|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-774 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1710.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASRDELAIELNIEGEEQTEALRRRLRAMERDGQLVFTRRQCYALPE 80
Cdd:PRK11642 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
Cdd:PRK11642 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 161 GVGFVVPDDSRLSFDILIPPEEIMGARMGYVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPPA 240
Cdd:PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 241 VEKQVSGLKEQVPEEAKAGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPGTPLDAEARSRG 320
Cdd:PRK11642 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHMLQGDQELREHY 400
Cdd:PRK11642 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 401 APLVKHIEELHNLYKVLESAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAQEP 480
Cdd:PRK11642 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 481 ALFRIHDKPTTEAITSFRTVLAELGLELPGGNKPEPRDYAELLTSIADRPDAEMLQTMLLRSMKQAVYDPENRGHFGLAL 560
Cdd:PRK11642 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNSTETGGWHYSMEEMLQLGQHCSMTERRADEATREVSDWLKCDFMQ 640
Cdd:PRK11642 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFML 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 641 DQVGNIFSGVIASVTGFGFFVRLNDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....
gi 488974776 721 DFTLISSERAPRNVGKTAREKAKKSTSGKPGGRRRQVGKQVNFEPDSAFRKEKE 774
Cdd:PRK11642 721 DFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKK 774
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
20-732 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1153.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 20 SREFILEHLTK-REKPASRDELAIELNIEGEEQTEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGF 98
Cdd:COG0557 4 SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFGF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 99 LRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILI 178
Cdd:COG0557 84 VIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDIFI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 179 PPEEIMGARMGYVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPPAVEKQVSGLKEQVPEEAKA 258
Cdd:COG0557 164 PPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEADLK 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 259 GRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPGTPLDAEARSRGTSVYFPSQVVPMLPEVLS 338
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLS 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 339 NGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHMLQG-DQELREHYAPLVKHIEELHNLYKVL 417
Cdd:COG0557 324 NGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELYELAKIL 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 418 ESAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAQEPALFRIHDKPTTEAITSF 497
Cdd:COG0557 404 RKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLEAL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 498 RTVLAELGLELPGGNKPEPRDYAELLTSIADRPDAEMLQTMLLRSMKQAVYDPENRGHFGLALQSYAHFTSPIRRYPDLS 577
Cdd:COG0557 484 REFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYPDLL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 578 LHRAIKYLLAKEQGhkgnsteTGGWHYSMEEMLQLGQHCSMTERRADEATREVSDWLKCDFMQDQVGNIFSGVIASVTGF 657
Cdd:COG0557 564 VHRALKAYLEGKRS-------PGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSF 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488974776 658 GFFVRLNDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVRVEAVNMDERKIDFTLISSERAPR 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: 1055.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 18 IPSREFILEHLTK-REKPASRDELAIELNIEGEEQTEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGY 96
Cdd:TIGR02063 1 SPLRELILEFLKSkKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 97 GFLRVEGRK-DDLYLSSEQMKTCIHGDQVLAQPLG-ADRKGRREARIVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSF 174
Cdd:TIGR02063 81 GFLRPEDDDeDDIFIPPRQMNGAMHGDRVLVRITGkPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 175 DILIPPEEIMGARMGYVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPPAVEKQVSGLKEQVPE 254
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 255 EAKAGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPGTPLDAEARSRGTSVYFPSQVVPMLP 334
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 335 EVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHMLQGDQELREHYAPLVKHIEELHNLY 414
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 415 KVLESAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAQEPALFRIHDKPTTEAI 494
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 495 TSFRTVLAELGLELPGG--NKPEPRDYAELLTSIADRPDAEMLQTMLLRSMKQAVYDPENRGHFGLALQSYAHFTSPIRR 572
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGtsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 573 YPDLSLHRAIKYLLAKEQGHKGNSTEtggwHYSMEEMLQLGQHCSMTERRADEATREVSDWLKCDFMQDQVGNIFSGVIA 652
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGENTTTEKER----EYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVIS 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488974776 653 SVTGFGFFVRLNDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVRVEAVNMDERKIDFTLI 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: 994.99 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 67 QLVFTrrQCYALPERLDLLKGTVIGHRDGYGFLR-VEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVL 145
Cdd:TIGR00358 1 QLLAT--LKYALPEKDDLVKGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 146 VPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEEI-MGARMGYVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAV 224
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 225 DMALRTHEIPYVWPPAVEKQVSGLKEQVPEEAKAGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSY 304
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 305 YVRPGTPLDAEARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYT 384
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 385 KVWHMLQGDQELREHYAPLVKHIEELHNLYKVLESAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMI 464
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 465 LANISAARFVEKAQEPALFRIHDKPTTEAITSFRTVLAELGLELPGGNKPE--PRDYAELLTSIADRPDAEMLQTMLLRS 542
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENvtTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 543 MKQAVYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQghkgnsTETGGwHYSMEEMLQLGQHCSMTERR 622
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ------TDTER-YQPQDELLQIAEHCSDTERR 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 623 ADEATREVSDWLKCDFMQDQVGNIFSGVIASVTGFGFFVRLNDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRL 702
Cdd:TIGR00358 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRI 631
|
650 660
....*....|....*....|...
gi 488974776 703 GDRVEVRVEAVNMDERKIDFTLI 725
Cdd:TIGR00358 632 GDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
260-588 |
1.20e-137 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 408.96 E-value: 1.20e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 260 RVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPGTPLDAEARSRGTSVYFPSQVVPMLPEVLSN 339
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 340 GLCSLNPQVDRLCMVCEMTISSKG-RLTGYKFYEAVMSSHARLTYTKVWHMLQgdqelrehyaplvkhieelhnlykvle 418
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 419 sareerggisfeseeaKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAQEPALFRIHDKPTTEAIT-SF 497
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAeLL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 498 RTVLAELGLELPGGnkPEPRDYAELLTSIADRPDAEMLQTMLLRSMKQAVYDPENRGHFGLALQSYAHFTSPIRRYPDLS 577
Cdd:smart00955 198 KEFLALLGLLLLGG--DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 488974776 578 LHRAIKYLLAK 588
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
260-586 |
7.02e-137 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 407.83 E-value: 7.02e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 260 RVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPGTPLDAEARSRGTSVYFPSQVVPMLPEVLSN 339
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 340 GLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHMLQGDQELREHyAPLVKHIEELHNLYKVLES 419
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 420 AREERGGISFESEEAKFIFNAERRIErIEQTQRNDAHKLIEECMILANISAARFVEKAQEPALFRIHDKPTTEAITSFRT 499
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 500 VLAELglelpggnkPEPRDYAELLTSIADRPDAemLQTMLLRSMKQAVYDPENRGHFGLALQSYAHFTSPIRRYPDLSLH 579
Cdd:pfam00773 239 LLQLL---------PDDKGLSKSLEKIKDDERL--LSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....*..
gi 488974776 580 RAIKYLL 586
Cdd:pfam00773 308 RQLKALL 314
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
87-720 |
2.80e-90 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 297.92 E-value: 2.80e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAQPLGAdrKGRREARIVRVLVPKTSQIVGRY-FTDaGVGFV 165
Cdd:COG4776 24 GVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVIRTE--KDKESAEPETLIEPFLTRFVGRVqKKD-GRLFV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 166 VPDDSRLSFDILIPPEEIMGA--RMGYVVVVELTQRPTRRTK-AVGKIVEVLGDNMGTGMAVDMALRTHEIPYVWPPAVE 242
Cdd:COG4776 100 VPDHPLIKDAIKARPKKGLEEglKEGDWVVAELKRHPLKGDRgFFAEITEFIADADDPFAPWWVTLARHNLEREAPEGDD 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 243 kQVSGLKEQVPeeakagRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPGTPLDAEARSRGTS 322
Cdd:COG4776 180 -EWELLDEGLE------REDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKEARQRAFT 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 323 VYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTG-YKFYEAVMSSHARLTYTKVWHMLQGDQELREHYA 401
Cdd:COG4776 253 NYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKGEWQPENE 332
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 402 PLVKHIEELHNLYKVLESAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAQEPA 481
Cdd:COG4776 333 EIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVLREHLGFG 412
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 482 LFRIHDKPTTEAITSFRTVLAELGLELPGGNKPEPRDYAELLTSIADRPDAEMlqTMLLRSMKQ-AVYDPENRGHFGLAL 560
Cdd:COG4776 413 IFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYL--DSRLRRFQTfAEISTEPGPHFGLGL 490
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNstetggwhysmEEMLQLGQHCsmteRRADE-ATREVSDWLKCDFM 639
Cdd:COG4776 491 DAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPD-----------EELTERLAER----RRLNRmAERDVADWLYARYL 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 640 QDQVGN--IFSGVIASVTGFGFFVRLND----LFIDG-LVHVsslDNDYYRFDQ-VGQRLIgeSGGQTYRLGDRVEVRVE 711
Cdd:COG4776 556 KPKVGSgqVFTAEIIDINRGGLRVRLLEngavAFIPAsFIHS---VRDELVCSQeEGTVYI--KGEVRYKLGDTIQVTLA 630
|
....*....
gi 488974776 712 AVNMDERKI 720
Cdd:COG4776 631 EVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
87-720 |
1.31e-75 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 258.27 E-value: 1.31e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 87 GTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAqpLGADRKGRREARIVRVLVPKTSQIVGRyftdagvgfVV 166
Cdd:PRK05054 24 GVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIA--VIHTEKDREIAEPEELIEPFLTRFVGR---------VQ 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 167 PDDSRLSfdiLIP--P--EEIMGARM----------GYVVVVELTQRPTR-----RTKAVGKIVEvlGDNMGTGMAVdmA 227
Cdd:PRK05054 92 KKDDRLS---IVPdhPllKDAIPCRAakglnhefkeGDWVVAELRRHPLKgdrgfYAEITQFITD--ADDHFAPWWV--T 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 228 LRTHEIPYVwPPAVEKQVSGLKEQVPeeakagRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVR 307
Cdd:PRK05054 165 LARHNLERE-APAGGVAWEMLDEGLE------REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIA 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 308 PGTPLDAEARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTG-YKFYEAVMSSHARLTYTKV 386
Cdd:PRK05054 238 EGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAYDNV 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 387 WHMLQGDQELREHYAPLVKHIEELHNLYKVLESAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILA 466
Cdd:PRK05054 318 SDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAA 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 467 NISAARFVEKAQEPALFRIH---DKPTTEAITSFrtvLAELGLE--------LPGgnkpeprdYAELLTSIADRPDaEML 535
Cdd:PRK05054 398 NICAARVLRDKLGFGIYNVHsgfDPANAEQAVAL---LKEHGLHfdaeelltLEG--------FCKLRRELDAQPT-GYL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 536 QTMLLRSMKQAVYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNstetggwhysmEEMLQLgqh 615
Cdd:PRK05054 466 DSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ-----------DEITVQ--- 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 616 csMTERRADE--ATREVSDWLKCDFMQDQVGN--IFSGVIASVTGFGFFVRLND----LFIDGlvhvSSLDNDYYRFDqv 687
Cdd:PRK05054 532 --LAERRRLNrmAERDVGDWLYARYLKDKAGTdtRFAAEIIDISRGGMRVRLLEngavAFIPA----SFLHAVRDELV-- 603
|
650 660 670
....*....|....*....|....*....|....*....
gi 488974776 688 gqrLIGESG-----GQT-YRLGDRVEVRVEAVNMDERKI 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 |
5.57e-39 |
|
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: 139.07 E-value: 5.57e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 643 VGNIFSGVIASVTGFGFFVRLNDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 488974776 723 TLI 725
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
164-238 |
2.88e-30 |
|
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: 113.64 E-value: 2.88e-30
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488974776 164 FVVPDDSRLSFDILIPPEEIMGARMGYVVVVELTQRPTRRtKAVGKIVEVLGDNMGTGMAVDMALRTHEIPYVWP 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 |
2.40e-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: 93.76 E-value: 2.40e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 488974776 87 GTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRV 144
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
649-720 |
3.73e-14 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 71.40 E-value: 3.73e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488974776 649 GVIASVTGFGFFVRLNDlfIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK08563 87 GEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
86-145 |
2.76e-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: 65.31 E-value: 2.76e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488974776 86 KGTVIGHRDGYGFLRVEGRKDDLYLSSEQ----MKTCIHGDQVLAQPLGADRKGRREARIVRVL 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 ... |
646-724 |
3.18e-13 |
|
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Pssm-ID: 239907 [Multi-domain] Cd Length: 99 Bit Score: 66.16 E-value: 3.18e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 646 IFSGVIASVTGFGFFVRLNDlfIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVRVEAVNMDER-----KI 720
Cdd:cd04460 2 VVEGEVVEVVDFGAFVRIGP--VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERrpresKI 79
|
....
gi 488974776 721 DFTL 724
Cdd:cd04460 80 GLTM 83
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
641-724 |
6.70e-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: 64.23 E-value: 6.70e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 641 DQVGNIFSGVIASVTGFGFFVRLnDLFIDGLVHVSSLDNDYYrfdqvgqrligESGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRI 68
|
....
gi 488974776 721 DFTL 724
Cdd:pfam00575 69 ILSI 72
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
642-724 |
8.15e-12 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 61.08 E-value: 8.15e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDNDYyrfdqvgqrliGESGGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
...
gi 488974776 722 FTL 724
Cdd:smart00316 69 LSL 71
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
22-85 |
3.72e-11 |
|
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: 59.34 E-value: 3.72e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488974776 22 EFILEHLTKREKPASRDELAIELNIEGEE-QTEALRRRLRAMERDGqlvFTRRQCYA---LPER-LDLL 85
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYAgreITEKgLEEL 66
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
649-720 |
7.08e-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: 50.07 E-value: 7.08e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488974776 649 GVIASVTGFGFFVRLNDlFIDGLVHVSSLDNDYYrfdqvgqrligESGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:cd00164 3 GKVVSITKFGVFVELED-GVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRI 62
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-720 |
3.79e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 53.63 E-value: 3.79e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDndyyrFDQVGQRLIgesggQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDIS-----WDKKGEEAV-----ELYKKGDEVEAVVLKVDVEKERI 439
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
644-723 |
6.57e-07 |
|
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: 47.23 E-value: 6.57e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 644 GNIFSGVIASVTGFGFFVrlnDLFI--DGLVHVSSLDNDYY--RFDQVGqrligesggqtyrLGDRVEVRVEAVNMDERK 719
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFV---DIGVkqDGLIHISKMADRFVshPSDVVS-------------VGDIVEVKVISIDEERGR 64
|
....
gi 488974776 720 IDFT 723
Cdd:cd05685 65 ISLS 68
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-720 |
7.19e-07 |
|
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: 47.10 E-value: 7.19e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488974776 644 GNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLdndyyrfdQVGQRliGESGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDI--------SWTQR--VRHPSEIYKKGQEVEAVVLNIDVERERI 66
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
644-680 |
1.34e-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: 46.85 E-value: 1.34e-06
10 20 30
....*....|....*....|....*....|....*....
gi 488974776 644 GNIFSGVIASVTGFGFFVRLNDL--FIDGLVHVSSLDND 680
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFE 39
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
636-722 |
1.48e-06 |
|
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Pssm-ID: 239919 [Multi-domain] Cd Length: 77 Bit Score: 46.45 E-value: 1.48e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 636 CDFMQDQVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDNDyyrfdqvgqrligesggqtYRLGDRVEVRVEAVNm 715
Cdd:cd04473 9 CTMEDLEVGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLLRD-------------------YEVGDEVIVQVTDIP- 67
|
....*..
gi 488974776 716 DERKIDF 722
Cdd:cd04473 68 ENGNIDL 74
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
643-727 |
1.54e-06 |
|
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 46.55 E-value: 1.54e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 643 VGNIFSGVIASVTGFGFFVRLNDLFIDGLVHVSSLDNDyyRFDQVGQRligesggqtYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN--RVADASKL---------FRVGDKVRAKVLKIDAEKKRISL 70
|
....*
gi 488974776 723 TLISS 727
Cdd:cd05708 71 GLKAS 75
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-720 |
1.92e-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: 50.81 E-value: 1.92e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDNDyyrfdqvgQRLigESGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEP-GVEGLVHISEMSWT--------KRV--AHPSDVVKVGDEVEVKVLDIDPEERRI 340
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
643-724 |
1.69e-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: 48.19 E-value: 1.69e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 643 VGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDNdyyrfDQVGQRLIgesggqTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSE-----NRDEDKTD------EIKVGDEVEAKVVDIDKKNRKVSL 513
|
..
gi 488974776 723 TL 724
Cdd:TIGR00717 514 SV 515
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-720 |
2.54e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 47.85 E-value: 2.54e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRD--RVEDATEVL---------KVGDEVEAKVINIDRKNRRI 525
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
643-752 |
2.63e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 47.18 E-value: 2.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 643 VGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSsldndyyrfdQVGQRLIGeSGGQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLP-GVEGLVHIS----------QISHKHIA-TPSEVLEEGQEVKVKVLEVNEEEKRISL 344
|
90 100 110
....*....|....*....|....*....|
gi 488974776 723 TLISSERAPRNVGKTAREKAKKSTSGKPGG 752
Cdd:PRK06676 345 SIKALEEAPAEEEDRREEYRQYELPEEETG 374
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
3.94e-05 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 47.25 E-value: 3.94e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGG--VDGLLHVSEI--SWGRVEKPSDVL---------KVGDEIKVYILDIDKENKKLS 542
|
...
gi 488974776 722 FTL 724
Cdd:PRK00087 543 LSL 545
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
602-720 |
7.74e-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: 7.74e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 602 WHYSM--EEMLQLGQHCSMTERRADEATREVSDWLKcDFMQD---------QVGNIFSGVIASVTGFGFFVRLNDlFIDG 670
Cdd:PRK00087 511 WGRVEkpSDVLKVGDEIKVYILDIDKENKKLSLSLK-KLLPDpwenveekyPVGSIVLGKVVRIAPFGAFVELEP-GVDG 588
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 488974776 671 LVHVSSLDNdyYRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK00087 589 LVHISQISW--KRIDKPEDVL---------SEGEEVKAKILEVDPEEKRI 627
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
643-720 |
7.75e-05 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 41.46 E-value: 7.75e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488974776 643 VGNIFSGVIASVTGFGFFVRLNDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKI 720
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHISDM--SWGRVKHPSEVV---------NVGDEVEVKVLKIDKERKRI 65
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
639-733 |
7.76e-05 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 46.17 E-value: 7.76e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 639 MQD-QVGNIFSGVIASVTGFGFFVrlnDLFI--DGLVHVSSLDNDYYR--FDQVgqrligesggqtyRLGDRVEVRVEAV 713
Cdd:COG2183 636 IEDlKPGMILEGTVTNVTDFGAFV---DIGVhqDGLVHISQLSDRFVKdpREVV-------------KVGDIVKVKVLEV 699
|
90 100
....*....|....*....|
gi 488974776 714 NMDERKIDFTLISSERAPRN 733
Cdd:COG2183 700 DLKRKRISLSMKLDDEAGAA 719
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
639-764 |
9.72e-05 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 42.86 E-value: 9.72e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 639 MQDQVGNIFSGVIASVTGFGFFVRLNDlfiD--GLVHVSSLDNDY----YRFDQVGQrligesggqtyrlgdrvEVRVEA 712
Cdd:COG1098 1 MSIEVGDIVEGKVTGITPFGAFVELPE---GttGLVHISEIADGYvkdiNDYLKVGD-----------------EVKVKV 60
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 488974776 713 VNMDER-KIDFTLisseraprnvgKTAREKAKKSTSGKPGGRRRQvgKQVNFE 764
Cdd:COG1098 61 LSIDEDgKISLSI-----------KQAEEKPKRPPRPRRNSRPKA--GFESFE 100
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
642-724 |
1.41e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 44.87 E-value: 1.41e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFVDIGG--VDGLVHISEL--SHERVEKPSEVV---------SVGQEVEVKVLSIDWETERIS 257
|
...
gi 488974776 722 FTL 724
Cdd:PRK06676 258 LSL 260
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
642-724 |
2.43e-04 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 44.66 E-value: 2.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVrlnDLF--IDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVRVeaVNMDER- 718
Cdd:PRK11824 620 EVGEIYEGKVVRIVDFGAFV---EILpgKDGLVHISEIADE--RVEKVEDVL---------KEGDEVKVKV--LEIDKRg 683
|
....*.
gi 488974776 719 KIDFTL 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 ... |
642-718 |
2.52e-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: 40.16 E-value: 2.52e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDLFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDER 718
Cdd:cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RVDDPSEVV---------DVGEKVWVKVIGREMKDK 67
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
642-751 |
2.61e-04 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 41.57 E-value: 2.61e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDLfIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDEE-TQGLVHISEITHGFVK--DIHDFL---------SVGDEVKVKVLSVDEEKGKIS 73
|
90 100 110
....*....|....*....|....*....|
gi 488974776 722 FTLISSERAPRnvGKTAREKAKKSTSGKPG 751
Cdd:PRK08059 74 LSIRATEEAPE--AKRKKGKILIPNPSEQG 101
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-720 |
2.99e-04 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 43.88 E-value: 2.99e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERKI 720
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG--VDGLLHISEI--SWGRVKHPSEVL---------KVGDEVEVKVLKIDREKERI 253
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
158-213 |
5.04e-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: 38.67 E-value: 5.04e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 488974776 158 TDAGVGFVVPDDSrlSFDILIPPEEIMGARMGYVVVVELTQrPTRRTKAVGKIVEV 213
Cdd:pfam08206 6 HKKGFGFLIPDDE--EDDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-724 |
7.01e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 43.11 E-value: 7.01e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLdndyyrfdqvGQRLIgESGGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISEL----------AERHV-EVPEQVVQVGDEVFVKVIDIDLERRRIS 359
|
...
gi 488974776 722 FTL 724
Cdd:PRK07899 360 LSL 362
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
640-731 |
7.51e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 42.72 E-value: 7.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 640 QDQVGNIFSGVIASVTGFGFFVRLNDlfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVRVEAVNMDERK 719
Cdd:PRK07899 205 QLQKGQVRKGVVSSIVNFGAFVDLGG--VDGLVHVSEL--SWKHIDHPSEVV---------EVGQEVTVEVLDVDMDRER 271
|
90
....*....|..
gi 488974776 720 IDFTLISSERAP 731
Cdd:PRK07899 272 VSLSLKATQEDP 283
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-720 |
9.49e-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: 42.41 E-value: 9.49e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 642 QVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVS--SLDNDyyrfdqvgqrliGESGGQTYRLGDRVEVRVEAVNMDERK 719
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSdiSWDKD------------GREADHLYKKGDEIEAVVLAVDKEKKR 424
|
.
gi 488974776 720 I 720
Cdd:TIGR00717 425 I 425
|
|
| TFIIE_beta |
pfam02186 |
TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, ... |
23-64 |
1.25e-03 |
|
TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.
Pssm-ID: 460479 Cd Length: 66 Bit Score: 37.90 E-value: 1.25e-03
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 488974776 23 FILEHLTKREKPASRDELAIELNIEGEEQTEALRRRLRAMER 64
Cdd:pfam02186 7 KAVEYLKKQDGPLTLEEILDYLSLDLGDKNWLLLEALKNNPK 48
|
|
| PRK05807 |
PRK05807 |
RNA-binding protein S1; |
639-681 |
3.10e-03 |
|
RNA-binding protein S1;
Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 38.57 E-value: 3.10e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 488974776 639 MQDQVGNIFSGVIASVTGFGFFVRLNDLfiDGLVHVSSLDNDY 681
Cdd:PRK05807 1 MTLKAGSILEGTVVNITNFGAFVEVEGK--TGLVHISEVADTY 41
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
639-774 |
3.98e-03 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 38.48 E-value: 3.98e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488974776 639 MQDQVGNIFSGVIASVTGFGFFVRLNDlFIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVRVEAVNmDER 718
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVK--DINDHL---------KVGDEVEVKVLNVE-DDG 67
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488974776 719 KIDFTLisseraprnvgKTAREKAKKSTSGKPGGRRRQVGKQVNFEPD-----SAFRKEKE 774
Cdd:PRK08582 68 KIGLSI-----------KKAKDRPKRQHDRPRHEDNRGGGNDVAPKEDfeqkmSRFLKDSE 117
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
644-718 |
8.35e-03 |
|
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: 35.60 E-value: 8.35e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488974776 644 GNIFSGVIASVTGFGFFVRlndlFI---DGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVRVeaVNMDER 718
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVE----ILpgkDGLVHISELSDE--RVEKVEDVL---------KVGDEVKVKV--IEVDDR 61
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
643-720 |
9.52e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 39.38 E-value: 9.52e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488974776 643 VGNIFSGVIASVTGFGFFVRL-NDlfIDGLVHVSSLDNDyyrfdqvgQRLIgeSGGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELeEG--IEGLVHVSEMSWT--------KKNK--HPSKVVSVGQEVEVMVLEIDEEKRRI 352
|
|
| |
