRLSgersgrsyrLGDPLEVVVARVDLDERKIDF 739
Cdd:PRK06676 192 EGDVVEGTVARLTDFGAFVDIGG--VDGLVHISEL--SHERVEKPSEVVS---------VGQEVEVKVLSIDWETERISL 258
|
..
gi 516238951 740 VL 741
Cdd:PRK06676 259 SL 260
|
|
| PRK07003 |
PRK07003 |
DNA polymerase III subunit gamma/tau; |
742-906 |
2.49e-04 |
|
DNA polymerase III subunit gamma/tau;
Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 45.23 E-value: 2.49e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 742 PASAGAPRVreerePRQKRGNRRRGAPAPAQE--PSALPVAETATETVSPEPERESRRSRNGRRRGTPAPAQ-------- 811
Cdd:PRK07003 368 PGGGVPARV-----AGAVPAPGARAAAAVGASavPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPAtadrgdda 442
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 812 ---EPSALPDAETATETVSPEPEREPRRSRNGRRRDAPTQEQGVAATVEAAPASVSPEPESEPRRSRSERRRATSSAQQ- 887
Cdd:PRK07003 443 adgDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAp 522
|
170
....*....|....*....
gi 516238951 888 QNASTPMPASVEATPSKSS 906
Cdd:PRK07003 523 AAAAPPAPEARPPTPAAAA 541
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
660-737 |
3.96e-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: 43.88 E-value: 3.96e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 660 VGETYAGVITAVTGFGLFVELSEvfVEGLVHVTAL-------PDDYYHfdsvhhrlsgersgrsyrLGDPLEVVVARVDL 732
Cdd:COG0539 189 EGDVVEGTVKNITDFGAFVDLGG--VDGLLHISEIswgrvkhPSEVLK------------------VGDEVEVKVLKIDR 248
|
....*
gi 516238951 733 DERKI 737
Cdd:COG0539 249 EKERI 253
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
661-694 |
4.85e-04 |
|
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: 39.91 E-value: 4.85e-04
10 20 30
....*....|....*....|....*....|....*.
gi 516238951 661 GETYAGVITAVTGFGLFVELSEV--FVEGLVHVTAL 694
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQL 36
|
|
| OB_Dis3 |
pfam17849 |
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ... |
193-236 |
8.06e-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: 8.06e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 516238951 193 GQFVQVRIDEWPTTFRQAQGEVVEILGDY--MAPgmEIEVALRSYD 236
Cdd:pfam17849 34 GKLFVVKIDDWPENSRYPLGHIVKVLGEIgdIET--ETEAILLENG 77
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
657-737 |
8.94e-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: 43.18 E-value: 8.94e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 657 KDRVGETYAGVITAVTGFGLFVELsEVFVEGLVHVtalpddyyhfdsvhHRLSGERSGR----SYRLGDPLEVVVARVDL 732
Cdd:TIGR00717 356 KHPVGDRVTGKIKKITDFGAFVEL-EGGIDGLIHL--------------SDISWDKDGReadhLYKKGDEIEAVVLAVDK 420
|
....*
gi 516238951 733 DERKI 737
Cdd:TIGR00717 421 EKKRI 425
|
|
| PRK07764 |
PRK07764 |
DNA polymerase III subunits gamma and tau; Validated |
742-931 |
9.14e-04 |
|
DNA polymerase III subunits gamma and tau; Validated
Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.44 E-value: 9.14e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 742 PASAGAPRVREEREPRQKRGNRRRGAPAPAQEPSA----------LPVAETATETVSPEPERESRRSRNGRRRGTPAPAQ 811
Cdd:PRK07764 601 PAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAApaeasaapapGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAA 680
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 812 EPSALPDAETATETVSPEPE---REPRRSRNGRRRDAPTQEQGVAATVEAAPASVSPEPESEPRRSRSERRRATSSAQQQ 888
Cdd:PRK07764 681 PPPAPAPAAPAAPAGAAPAQpapAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPP 760
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 516238951 889 NASTPMPASVEATPSKSSRQDDQLL--------GNTDVRRSRAVKQALLAE 931
Cdd:PRK07764 761 PPAPAPAAAPAAAPPPSPPSEEEEMaeddapsmDDEDRRDAEEVAMELLEE 811
|
|
| PRK12323 |
PRK12323 |
DNA polymerase III subunit gamma/tau; |
742-907 |
1.27e-03 |
|
DNA polymerase III subunit gamma/tau;
Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 42.94 E-value: 1.27e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 742 PASAGAPRVREEREPRQKRGNRRRGAPAPAQEPSALPVAETATETVSPEPERESRRSRNGRRRG------------TPAP 809
Cdd:PRK12323 381 PVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPggapapapapaaAPAA 460
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 810 AQEPSALPDAETATETVSPEPEREPRRSRNGRRRDAPTQEQGVAATVEAAPASVSPEPESEPRRSRSERRRATSSAQQQN 889
Cdd:PRK12323 461 AARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFET 540
|
170
....*....|....*...
gi 516238951 890 ASTPMPASVEATPSKSSR 907
Cdd:PRK12323 541 LAPAPAAAPAPRAAAATE 558
|
|
| S1_RPS1_repeat_ec4 |
cd05689 |
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
661-737 |
1.31e-03 |
|
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240194 [Multi-domain] Cd Length: 72 Bit Score: 38.33 E-value: 1.31e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516238951 661 GETYAGVITAVTGFGLFVELSEvFVEGLVHVTALpdDYYHfDSVHhrlsgerSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:cd05689 4 GTRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEM--DWTN-KNIH-------PSKVVSLGDEVEVMVLDIDEERRRI 69
|
|
| PRK06347 |
PRK06347 |
1,4-beta-N-acetylmuramoylhydrolase; |
808-969 |
1.31e-03 |
|
1,4-beta-N-acetylmuramoylhydrolase;
Pssm-ID: 180536 [Multi-domain] Cd Length: 592 Bit Score: 42.76 E-value: 1.31e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 808 APAQEPSALPDAETATE---TVSPE----PEREPRRSRNGRRRDAPTQEQGVAATVEAAPASvspepeseprrsrserrR 880
Cdd:PRK06347 56 APADEASKSAEANTTKEapaTATPEnttePTVEPKQTETKEQTKTPEEKQPAAKQVEKAPAE-----------------P 118
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 881 ATSSAQQQNASTPMP--------------ASVEATPSKSSRQDDQLLGNTDVRRSRAVKQALLAEA---KVEGGKPK--- 940
Cdd:PRK06347 119 ATVSNPDNATSSSTPatynllqksalrsgATVQSFIQTIQASSSQIAAENDLYASVMIAQAILESAygtSELGSAPNynl 198
|
170 180 190
....*....|....*....|....*....|....*..
gi 516238951 941 --TVGKANGKAKGNA---DKGKA---SDTAKTRTAPA 969
Cdd:PRK06347 199 fgIKGAYNGQSYTKQtleDDGKGnyyTITAKFRKYPS 235
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
660-761 |
3.01e-03 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 38.87 E-value: 3.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 660 VGETYAGVITAVTGFGLFVELSEVfVEGLVHVTALPDDYyhFDSVHHRLSgersgrsyrLGDPLEVVVARVDLDERKIDF 739
Cdd:PRK08059 7 VGSVVTGKVTGIQPYGAFVALDEE-TQGLVHISEITHGF--VKDIHDFLS---------VGDEVKVKVLSVDEEKGKISL 74
|
90 100
....*....|....*....|..
gi 516238951 740 VLPASAGAPrvreEREPRQKRG 761
Cdd:PRK08059 75 SIRATEEAP----EAKRKKGKI 92
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
666-735 |
3.17e-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: 37.26 E-value: 3.17e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 666 GVITAVTGFGLFVELSEvFVEGLVHVTALPDDYyhFDSVHHRLsgersgrsyRLGDPLEVVVARVDLDER 735
Cdd:cd05692 6 GTVTRLKPFGAFVELGG-GISGLVHISQIAHKR--VKDVKDVL---------KEGDKVKVKVLSIDARGR 63
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
639-737 |
5.14e-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: 40.49 E-value: 5.14e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 639 RADEATRDVSNWLK-------CEFMKD-RVGETYAGVITAVTGFGLFVELSEVfVEGLVHVTALPDDYyhfdsvhhrlSG 710
Cdd:TIGR00717 243 KFDKEKGRISLSLKqlgedpwEAIEKKfPVGDKITGRVTNLTDYGVFVEIEEG-IEGLVHVSEMSWVK----------KN 311
|
90 100
....*....|....*....|....*..
gi 516238951 711 ERSGRSYRLGDPLEVVVARVDLDERKI 737
Cdd:TIGR00717 312 SHPSKVVKKGDEVEVMILDIDPERRRL 338
|
|
| PRK14951 |
PRK14951 |
DNA polymerase III subunits gamma and tau; Provisional |
735-895 |
6.43e-03 |
|
DNA polymerase III subunits gamma and tau; Provisional
Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 40.47 E-value: 6.43e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 735 RKIDFVLPASAGAPRVREEREPrqkrgnrrrgAPAPAQEPSALPVAETATETVSPEPERESRRsrngrrrgtPAPAQEPS 814
Cdd:PRK14951 360 RLLAFKPAAAAEAAAPAEKKTP----------ARPEAAAPAAAPVAQAAAAPAPAAAPAAAAS---------APAAPPAA 420
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 815 ALPDAETATETVSPEPEREPRRSRNGRRRDAPTQeqgvaatveAAPASVSPEPESEPRRSRSERRRATSSAQQQNASTPM 894
Cdd:PRK14951 421 APPAPVAAPAAAAPAAAPAAAPAAVALAPAPPAQ---------AAPETVAIPVRVAPEPAVASAAPAPAAAPAAARLTPT 491
|
.
gi 516238951 895 P 895
Cdd:PRK14951 492 E 492
|
|
| PRK07994 |
PRK07994 |
DNA polymerase III subunits gamma and tau; Validated |
767-931 |
7.87e-03 |
|
DNA polymerase III subunits gamma and tau; Validated
Pssm-ID: 236138 [Multi-domain] Cd Length: 647 Bit Score: 40.23 E-value: 7.87e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 767 APAPAQEPSALPVAETATETVSPEPERESRRSRNGRRRGTPAPAQEPSALPDAETATETVSPEPEReprrsrngrrrdap 846
Cdd:PRK07994 365 LPEPEVPPQSAAPAASAQATAAPTAAVAPPQAPAVPPPPASAPQQAPAVPLPETTSQLLAARQQLQ-------------- 430
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516238951 847 tQEQGVAATVEAAPASVSPEPESEPRRSRSerrraTSSAQQQNASTPMPASVEATPSKSsrQDDQLLGNTDVRRSRAVKQ 926
Cdd:PRK07994 431 -RAQGATKAKKSEPAAASRARPVNSALERL-----ASVRPAPSALEKAPAKKEAYRWKA--TNPVEVKKEPVATPKALKK 502
|
....*
gi 516238951 927 ALLAE 931
Cdd:PRK07994 503 ALEHE 507
|
|
| |
