|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-797 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1245.02 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 1 MSQkDPFLEREAEKYENPIASREMILDLIKGHEKPMSREELAKVLKLTEEEPLEALRRRLRAMERDGQLVFTRNQCYALP 80
Cdd:PRK11642 1 MSQ-DPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 81 DRLNLVKGYVLGHKDGFGFLRPEGGGPDLFLNNREMQRLMHGDYALVQPTEIDRKGRQEARLVRLLKSREADIVGRYFVE 160
Cdd:PRK11642 80 ERLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTD 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 161 NGVGFVVPDDSRIGQDIIIPEGENKGARQSQVVVVRINQRATARFNAVGTVLEVLGENMAPGMEIEIALRTHGIPHTWPE 240
Cdd:PRK11642 160 AGVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQ 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 241 EVTKEVAGLGEQVPEKAKEGRIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYVKPGTALDTEAYQR 320
Cdd:PRK11642 240 AVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 321 GNSVYFPEFVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAAGRMSGYKFYEAVMNSHARMTYTKVAAILEGDPKLRQQ 400
Cdd:PRK11642 320 GTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQ 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 401 YEPLVGHIEELNNLYKALKHARHQRGAVEFESEETRFIFNAQRKIDRIVPLVRNDAHKIIEECMIQANVAAARYIEKNEA 480
Cdd:PRK11642 400 YAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKE 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 481 AALFRVHDRPGEERLTGFRDFLAELGLELKGGLEPEPKDFADLAAKFEGRPDAELLSTMLLRSMRQAIYQADNIGHFGLA 560
Cdd:PRK11642 480 PALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLA 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 561 LKSYAHFTSPIRRYPDLILHRAIKYQTAKEQqaNLRHKWTPSGGYHYQLEEVDPMGEHCSMTERRADDATRDVADWLKCE 640
Cdd:PRK11642 560 LQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQ--GHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCD 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 641 YMLDHVGDEFDGVIASVTGFGFFVRLAEIHIDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRYRLGDKVRVKVMGVNLDD 720
Cdd:PRK11642 638 FMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDE 717
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 721 RKIDFVMVEEPLKA--TGKNAKEMARKQAEIKKEKAK------------SAQRHEKRKEGKDHGKSDKGGRaKPSNRRPS 786
Cdd:PRK11642 718 RKIDFSLISSERAPrnVGKTAREKAKKGDAGKKGGKRrqvgkkvnfepdSAFRGEKKAKPKAAKKDARKAK-KPSAKTQK 796
|
810
....*....|.
gi 511289175 787 KKARDKAKSTK 797
Cdd:PRK11642 797 IAAATKAKRAA 807
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
15-734 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1127.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 15 YENpiaSREMILDLIK-GHEKPMSREELAKVLKLTEEEPLEALRRRLRAMERDGQLVFTRNQCYALPDRLNLVKGYVLGH 93
Cdd:COG0557 1 YEN---SRETILAFLKeDAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGH 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 94 KDGFGFLRPEGGGPDLFLNNREMQRLMHGDYALVQPTEIDRKGRQEARLVRLLKSREADIVGRYFVENGVGFVVPDDSRI 173
Cdd:COG0557 78 RDGFGFVIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 174 GQDIIIPEGENKGARQSQVVVVRINQRATARFNAVGTVLEVLGENMAPGMEIEIALRTHGIPHTWPEEVTKEVAGLGEQV 253
Cdd:COG0557 158 LQDIFIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEV 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 254 PEKAKEGRIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYVKPGTALDTEAYQRGNSVYFPEFVVPM 333
Cdd:COG0557 238 PEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPM 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 334 LPEVLSNGLCSLNPQVDRLCMVCEMTISAAGRMSGYKFYEAVMNSHARMTYTKVAAILEG-DPKLRQQYEPLVGHIEELN 412
Cdd:COG0557 318 LPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELY 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 413 NLYKALKHARHQRGAVEFESEETRFIFNAQRKIDRIVPLVRNDAHKIIEECMIQANVAAARYIEKNEAAALFRVHDRPGE 492
Cdd:COG0557 398 ELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDP 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 493 ERLTGFRDFLAELGLELKGGLEPEPKDFADLAAKFEGRPDAELLSTMLLRSMRQAIYQADNIGHFGLALKSYAHFTSPIR 572
Cdd:COG0557 478 EKLEALREFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIR 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 573 RYPDLILHRAIKyqtakeqqANLRHKwTPSGGYHYQLEEVDPMGEHCSMTERRADDATRDVADWLKCEYMLDHVGDEFDG 652
Cdd:COG0557 558 RYPDLLVHRALK--------AYLEGK-RSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEG 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 653 VIASVTGFGFFVRLAEIHIDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRYRLGDKVRVKVMGVNLDDRKIDFVMVEEPL 732
Cdd:COG0557 629 VISGVTSFGLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGS 708
|
..
gi 511289175 733 KA 734
Cdd:COG0557 709 EA 710
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
19-728 |
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: 966.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 19 IASREMILDLIKGHE-KPMSREELAKVLKLTEEEPLEALRRRLRAMERDGQLVFTRNQCYALPDRLNLVKGYVLGHKDGF 97
Cdd:TIGR02063 1 SPLRELILEFLKSKKgKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 98 GFLRPEGG-GPDLFLNNREMQRLMHGDYALVQPTE-IDRKGRQEARLVRLLKSREADIVGRYFVENGVGFVVPDDSRIGQ 175
Cdd:TIGR02063 81 GFLRPEDDdEDDIFIPPRQMNGAMHGDRVLVRITGkPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 176 DIIIPEGENKGARQSQVVVVRINQRATARFNAVGTVLEVLGENMAPGMEIEIALRTHGIPHTWPEEVTKEVAGLGEQVPE 255
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 256 KAKEGRIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYVKPGTALDTEAYQRGNSVYFPEFVVPMLP 335
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 336 EVLSNGLCSLNPQVDRLCMVCEMTISAAGRMSGYKFYEAVMNSHARMTYTKVAAILEGDPKLRQQYEPLVGHIEELNNLY 415
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 416 KALKHARHQRGAVEFESEETRFIFNAQRKIDRIVPLVRNDAHKIIEECMIQANVAAARYIEKNEAAALFRVHDRPGEERL 495
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 496 TGFRDFLAELGLELKGGL--EPEPKDFADLAAKFEGRPDAELLSTMLLRSMRQAIYQADNIGHFGLALKSYAHFTSPIRR 573
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGTsdKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 574 YPDLILHRAIKYQTAKEQqanlrhKWTPSGGYHYQLEEVDPMGEHCSMTERRADDATRDVADWLKCEYMLDHVGDEFDGV 653
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGE------NTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGV 634
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 511289175 654 IASVTGFGFFVRLAEIHIDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRYRLGDKVRVKVMGVNLDDRKIDFVMV 728
Cdd:TIGR02063 635 ISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
68-728 |
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: 843.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 68 QLVFTrnQCYALPDRLNLVKGYVLGHKDGFGFLRPEGGG-PDLFLNNREMQRLMHGDYALVQPTEIDRKGRQEARLVRLL 146
Cdd:TIGR00358 1 QLLAT--LKYALPEKDDLVKGVVKAHNKGFGFLRPDDDDkKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 147 KSREADIVGRYFVENGVGFVVPDDSRIGQDIIIP-EGENKGARQSQVVVVRINQRATARFNAVGTVLEVLGENMAPGMEI 225
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPkASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 226 EIALRTHGIPHTWPEEVTKEVAGLGEQVPEKAKEGRIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSA 305
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 306 YVKPGTALDTEAYQRGNSVYFPEFVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAAGRMSGYKFYEAVMNSHARMTYT 385
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 386 KVAAILEGDPKLRQQYEPLVGHIEELNNLYKALKHARHQRGAVEFESEETRFIFNAQRKIDRIVPLVRNDAHKIIEECMI 465
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 466 QANVAAARYIEKNEAAALFRVHDRPGEERLTGFRDFLAELGLELKGGLEPE--PKDFADLAAKFEGRPDAELLSTMLLRS 543
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENvtTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 544 MRQAIYQADNIGHFGLALKSYAHFTSPIRRYPDLILHRAIKYQTAKEQQANLRHKWTpsggyhyqlEEVDPMGEHCSMTE 623
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQ---------DELLQIAEHCSDTE 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 624 RRADDATRDVADWLKCEYMLDHVGDEFDGVIASVTGFGFFVRLAEIHIDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRY 703
Cdd:TIGR00358 550 RRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVY 629
|
650 660
....*....|....*....|....*
gi 511289175 704 RLGDKVRVKVMGVNLDDRKIDFVMV 728
Cdd:TIGR00358 630 RIGDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
261-584 |
3.99e-136 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 404.73 E-value: 3.99e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 261 RIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYVKPGTALDTEAYQRGNSVYFPEFVVPMLPEVLSN 340
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 341 GLCSLNPQVDRLCMVCEMTISAAG-RMSGYKFYEAVMNSHARMTYTKVAAILEgdpklrqqyeplvghieelnnlykalk 419
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 420 harhqrgavefeseetRFIFNAQRKIDRIVPLVRNDAHKIIEECMIQANVAAARYIEKNEAAALFRVHDRPGEERLTG-F 498
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAElL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 499 RDFLAELGLELKGglEPEPKDFADLAAKFEGRPDAELLSTMLLRSMRQAIYQADNIGHFGLALKSYAHFTSPIRRYPDLI 578
Cdd:smart00955 198 KEFLALLGLLLLG--GDGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
....*.
gi 511289175 579 LHRAIK 584
Cdd:smart00955 276 VHRQLK 281
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
261-584 |
2.51e-133 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 398.58 E-value: 2.51e-133
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 261 RIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYVKPGTALDTEAYQRGNSVYFPEFVVPMLPEVLSN 340
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 341 GLCSLNPQVDRLCMVCEMTISAAGRMSGYKFYEAVMNSHARMTYTKVAAILEGDPKLRQQYEpLVGHIEELNNLYKALKH 420
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKPD-LAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 421 ARHQRGAVEFESEETRFIFNAQRKIDrIVPLVRNDAHKIIEECMIQANVAAARYIEKNEAAALFRVHDRPGEERLTGFRD 500
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 501 FLAelglelkggLEPEPKDFADLAAKFEGrpDAELLSTMLLRSMRQAIYQADNIGHFGLALKSYAHFTSPIRRYPDLILH 580
Cdd:pfam00773 239 LLQ---------LLPDDKGLSKSLEKIKD--DERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....
gi 511289175 581 RAIK 584
Cdd:pfam00773 308 RQLK 311
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
86-723 |
1.15e-93 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 306.39 E-value: 1.15e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 86 VKGYVLGHKDGFGFLRPEGGgPDLFLNNREMQRLMHGDY--ALVQpTEidrKGRQEARLVRLLKSREADIVGRYFVENGV 163
Cdd:COG4776 22 VEGVVKATDKGFGFLEVDDQ-KSYFIPPPQMKKVMHGDRikAVIR-TE---KDKESAEPETLIEPFLTRFVGRVQKKDGR 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 164 GFVVPDDSRIGQDIIIP--EGENKGARQSQVVVVRINQ---RATARFNAvgTVLEVLGENMAPGMEIEIALRTHGIPHTW 238
Cdd:COG4776 97 LFVVPDHPLIKDAIKARpkKGLEEGLKEGDWVVAELKRhplKGDRGFFA--EITEFIADADDPFAPWWVTLARHNLEREA 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 239 PEevtkevaglGEQVPEKAKEG--RIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYVKPGTALDTE 316
Cdd:COG4776 175 PE---------GDDEWELLDEGleREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 317 AYQRGNSVYFPEFVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAAGRMSG-YKFYEAVMNSHARMTYTKVAAILEGDP 395
Cdd:COG4776 246 ARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKG 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 396 KLRQQYEPLVGHIEELNNLYKALKHARHQRGAVEFESEETRFIFNAQRKIDRIVPLVRNDAHKIIEECMIQANVAAARYI 475
Cdd:COG4776 326 EWQPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 476 EKNEAAALFRVHdrpgeerlTGFRDFLAELGLEL--KGGLEPEPKDFADLAA------KFEGRPDAELLStmLLRSMRQ- 546
Cdd:COG4776 406 REHLGFGIFNVH--------SGFDPEKLEQAVELlaEHGIEFDPEQLLTLEGfcalrrELDAQPTSYLDS--RLRRFQTf 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 547 AIYQADNIGHFGLALKSYAHFTSPIRRYPDLILHRAIKyQTAKEQQANlrhkwTPSggyhyqlEEVdpmGEHcsMTERRA 626
Cdd:COG4776 476 AEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIK-AVILGQPAE-----KPD-------EEL---TER--LAERRR 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 627 DD--ATRDVADWLKCEYMLDHVGDE--FDGVIASVTGFGFFVRLAEIHIDGLVHVSTLTN--DYYQFDP--LHQQLIGEn 698
Cdd:COG4776 538 LNrmAERDVADWLYARYLKPKVGSGqvFTAEIIDINRGGLRVRLLENGAVAFIPASFIHSvrDELVCSQeeGTVYIKGE- 616
|
650 660
....*....|....*....|....*
gi 511289175 699 frRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:COG4776 617 --VRYKLGDTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
86-723 |
1.56e-77 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 263.28 E-value: 1.56e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 86 VKGYVLGHKDGFGFLRPEGGgPDLFLNNREMQRLMHGD--YALVQpTEIDRKGRQEARLVRLLKSReadIVGRYFVENGV 163
Cdd:PRK05054 22 VEGVVKATEKGFGFLEVDAQ-KSYFIPPPQMKKVMHGDriIAVIH-TEKDREIAEPEELIEPFLTR---FVGRVQKKDDR 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 164 GFVVPDDSRIGQDIiipegenkGARQSQV----------VVVRINQ---RATARFNAVGTVLEVLGE-NMAPGMeieIAL 229
Cdd:PRK05054 97 LSIVPDHPLLKDAI--------PCRAAKGlnhefkegdwVVAELRRhplKGDRGFYAEITQFITDADdHFAPWW---VTL 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 230 RTHGIPHTWPEevtkevaglGEQVPEKAKEG--RIDLRALPLVTIDGEDARDFDDAVFCEAKRGGGWRLWVAIADVSAYV 307
Cdd:PRK05054 166 ARHNLEREAPA---------GGVAWEMLDEGleREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYI 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 308 KPGTALDTEAYQRGNSVYFPEFVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISAAGRMSG-YKFYEAVMNSHARMTYTK 386
Cdd:PRK05054 237 AEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAYDN 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 387 VAAILEGDPKLRQQYEPLVGHIEELNNLYKALKHARHQRGAVEFESEETRFIFNAQRKIDRIVPLVRNDAHKIIEECMIQ 466
Cdd:PRK05054 317 VSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 467 ANVAAARYIEKNEAAALFRVHdrpgeerlTGFRDFLAELGLEL--KGGLEPEPKDFADLAAKFEGRPDAELLSTMLLRSm 544
Cdd:PRK05054 397 ANICAARVLRDKLGFGIYNVH--------SGFDPANAEQAVALlkEHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDS- 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 545 RQAIYQA-DNIG-----HFGLALKSYAHFTSPIRRYPDLILHRAIKYQTAKEQQAnlrhkwTPSggyhyqleevDPMGEH 618
Cdd:PRK05054 468 RIRRFQSfAEIStepgpHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAE------RPQ----------DEITVQ 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 619 csMTERRADD--ATRDVADWLKCEYMLDHVGDE--FDGVIASVTGFGFFVRLAEIHIDGLVHVSTLTNDYYQFDpLHQQL 694
Cdd:PRK05054 532 --LAERRRLNrmAERDVGDWLYARYLKDKAGTDtrFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELV-CNQEN 608
|
650 660 670
....*....|....*....|....*....|....
gi 511289175 695 I-----GEnfrRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:PRK05054 609 GtvqikGE---TVYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
646-728 |
8.47e-41 |
|
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: 144.08 E-value: 8.47e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEIHIDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRYRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 511289175 726 VMV 728
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
165-239 |
3.96e-28 |
|
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.
Pssm-ID: 465546 [Multi-domain] Cd Length: 74 Bit Score: 107.86 E-value: 3.96e-28
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 511289175 165 FVVPDDSRIGQDIIIPEGENKGARQSQVVVVRINQRATARfNAVGTVLEVLGENMAPGMEIEIALRTHGIPHTWP 239
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYPDGK-NPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
88-144 |
1.24e-19 |
|
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: 82.97 E-value: 1.24e-19
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 511289175 88 GYVLGHKDGFGFLRPEGGGPDLFLNNREMQRLMHGDYALVQPTEIDRKGRQEARLVR 144
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVR 57
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
651-727 |
2.51e-15 |
|
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: 72.32 E-value: 2.51e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 651 DGVIASVTGFGFFVRLAEIhiDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRYRLGDKVRVKVMGVNLDDR-----KIDF 725
Cdd:cd04460 4 EGEVVEVVDFGAFVRIGPV--DGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERrpresKIGL 81
|
..
gi 511289175 726 VM 727
Cdd:cd04460 82 TM 83
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
651-723 |
5.40e-15 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 74.09 E-value: 5.40e-15
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 511289175 651 DGVIASVTGFGFFVRLAEIhiDGLVHVSTLTNDYYQFDPLHQQLIGENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:PRK08563 86 EGEVVEVVEFGAFVRIGPV--DGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
646-725 |
1.96e-12 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 63.01 E-value: 1.96e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYyqfdplhqqliGENFRRRYRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:smart00316 2 VGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
645-727 |
2.91e-11 |
|
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: 60.04 E-value: 2.91e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 645 HVGDEFDGVIASVTGFGFFVRLAEIHIDGLVHVSTLTNDyyqfdplhqqlIGENFRRRYRLGDKVRVKVMGVNLDDRKID 724
Cdd:cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRIS 69
|
...
gi 511289175 725 FVM 727
Cdd:cd05708 70 LGL 72
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
646-725 |
3.96e-10 |
|
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 56.53 E-value: 3.96e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLaEIHIDGLVHVSTLTNDYYQfDPLhqqligenfrRRYRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:pfam00575 3 KGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVE-DPD----------EVIKVGDEVKVKVLKVDKDRRRIIL 70
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
23-78 |
9.59e-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: 55.10 E-value: 9.59e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 511289175 23 EMILDLIKGHEKPMSREELAKVLKLTEEE-PLEALRRRLRAMERDGqlvFTRNQCYA 78
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYA 54
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
87-146 |
9.87e-10 |
|
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 54.91 E-value: 9.87e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 511289175 87 KGYVLGHKDGFGFLRPEGGGPDLFL----NNREMQRLMHGDYALVQPTEIDRKGRQEARLVRLL 146
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVhpsqIQGGLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
647-723 |
5.39e-09 |
|
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: 53.01 E-value: 5.39e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAeIHIDGLVHVSTLTNDYYQfDPLHQQLIGenfrrryrlgDKVRVKVMGVNLDDRKI 723
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMADRFVS-HPSDVVSVG----------DIVEVKVISIDEERGRI 65
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
646-723 |
4.58e-08 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 56.71 E-value: 4.58e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLaEIHIDGLVHVSTLTNDyyqfdplhqqLIGENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGL-EGGIDGLVHLSDISWD----------KKGEEAVELYKKGDEVEAVVLKVDVEKERI 439
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
645-759 |
4.76e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 52.96 E-value: 4.76e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 645 HVGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYyqfdplhqqlIGeNFRRRYRLGDKVRVKVMGVNLDDRKID 724
Cdd:PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQISHKH----------IA-TPSEVLEEGQEVKVKVLEVNEEEKRIS 343
|
90 100 110
....*....|....*....|....*....|....*
gi 511289175 725 FvmveePLKATGKNAKEMARKQAEIKKEKAKSAQR 759
Cdd:PRK06676 344 L-----SIKALEEAPAEEEDRREEYRQYELPEEET 373
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
650-723 |
6.25e-07 |
|
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: 47.38 E-value: 6.25e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 511289175 650 FDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:cd00164 1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRI 62
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
645-723 |
1.40e-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: 1.40e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 511289175 645 HVGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTndyyqfdpLHQQLigENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEP-GVEGLVHISEMS--------WTKRV--AHPSDVVKVGDEVEVKVLDIDPEERRI 340
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
647-723 |
2.08e-06 |
|
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240195 [Multi-domain] Cd Length: 69 Bit Score: 45.95 E-value: 2.08e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTndyyqfdplhQQLIGENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDIS----------WTQRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
645-723 |
5.17e-06 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 49.27 E-value: 5.17e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 645 HVGDEFDGVIASVTGFGFFVRLAeiHIDGLVHVSTLT-------NDYYQfdplhqqligenfrrryrLGDKVRVKVMGVN 717
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLG--GVDGLLHISEISwgrvkhpSEVLK------------------VGDEVEVKVLKID 247
|
....*.
gi 511289175 718 LDDRKI 723
Cdd:COG0539 248 REKERI 253
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
646-777 |
5.21e-06 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 46.33 E-value: 5.21e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNlDDRKIDF 725
Cdd:COG1098 5 VGDIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGYV-----------KDINDYLKVGDEVKVKVLSID-EDGKISL 71
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 511289175 726 VM---VEEPLKATGKNAKEMARKQAEIKKEKAKSAQRH--EKRKEGKDHGKSDKGGR 777
Cdd:COG1098 72 SIkqaEEKPKRPPRPRRNSRPKAGFESFEDKLSKFLKDsdERLSDLKKRTESKRGGR 128
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
646-757 |
5.43e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 49.78 E-value: 5.43e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYyqfdplhqqliGENFRRRYRLGDKVRVKVMGVNLDDRKIdf 725
Cdd:PRK06299 460 KGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDR-----------VEDATEVLKVGDEVEAKVINIDRKNRRI-- 525
|
90 100 110
....*....|....*....|....*....|..
gi 511289175 726 vmveePLKATgknAKEMARKQAEIKKEKAKSA 757
Cdd:PRK06299 526 -----SLSIK---ALDEAEEKEAIAEYNSASD 549
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
645-723 |
9.85e-06 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 49.25 E-value: 9.85e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 511289175 645 HVGDEFDGVIASVTGFGFFVRLAeIHIDGLVHVSTLTNDYYQfDPlHQQLigenfrrryRLGDKVRVKVMGVNLDDRKI 723
Cdd:COG2183 640 KPGMILEGTVTNVTDFGAFVDIG-VHQDGLVHISQLSDRFVK-DP-REVV---------KVGDIVKVKVLEVDLKRKRI 706
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
646-765 |
1.34e-05 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 45.41 E-value: 1.34e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNlDDRKIDF 725
Cdd:PRK08582 5 VGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYV-----------KDINDHLKVGDEVEVKVLNVE-DDGKIGL 71
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 511289175 726 VMveeplkatgKNAKEMARKQ-AEIKKEKAKSAQRHEKRKE 765
Cdd:PRK08582 72 SI---------KKAKDRPKRQhDRPRHEDNRGGGNDVAPKE 103
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
646-723 |
1.48e-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: 48.58 E-value: 1.48e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLaEIHIDGLVHVSTLTNDYYQFDPLHQqligenfrrrYRLGDKVRVKVMGVNLDDRKI 723
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVEL-EGGIDGLIHLSDISWDKDGREADHL----------YKKGDEIEAVVLAVDKEKKRI 425
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
646-729 |
1.58e-05 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 48.51 E-value: 1.58e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVrlaEIH--IDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVnlDDR-K 722
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFV---EILpgKDGLVHISEIADERV-----------EKVEDVLKEGDEVKVKVLEI--DKRgR 684
|
....*..
gi 511289175 723 IDFVMVE 729
Cdd:PRK11824 685 IRLSRKA 691
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
647-724 |
1.72e-05 |
|
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: 43.04 E-value: 1.72e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNlDDRKID 724
Cdd:cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRV-----------KDVKDVLKEGDKVKVKVLSID-ARGRIS 65
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
646-725 |
2.32e-05 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 47.81 E-value: 2.32e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSENRD-----------EDKTDEIKVGDEVEAKVVDIDKKNRKVSL 513
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
650-716 |
3.27e-05 |
|
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Pssm-ID: 240189 [Multi-domain] Cd Length: 79 Bit Score: 42.61 E-value: 3.27e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 511289175 650 FDGVIASVTGFGFFVRLA--EIHIDGLVHVSTLTNDYYQFDPlhqqliGENFRRryrlGDKVRVKVMGV 716
Cdd:cd05684 4 YKGKVTSIMDFGCFVQLEglKGRKEGLVHISQLSFEGRVANP------SDVVKR----GQKVKVKVISI 62
|
|
| PRK05807 |
PRK05807 |
RNA-binding protein S1; |
646-759 |
4.25e-05 |
|
RNA-binding protein S1;
Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 43.97 E-value: 4.25e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAeiHIDGLVHVSTLTNDYYQfdplhqqligeNFRRRYRLGDKVRVKVMGVNlDDRKIDF 725
Cdd:PRK05807 5 AGSILEGTVVNITNFGAFVEVE--GKTGLVHISEVADTYVK-----------DIREHLKEQDKVKVKVISID-DNGKISL 70
|
90 100 110
....*....|....*....|....*....|....
gi 511289175 726 VMveeplKATGKNAKemARKQAEIKKEKAKSAQR 759
Cdd:PRK05807 71 SI-----KQAMKQKK--SVKPAEIDWQKEKNKNN 97
|
|
| S1_Rrp5_repeat_hs5 |
cd05697 |
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ... |
647-723 |
4.99e-05 |
|
S1_Rrp5_repeat_hs5: 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 H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240202 [Multi-domain] Cd Length: 69 Bit Score: 41.84 E-value: 4.99e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAEiHIDGLVHvstltndyyqfdPLH-QQLIGENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:cd05697 1 GQVVKGTIRKLRPSGIFVKLSD-HIKGLVP------------PMHlADVRLKHPEKKFKPGLKVKCRVLSVEPERKRL 65
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
647-721 |
1.39e-04 |
|
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Pssm-ID: 239918 [Multi-domain] Cd Length: 68 Bit Score: 40.60 E-value: 1.39e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAEIHiDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNLDDR 721
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVEILPGK-DGLVHISELSDERV-----------EKVEDVLKVGDEVKVKVIEVDDRGR 63
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
646-723 |
1.74e-04 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 40.30 E-value: 1.74e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEIhiDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGGV--DGLLHISDMSWGRV-----------KHPSEVVNVGDEVEVKVLKIDKERKRI 65
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
645-723 |
1.74e-04 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 44.94 E-value: 1.74e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 511289175 645 HVGDEFDGVIASVTGFGFFVRLaEIHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVEL-EPGVDGLVHISQISWKRI-----------DKPEDVLSEGEEVKAKILEVDPEEKRI 627
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
646-725 |
2.63e-04 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 44.70 E-value: 2.63e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYyQFDPlhqqliGENFRRrYRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVENR-DGDP------GEALRK-YAVGDRVKAVIVDMNVKDRKVAF 822
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
646-735 |
6.22e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 42.94 E-value: 6.22e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEihIDGLVHVSTLTNDyyqfdplHQQLIGENFrrryRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:PRK06676 192 EGDVVEGTVARLTDFGAFVDIGG--VDGLVHISELSHE-------RVEKPSEVV----SVGQEVEVKVLSIDWETERISL 258
|
90
....*....|
gi 511289175 726 VmveepLKAT 735
Cdd:PRK06676 259 S-----LKDT 263
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
647-723 |
1.06e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.46 E-value: 1.06e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAEIhiDGLVHVSTLTndYYQFdplhqqligENFRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:PRK06299 202 GQVVEGVVKNITDYGAFVDLGGV--DGLLHITDIS--WKRV---------NHPSEVVNVGDEVKVKVLKFDKEKKRV 265
|
|
| COG2345 |
COG2345 |
Predicted transcriptional regulator, ArsR family [Transcription]; |
21-73 |
1.52e-03 |
|
Predicted transcriptional regulator, ArsR family [Transcription];
Pssm-ID: 441914 [Multi-domain] Cd Length: 217 Bit Score: 40.68 E-value: 1.52e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 511289175 21 SREMILDLIKGHEkPMSREELAKVLKLTEeeplEALRRRLRAMERDGQLVFTR 73
Cdd:COG2345 14 TRRRILELLKRAG-PVTAAELAEALGLTP----NAVRRHLDALEEEGLVERET 61
|
|
| S1_Rrp5_repeat_sc11 |
cd05707 |
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
647-724 |
1.76e-03 |
|
S1_Rrp5_repeat_sc11: 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 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240212 [Multi-domain] Cd Length: 68 Bit Score: 37.66 E-value: 1.76e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 647 GDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYQfdplhqqligeNFRRRYRLGDKVRVKVMGVNLDDRKID 724
Cdd:cd05707 1 GDVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDSYLK-----------DWKKRFKVGQLVKGKIVSIDPDNGRIE 66
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
646-723 |
2.29e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 41.26 E-value: 2.29e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYQFDPlhqqligenfRRRYRLGDKVRVKVMGVNLDDRKI 723
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEE-GIEGLVHVSEMSWVKKNSHP----------SKVVKKGDEVEVMILDIDPERRRL 338
|
|
| S1_pNO40 |
cd05686 |
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
650-721 |
2.35e-03 |
|
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: 37.46 E-value: 2.35e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 511289175 650 FDGVIASVTGFGFFVRLAEIHIDGLVHVStltndyyQFDPLHQQLIGENFRRryrlGDKVRVKVMGVNLDDR 721
Cdd:cd05686 7 FKGEVASVTEYGAFVKIPGCRKQGLVHKS-------HMSSCRVDDPSEVVDV----GEKVWVKVIGREMKDK 67
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
646-756 |
2.40e-03 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 38.49 E-value: 2.40e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 646 VGDEFDGVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYqfdplhqqligENFRRRYRLGDKVRVKVMGVNLDDRKIDF 725
Cdd:PRK08059 7 VGSVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFV-----------KDIHDFLSVGDEVKVKVLSVDEEKGKISL 74
|
90 100 110
....*....|....*....|....*....|.
gi 511289175 726 vmveePLKATGKNAKEMARKQAEIKKEKAKS 756
Cdd:PRK08059 75 -----SIRATEEAPEAKRKKGKILIPNPSEQ 100
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
652-723 |
2.79e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 41.18 E-value: 2.79e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 511289175 652 GVIASVTGFGFFVRLAEiHIDGLVHVSTLTNDYYQfdpLHQQLIGenfrrryrLGDKVRVKVMGVNLDDRKI 723
Cdd:PRK07899 299 GKVTKLVPFGAFVRVEE-GIEGLVHISELAERHVE---VPEQVVQ--------VGDEVFVKVIDIDLERRRI 358
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
652-735 |
7.71e-03 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 39.64 E-value: 7.71e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 511289175 652 GVIASVTGFGFFVRLAeiHIDGLVHVSTLTndYYQFDplHQQLIGEnfrrryrLGDKVRVKVMGVNLDDRKidfvmVEEP 731
Cdd:PRK07899 214 GVVSSIVNFGAFVDLG--GVDGLVHVSELS--WKHID--HPSEVVE-------VGQEVTVEVLDVDMDRER-----VSLS 275
|
....
gi 511289175 732 LKAT 735
Cdd:PRK07899 276 LKAT 279
|
|
| |
