|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-803 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1696.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 1 MSHDPFQEREAEKYANPIPSREFILEHLTKREKPANRDELASELGIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
Cdd:PRK11642 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 81 RLDLQKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDIVLAQPLGSDRKGRREARIVRVLVPKQSNIVGRYFTDA 160
Cdd:PRK11642 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 161 GVGFVVPDDSRLSFDILIPPEEVMGARMGYVVVVELTQRPTRRTKAIGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPKA 240
Cdd:PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 241 VEEQIAHLKEEVPEEAKVGRVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVRPPTPLDNEARNRG 320
Cdd:PRK11642 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDEDLRSQY 400
Cdd:PRK11642 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 401 QPLVKHLEELHTLYKALEEARTERGGISFESEEAKFIFNAERRIDRIEQTQRNDAHKLIEECMILANISAARFVEKHKEP 480
Cdd:PRK11642 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 481 ALFRIHDRPTNEAITSFRSVLAELGLELPGGNKPEPRDYAELLDSIADRPDHEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
Cdd:PRK11642 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 561 QSYAHFTSPIRRYPDLTLHRAIKYLIAKEQGHEGNTTESGGWHYTMEEMLQLGQHCSMTERRADEATREVADWLKCDFMQ 640
Cdd:PRK11642 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFML 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 641 DQVGQTFSGVISSVTGFGFFVRLTDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDERKI 720
Cdd:PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 721 DFSLISSERGPRNVGKTAREREKRGG-GAKNRSRRQVGKRQNFEPNEAFRSEKGRGKVKKdgaaraeksDKPAKSSKKPS 799
Cdd:PRK11642 721 DFSLISSERAPRNVGKTAREKAKKGDaGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAA---------KKDARKAKKPS 791
|
....
gi 495127521 800 AKTQ 803
Cdd:PRK11642 792 AKTQ 795
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
20-732 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1152.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 20 SREFILEHLTK-REKPANRDELASELGIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPERLDLQKGTVIGHRDGYGF 98
Cdd:COG0557 4 SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFGF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 99 LRVEGRKDDLYLSSEQMKTCIHGDIVLAQPLGSDRKGRREARIVRVLVPKQSNIVGRYFTDAGVGFVVPDDSRLSFDILI 178
Cdd:COG0557 84 VIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDIFI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 179 PPEEVMGARMGYVVVVELTQRPTRRTKAIGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPKAVEEQIAHLKEEVPEEAKV 258
Cdd:COG0557 164 PPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEADLK 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 259 GRVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVRPPTPLDNEARNRGTSVYFPSQVVPMLPEVLS 338
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLS 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 339 NGLCSLNPQVDRLCMVCEMTISAKGRLTGYKFYEAVMSSHARLTYTKVWHILQG-DEDLRSQYQPLVKHLEELHTLYKAL 417
Cdd:COG0557 324 NGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELYELAKIL 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 418 EEARTERGGISFESEEAKFIFNAERRIDRIEQTQRNDAHKLIEECMILANISAARFVEKHKEPALFRIHDRPTNEAITSF 497
Cdd:COG0557 404 RKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLEAL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 498 RSVLAELGLELPGGNKPEPRDYAELLDSIADRPDHEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLT 577
Cdd:COG0557 484 REFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYPDLL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 578 LHRAIKYLIAKEQGhegntteSGGWHYTMEEMLQLGQHCSMTERRADEATREVADWLKCDFMQDQVGQTFSGVISSVTGF 657
Cdd:COG0557 564 VHRALKAYLEGKRS-------PGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSF 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495127521 658 GFFVRLTDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDERKIDFSLISSERGPR 732
Cdd:COG0557 637 GLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEAP 711
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
18-725 |
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: 1047.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 18 IPSREFILEHLTK-REKPANRDELASELGIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPERLDLQKGTVIGHRDGY 96
Cdd:TIGR02063 1 SPLRELILEFLKSkKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 97 GFLRVEGRK-DDLYLSSEQMKTCIHGDIVLAQPLGS-DRKGRREARIVRVLVPKQSNIVGRYFTDAGVGFVVPDDSRLSF 174
Cdd:TIGR02063 81 GFLRPEDDDeDDIFIPPRQMNGAMHGDRVLVRITGKpDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 175 DILIPPEEVMGARMGYVVVVELTQRPTRRTKAIGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPKAVEEQIAHLKEEVPE 254
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 255 EAKVGRVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVRPPTPLDNEARNRGTSVYFPSQVVPMLP 334
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 335 EVLSNGLCSLNPQVDRLCMVCEMTISAKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDEDLRSQYQPLVKHLEELHTLY 414
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 415 KALEEARTERGGISFESEEAKFIFNAERRIDRIEQTQRNDAHKLIEECMILANISAARFVEKHKEPALFRIHDRPTNEAI 494
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 495 TSFRSVLAELGLELPGG--NKPEPRDYAELLDSIADRPDHEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRR 572
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGtsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 573 YPDLTLHRAIKYLIAKEQghegNTTESGGWHYTMEEMLQLGQHCSMTERRADEATREVADWLKCDFMQDQVGQTFSGVIS 652
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGE----NTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVIS 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495127521 653 SVTGFGFFVRLTDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDERKIDFSLI 725
Cdd:TIGR02063 637 GVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
67-725 |
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: 992.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 67 QLVFTrrQCYALPERLDLQKGTVIGHRDGYGFLR-VEGRKDDLYLSSEQMKTCIHGDIVLAQPLGSDRKGRREARIVRVL 145
Cdd:TIGR00358 1 QLLAT--LKYALPEKDDLVKGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 146 VPKQSNIVGRYFTDAGVGFVVPDDSRLSFDILIPPEEV-MGARMGYVVVVELTQRPTRRTKAIGKIVEVLGDNMGTGMAV 224
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 225 DMALRTHEIPYVWPKAVEEQIAHLKEEVPEEAKVGRVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSY 304
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 305 YVRPPTPLDNEARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAKGRLTGYKFYEAVMSSHARLTYT 384
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 385 KVWHILQGDEDLRSQYQPLVKHLEELHTLYKALEEARTERGGISFESEEAKFIFNAERRIDRIEQTQRNDAHKLIEECMI 464
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 465 LANISAARFVEKHKEPALFRIHDRPTNEAITSFRSVLAELGLELPGGNKPE--PRDYAELLDSIADRPDHEMLQTMLLRS 542
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENvtTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 543 MKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLIAKEQghegntTESGGwHYTMEEMLQLGQHCSMTERR 622
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ------TDTER-YQPQDELLQIAEHCSDTERR 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 623 ADEATREVADWLKCDFMQDQVGQTFSGVISSVTGFGFFVRLTDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRL 702
Cdd:TIGR00358 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRI 631
|
650 660
....*....|....*....|...
gi 495127521 703 GDRVEVKVEAVNMDERKIDFSLI 725
Cdd:TIGR00358 632 GDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
260-588 |
3.88e-137 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 407.81 E-value: 3.88e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 260 RVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVRPPTPLDNEARNRGTSVYFPSQVVPMLPEVLSN 339
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 340 GLCSLNPQVDRLCMVCEMTISAKG-RLTGYKFYEAVMSSHARLTYTKVWHILQgdedlrsqyqplvkhleelhtlykale 418
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 419 earterggisfeseeaKFIFNAERRIDRIEQTQRNDAHKLIEECMILANISAARFVEKHKEPALFRIHDRPTNEAIT-SF 497
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAeLL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 498 RSVLAELGLELPGGnkPEPRDYAELLDSIADRPDHEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLT 577
Cdd:smart00955 198 KEFLALLGLLLLGG--DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 495127521 578 LHRAIKYLIAK 588
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
260-583 |
3.06e-135 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 403.97 E-value: 3.06e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 260 RVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVRPPTPLDNEARNRGTSVYFPSQVVPMLPEVLSN 339
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 340 GLCSLNPQVDRLCMVCEMTISAKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDEDLRSQYQpLVKHLEELHTLYKALEE 419
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKPD-LAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 420 ARTERGGISFESEEAKFIFNAERRIDrIEQTQRNDAHKLIEECMILANISAARFVEKHKEPALFRIHDRPTNEAITSFRS 499
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 500 VLAelglelpggnkpEPRDYAELLDSIADRPDHEM-LQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTL 578
Cdd:pfam00773 239 LLQ------------LLPDDKGLSKSLEKIKDDERlLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIV 306
|
....*
gi 495127521 579 HRAIK 583
Cdd:pfam00773 307 HRQLK 311
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
87-720 |
1.40e-89 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 295.99 E-value: 1.40e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDIVLAQpLGSDrKGRREARIVRVLVPKQSNIVGRY-FTDaGVGFV 165
Cdd:COG4776 24 GVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAV-IRTE-KDKESAEPETLIEPFLTRFVGRVqKKD-GRLFV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 166 VPDDSRLSFDILIPPEEVMGA--RMGYVVVVELTQRPTRR-----TKAIGKIVEVlgDNMGTGMAVdmALRTHEIPYVWP 238
Cdd:COG4776 100 VPDHPLIKDAIKARPKKGLEEglKEGDWVVAELKRHPLKGdrgffAEITEFIADA--DDPFAPWWV--TLARHNLEREAP 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 239 KAVEE-QIahLKEEVPeeakvgRVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVRPPTPLDNEAR 317
Cdd:COG4776 176 EGDDEwEL--LDEGLE------REDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKEAR 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 318 NRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAKGRLTG-YKFYEAVMSSHARLTYTKVWHILQGDEDL 396
Cdd:COG4776 248 QRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKGEW 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 397 RSQYQPLVKHLEELHTLYKALEEARTERGGISFESEEAKFIFNAERRIDRIEQTQRNDAHKLIEECMILANISAARFVEK 476
Cdd:COG4776 328 QPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVLRE 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 477 HKEPALFRIHDRPTNEAITSFRSVLAELGLELPGGNKPEPRDYAELLDSIADRPDhEMLQTMLLRSMKQAIYDPENRGHF 556
Cdd:COG4776 408 HLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPT-SYLDSRLRRFQTFAEISTEPGPHF 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 557 GLALQSYAHFTSPIRRYPDLTLHRAIKYLIAKEQGHEGNttesggwhytmEEMLQLGQHCsmteRRADE-ATREVADWLK 635
Cdd:COG4776 487 GLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPD-----------EELTERLAER----RRLNRmAERDVADWLY 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 636 CDFMQDQVG--QTFSGVISSVTGFGFFVRLTD----LFIDG-LVHVsslDNDYYRFDQ-VGQRLIgeSGGQTYRLGDRVE 707
Cdd:COG4776 552 ARYLKPKVGsgQVFTAEIIDINRGGLRVRLLEngavAFIPAsFIHS---VRDELVCSQeEGTVYI--KGEVRYKLGDTIQ 626
|
650
....*....|...
gi 495127521 708 VKVEAVNMDERKI 720
Cdd:COG4776 627 VTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
87-720 |
1.52e-74 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 255.57 E-value: 1.52e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDIVLAQpLGSDrKGRREARIVRVLVPKQSNIVGRyftdagvgfVV 166
Cdd:PRK05054 24 GVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIAV-IHTE-KDREIAEPEELIEPFLTRFVGR---------VQ 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 167 PDDSRLSfdiLIP--P--EEVMGARM----------GYVVVVELTQRPTR-----RTKAIGKIVEvlGDNMGTGMAVdmA 227
Cdd:PRK05054 92 KKDDRLS---IVPdhPllKDAIPCRAakglnhefkeGDWVVAELRRHPLKgdrgfYAEITQFITD--ADDHFAPWWV--T 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 228 LRTHEIPYVWPKAVEEQIAHlkeevpeEAKVGRVDLRNLPLVTIDGEDARDFDDAVFCEKKRGGGWRLWVAIADVSYYVR 307
Cdd:PRK05054 165 LARHNLEREAPAGGVAWEML-------DEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIA 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 308 PPTPLDNEARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAKGRLTG-YKFYEAVMSSHARLTYTKV 386
Cdd:PRK05054 238 EGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAYDNV 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 387 WHILQGDEDLRSQYQPLVKHLEELHTLYKALEEARTERGGISFESEEAKFIFNAERRIDRIEQTQRNDAHKLIEECMILA 466
Cdd:PRK05054 318 SDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAA 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 467 NISAARFVEKHKEPALFRIHDRPTNEAITSFRSVLAELGLE--------LPGgnkpeprdYAELLDSIADRPDhEMLQTM 538
Cdd:PRK05054 398 NICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEHGLHfdaeelltLEG--------FCKLRRELDAQPT-GYLDSR 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 539 LLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLIAKEQghegNTTESggwhytmEEMLQLgqhcsM 618
Cdd:PRK05054 469 IRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGET----AERPQ-------DEITVQ-----L 532
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 619 TERRADE--ATREVADWLKCDFMQDQVG--QTFSGVISSVTGFGFFVRLTD----LFIDGlvhvSSLDNDYYRFDqvgqr 690
Cdd:PRK05054 533 AERRRLNrmAERDVGDWLYARYLKDKAGtdTRFAAEIIDISRGGMRVRLLEngavAFIPA----SFLHAVRDELV----- 603
|
650 660 670
....*....|....*....|....*....|....*.
gi 495127521 691 LIGESG-----GQT-YRLGDRVEVKVEAVNMDERKI 720
Cdd:PRK05054 604 CNQENGtvqikGETvYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
643-725 |
1.88e-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: 143.31 E-value: 1.88e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDERKIDF 722
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 495127521 723 SLI 725
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
164-238 |
2.08e-29 |
|
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: 111.33 E-value: 2.08e-29
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495127521 164 FVVPDDSRLSFDILIPPEEVMGARMGYVVVVELTQRPTRRtKAIGKIVEVLGDNMGTGMAVDMALRTHEIPYVWP 238
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYPDGK-NPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
87-144 |
2.63e-23 |
|
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: 93.37 E-value: 2.63e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 495127521 87 GTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDIVLAQPLGSDRKGRREARIVRV 144
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
641-724 |
5.27e-14 |
|
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: 67.31 E-value: 5.27e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 641 DQVGQTFSGVISSVTGFGFFVRLtDLFIDGLVHVSSLDNDYYrfdqvgqrligESGGQTYRLGDRVEVKVEAVNMDERKI 720
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRI 68
|
....
gi 495127521 721 DFSL 724
Cdd:pfam00575 69 ILSI 72
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
649-748 |
5.46e-14 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 71.01 E-value: 5.46e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 649 GVISSVTGFGFFVRLTDlfIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDERkidfslisSE 728
Cdd:PRK08563 87 GEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKER--------RP 156
|
90 100 110
....*....|....*....|....*....|..
gi 495127521 729 RGPRnVGKTAR------------EREKRGGGA 748
Cdd:PRK08563 157 RGSK-IGLTMRqpglgklewieeEKKKAKKEA 187
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
86-145 |
3.06e-13 |
|
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: 64.93 E-value: 3.06e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495127521 86 KGTVIGHRDGYGFLRVEGRKDDLYLSSEQ----MKTCIHGDIVLAQPLGSDRKGRREARIVRVL 145
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 ... |
649-725 |
1.45e-12 |
|
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: 64.23 E-value: 1.45e-12
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495127521 649 GVISSVTGFGFFVRLTDlfIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDERKIDFSLI 725
Cdd:cd04460 5 GEVVEVVDFGAFVRIGP--VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
642-724 |
8.76e-12 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 61.08 E-value: 8.76e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLtDLFIDGLVHVSSLDNDYyrfdqvgqrliGESGGQTYRLGDRVEVKVEAVNMDERKID 721
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDL-GNGVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
...
gi 495127521 722 FSL 724
Cdd:smart00316 69 LSL 71
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
22-81 |
2.46e-09 |
|
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: 53.94 E-value: 2.46e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495127521 22 EFILEHLTKREKPANRDELASELGIEGEE-QLEALRRRLRAMERDGqlvFTRRQCYA---LPER 81
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYAgreITEK 61
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
643-727 |
1.59e-08 |
|
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: 51.95 E-value: 1.59e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDLFIDGLVHVSSLDNDyyRFDQVGQRligesggqtYRLGDRVEVKVEAVNMDERKIDF 722
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN--RVADASKL---------FRVGDKVRAKVLKIDAEKKRISL 70
|
....*
gi 495127521 723 SLISS 727
Cdd:cd05708 71 GLKAS 75
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
649-723 |
3.00e-08 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 50.84 E-value: 3.00e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495127521 649 GVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDYYrfdqvgqrligESGGQTYRLGDRVEVKVEAVNMDERKIDFS 723
Cdd:cd00164 3 GKVVSITKFGVFVELED-GVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
644-723 |
7.72e-08 |
|
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: 49.92 E-value: 7.72e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 644 GQTFSGVISSVTGFGFFVrltDLFI--DGLVHVSSLDNDYY--RFDQVGqrligesggqtyrLGDRVEVKVEAVNMDERK 719
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFV---DIGVkqDGLIHISKMADRFVshPSDVVS-------------VGDIVEVKVISIDEERGR 64
|
....
gi 495127521 720 IDFS 723
Cdd:cd05685 65 ISLS 68
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
4.27e-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: 52.74 E-value: 4.27e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyrfdqvgQRLigESGGQTYRLGDRVEVKVEAVNMDERKID 721
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEP-GVEGLVHISEMSWT--------KRV--AHPSDVVKVGDEVEVKVLDIDPEERRIS 341
|
...
gi 495127521 722 FSL 724
Cdd:COG0539 342 LSI 344
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
639-763 |
4.34e-07 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 49.79 E-value: 4.34e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 639 MQDQVGQTFSGVISSVTGFGFFVRL----TdlfidGLVHVSSLDNDYyrfdqVgqrligESGGQTYRLGDRVEVKVeaVN 714
Cdd:COG1098 1 MSIEVGDIVEGKVTGITPFGAFVELpegtT-----GLVHISEIADGY-----V------KDINDYLKVGDEVKVKV--LS 62
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 495127521 715 MDER-KIDFSLissergprnvgKTAREREKRGGGAKNRSRRQVGKrQNFE 763
Cdd:COG1098 63 IDEDgKISLSI-----------KQAEEKPKRPPRPRRNSRPKAGF-ESFE 100
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-724 |
7.48e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 52.86 E-value: 7.48e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDndyyrFDQVGQRLIgesggQTYRLGDRVEVKVEAVNMDERKId 721
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDIS-----WDKKGEEAV-----ELYKKGDEVEAVVLKVDVEKERI- 439
|
...
gi 495127521 722 fSL 724
Cdd:PRK06299 440 -SL 441
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
642-731 |
1.03e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 51.80 E-value: 1.03e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVrltDL-FIDGLVHVSSLDndYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKI 720
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFV---DIgGVDGLVHISELS--HERVEKPSEVV---------SVGQEVEVKVLSIDWETERI 256
|
90
....*....|.
gi 495127521 721 DFSLISSERGP 731
Cdd:PRK06676 257 SLSLKDTLPGP 267
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-720 |
2.48e-06 |
|
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240195 [Multi-domain] Cd Length: 69 Bit Score: 45.56 E-value: 2.48e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 495127521 644 GQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLdndyyrfdQVGQRliGESGGQTYRLGDRVEVKVEAVNMDERKI 720
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDI--------SWTQR--VRHPSEIYKKGQEVEAVVLNIDVERERI 66
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
643-724 |
3.33e-06 |
|
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: 50.50 E-value: 3.33e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyrfdQVGQRLIgesggqTYRLGDRVEVKVEAVNMDERKIDF 722
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSEN-----RDEDKTD------EIKVGDEVEAKVVDIDKKNRKVSL 513
|
..
gi 495127521 723 SL 724
Cdd:TIGR00717 514 SV 515
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
4.42e-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: 4.42e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVrltDL-FIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKI 720
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFV---DLgGVDGLLHISEI--SWGRVKHPSEVL---------KVGDEVEVKVLKIDREKERI 253
|
....
gi 495127521 721 DFSL 724
Cdd:COG0539 254 SLSL 257
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
5.36e-06 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 49.95 E-value: 5.36e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKID 721
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGG--VDGLLHVSEI--SWGRVEKPSDVL---------KVGDEIKVYILDIDKENKKLS 542
|
...
gi 495127521 722 FSL 724
Cdd:PRK00087 543 LSL 545
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
643-723 |
7.16e-06 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 44.16 E-value: 7.16e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDlfIDGLVHVSSLDndYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKIDF 722
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHISDMS--WGRVKHPSEVV---------NVGDEVEVKVLKIDKERKRISL 67
|
.
gi 495127521 723 S 723
Cdd:cd05688 68 G 68
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
642-724 |
9.12e-06 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 49.28 E-value: 9.12e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVeaVNMDER-KI 720
Cdd:PRK11824 620 EVGEIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADE--RVEKVEDVL---------KEGDEVKVKV--LEIDKRgRI 685
|
....
gi 495127521 721 DFSL 724
Cdd:PRK11824 686 RLSR 689
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
640-731 |
1.68e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 48.12 E-value: 1.68e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 640 QDQVGQTFSGVISSVTGFGFFVRLTDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERK 719
Cdd:PRK07899 205 QLQKGQVRKGVVSSIVNFGAFVDLGG--VDGLVHVSEL--SWKHIDHPSEVV---------EVGQEVTVEVLDVDMDRER 271
|
90
....*....|..
gi 495127521 720 IDFSLISSERGP 731
Cdd:PRK07899 272 VSLSLKATQEDP 283
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-723 |
1.68e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 48.24 E-value: 1.68e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKID 721
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRD--RVEDATEVL---------KVGDEVEAKVINIDRKNRRIS 526
|
..
gi 495127521 722 FS 723
Cdd:PRK06299 527 LS 528
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-724 |
2.01e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 48.12 E-value: 2.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLdndyyrfdqvGQRLIgESGGQTYRLGDRVEVKVEAVNMDERKID 721
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISEL----------AERHV-EVPEQVVQVGDEVFVKVIDIDLERRRIS 359
|
...
gi 495127521 722 FSL 724
Cdd:PRK07899 360 LSL 362
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
639-770 |
2.12e-05 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 45.02 E-value: 2.12e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 639 MQDQVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVEAVNmDER 718
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVK--DINDHL---------KVGDEVEVKVLNVE-DDG 67
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 495127521 719 KIDFSLissergprnvgKTAREREKRgGGAKNRSRRQVGKRQNFEPNEAFRS 770
Cdd:PRK08582 68 KIGLSI-----------KKAKDRPKR-QHDRPRHEDNRGGGNDVAPKEDFEQ 107
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
639-733 |
2.19e-05 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 48.10 E-value: 2.19e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 639 MQD-QVGQTFSGVISSVTGFGFFVrltDLFI--DGLVHVSSLDNDYYR--FDQVgqrligesggqtyRLGDRVEVKVEAV 713
Cdd:COG2183 636 IEDlKPGMILEGTVTNVTDFGAFV---DIGVhqDGLVHISQLSDRFVKdpREVV-------------KVGDIVKVKVLEV 699
|
90 100
....*....|....*....|
gi 495127521 714 NMDERKIDFSLISSERGPRN 733
Cdd:COG2183 700 DLKRKRISLSMKLDDEAGAA 719
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
644-710 |
4.14e-05 |
|
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: 42.61 E-value: 4.14e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 495127521 644 GQTFSGVISSVTGFGFFVRLTDL--FIDGLVHVSSLDNDyyrfdqvgqRLIGESgGQTYRLGDRVEVKV 710
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFE---------GRVANP-SDVVKRGQKVKVKV 59
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
636-723 |
6.26e-05 |
|
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: 41.82 E-value: 6.26e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 636 CDFMQDQVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyrfdqvgqrligesggqtYRLGDRVEVKVEAVNm 715
Cdd:cd04473 9 CTMEDLEVGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLLRD-------------------YEVGDEVIVQVTDIP- 67
|
....*...
gi 495127521 716 DERKIDFS 723
Cdd:cd04473 68 ENGNIDLI 75
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-733 |
8.58e-05 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 46.09 E-value: 8.58e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNdyYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKID 721
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISW--KRIDKPEDVL---------SEGEEVKAKILEVDPEEKRIR 628
|
90
....*....|..
gi 495127521 722 FSLISSERGPRN 733
Cdd:PRK00087 629 LSIKEVEEEPGD 640
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
643-724 |
1.00e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 45.64 E-value: 1.00e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSsldndyyrfdQVGQRLIGeSGGQTYRLGDRVEVKVEAVNMDERKIDF 722
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLP-GVEGLVHIS----------QISHKHIA-TPSEVLEEGQEVKVKVLEVNEEEKRISL 344
|
..
gi 495127521 723 SL 724
Cdd:PRK06676 345 SI 346
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
644-723 |
2.06e-04 |
|
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: 40.22 E-value: 2.06e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 644 GQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVeaVNMDER-KIDF 722
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDE--RVEKVEDVL---------KVGDEVKVKV--IEVDDRgRISL 66
|
.
gi 495127521 723 S 723
Cdd:cd04472 67 S 67
|
|
| S1_pNO40 |
cd05686 |
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
642-724 |
3.75e-04 |
|
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Pssm-ID: 240191 [Multi-domain] Cd Length: 73 Bit Score: 39.77 E-value: 3.75e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDLFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDErKID 721
Cdd:cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RVDDPSEVV---------DVGEKVWVKVIGREMKD-KMK 69
|
...
gi 495127521 722 FSL 724
Cdd:cd05686 70 LSL 72
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
643-729 |
4.48e-04 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 43.93 E-value: 4.48e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyRFDQVGQRLigesggQTYRLGDRVEVKVEAVNMDERKIDF 722
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVEN--RDGDPGEAL------RKYAVGDRVKAVIVDMNVKDRKVAF 822
|
....*..
gi 495127521 723 SLISSER 729
Cdd:PRK12269 823 SVRDYQR 829
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
643-724 |
4.94e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 43.61 E-value: 4.94e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 643 VGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDyyrfdqvgQRLIgeSGGQTYRLGDRVEVKVEAVNMDERKIDF 722
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWT--------KKNK--HPSKVVSVGQEVEVMVLEIDEEKRRISL 354
|
..
gi 495127521 723 SL 724
Cdd:PRK06299 355 GL 356
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
158-213 |
9.50e-04 |
|
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: 37.90 E-value: 9.50e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 495127521 158 TDAGVGFVVPDDSrlSFDILIPPEEVMGARMGYVVVVELTQrPTRRTKAIGKIVEV 213
Cdd:pfam08206 6 HKKGFGFLIPDDE--EDDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-724 |
2.80e-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: 41.26 E-value: 2.80e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVS--SLDNDyyrfdqvgqrliGESGGQTYRLGDRVEVKVEAVNMDERK 719
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSdiSWDKD------------GREADHLYKKGDEIEAVVLAVDKEKKR 424
|
....*
gi 495127521 720 IDFSL 724
Cdd:TIGR00717 425 ISLGV 429
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
607-724 |
3.75e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 40.87 E-value: 3.75e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 607 EEMLQLGQHCSMTERRADEATREVADWLKcDFMQD---------QVGQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSL 677
Cdd:TIGR00717 228 SEYVKVGQEVKVKVIKFDKEKGRISLSLK-QLGEDpweaiekkfPVGDKITGRVTNLTDYGVFVEIEE-GIEGLVHVSEM 305
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 495127521 678 DNDyyrfdqvgQRLIGESggQTYRLGDRVEVKVEAVNMDERKIDFSL 724
Cdd:TIGR00717 306 SWV--------KKNSHPS--KVVKKGDEVEVMILDIDPERRRLSLGL 342
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
642-752 |
4.81e-03 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 37.72 E-value: 4.81e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 642 QVGQTFSGVISSVTGFGFFVRLtDLFIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVEAVNMDERKID 721
Cdd:PRK08059 6 EVGSVVTGKVTGIQPYGAFVAL-DEETQGLVHISEITHGFVK--DIHDFL---------SVGDEVKVKVLSVDEEKGKIS 73
|
90 100 110
....*....|....*....|....*....|.
gi 495127521 722 FSLISSERGPrnvgktAREREKRGGGAKNRS 752
Cdd:PRK08059 74 LSIRATEEAP------EAKRKKGKILIPNPS 98
|
|
| COG2345 |
COG2345 |
Predicted transcriptional regulator, ArsR family [Transcription]; |
1-74 |
6.33e-03 |
|
Predicted transcriptional regulator, ArsR family [Transcription];
Pssm-ID: 441914 [Multi-domain] Cd Length: 217 Bit Score: 39.14 E-value: 6.33e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 495127521 1 MSHDPFQEREAEkyanpiPSREFILEHLtKREKPANRDELASELGIEGeeqlEALRRRLRAMERDGQLVFTRRQ 74
Cdd:COG2345 1 MTDTPALAALAD------PTRRRILELL-KRAGPVTAAELAEALGLTP----NAVRRHLDALEEEGLVERETER 63
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-723 |
6.72e-03 |
|
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240197 [Multi-domain] Cd Length: 69 Bit Score: 36.11 E-value: 6.72e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 644 GQTFSGVISSVTGFGFFVRLTDlFIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVeaVNMDER-KIDF 722
Cdd:cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVK--DVKDVL---------KEGDKVKVKV--LSIDARgRISL 66
|
.
gi 495127521 723 S 723
Cdd:cd05692 67 S 67
|
|
| RNase_II_C_S1 |
pfam18614 |
RNase II-type exonuclease C-terminal S1 domain; This entry describes the C-terminal S1 domain ... |
645-724 |
9.20e-03 |
|
RNase II-type exonuclease C-terminal S1 domain; This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interacts with a flexible loop that connects two beta-strands from the conserved C-terminal S1 domain, forming a beta-wing fold common in wHTH domains.
Pssm-ID: 436621 [Multi-domain] Cd Length: 59 Bit Score: 35.22 E-value: 9.20e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495127521 645 QTFSGVISSVTGFGFFVRLTDLFIDGLVhvssldndyyrfdqvgqrligeSGGQTYRLGDRVEVKVEAVNMDERKIDFSL 724
Cdd:pfam18614 1 ETFDAVVVDADERGATVQLADPAVEARC----------------------VGGDGLPLGDRVRVRLVEADVATGTVRFAV 58
|
|
| |
