|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-801 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1696.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPANRDELAAELNIEGEEQQEALRRRLRAMERDGQLVFTRRQCYALPE 80
Cdd:PRK11642 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
Cdd:PRK11642 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 161 GVGFVVPDDSRLSFDILIPPEEVMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTSMAVDMALRTHEIPYIWPQA 240
Cdd:PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 241 VEKQVAGLKEEVPEEAKIGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDQEARSRG 320
Cdd:PRK11642 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGFKFYEAVMSSHARLTYTKVWHMLQGDQELREQY 400
Cdd:PRK11642 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 401 APLVKHIEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMIMANISAARFVEKAKEP 480
Cdd:PRK11642 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 481 ALFRIHDKPTTEAINSFRSVLAELGLELPGGNKPEPRDYAELLESIADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
Cdd:PRK11642 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAQEQGHKGNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVSDWLKCDFML 640
Cdd:PRK11642 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFML 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 641 DQVGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 721 DFSLISSERAPRNEGKTAREKAKKSDAGKNTGKRRQMGKKVNFEPDSAFRGEKKGRAKPQAEKnaaekkgDKKAKKPSAK 800
Cdd:PRK11642 721 DFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKD-------ARKAKKPSAK 793
|
.
gi 489115763 801 T 801
Cdd:PRK11642 794 T 794
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
20-732 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1146.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 20 SREFILEHLTK-REKPANRDELAAELNIEGEEQQEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGF 98
Cdd:COG0557 4 SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFGF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 99 LRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILI 178
Cdd:COG0557 84 VIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDIFI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 179 PPEEVMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTSMAVDMALRTHEIPYIWPQAVEKQVAGLKEEVPEEAKI 258
Cdd:COG0557 164 PPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEADLK 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 259 GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDQEARSRGTSVYFPSQVVPMLPEVLS 338
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLS 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 339 NGLCSLNPQVDRLCMVCEMTISSKGRLTGFKFYEAVMSSHARLTYTKVWHMLQG-DQELREQYAPLVKHIEELHNLYKVL 417
Cdd:COG0557 324 NGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELYELAKIL 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 418 DKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMIMANISAARFVEKAKEPALFRIHDKPTTEAINSF 497
Cdd:COG0557 404 RKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLEAL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 498 RSVLAELGLELPGGNKPEPRDYAELLESIADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLS 577
Cdd:COG0557 484 REFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYPDLL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 578 LHRAIKYLLAqeqghkgNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVSDWLKCDFMLDQVGNVFKGVIASVTGF 657
Cdd:COG0557 564 VHRALKAYLE-------GKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSF 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489115763 658 GFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRLGDRVEVRVEAVNMDERKIDFSLISSERAPR 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: 1056.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 18 IPSREFILEHLTK-REKPANRDELAAELNIEGEEQQEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGY 96
Cdd:TIGR02063 1 SPLRELILEFLKSkKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 97 GFLRVEGRK-DDLYLSSEQMKTCIHGDQVLAQPLG-ADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSF 174
Cdd:TIGR02063 81 GFLRPEDDDeDDIFIPPRQMNGAMHGDRVLVRITGkPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 175 DILIPPEEVMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTSMAVDMALRTHEIPYIWPQAVEKQVAGLKEEVPE 254
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 255 EAKIGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDQEARSRGTSVYFPSQVVPMLP 334
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 335 EVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGFKFYEAVMSSHARLTYTKVWHMLQGDQELREQYAPLVKHIEELHNLY 414
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 415 KVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMIMANISAARFVEKAKEPALFRIHDKPTTEAI 494
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 495 NSFRSVLAELGLELPGG--NKPEPRDYAELLESIADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRR 572
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGtsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 573 YPDLSLHRAIKYLLAQEQGHKGNTTetggYHYSMEEMLQLGQHCSMAERRADEATRDVSDWLKCDFMLDQVGNVFKGVIA 652
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGENTTTEKE----REYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVIS 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489115763 653 SVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRLGDRVEVRVEAVNMDERKIDFSLI 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: 999.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 67 QLVFTrrQCYALPERLDLLKGTVIGHRDGYGFLR-VEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVL 145
Cdd:TIGR00358 1 QLLAT--LKYALPEKDDLVKGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 146 VPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEEV-MGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTSMAV 224
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 225 DMALRTHEIPYIWPQAVEKQVAGLKEEVPEEAKIGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSY 304
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 305 YVRPPTPLDQEARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGFKFYEAVMSSHARLTYT 384
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 385 KVWHMLQGDQELREQYAPLVKHIEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMI 464
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 465 MANISAARFVEKAKEPALFRIHDKPTTEAINSFRSVLAELGLELPGGNKPE--PRDYAELLESIADRPDAEMLQTMLLRS 542
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENvtTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 543 MKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAQEQghkgntTETGGYhYSMEEMLQLGQHCSMAERR 622
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ------TDTERY-QPQDELLQIAEHCSDTERR 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 623 ADEATRDVSDWLKCDFMLDQVGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRL 702
Cdd:TIGR00358 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRI 631
|
650 660
....*....|....*....|...
gi 489115763 703 GDRVEVRVEAVNMDERKIDFSLI 725
Cdd:TIGR00358 632 GDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
260-588 |
1.22e-136 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 406.65 E-value: 1.22e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 260 RVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDQEARSRGTSVYFPSQVVPMLPEVLSN 339
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 340 GLCSLNPQVDRLCMVCEMTISSKG-RLTGFKFYEAVMSSHARLTYTKVWHMLQgdqelreqyaplvkhieelhnlykvld 418
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 419 kareerggisfeseeaKFIFNAERRIERIEQTQRNDAHKLIEECMIMANISAARFVEKAKEPALFRIHDKPTTEAI-NSF 497
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLaELL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 498 RSVLAELGLELPGGnkPEPRDYAELLESIADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLS 577
Cdd:smart00955 198 KEFLALLGLLLLGG--DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 489115763 578 LHRAIKYLLAQ 588
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
260-586 |
1.34e-135 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 405.13 E-value: 1.34e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 260 RVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDQEARSRGTSVYFPSQVVPMLPEVLSN 339
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 340 GLCSLNPQVDRLCMVCEMTISSKGRLTGFKFYEAVMSSHARLTYTKVWHMLQGDQELREQyAPLVKHIEELHNLYKVLDK 419
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 420 AREERGGISFESEEAKFIFNAERRIErIEQTQRNDAHKLIEECMIMANISAARFVEKAKEPALFRIHDKPTTEAINSFRS 499
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 500 VLAELglelpggnkPEPRDYAELLESIADRPDAemLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLH 579
Cdd:pfam00773 239 LLQLL---------PDDKGLSKSLEKIKDDERL--LSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....*..
gi 489115763 580 RAIKYLL 586
Cdd:pfam00773 308 RQLKALL 314
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
87-720 |
9.81e-91 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 299.08 E-value: 9.81e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAQPLGAdrKGRREARIVRVLVPKTSQIVGRY-FTDaGVGFV 165
Cdd:COG4776 24 GVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVIRTE--KDKESAEPETLIEPFLTRFVGRVqKKD-GRLFV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 166 VPDDSRLSFDILIPPEEVMGA--RMGFVVVVELTQRPTRRTK-AVGKIVEVLGDnmgtsmaVD-------MALRTHEIPY 235
Cdd:COG4776 100 VPDHPLIKDAIKARPKKGLEEglKEGDWVVAELKRHPLKGDRgFFAEITEFIAD-------ADdpfapwwVTLARHNLER 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 236 IWPQAVEkQVAGLKEEVPeeakigRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDQE 315
Cdd:COG4776 173 EAPEGDD-EWELLDEGLE------REDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 316 ARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTG-FKFYEAVMSSHARLTYTKVWHMLQGDQ 394
Cdd:COG4776 246 ARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKG 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 395 ELREQYAPLVKHIEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMIMANISAARFV 474
Cdd:COG4776 326 EWQPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 475 EKAKEPALFRIHDKPTTEAINSFRSVLAELGLELPGGNKPEPRDYAELLESIADRPDAEMlqTMLLRSMKQ-AIYDPENR 553
Cdd:COG4776 406 REHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYL--DSRLRRFQTfAEISTEPG 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 554 GHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAQEQGHKGNttetggyhysmEEMLQLGQHCSMAERRADeatRDVSDW 633
Cdd:COG4776 484 PHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPD-----------EELTERLAERRRLNRMAE---RDVADW 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 634 LKCDFMLDQVGN--VFKGVIASVTGFGFFVRLDE----LFIDGlvhvSSLDNDYYRFDQVGQRLTGESSGQM-YRLGDRV 706
Cdd:COG4776 550 LYARYLKPKVGSgqVFTAEIIDINRGGLRVRLLEngavAFIPA----SFIHSVRDELVCSQEEGTVYIKGEVrYKLGDTI 625
|
650
....*....|....
gi 489115763 707 EVRVEAVNMDERKI 720
Cdd:COG4776 626 QVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
87-720 |
1.72e-74 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 255.57 E-value: 1.72e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAqpLGADRKGRREARIVRVLVPKTSQIVGRyftdagvgfVV 166
Cdd:PRK05054 24 GVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIA--VIHTEKDREIAEPEELIEPFLTRFVGR---------VQ 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 167 PDDSRLSfdiLIP--P--EEVMGARM----------GFVVVVELTQRPTR-----RTKAVGKIVEvlGDNMGTSMAVdmA 227
Cdd:PRK05054 92 KKDDRLS---IVPdhPllKDAIPCRAakglnhefkeGDWVVAELRRHPLKgdrgfYAEITQFITD--ADDHFAPWWV--T 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 228 LRTHEIPYIWPQ---AVEKQVAGLKeevpeeakigRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSY 304
Cdd:PRK05054 165 LARHNLEREAPAggvAWEMLDEGLE----------REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTA 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 305 YVRPPTPLDQEARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTG-FKFYEAVMSSHARLTY 383
Cdd:PRK05054 235 YIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAY 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 384 TKVWHMLQGDQELREQYAPLVKHIEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECM 463
Cdd:PRK05054 315 DNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESM 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 464 IMANISAARFVEKAKEPALFRIHDKPTTEAINSFRSVLAELGLE--------LPGgnkpeprdYAELLESIADRPDaEML 535
Cdd:PRK05054 395 IAANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEHGLHfdaeelltLEG--------FCKLRRELDAQPT-GYL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 536 QTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAQEQGHKGNttetggyhysmEEMLQLgqh 615
Cdd:PRK05054 466 DSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ-----------DEITVQ--- 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 616 csMAERRADE--ATRDVSDWLKCDFMLDQVGN--VFKGVIASVTGFGFFVRLDE----LFIDGlvhvSSLDNDYYRFDQV 687
Cdd:PRK05054 532 --LAERRRLNrmAERDVGDWLYARYLKDKAGTdtRFAAEIIDISRGGMRVRLLEngavAFIPA----SFLHAVRDELVCN 605
|
650 660 670
....*....|....*....|....*....|....
gi 489115763 688 GQRLTGESSGQM-YRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK05054 606 QENGTVQIKGETvYKLGDVIDVTLAEVRMETRSI 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 |
7.04e-40 |
|
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Pssm-ID: 239917 [Multi-domain] Cd Length: 83 Bit Score: 141.38 E-value: 7.04e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 489115763 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 |
1.03e-27 |
|
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: 106.71 E-value: 1.03e-27
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489115763 164 FVVPDDSRLSFDILIPPEEVMGARMGFVVVVELTQRPTRRtKAVGKIVEVLGDNMGTSMAVDMALRTHEIPYIWP 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 |
3.01e-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: 3.01e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 489115763 87 GTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRV 144
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
646-720 |
9.67e-14 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 70.24 E-value: 9.67e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489115763 646 VFKGVIASVTGFGFFVRLDElfIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK08563 84 VVEGEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
641-724 |
1.18e-13 |
|
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: 66.54 E-value: 1.18e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 641 DQVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYrfdqvgqrltgESSGQMYRLGDRVEVRVEAVNMDERKI 720
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDLGN-GVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRI 68
|
....
gi 489115763 721 DFSL 724
Cdd:pfam00575 69 ILSI 72
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
86-145 |
2.94e-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: 2.94e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489115763 86 KGTVIGHRDGYGFLRVEGRKDDLYLSSEQ----MKTCIHGDQVLAQPLGADRKGRREARIVRVL 145
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQiqggLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
642-724 |
6.71e-13 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 64.16 E-value: 6.71e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYyrfdqvgqrltGESSGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
...
gi 489115763 722 FSL 724
Cdd:smart00316 69 LSL 71
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
646-725 |
1.64e-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: 1.64e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 646 VFKGVIASVTGFGFFVRLDElfIDGLVHVSSLDNDYYRFDQVGQRLTGESSGQMYRLGDRVEVRVEAVNMDERKIDFSLI 725
Cdd:cd04460 2 VVEGEVVEVVDFGAFVRIGP--VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
22-85 |
1.72e-10 |
|
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: 57.41 E-value: 1.72e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489115763 22 EFILEHLTKREKPANRDELAAELNIEGEE-QQEALRRRLRAMERDGqlvFTRRQCYA---LPER-LDLL 85
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYAgreITEKgLEEL 66
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-724 |
2.75e-09 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 60.56 E-value: 2.75e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgqrLTGESSGQMYRLGDRVEVRVEAVNMDERKId 721
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISWD----------KKGEEAVELYKKGDEVEAVVLKVDVEKERI- 439
|
...
gi 489115763 722 fSL 724
Cdd:PRK06299 440 -SL 441
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
647-723 |
6.91e-09 |
|
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: 52.77 E-value: 6.91e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489115763 647 FKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYrfdqvgqrltgESSGQMYRLGDRVEVRVEAVNMDERKIDFS 723
Cdd:cd00164 1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
643-727 |
7.33e-09 |
|
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: 53.10 E-value: 7.33e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDyyrfdqvgqrlTGESSGQMYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRISL 70
|
....*
gi 489115763 723 SLISS 727
Cdd:cd05708 71 GLKAS 75
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
1.76e-08 |
|
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: 56.98 E-value: 1.76e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgQRLtgESSGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEP-GVEGLVHISEMSWT--------KRV--AHPSDVVKVGDEVEVKVLDIDPEERRIS 341
|
...
gi 489115763 722 FSL 724
Cdd:COG0539 342 LSI 344
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-724 |
3.36e-08 |
|
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240195 [Multi-domain] Cd Length: 69 Bit Score: 50.96 E-value: 3.36e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 644 GNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDndyyrfdqvgQRLTGESSGQMYRLGDRVEVRVeaVNMDERKIDFS 723
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVV--LNIDVERERIS 67
|
.
gi 489115763 724 L 724
Cdd:cd05690 68 L 68
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
643-752 |
1.45e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 54.50 E-value: 1.45e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVrldELF--IDGLVHVSSLDNdyyrfdqvgQRLtgESSGQMYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFV---EVLpgVEGLVHISQISH---------KHI--ATPSEVLEEGQEVKVKVLEVNEEEKRI 342
|
90 100 110
....*....|....*....|....*....|..
gi 489115763 721 DFSLISSERAPRNEGKTAREKAKKSDAGKNTG 752
Cdd:PRK06676 343 SLSIKALEEAPAEEEDRREEYRQYELPEEETG 374
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-751 |
1.99e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 54.40 E-value: 1.99e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyRFDQVGQRLTgessgqmyrLGDRVEVRVEAVNMDERKID 721
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRD--RVEDATEVLK---------VGDEVEAKVINIDRKNRRIS 526
|
90 100 110
....*....|....*....|....*....|
gi 489115763 722 FSLISSERAprnEGKTAREKAKKSDAGKNT 751
Cdd:PRK06299 527 LSIKALDEA---EEKEAIAEYNSASDSKTT 553
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
643-724 |
1.28e-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: 52.04 E-value: 1.28e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdQVGQRLtgessgQMYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSEN-----RDEDKT------DEIKVGDEVEAKVVDIDKKNRKVSL 513
|
..
gi 489115763 723 SL 724
Cdd:TIGR00717 514 SV 515
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
1.47e-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: 51.20 E-value: 1.47e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVgqrltgessGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG--VDGLLHISEI--SWGRVKHP---------SEVLKVGDEVEVKVLKIDREKERIS 254
|
...
gi 489115763 722 FSL 724
Cdd:COG0539 255 LSL 257
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
642-724 |
1.53e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 51.41 E-value: 1.53e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLTgessgqmyrLGDRVEVRVEAVNMDERKID 721
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFVDIGG--VDGLVHISEL--SHERVEKPSEVVS---------VGQEVEVKVLSIDWETERIS 257
|
...
gi 489115763 722 FSL 724
Cdd:PRK06676 258 LSL 260
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
642-751 |
1.60e-06 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 47.73 E-value: 1.60e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDELfIDGLVHVSSLDNDYYRfdQVGQRLTgessgqmyrLGDRVEVRVEAVNMDERKID 721
Cdd:PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDEE-TQGLVHISEITHGFVK--DIHDFLS---------VGDEVKVKVLSVDEEKGKIS 73
|
90 100 110
....*....|....*....|....*....|.
gi 489115763 722 FSLISSERAPRNEGKTAREKAKK-SDAGKNT 751
Cdd:PRK08059 74 LSIRATEEAPEAKRKKGKILIPNpSEQGFNT 104
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
644-723 |
2.38e-06 |
|
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 45.69 E-value: 2.38e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 644 GNVFKGVIASVTGFGFFVRLDeLFIDGLVHVSSLDNDYY--RFDQVGqrltgessgqmyrLGDRVEVRVEAVNMDERKID 721
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMADRFVshPSDVVS-------------VGDIVEVKVISIDEERGRIS 66
|
..
gi 489115763 722 FS 723
Cdd:cd05685 67 LS 68
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
644-680 |
2.67e-06 |
|
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: 45.69 E-value: 2.67e-06
10 20 30
....*....|....*....|....*....|....*....
gi 489115763 644 GNVFKGVIASVTGFGFFVRLDEL--FIDGLVHVSSLDND 680
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFE 39
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
3.23e-06 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 50.72 E-value: 3.23e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLTgessgqmyrLGDRVEVRVEAVNMDERKID 721
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGG--VDGLLHVSEI--SWGRVEKPSDVLK---------VGDEIKVYILDIDKENKKLS 542
|
...
gi 489115763 722 FSL 724
Cdd:PRK00087 543 LSL 545
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
642-764 |
4.18e-06 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 46.71 E-value: 4.18e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYRfdQVGQRLTgessgqmyrLGDRVEVRVeaVNMDER-KI 720
Cdd:COG1098 4 EVGDIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGYVK--DINDYLK---------VGDEVKVKV--LSIDEDgKI 69
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 489115763 721 DFSLisseraprnegKTAREKAKKSDAGKNTGKRRQmgKKVNFE 764
Cdd:COG1098 70 SLSI-----------KQAEEKPKRPPRPRRNSRPKA--GFESFE 100
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
642-724 |
4.51e-06 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 50.43 E-value: 4.51e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVrldELF--IDGLVHVSSLDNDyyRFDQVGQRLTgessgqmyrLGDRVEVRVeaVNMDER- 718
Cdd:PRK11824 620 EVGEIYEGKVVRIVDFGAFV---EILpgKDGLVHISEIADE--RVEKVEDVLK---------EGDEVKVKV--LEIDKRg 683
|
....*.
gi 489115763 719 KIDFSL 724
Cdd:PRK11824 684 RIRLSR 689
|
|
| S1_pNO40 |
cd05686 |
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
642-724 |
1.28e-05 |
|
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: 43.62 E-value: 1.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDyyRFDQVGQRLTgessgqmyrLGDRVEVRVEAVNMDErKID 721
Cdd:cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RVDDPSEVVD---------VGEKVWVKVIGREMKD-KMK 69
|
...
gi 489115763 722 FSL 724
Cdd:cd05686 70 LSL 72
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-731 |
2.49e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 47.73 E-value: 2.49e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQvgqrltgesSGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLGG--VDGLVHVSEL--SWKHIDH---------PSEVVEVGQEVTVEVLDVDMDRERVS 273
|
90
....*....|
gi 489115763 722 FSLISSERAP 731
Cdd:PRK07899 274 LSLKATQEDP 283
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-724 |
3.23e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 47.35 E-value: 3.23e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYrfdqvgqrltgESSGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAERHV-----------EVPEQVVQVGDEVFVKVIDIDLERRRIS 359
|
...
gi 489115763 722 FSL 724
Cdd:PRK07899 360 LSL 362
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
643-723 |
3.24e-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: 42.59 E-value: 3.24e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgqrltgessgqmYRLGDRVEVRVEAVNmDERKIDF 722
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLLRD-------------------YEVGDEVIVQVTDIP-ENGNIDL 74
|
.
gi 489115763 723 S 723
Cdd:cd04473 75 I 75
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
3.28e-05 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 47.63 E-value: 3.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLdELFIDGLVHVSSLDNdyYRFDQVGQRLTgessgqmyrLGDRVEVRVEAVNMDERKID 721
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVEL-EPGVDGLVHISQISW--KRIDKPEDVLS---------EGEEVKAKILEVDPEEKRIR 628
|
...
gi 489115763 722 FSL 724
Cdd:PRK00087 629 LSI 631
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-724 |
4.28e-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: 47.04 E-value: 4.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgqrLTGESSGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWD----------KDGREADHLYKKGDEIEAVVLAVDKEKKRIS 426
|
...
gi 489115763 722 FSL 724
Cdd:TIGR00717 427 LGV 429
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
642-733 |
1.17e-04 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 45.79 E-value: 1.17e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVrlDelfI----DGLVHVSSLDNDYYR--FDQVgqrltgessgqmyRLGDRVEVRVEAVNM 715
Cdd:COG2183 640 KPGMILEGTVTNVTDFGAFV--D---IgvhqDGLVHISQLSDRFVKdpREVV-------------KVGDIVKVKVLEVDL 701
|
90
....*....|....*...
gi 489115763 716 DERKIDFSLISSERAPRN 733
Cdd:COG2183 702 KRKRISLSMKLDDEAGAA 719
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
643-723 |
1.28e-04 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 40.69 E-value: 1.28e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLTgessgqmyrLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHISDM--SWGRVKHPSEVVN---------VGDEVEVKVLKIDKERKRISL 67
|
.
gi 489115763 723 S 723
Cdd:cd05688 68 G 68
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
639-766 |
2.43e-04 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 41.94 E-value: 2.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 639 MLDQVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYRfdQVGQRLTgessgqmyrLGDRVEVRVEAVNmDER 718
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVK--DINDHLK---------VGDEVEVKVLNVE-DDG 67
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 489115763 719 KIDFSLisseraprnegKTAREKAKKSDAGKNTGKRRQMGKKVNFEPD 766
Cdd:PRK08582 68 KIGLSI-----------KKAKDRPKRQHDRPRHEDNRGGGNDVAPKED 104
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
607-724 |
2.84e-04 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 44.34 E-value: 2.84e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 607 EEMLQLGQHCSMAERRADEATRDVSDWLKcdfMLDQ-----------VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVS 675
Cdd:TIGR00717 228 SEYVKVGQEVKVKVIKFDKEKGRISLSLK---QLGEdpweaiekkfpVGDKITGRVTNLTDYGVFVEIEE-GIEGLVHVS 303
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 489115763 676 SLDNDYyrfdqvgqrlTGESSGQMYRLGDRVEVRVEAVNMDERKIDFSL 724
Cdd:TIGR00717 304 EMSWVK----------KNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
644-723 |
4.38e-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: 39.06 E-value: 4.38e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 644 GNVFKGVIASVTGFGFFVrldELF--IDGLVHVSSLDNDyyRFDQVGQRLTgessgqmyrLGDRVEVRVeaVNMDER-KI 720
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFV---EILpgKDGLVHISELSDE--RVEKVEDVLK---------VGDEVKVKV--IEVDDRgRI 64
|
...
gi 489115763 721 DFS 723
Cdd:cd04472 65 SLS 67
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
158-213 |
7.06e-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: 38.29 E-value: 7.06e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 489115763 158 TDAGVGFVVPDDSrlSFDILIPPEEVMGARMGFVVVVELTQrPTRRTKAVGKIVEV 213
Cdd:pfam08206 6 HKKGFGFLIPDDE--EDDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
643-724 |
7.57e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.84 E-value: 7.57e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgQRLTgeSSGQMYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWT--------KKNK--HPSKVVSVGQEVEVMVLEIDEEKRRISL 354
|
..
gi 489115763 723 SL 724
Cdd:PRK06299 355 GL 356
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-723 |
7.94e-04 |
|
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240197 [Multi-domain] Cd Length: 69 Bit Score: 38.42 E-value: 7.94e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 644 GNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYRfdqvgqrltgeSSGQMYRLGDRVEVRVeaVNMDER-KIDF 722
Cdd:cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVK-----------DVKDVLKEGDKVKVKV--LSIDARgRISL 66
|
.
gi 489115763 723 S 723
Cdd:cd05692 67 S 67
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-769 |
2.77e-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: 2.77e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSsldndyyrfDQVGQRLTGESsgQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDLGG--VDGLLHIT---------DMSWKRVKHPS--EYVKVGQEVKVKVIKFDKEKGRIS 252
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 489115763 722 FSLISSERAPRNEGKtarEKAKKSDAGKntgkrrqmGKKVNFEPDSAF 769
Cdd:TIGR00717 253 LSLKQLGEDPWEAIE---KKFPVGDKIT--------GRVTNLTDYGVF 289
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
643-751 |
2.81e-03 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 41.24 E-value: 2.81e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyRFDQVGQRLtgessgQMYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVEN--RDGDPGEAL------RKYAVGDRVKAVIVDMNVKDRKVAF 822
|
90 100 110
....*....|....*....|....*....|
gi 489115763 723 SLISSER-APRNEGKTAREKAKKSDAGKNT 751
Cdd:PRK12269 823 SVRDYQRkVQRDELSRYMSAPRGEDEGSFT 852
|
|
| HTH_ARSR |
cd00090 |
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ... |
19-85 |
2.84e-03 |
|
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Pssm-ID: 238042 [Multi-domain] Cd Length: 78 Bit Score: 37.28 E-value: 2.84e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489115763 19 PSREFILEHLTKREKPANrdELAAELNIEgeeqQEALRRRLRAMERDGqLVFTRRQ----CYALPERLDLL 85
Cdd:cd00090 7 PTRLRILRLLLEGPLTVS--ELAERLGLS----QSTVSRHLKKLEEAG-LVESRREgrrvYYSLTDAERLL 70
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-724 |
7.93e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 39.76 E-value: 7.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489115763 642 QVGNVFKGVIASVTGFGFFVRLDelFIDGLVHVSslDNDYYRFdqvgqrltgESSGQMYRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK06299 200 EEGQVVEGVVKNITDYGAFVDLG--GVDGLLHIT--DISWKRV---------NHPSEVVNVGDEVKVKVLKFDKEKKRVS 266
|
...
gi 489115763 722 FSL 724
Cdd:PRK06299 267 LGL 269
|
|
| |
