|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-796 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1697.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 1 MSHDPFQEREAEKYANPIPSREFIIEHLTKREKPANREELAVELNIEGEEQIEALRRRLRAMERDGQLVFTRRQCYALPE 80
Cdd:PRK11642 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 81 RLDLLKGTVIGHRDGFGFLRVEGRKDDLYLSSEQMKMCIHGDQILAQPLGADRKGRREARVVRVLVPKTSQIVGRYFTDA 160
Cdd:PRK11642 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 161 GVGFVVPDDSRLSFDILIPPEEVMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTTMAVDMALRTHEIPYIWPKA 240
Cdd:PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 241 VEDQIESLREEVPEESKVGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPHTPLDNEARSRG 320
Cdd:PRK11642 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISTKGRLTGYKFYEAVMSSHARLTYTKVWHMLQGDQDLREQY 400
Cdd:PRK11642 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 401 APLVKHIEELHNLYKTLDQAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
Cdd:PRK11642 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 481 ALFRIHDKPTTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESIGDRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
Cdd:PRK11642 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAQEQGHKGNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFML 640
Cdd:PRK11642 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFML 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 641 DQVGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDDRKI 720
Cdd:PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556425213 721 DFSLISSERAPRNVGKTERERAKKTGNGKPgGGKRRQAGKKVNFEPDSAFRGEKKQKPKAAKKEARSAKKPSAKTQ 796
Cdd:PRK11642 721 DFSLISSERAPRNVGKTAREKAKKGDAGKK-GGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKTQ 795
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
20-732 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1136.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 20 SREFIIEHLTK-REKPANREELAVELNIEGEEQIEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGFGF 98
Cdd:COG0557 4 SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFGF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 99 LRVEGRKDDLYLSSEQMKMCIHGDQILAQPLGADRKGRREARVVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILI 178
Cdd:COG0557 84 VIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDIFI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 179 PPEEVMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTTMAVDMALRTHEIPYIWPKAVEDQIESLREEVPEESKV 258
Cdd:COG0557 164 PPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEADLK 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 259 GRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPHTPLDNEARSRGTSVYFPSQVVPMLPEVLS 338
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLS 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 339 NGLCSLNPQVDRLCMVCEMTISTKGRLTGYKFYEAVMSSHARLTYTKVWHMLQG-DQDLREQYAPLVKHIEELHNLYKTL 417
Cdd:COG0557 324 NGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELYELAKIL 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 418 DQAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPTTEAITSF 497
Cdd:COG0557 404 RKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLEAL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 498 RSVLAELGLELPGGNKPEPRDYAELLESIGDRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLS 577
Cdd:COG0557 484 REFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYPDLL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 578 LHRAIKYLLAqeqghkgNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVIASVTGF 657
Cdd:COG0557 564 VHRALKAYLE-------GKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSF 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556425213 658 GFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDDRKIDFSLISSERAPR 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 556425213 18 IPSREFIIEHLTK-REKPANREELAVELNIEGEEQIEALRRRLRAMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGF 96
Cdd:TIGR02063 1 SPLRELILEFLKSkKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 97 GFLRVEGRK-DDLYLSSEQMKMCIHGDQILAQPLG-ADRKGRREARVVRVLVPKTSQIVGRYFTDAGVGFVVPDDSRLSF 174
Cdd:TIGR02063 81 GFLRPEDDDeDDIFIPPRQMNGAMHGDRVLVRITGkPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 175 DILIPPEEVMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTTMAVDMALRTHEIPYIWPKAVEDQIESLREEVPE 254
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 255 ESKVGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPHTPLDNEARSRGTSVYFPSQVVPMLP 334
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 335 EVLSNGLCSLNPQVDRLCMVCEMTISTKGRLTGYKFYEAVMSSHARLTYTKVWHMLQGDQDLREQYAPLVKHIEELHNLY 414
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 415 KTLDQAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPTTEAI 494
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 495 TSFRSVLAELGLELPGG--NKPEPRDYAELLESIGDRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRR 572
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGtsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 573 YPDLSLHRAIKYLLAQEQGHKGNTTetggYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVIA 652
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGENTTTEKE----REYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVIS 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556425213 653 SVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDDRKIDFSLI 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: 989.99 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 67 QLVFTrrQCYALPERLDLLKGTVIGHRDGFGFLR-VEGRKDDLYLSSEQMKMCIHGDQILAQPLGADRKGRREARVVRVL 145
Cdd:TIGR00358 1 QLLAT--LKYALPEKDDLVKGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 146 VPKTSQIVGRYFTDAGVGFVVPDDSRLSFDILIPPEEV-MGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTTMAV 224
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKASVkNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 225 DMALRTHEIPYIWPKAVEDQIESLREEVPEESKVGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSY 304
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 305 YVRPHTPLDNEARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISTKGRLTGYKFYEAVMSSHARLTYT 384
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 385 KVWHMLQGDQDLREQYAPLVKHIEELHNLYKTLDQAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMI 464
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 465 LANISAARFVEKAKEPALFRIHDKPTTEAITSFRSVLAELGLELPGGNKPE--PRDYAELLESIGDRPDAEMLQTMLLRS 542
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENvtTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 543 MKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAQEQghkgntTETGGYhYSMEEMLQLGQHCSMAERR 622
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ------TDTERY-QPQDELLQIAEHCSDTERR 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 623 ADEATRDVADWLKCDFMLDQVGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRL 702
Cdd:TIGR00358 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRI 631
|
650 660
....*....|....*....|...
gi 556425213 703 GDRVEVKVEAVNMDDRKIDFSLI 725
Cdd:TIGR00358 632 GDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
260-588 |
4.59e-136 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 404.73 E-value: 4.59e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 260 RVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPHTPLDNEARSRGTSVYFPSQVVPMLPEVLSN 339
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 340 GLCSLNPQVDRLCMVCEMTISTKG-RLTGYKFYEAVMSSHARLTYTKVWHMLQgdqdlreqyaplvkhieelhnlyktld 418
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 419 qareerggisfeseeaKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPTTEAIT-SF 497
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAeLL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 498 RSVLAELGLELPGGnkPEPRDYAELLESIGDRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLS 577
Cdd:smart00955 198 KEFLALLGLLLLGG--DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 556425213 578 LHRAIKYLLAQ 588
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
260-586 |
8.63e-135 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 402.82 E-value: 8.63e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 260 RVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPHTPLDNEARSRGTSVYFPSQVVPMLPEVLSN 339
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 340 GLCSLNPQVDRLCMVCEMTISTKGRLTGYKFYEAVMSSHARLTYTKVWHMLQGDQDLREQyAPLVKHIEELHNLYKTLDQ 419
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 420 AREERGGISFESEEAKFIFNAERRIErIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPTTEAITSFRS 499
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 500 VLAELglelpggnkPEPRDYAELLESIGDRPDAemLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLH 579
Cdd:pfam00773 239 LLQLL---------PDDKGLSKSLEKIKDDERL--LSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....*..
gi 556425213 580 RAIKYLL 586
Cdd:pfam00773 308 RQLKALL 314
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
87-720 |
4.66e-92 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 302.54 E-value: 4.66e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 87 GTVIGHRDGFGFLRVEGRKDdLYLSSEQMKMCIHGDQILAQPLGAdrKGRREARVVRVLVPKTSQIVGRY-FTDaGVGFV 165
Cdd:COG4776 24 GVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVIRTE--KDKESAEPETLIEPFLTRFVGRVqKKD-GRLFV 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 166 VPDDSRLSFDILIPPEEVMGA--RMGFVVVVELTQRPTRRTK-AVGKIVEVLGDnmgttmaVD-------MALRTHEIPY 235
Cdd:COG4776 100 VPDHPLIKDAIKARPKKGLEEglKEGDWVVAELKRHPLKGDRgFFAEITEFIAD-------ADdpfapwwVTLARHNLER 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 236 IWPKAVEDQieSLREEVPEeskvgRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPHTPLDNE 315
Cdd:COG4776 173 EAPEGDDEW--ELLDEGLE-----REDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 316 ARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISTKGRLTG-YKFYEAVMSSHARLTYTKVWHMLQGDQ 394
Cdd:COG4776 246 ARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKG 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 395 DLREQYAPLVKHIEELHNLYKTLDQAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFV 474
Cdd:COG4776 326 EWQPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 475 EKAKEPALFRIHDKPTTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESIGDRPDAEMlqTMLLRSMKQ-AIYDPENR 553
Cdd:COG4776 406 REHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYL--DSRLRRFQTfAEISTEPG 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 554 GHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAQEQGHKGNttetggyhysmEEMLQLGQHCSMAERRADeatRDVADW 633
Cdd:COG4776 484 PHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPD-----------EELTERLAERRRLNRMAE---RDVADW 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 634 LKCDFMLDQVGN--VFKGVIASVTGFGFFVRLDE----LFIDG-LVHVsslDNDYYRFDQ-VGQRLIgeSGGQTYRLGDR 705
Cdd:COG4776 550 LYARYLKPKVGSgqVFTAEIIDINRGGLRVRLLEngavAFIPAsFIHS---VRDELVCSQeEGTVYI--KGEVRYKLGDT 624
|
650
....*....|....*
gi 556425213 706 VEVKVEAVNMDDRKI 720
Cdd:COG4776 625 IQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
87-720 |
1.14e-77 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 264.05 E-value: 1.14e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 87 GTVIGHRDGFGFLRVEGRKDdLYLSSEQMKMCIHGDQILAQplgADRKGRREARVVRVLV-PKTSQIVGRyftdagvgfV 165
Cdd:PRK05054 24 GVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIAV---IHTEKDREIAEPEELIePFLTRFVGR---------V 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 166 VPDDSRLSfdiLIP--P--EEVMGARM----------GFVVVVELTQRPTR-----RTKAVGKIVEvlGDNMGTTMAVdm 226
Cdd:PRK05054 91 QKKDDRLS---IVPdhPllKDAIPCRAakglnhefkeGDWVVAELRRHPLKgdrgfYAEITQFITD--ADDHFAPWWV-- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 227 ALRTHEIPYIWPKAVEDQIesLREEVPEeskvgRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYV 306
Cdd:PRK05054 164 TLARHNLEREAPAGGVAWE--MLDEGLE-----REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYI 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 307 RPHTPLDNEARSRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISTKGRLTG-YKFYEAVMSSHARLTYTK 385
Cdd:PRK05054 237 AEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAYDN 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 386 VWHMLQGDQDLREQYAPLVKHIEELHNLYKTLDQAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMIL 465
Cdd:PRK05054 317 VSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 466 ANISAARFVEKAKEPALFRIH---DKPTTEAITSFrsvLAELGLE--------LPGgnkpeprdYAELLESIGDRPDaEM 534
Cdd:PRK05054 397 ANICAARVLRDKLGFGIYNVHsgfDPANAEQAVAL---LKEHGLHfdaeelltLEG--------FCKLRRELDAQPT-GY 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 535 LQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAQEQGHKGNttetggyhysmEEMLQLgq 614
Cdd:PRK05054 465 LDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ-----------DEITVQ-- 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 615 hcsMAERRADE--ATRDVADWLKCDFMLDQVGN--VFKGVIASVTGFGFFVRLDE----LFIDGlvhvSSLDNDYYRFDq 686
Cdd:PRK05054 532 ---LAERRRLNrmAERDVGDWLYARYLKDKAGTdtRFAAEIIDISRGGMRVRLLEngavAFIPA----SFLHAVRDELV- 603
|
650 660 670 680
....*....|....*....|....*....|....*....|
gi 556425213 687 vgqrLIGESG-----GQT-YRLGDRVEVKVEAVNMDDRKI 720
Cdd:PRK05054 604 ----CNQENGtvqikGETvYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
643-725 |
1.77e-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: 140.23 E-value: 1.77e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDDRKIDF 722
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 556425213 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 |
3.50e-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: 105.16 E-value: 3.50e-27
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556425213 164 FVVPDDSRLSFDILIPPEEVMGARMGFVVVVELTQRPTRRtKAVGKIVEVLGDNMGTTMAVDMALRTHEIPYIWP 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 |
7.53e-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: 92.22 E-value: 7.53e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 556425213 87 GTVIGHRDGFGFLRVEGRKDDLYLSSEQMKMCIHGDQILAQPLGADRKGRREARVVRV 144
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
641-724 |
2.15e-14 |
|
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 68.47 E-value: 2.15e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 641 DQVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYrfdqvgqrligESGGQTYRLGDRVEVKVEAVNMDDRKI 720
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDLGN-GVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRI 68
|
....
gi 556425213 721 DFSL 724
Cdd:pfam00575 69 ILSI 72
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
642-724 |
6.79e-13 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 64.16 E-value: 6.79e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYyrfdqvgqrliGESGGQTYRLGDRVEVKVEAVNMDDRKID 721
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
...
gi 556425213 722 FSL 724
Cdd:smart00316 69 LSL 71
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
646-720 |
7.34e-13 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 67.93 E-value: 7.34e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 556425213 646 VFKGVIASVTGFGFFVRLDElfIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDDRKI 720
Cdd:PRK08563 84 VVEGEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
86-145 |
7.24e-12 |
|
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: 61.08 E-value: 7.24e-12
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556425213 86 KGTVIGHRDGFGFLRVEGRKDDLYLSSEQ----MKMCIHGDQILAQPLGADRKGRREARVVRVL 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 ... |
646-725 |
8.19e-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: 62.30 E-value: 8.19e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 646 VFKGVIASVTGFGFFVRLDElfIDGLVHVSSLDNDYYRFDQVGQRLIGESGGQTYRLGDRVEVKVEAVNMDDRKIDFSLI 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 |
6.83e-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: 55.49 E-value: 6.83e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556425213 22 EFIIEHLTKREKPANREELAVELNIEGEE-QIEALRRRLRAMERDGqlvFTRRQCYA---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 ... |
647-723 |
5.98e-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: 5.98e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 556425213 647 FKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYrfdqvgqrligESGGQTYRLGDRVEVKVEAVNMDDRKIDFS 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 |
8.26e-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: 8.26e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDyyRFDQVGQRligesggqtYRLGDRVEVKVEAVNMDDRKIDF 722
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN--RVADASKL---------FRVGDKVRAKVLKIDAEKKRISL 70
|
....*
gi 556425213 723 SLISS 727
Cdd:cd05708 71 GLKAS 75
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-724 |
9.40e-09 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 58.64 E-value: 9.40e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDndyyrFDQVGQRLIgesggQTYRLGDRVEVKVEAVNMDDRKId 721
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDIS-----WDKKGEEAV-----ELYKKGDEVEAVVLKVDVEKERI- 439
|
...
gi 556425213 722 fSL 724
Cdd:PRK06299 440 -SL 441
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-724 |
1.26e-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: 49.41 E-value: 1.26e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 644 GNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLdndyyrfdQVGQRliGESGGQTYRLGDRVEVKVeaVNMDDRKIDFS 723
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDI--------SWTQR--VRHPSEIYKKGQEVEAVV--LNIDVERERIS 67
|
.
gi 556425213 724 L 724
Cdd:cd05690 68 L 68
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
1.33e-07 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 54.28 E-value: 1.33e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgQRLigESGGQTYRLGDRVEVKVEAVNMDDRKID 721
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEP-GVEGLVHISEMSWT--------KRV--AHPSDVVKVGDEVEVKVLDIDPEERRIS 341
|
...
gi 556425213 722 FSL 724
Cdd:COG0539 342 LSI 344
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
643-752 |
1.57e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 54.50 E-value: 1.57e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVrldELF--IDGLVHVSsldndyyrfdQVGQRLIGeSGGQTYRLGDRVEVKVEAVNMDDRKI 720
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFV---EVLpgVEGLVHIS----------QISHKHIA-TPSEVLEEGQEVKVKVLEVNEEEKRI 342
|
90 100 110
....*....|....*....|....*....|..
gi 556425213 721 DFSLISSERAPRNVGKTERERAKKTGNGKPGG 752
Cdd:PRK06676 343 SLSIKALEEAPAEEEDRREEYRQYELPEEETG 374
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
643-724 |
5.20e-07 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 53.20 E-value: 5.20e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdQVGQRLIgesggqTYRLGDRVEVKVEAVNMDDRKIDF 722
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSEN-----RDEDKTD------EIKVGDEVEAKVVDIDKKNRKVSL 513
|
..
gi 556425213 723 SL 724
Cdd:TIGR00717 514 SV 515
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
642-724 |
9.02e-07 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 52.36 E-value: 9.02e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVrldELF--IDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVeaVNMDDR- 718
Cdd:PRK11824 620 EVGEIYEGKVVRIVDFGAFV---EILpgKDGLVHISEIADE--RVEKVEDVL---------KEGDEVKVKV--LEIDKRg 683
|
....*.
gi 556425213 719 KIDFSL 724
Cdd:PRK11824 684 RIRLSR 689
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
642-765 |
1.00e-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: 48.64 E-value: 1.00e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYyrfdqVgqrligESGGQTYRLGDRVEVKVeaVNMDDR-KI 720
Cdd:COG1098 4 EVGDIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGY-----V------KDINDYLKVGDEVKVKV--LSIDEDgKI 69
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 556425213 721 DFSLisseraprnvgKTEREraKKTGNGKPGGGKRRQAGKKvNFE 765
Cdd:COG1098 70 SLSI-----------KQAEE--KPKRPPRPRRNSRPKAGFE-SFE 100
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
642-724 |
1.28e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 51.41 E-value: 1.28e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLDndYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFVDIGG--VDGLVHISELS--HERVEKPSEVV---------SVGQEVEVKVLSIDWETERIS 257
|
...
gi 556425213 722 FSL 724
Cdd:PRK06676 258 LSL 260
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
1.34e-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: 1.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG--VDGLLHISEI--SWGRVKHPSEVL---------KVGDEVEVKVLKIDREKERIS 254
|
...
gi 556425213 722 FSL 724
Cdd:COG0539 255 LSL 257
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
644-723 |
1.85e-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: 46.07 E-value: 1.85e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 644 GNVFKGVIASVTGFGFFVRLDeLFIDGLVHVSSLDNDYY--RFDQVGqrligesggqtyrLGDRVEVKVEAVNMDDRKID 721
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMADRFVshPSDVVS-------------VGDIVEVKVISIDEERGRIS 66
|
..
gi 556425213 722 FS 723
Cdd:cd05685 67 LS 68
|
|
| S1_pNO40 |
cd05686 |
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
642-724 |
2.09e-06 |
|
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: 45.93 E-value: 2.09e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDELFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDrKID 721
Cdd:cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RVDDPSEVV---------DVGEKVWVKVIGREMKD-KMK 69
|
...
gi 556425213 722 FSL 724
Cdd:cd05686 70 LSL 72
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
644-710 |
2.15e-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: 46.08 E-value: 2.15e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 556425213 644 GNVFKGVIASVTGFGFFVRLDEL--FIDGLVHVSSLDNDyyrfdqvgqRLIGESgGQTYRLGDRVEVKV 710
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFE---------GRVANP-SDVVKRGQKVKVKV 59
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
2.56e-06 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 51.10 E-value: 2.56e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGG--VDGLLHVSEI--SWGRVEKPSDVL---------KVGDEIKVYILDIDKENKKLS 542
|
...
gi 556425213 722 FSL 724
Cdd:PRK00087 543 LSL 545
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
639-765 |
3.29e-06 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 47.33 E-value: 3.29e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 639 MLDQVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVEAVNmDDR 718
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVK--DINDHL---------KVGDEVEVKVLNVE-DDG 67
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 556425213 719 KIDFSLISSERAPRnvgkteRERAKKTGNGKPGGGKRRQagKKVNFE 765
Cdd:PRK08582 68 KIGLSIKKAKDRPK------RQHDRPRHEDNRGGGNDVA--PKEDFE 106
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-752 |
6.57e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 49.78 E-value: 6.57e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRD--RVEDATEVL---------KVGDEVEAKVINIDRKNRRIS 526
|
90 100 110
....*....|....*....|....*....|.
gi 556425213 722 FSLISSERAprnvgkTERERAKKTGNGKPGG 752
Cdd:PRK06299 527 LSIKALDEA------EEKEAIAEYNSASDSK 551
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
642-751 |
8.85e-06 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 45.81 E-value: 8.85e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDELfIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDEE-TQGLVHISEITHGFVK--DIHDFL---------SVGDEVKVKVLSVDEEKGKIS 73
|
90 100 110
....*....|....*....|....*....|
gi 556425213 722 FSLISSERAPRnvGKTERERAKKTGNGKPG 751
Cdd:PRK08059 74 LSIRATEEAPE--AKRKKGKILIPNPSEQG 101
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-724 |
1.63e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 48.12 E-value: 1.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLdndyyrfdqvGQRLIgESGGQTYRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISEL----------AERHV-EVPEQVVQVGDEVFVKVIDIDLERRRIS 359
|
...
gi 556425213 722 FSL 724
Cdd:PRK07899 360 LSL 362
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-724 |
1.72e-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: 1.72e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElFIDGLVHVS--SLDNDyyrfdqvgqrliGESGGQTYRLGDRVEVKVEAVNMDDRK 719
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSdiSWDKD------------GREADHLYKKGDEIEAVVLAVDKEKKR 424
|
....*
gi 556425213 720 IDFSL 724
Cdd:TIGR00717 425 ISLGV 429
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-740 |
3.37e-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: 3.37e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLdELFIDGLVHVSSLDNdyYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVEL-EPGVDGLVHISQISW--KRIDKPEDVL---------SEGEEVKAKILEVDPEEKRIR 628
|
90
....*....|....*....
gi 556425213 722 FSLissERAPRNVGKTERE 740
Cdd:PRK00087 629 LSI---KEVEEEPGDIEKV 644
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-731 |
4.59e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 46.96 E-value: 4.59e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKID 721
Cdd:PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLGG--VDGLVHVSEL--SWKHIDHPSEVV---------EVGQEVTVEVLDVDMDRERVS 273
|
90
....*....|
gi 556425213 722 FSLISSERAP 731
Cdd:PRK07899 274 LSLKATQEDP 283
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
643-723 |
5.46e-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: 42.21 E-value: 5.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgqrligesggqtYRLGDRVEVKVEAVNmDDRKIDF 722
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLLRD-------------------YEVGDEVIVQVTDIP-ENGNIDL 74
|
.
gi 556425213 723 S 723
Cdd:cd04473 75 I 75
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
642-733 |
1.18e-04 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 45.79 E-value: 1.18e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVrlDelfI----DGLVHVSSLDNDYYR--FDQVgqrligesggqtyRLGDRVEVKVEAVNM 715
Cdd:COG2183 640 KPGMILEGTVTNVTDFGAFV--D---IgvhqDGLVHISQLSDRFVKdpREVV-------------KVGDIVKVKVLEVDL 701
|
90
....*....|....*...
gi 556425213 716 DDRKIDFSLISSERAPRN 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 |
2.46e-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: 39.92 E-value: 2.46e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSLdnDYYRFDQVGQRLigesggqtyRLGDRVEVKVEAVNMDDRKIDF 722
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHISDM--SWGRVKHPSEVV---------NVGDEVEVKVLKIDKERKRISL 67
|
.
gi 556425213 723 S 723
Cdd:cd05688 68 G 68
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-723 |
2.86e-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: 39.96 E-value: 2.86e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 644 GNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVEAVNmDDRKIDFS 723
Cdd:cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVK--DVKDVL---------KEGDKVKVKVLSID-ARGRISLS 67
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
644-723 |
2.93e-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: 39.83 E-value: 2.93e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 644 GNVFKGVIASVTGFGFFVrldELF--IDGLVHVSSLDNDyyRFDQVGQRLigesggqtyRLGDRVEVKVeaVNMDDR-KI 720
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFV---EILpgKDGLVHISELSDE--RVEKVEDVL---------KVGDEVKVKV--IEVDDRgRI 64
|
...
gi 556425213 721 DFS 723
Cdd:cd04472 65 SLS 67
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
643-724 |
3.10e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 44.38 E-value: 3.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyrfdqvgQRLIgeSGGQTYRLGDRVEVKVEAVNMDDRKIDF 722
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWT--------KKNK--HPSKVVSVGQEVEVMVLEIDEEKRRISL 354
|
..
gi 556425213 723 SL 724
Cdd:PRK06299 355 GL 356
|
|
| PRK05807 |
PRK05807 |
RNA-binding protein S1; |
639-724 |
7.08e-04 |
|
RNA-binding protein S1;
Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 40.50 E-value: 7.08e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 639 MLDQVGNVFKGVIASVTGFGFFVRLDELfiDGLVHVSSLDNDYYRfdQVGQRLigesggqtyRLGDRVEVKVeaVNMDDR 718
Cdd:PRK05807 1 MTLKAGSILEGTVVNITNFGAFVEVEGK--TGLVHISEVADTYVK--DIREHL---------KEQDKVKVKV--ISIDDN 65
|
....*..
gi 556425213 719 -KIDFSL 724
Cdd:PRK05807 66 gKISLSI 72
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
643-752 |
8.46e-04 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 43.16 E-value: 8.46e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 643 VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVSSLDNDyyRFDQVGQRLigesggQTYRLGDRVEVKVEAVNMDDRKIDF 722
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVEN--RDGDPGEAL------RKYAVGDRVKAVIVDMNVKDRKVAF 822
|
90 100 110
....*....|....*....|....*....|
gi 556425213 723 SLISSErapRNVGKTERERAKKTGNGKPGG 752
Cdd:PRK12269 823 SVRDYQ---RKVQRDELSRYMSAPRGEDEG 849
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
158-213 |
8.97e-04 |
|
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 37.90 E-value: 8.97e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 556425213 158 TDAGVGFVVPDDSrlSFDILIPPEEVMGARMGFVVVVELTQrPTRRTKAVGKIVEV 213
Cdd:pfam08206 6 HKKGFGFLIPDDE--EDDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
607-724 |
4.72e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 40.49 E-value: 4.72e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 607 EEMLQLGQHCSMAERRADEATRDVADWLKcdfMLDQ-----------VGNVFKGVIASVTGFGFFVRLDElFIDGLVHVS 675
Cdd:TIGR00717 228 SEYVKVGQEVKVKVIKFDKEKGRISLSLK---QLGEdpweaiekkfpVGDKITGRVTNLTDYGVFVEIEE-GIEGLVHVS 303
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 556425213 676 SLDNDyyrfdqvgQRLIGESggQTYRLGDRVEVKVEAVNMDDRKIDFSL 724
Cdd:TIGR00717 304 EMSWV--------KKNSHPS--KVVKKGDEVEVMILDIDPERRRLSLGL 342
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-770 |
6.83e-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: 39.72 E-value: 6.83e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556425213 642 QVGNVFKGVIASVTGFGFFVRLDElfIDGLVHVSSL----DNDYYRFdqvgqrligesggqtYRLGDRVEVKVEAVNMDD 717
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDLGG--VDGLLHITDMswkrVKHPSEY---------------VKVGQEVKVKVIKFDKEK 248
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 556425213 718 RKIDFSLISSERAPRNvgkterERAKKTGNGKpgggkrRQAGKKVNFEPDSAF 770
Cdd:TIGR00717 249 GRISLSLKQLGEDPWE------AIEKKFPVGD------KITGRVTNLTDYGVF 289
|
|
| |
