|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-732 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1223.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 1 MIVDPNYQKELEKYENPVPSREFILQTIRDYDAPMSREELLEAFHLYDEERQEAVRRRLRAMENDGQLVFTKKKRYALPE 80
Cdd:PRK11642 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 81 KMDLIKGTVIGHRDGYGFLQVEG-DDDWFIPNSQMNRVMHGDFVLAQPNGIDRRGRKEVRIVRVLEARKKQIVGRFFTES 159
Cdd:PRK11642 81 RLDLLKGTVIGHRDGYGFLRVEGrKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 160 GINYVVPDDSRINQDILIPEEHRLGARMGQVVVVELQPRKADFKRPVGVITEILGDNLAPGMEIEIALRNHDIPHVWPEG 239
Cdd:PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 240 VEKQVRQFNEEVPEEAKIGRVDLRDLPLVTIDGESARDFDDAVFCQ-KESNGWRLWVAIADVSYYVRPKTALDLEAQQRG 318
Cdd:PRK11642 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEkKRGGGWRLWVAIADVSYYVRPPTPLDREARNRG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 319 NSVYFPNRVIPMLPEVLSNGLCSLNPQVDRLCLVAEMAVSESGKLLGYKFYEAVMNSHARLTYTKVWNILEGDEALRERY 398
Cdd:PRK11642 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 399 FYLVPHLEELHAMYKVLLNTRHQRGAIEFETVENQFIFNPQGRIERIEPVIRNDAHKIIEECMILANIASARFVEEANEP 478
Cdd:PRK11642 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 479 ALFRIHAQPSEEKLTSFRTFLKECGLCLNGGLRPTPKDYAELLEQVKERPDAELIQTMLLRSLKQAVYSPDNEGHFGLAL 558
Cdd:PRK11642 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 559 TEYAHFTSPIRRYPDLLLHRAIKYLIEKEKGNKRHYTDGGGYHYQIDDMDIFGEKCSATERRADEATREVADWLKCEYMQ 638
Cdd:PRK11642 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFML 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 639 DHIGEVFDGVISSVTGFGLFVKLNELLIDGLVHISTLDNGYYHFDSDRQRLVGEN-GVMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESsGQTYRLGDRVEVRVEAVNMDERKI 720
|
730
....*....|....*
gi 1800573186 718 DFALVTSLRKARGEG 732
Cdd:PRK11642 721 DFSLISSERAPRNVG 735
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
14-729 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1125.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 14 YENpvpSREFILQTIRD-YDAPMSREELLEAFHLYDEERQEAVRRRLRAMENDGQLVFTKKKRYALPEKMDLIKGTVIGH 92
Cdd:COG0557 1 YEN---SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGH 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 93 RDGYGFLQVE-GDDDWFIPNSQMNRVMHGDFVLAQPNGIDRRGRKEVRIVRVLEARKKQIVGRFFTESGINYVVPDDSRI 171
Cdd:COG0557 78 RDGFGFVIPDdGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 172 NQDILIPEEHRLGARMGQVVVVELQPRKADFKRPVGVITEILGDNLAPGMEIEIALRNHDIPHVWPEGVEKQVRQFNEEV 251
Cdd:COG0557 158 LQDIFIPPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEV 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 252 PEEAKIGRVDLRDLPLVTIDGESARDFDDAVFCQK-ESNGWRLWVAIADVSYYVRPKTALDLEAQQRGNSVYFPNRVIPM 330
Cdd:COG0557 238 PEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKlDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPM 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 331 LPEVLSNGLCSLNPQVDRLCLVAEMAVSESGKLLGYKFYEAVMNSHARLTYTKVWNILEG-DEALRERYFYLVPHLEELH 409
Cdd:COG0557 318 LPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELY 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 410 AMYKVLLNTRHQRGAIEFETVENQFIFNPQGRIERIEPVIRNDAHKIIEECMILANIASARFVEEANEPALFRIHAQPSE 489
Cdd:COG0557 398 ELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDP 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 490 EKLTSFRTFLKECGLCLNGGLRPTPKDYAELLEQVKERPDAELIQTMLLRSLKQAVYSPDNEGHFGLALTEYAHFTSPIR 569
Cdd:COG0557 478 EKLEALREFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIR 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 570 RYPDLLLHRAIKYLIEKEKGNKRhytdgggYHYQIDDMDIFGEKCSATERRADEATREVADWLKCEYMQDHIGEVFDGVI 649
Cdd:COG0557 558 RYPDLLVHRALKAYLEGKRSPGL-------QEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVI 630
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 650 SSVTGFGLFVKLNELLIDGLVHISTLDNGYYHFDSDRQRLVGE-NGVMYRLGDPVRVKVIGVNLDDKKIDFALVTSLRKA 728
Cdd:COG0557 631 SGVTSFGLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGErTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEA 710
|
.
gi 1800573186 729 R 729
Cdd:COG0557 711 P 711
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
18-722 |
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: 949.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 18 VPSREFILQTIRDYDA-PMSREELLEAFHLYDEERQEAVRRRLRAMENDGQLVFTKKKRYALPEKMDLIKGTVIGHRDGY 96
Cdd:TIGR02063 1 SPLRELILEFLKSKKGkPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 97 GFLQVEGDD--DWFIPNSQMNRVMHGDFVLAQPNG-IDRRGRKEVRIVRVLEARKKQIVGRFFTESGINYVVPDDSRINQ 173
Cdd:TIGR02063 81 GFLRPEDDDedDIFIPPRQMNGAMHGDRVLVRITGkPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 174 DILIPEEHRLGARMGQVVVVELQPRKADFKRPVGVITEILGDNLAPGMEIEIALRNHDIPHVWPEGVEKQVRQFNEEVPE 253
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 254 EAKIGRVDLRDLPLVTIDGESARDFDDAVFCQKESNG-WRLWVAIADVSYYVRPKTALDLEAQQRGNSVYFPNRVIPMLP 332
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGnYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 333 EVLSNGLCSLNPQVDRLCLVAEMAVSESGKLLGYKFYEAVMNSHARLTYTKVWNILEGDEALRERYFYLVPHLEELHAMY 412
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 413 KVLLNTRHQRGAIEFETVENQFIFNPQGRIERIEPVIRNDAHKIIEECMILANIASARFVEEANEPALFRIHAQPSEEKL 492
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 493 TSFRTFLKECGLCLNGGLR--PTPKDYAELLEQVKERPDAELIQTMLLRSLKQAVYSPDNEGHFGLALTEYAHFTSPIRR 570
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGTSdkPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 571 YPDLLLHRAIKYLIEKEKGnkrhYTDGGGYHYQIDDMDIFGEKCSATERRADEATREVADWLKCEYMQDHIGEVFDGVIS 650
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGEN----TTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVIS 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1800573186 651 SVTGFGLFVKLNELLIDGLVHISTLDNGYYHFDSDRQRLVGEN-GVMYRLGDPVRVKVIGVNLDDKKIDFALV 722
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 ... |
67-722 |
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: 873.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 67 QLVFTKkkRYALPEKMDLIKGTVIGHRDGYGFLQVEGDD--DWFIPNSQMNRVMHGDFVLAQPNGIDRRGRKEVRIVRVL 144
Cdd:TIGR00358 1 QLLATL--KYALPEKDDLVKGVVKAHNKGFGFLRPDDDDkkDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 145 EARKKQIVGRFFTESGINYVVPDDSRINQDILIP-EEHRLGARMGQVVVVELQPRKADFKRPVGVITEILGDNLAPGMEI 223
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPkASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 224 EIALRNHDIPHVWPEGVEKQVRQFNEEVPEEAKIGRVDLRDLPLVTIDGESARDFDDAVFCQKES-NGWRLWVAIADVSY 302
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPdGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 303 YVRPKTALDLEAQQRGNSVYFPNRVIPMLPEVLSNGLCSLNPQVDRLCLVAEMAVSESGKLLGYKFYEAVMNSHARLTYT 382
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 383 KVWNILEGDEALRERYFYLVPHLEELHAMYKVLLNTRHQRGAIEFETVENQFIFNPQGRIERIEPVIRNDAHKIIEECMI 462
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 463 LANIASARFVEEANEPALFRIHAQPSEEKLTSFRTFLKECGLCLNGGLRP--TPKDYAELLEQVKERPDAELIQTMLLRS 540
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAEnvTTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 541 LKQAVYSPDNEGHFGLALTEYAHFTSPIRRYPDLLLHRAIKYLIEKEKgnkrhyTDGGGYHYQiDDMDIFGEKCSATERR 620
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ------TDTERYQPQ-DELLQIAEHCSDTERR 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 621 ADEATREVADWLKCEYMQDHIGEVFDGVISSVTGFGLFVKLNELLIDGLVHISTLDNGYYHFDSDRQRLVGEN-GVMYRL 699
Cdd:TIGR00358 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGtGKVYRI 631
|
650 660
....*....|....*....|...
gi 1800573186 700 GDPVRVKVIGVNLDDKKIDFALV 722
Cdd:TIGR00358 632 GDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
259-581 |
3.23e-135 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 402.43 E-value: 3.23e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 259 RVDLRDLPLVTIDGESARDFDDAVFCQKESNG-WRLWVAIADVSYYVRPKTALDLEAQQRGNSVYFPNRVIPMLPEVLSN 337
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGgYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 338 GLCSLNPQVDRLCLVAEMAVSESGKLLGYKFYEAVMNSHARLTYTKVWNILEGDEALRERYFyLVPHLEELHAMYKVLLN 417
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKPD-LAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 418 TRHQRGAIEFETVENQFIFNPQGRIErIEPVIRNDAHKIIEECMILANIASARFVEEANEPALFRIHAQPSEEKLTSFRT 497
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 498 FLKecglclnggLRPTPKDYAELLEQVKErpDAELIQTMLLRSLKQAVYSPDNEGHFGLALTEYAHFTSPIRRYPDLLLH 577
Cdd:pfam00773 239 LLQ---------LLPDDKGLSKSLEKIKD--DERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....
gi 1800573186 578 RAIK 581
Cdd:pfam00773 308 RQLK 311
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
259-586 |
5.17e-135 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 400.88 E-value: 5.17e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 259 RVDLRDLPLVTIDGESARDFDDAVFCQKESNG-WRLWVAIADVSYYVRPKTALDLEAQQRGNSVYFPNRVIPMLPEVLSN 337
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGgYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 338 GLCSLNPQVDRLCLVAEMAVS-ESGKLLGYKFYEAVMNSHARLTYTKVWNILEgdealreryfylvphleelhamykvll 416
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDaDGGEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 417 ntrhqrgaiefetvenQFIFNPQGRIERIEPVIRNDAHKIIEECMILANIASARFVEEANEPALFRIHAQPSEEKLT-SF 495
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAeLL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 496 RTFLKECGLCLNGGlrPTPKDYAELLEQVKERPDAELIQTMLLRSLKQAVYSPDNEGHFGLALTEYAHFTSPIRRYPDLL 575
Cdd:smart00955 198 KEFLALLGLLLLGG--DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 1800573186 576 LHRAIKYLIEK 586
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
80-717 |
3.62e-104 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 333.36 E-value: 3.62e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 80 EKMDLIKGTVIGHRDGYGFLQVEGDDDWFIPNSQMNRVMHGDFVLAQpngIDRRGRKEV------------RIVrvleAR 147
Cdd:COG4776 17 EQTPRVEGVVKATDKGFGFLEVDDQKSYFIPPPQMKKVMHGDRIKAV---IRTEKDKESaepetliepfltRFV----GR 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 148 KKQIVGRFFtesginyVVPDDSRINQDILIPEEHRLGA--RMGQVVVVEL--QPRKAD--FkrpVGVITEILGDNLAPGM 221
Cdd:COG4776 90 VQKKDGRLF-------VVPDHPLIKDAIKARPKKGLEEglKEGDWVVAELkrHPLKGDrgF---FAEITEFIADADDPFA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 222 EIEIALRNHDIPHVWPEGVEKQvrQFNEEVPEeakigRVDLRDLPLVTIDGESARDFDDAVFCQKESNG-WRLWVAIADV 300
Cdd:COG4776 160 PWWVTLARHNLEREAPEGDDEW--ELLDEGLE-----REDLTALPFVTIDSESTEDMDDALYIEKLENGgWKLTVAIADP 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 301 SYYVRPKTALDLEAQQRGNSVYFPNRVIPMLPEVLSNGLCSLNPQVDRLCLVAEMAVSESGKLLG-YKFYEAVMNSHARL 379
Cdd:COG4776 233 TAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKL 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 380 TYTKVWNILEG-------DEALRERyfylvphLEELHAMYKVLLNTRHQRGAIEFETVENQFIFNPQGRIERIEPVIRND 452
Cdd:COG4776 313 AYDNVSDWLEGkgewqpeNEEIAEQ-------IRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRI 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 453 AHKIIEECMILANIASARFVEEANEPALFRIHAQPSEEKLTSFRTFLKECGLCLNGGLRPTPKDYAELLEQVKERPDAEL 532
Cdd:COG4776 386 ANRIVEEAMIAANICAARVLREHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 533 iqTMLLRSLKQ-AVYSPDNEGHFGLALTEYAHFTSPIRRYPDLLLHRAIKYLIEKEKGNKrhytdgggyhyqIDdmDIFG 611
Cdd:COG4776 466 --DSRLRRFQTfAEISTEPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEK------------PD--EELT 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 612 EKCSATERRADEATREVADWLKCEYMQDHIGE--VFDGVISSVTGFGLFVKLnellidglvhistLDNGYYHF------D 683
Cdd:COG4776 530 ERLAERRRLNRMAERDVADWLYARYLKPKVGSgqVFTAEIIDINRGGLRVRL-------------LENGAVAFipasfiH 596
|
650 660 670 680
....*....|....*....|....*....|....*....|...
gi 1800573186 684 SDRQRLV--GENG-------VMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:COG4776 597 SVRDELVcsQEEGtvyikgeVRYKLGDTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
85-717 |
2.57e-86 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 286.00 E-value: 2.57e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 85 IKGTVIGHRDGYGFLQVEGDDDWFIPNSQMNRVMHGDFVLAQpngIDRRGRKE-VRIVRVLEARKKQIVGRFFTESGINY 163
Cdd:PRK05054 22 VEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAV---IHTEKDREiAEPEELIEPFLTRFVGRVQKKDDRLS 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 164 VVPDDSRINQDILIPEEHRL--GARMGQVVVVEL--QPRKAD---FKRPVGVITEIlGDNLAPGMeieIALRNHDIPHVW 236
Cdd:PRK05054 99 IVPDHPLLKDAIPCRAAKGLnhEFKEGDWVVAELrrHPLKGDrgfYAEITQFITDA-DDHFAPWW---VTLARHNLEREA 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 237 PEGVEKQvrQFNEEVPEeakigRVDLRDLPLVTIDGESARDFDDAVFCQK-ESNGWRLWVAIADVSYYVRPKTALDLEAQ 315
Cdd:PRK05054 175 PAGGVAW--EMLDEGLE-----REDLTALDFVTIDSASTEDMDDALYVEKlPDGGLQLTVAIADPTAYIAEGSKLDKAAR 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 316 QRGNSVYFPNRVIPMLPEVLSNGLCSLNPQVDRLCLVAEMAVSESGKLLG-YKFYEAVMNSHARLTYTKVWNILEGDEAL 394
Cdd:PRK05054 248 QRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESKAKLAYDNVSDWLENGGDW 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 395 RERYFYLVPHLEELHAMYKVLLNTRHQRGAIEFETVENQFIFNPQGRIERI--EPviRNDAHKIIEECMILANIASARFV 472
Cdd:PRK05054 328 QPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIvaEP--RRIANRIVEESMIAANICAARVL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 473 EEANEPALFRIHAQPSEEKLTSFRTFLKEcglclnGGLRPTPKDYAELLEQVKERPDAELIQTMLL-----RSLKQAVYS 547
Cdd:PRK05054 406 RDKLGFGIYNVHSGFDPANAEQAVALLKE------HGLHFDAEELLTLEGFCKLRRELDAQPTGYLdsrirRFQSFAEIS 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 548 PDNEGHFGLALTEYAHFTSPIRRYPDLLLHRAIKYLIEKEKGNKrhytdgggyhyqIDDmDIfGEKCSATERRADEATRE 627
Cdd:PRK05054 480 TEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAER------------PQD-EI-TVQLAERRRLNRMAERD 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 628 VADWLKCEYMQDHIGE--VFDGVISSVTGFGLFVKLnellidglvhistLDNGYYHF------DSDRQRLV--GENG--- 694
Cdd:PRK05054 546 VGDWLYARYLKDKAGTdtRFAAEIIDISRGGMRVRL-------------LENGAVAFipasflHAVRDELVcnQENGtvq 612
|
650 660
....*....|....*....|....*..
gi 1800573186 695 ----VMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK05054 613 ikgeTVYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
641-722 |
1.61e-37 |
|
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: 134.84 E-value: 1.61e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNELLIDGLVHISTLDNGYYHFDSDRQRLVGEN-GVMYRLGDPVRVKVIGVNLDDKKIDF 719
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERtGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 1800573186 720 ALV 722
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
163-237 |
1.09e-29 |
|
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.
Pssm-ID: 465546 [Multi-domain] Cd Length: 74 Bit Score: 112.10 E-value: 1.09e-29
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1800573186 163 YVVPDDSRINQDILIPEEHRLGARMGQVVVVEL--QPrkaDFKRPVGVITEILGDNLAPGMEIEIALRNHDIPHVWP 237
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEIteYP---DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
87-143 |
3.89e-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: 92.99 E-value: 3.89e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1800573186 87 GTVIGHRDGYGFLQVEG-DDDWFIPNSQMNRVMHGDFVLAQPNGIDRRGRKEVRIVRV 143
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDeEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
641-717 |
2.90e-13 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 68.70 E-value: 2.90e-13
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNEllIDGLVHISTLDNGYYHFDSDRQRLVG-ENGVMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGkESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
643-713 |
1.28e-11 |
|
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: 61.53 E-value: 1.28e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1800573186 643 EVFDGVISSVTGFGLFVKLNEllIDGLVHISTLDNGYYHFDSDRQRLVGEN-GVMYRLGDPVRVKVIGVNLD 713
Cdd:cd04460 1 EVVEGEVVEVVDFGAFVRIGP--VDGLLHISQIMDDYISYDPKNKRLIGEEtKRVLKVGDVVRARIVAVSLK 70
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
641-719 |
4.75e-11 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 59.15 E-value: 4.75e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNELlIDGLVHISTLDNGYYHFDSDRqrlvgengvmYRLGDPVRVKVIGVNLDDKKIDF 719
Cdd:smart00316 2 VGDVVEGTVTEITPGGAFVDLGNG-VEGLIPISELSDKRVKDPEEV----------LKVGDEVKVKVLSVDEEKGRIIL 69
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
640-725 |
1.62e-10 |
|
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: 57.72 E-value: 1.62e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 640 HIGEVFDGVISSVTGFGLFVKLNELLIDGLVHISTLDNGYyhfDSDRQRLvgengvmYRLGDPVRVKVIGVNLDDKKIDF 719
Cdd:cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR---VADASKL-------FRVGDKVRAKVLKIDAEKKRISL 70
|
....*.
gi 1800573186 720 ALVTSL 725
Cdd:cd05708 71 GLKASY 76
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
641-721 |
2.14e-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: 57.30 E-value: 2.14e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLnELLIDGLVHISTLDNgyyhfdsdrqRLVGENGVMYRLGDPVRVKVIGVNLDDKKIDFA 720
Cdd:pfam00575 3 KGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSD----------DHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
|
.
gi 1800573186 721 L 721
Cdd:pfam00575 72 I 72
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
86-144 |
9.41e-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: 9.41e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1800573186 86 KGTVIGHRDGYGFLQVE-GDDDWFIPNSQ----MNRVMHGDFVLAQPNGIDRRGRKEVRIVRVL 144
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDdGGKDVFVHPSQiqggLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
642-710 |
2.02e-08 |
|
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: 51.86 E-value: 2.02e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNELLI--DGLVHISTLDNGyyhfdsdrQRLVGENGVMYRlGDPVRVKVIGV 710
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGrkEGLVHISQLSFE--------GRVANPSDVVKR-GQKVKVKVISI 62
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
641-728 |
2.29e-08 |
|
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];
Pssm-ID: 440715 [Multi-domain] Cd Length: 130 Bit Score: 53.26 E-value: 2.29e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNELLIdGLVHISTLDNGYyhfdsdrqrlVGENGVMYRLGDPVRVKVIGVNlDDKKIDFa 720
Cdd:COG1098 5 VGDIVEGKVTGITPFGAFVELPEGTT-GLVHISEIADGY----------VKDINDYLKVGDEVKVKVLSID-EDGKISL- 71
|
....*...
gi 1800573186 721 lvtSLRKA 728
Cdd:COG1098 72 ---SIKQA 76
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
642-717 |
2.82e-08 |
|
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 51.08 E-value: 2.82e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNeLLIDGLVHISTLDNgyyHFDSDRQRLVGengvmyrLGDPVRVKVIGVNLDDKKI 717
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMAD---RFVSHPSDVVS-------VGDIVEVKVISIDEERGRI 65
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
640-717 |
8.55e-08 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 55.05 E-value: 8.55e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 640 HIGEVFDGVISSVTGFGLFVKLNEllIDGLVHIStlDNGYYHFD--SDrqrlvgengvMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG--VDGLLHIS--EISWGRVKhpSE----------VLKVGDEVEVKVLKIDREKERI 253
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
22-81 |
3.55e-07 |
|
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: 47.78 E-value: 3.55e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1800573186 22 EFILQTIRDYDAPMSREELLEAFHLYDEE-RQEAVRRRLRAMENDGqlvFTKKKRYA---LPEK 81
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYAgreITEK 61
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
641-719 |
4.24e-07 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 53.51 E-value: 4.24e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVklnELL--IDGLVHISTLDNgyyhfdsdrQRlVGENGVMYRLGDPVRVKVIGVnlDDK-KI 717
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFV---EILpgKDGLVHISEIAD---------ER-VEKVEDVLKEGDEVKVKVLEI--DKRgRI 685
|
..
gi 1800573186 718 DF 719
Cdd:PRK11824 686 RL 687
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
641-717 |
5.19e-07 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 53.24 E-value: 5.19e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLnELLIDGLVHISTLdngyyhfDSDRQrlvGENGV-MYRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGL-EGGIDGLVHLSDI-------SWDKK---GEEAVeLYKKGDEVEAVVLKVDVEKERI 439
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
645-717 |
5.25e-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: 5.25e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1800573186 645 FDGVISSVTGFGLFVKLNELlIDGLVHISTLDNGYyhfdsdrqrlVGENGVMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:cd00164 1 VTGKVVSITKFGVFVELEDG-VEGLVHISELSDKF----------VKDPSEVFKVGDEVEVKVLEVDPEKGRI 62
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
641-717 |
1.25e-06 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 46.47 E-value: 1.25e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNEllIDGLVHIStlDNGYYHFDSDRQRLvgengvmyRLGDPVRVKVIGVNLDDKKI 717
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHIS--DMSWGRVKHPSEVV--------NVGDEVEVKVLKIDKERKRI 65
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
642-711 |
2.39e-06 |
|
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: 45.61 E-value: 2.39e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1800573186 642 GEVFDGVISSVTGFGLFVklnELL--IDGLVHISTLDNGYYHFDSDrqrlvgengvMYRLGDPVRVKVIGVN 711
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFV---EILpgKDGLVHISELSDERVEKVED----------VLKVGDEVKVKVIEVD 59
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
642-717 |
2.63e-06 |
|
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240195 [Multi-domain] Cd Length: 69 Bit Score: 45.56 E-value: 2.63e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNElLIDGLVHISTLdngyyhfdSDRQRlVGENGVMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDI--------SWTQR-VRHPSEIYKKGQEVEAVVLNIDVERERI 66
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
640-717 |
7.39e-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: 48.89 E-value: 7.39e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1800573186 640 HIGEVFDGVISSVTGFGLFVKLnELLIDGLVHISTLDNgyyhfdSDRQRLVGEngvMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVEL-EPGVEGLVHISEMSW------TKRVAHPSD---VVKVGDEVEVKVLDIDPEERRI 340
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
640-717 |
8.11e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 48.72 E-value: 8.11e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 640 HIGEVFDGVISSVTGFGLFVklnELL--IDGLVHISTLDNGyyHFDSDRQRLvgengvmyRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK06676 276 PEGDVIEGTVKRLTDFGAFV---EVLpgVEGLVHISQISHK--HIATPSEVL--------EEGQEVKVKVLEVNEEEKRI 342
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-717 |
1.26e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 48.62 E-value: 1.26e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNelLIDGLVHISTLD-NGYYHFdSDrqrlvgengvMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK06299 202 GQVVEGVVKNITDYGAFVDLG--GVDGLLHITDISwKRVNHP-SE----------VVNVGDEVKVKVLKFDKEKKRV 265
|
|
| S1_pNO40 |
cd05686 |
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
643-715 |
1.36e-05 |
|
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Pssm-ID: 240191 [Multi-domain] Cd Length: 73 Bit Score: 43.62 E-value: 1.36e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1800573186 643 EVFDGVISSVTGFGLFVKLNELLIDGLVHIStldngyyHFDSDRQRLVGEngvMYRLGDPVRVKVIGVNLDDK 715
Cdd:cd05686 5 QIFKGEVASVTEYGAFVKIPGCRKQGLVHKS-------HMSSCRVDDPSE---VVDVGEKVWVKVIGREMKDK 67
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
641-721 |
1.55e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 48.12 E-value: 1.55e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNELlIDGLVHISTLdngyyhfdSDRQRLVGENGVmyRLGDPVRVKVIGVNLDDKKIDFA 720
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEG-IEGLVHISEL--------AERHVEVPEQVV--QVGDEVFVKVIDIDLERRRISLS 361
|
.
gi 1800573186 721 L 721
Cdd:PRK07899 362 L 362
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
642-721 |
2.06e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 47.56 E-value: 2.06e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNEllIDGLVHISTLdnGYYHFDSDRQRLvgengvmyRLGDPVRVKVIGVNLDDKKIDFAL 721
Cdd:PRK06676 193 GDVVEGTVARLTDFGAFVDIGG--VDGLVHISEL--SHERVEKPSEVV--------SVGQEVEVKVLSIDWETERISLSL 260
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
637-732 |
4.37e-05 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 46.94 E-value: 4.37e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 637 MQD-HIGEVFDGVISSVTGFGLFVKlnellI----DGLVHISTLDNgyyHFDSDRQRLVgengvmyRLGDPVRVKVIGVN 711
Cdd:COG2183 636 IEDlKPGMILEGTVTNVTDFGAFVD-----IgvhqDGLVHISQLSD---RFVKDPREVV-------KVGDIVKVKVLEVD 700
|
90 100
....*....|....*....|.
gi 1800573186 712 LDDKKIdfALvtSLRKARGEG 732
Cdd:COG2183 701 LKRKRI--SL--SMKLDDEAG 717
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-721 |
4.37e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 46.58 E-value: 4.37e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNEllIDGLVHISTLDngYYHFDSDRQrlvgengvMYRLGDPVRVKVIGVNLDDKKIDFAL 721
Cdd:PRK07899 209 GQVRKGVVSSIVNFGAFVDLGG--VDGLVHVSELS--WKHIDHPSE--------VVEVGQEVTVEVLDVDMDRERVSLSL 276
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-721 |
9.81e-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: 45.50 E-value: 9.81e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNELlIDGLVHISTLDNGYyhfDSDRQRlvgengvMYRLGDPVRVKVIGVNLDDKKIDFAL 721
Cdd:TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGG-VEGLIRNSELSENR---DEDKTD-------EIKVGDEVEAKVVDIDKKNRKVSLSV 515
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
637-728 |
1.07e-04 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 42.71 E-value: 1.07e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 637 MQDHIGEVFDGVISSVTGFGLFVKLNELLiDGLVHISTLDNGYyhfdsdrqrlVGENGVMYRLGDPVRVKVIGVNlDDKK 716
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPEGK-TGLVHISEVADNY----------VKDINDHLKVGDEVEVKVLNVE-DDGK 68
|
90
....*....|..
gi 1800573186 717 IDFalvtSLRKA 728
Cdd:PRK08582 69 IGL----SIKKA 76
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
640-717 |
1.09e-04 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 45.71 E-value: 1.09e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1800573186 640 HIGEVFDGVISSVTGFGLFVKLnELLIDGLVHISTLDNGyyHFDSDRQRLvgengvmyRLGDPVRVKVIGVNLDDKKI 717
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVEL-EPGVDGLVHISQISWK--RIDKPEDVL--------SEGEEVKAKILEVDPEEKRI 627
|
|
| PRK05807 |
PRK05807 |
RNA-binding protein S1; |
637-728 |
1.55e-04 |
|
RNA-binding protein S1;
Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 42.43 E-value: 1.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 637 MQDHIGEVFDGVISSVTGFGLFVKLNELliDGLVHISTLDNGYYhfdSDRQRLVGENgvmyrlgDPVRVKVIGVNlDDKK 716
Cdd:PRK05807 1 MTLKAGSILEGTVVNITNFGAFVEVEGK--TGLVHISEVADTYV---KDIREHLKEQ-------DKVKVKVISID-DNGK 67
|
90
....*....|..
gi 1800573186 717 IDFalvtSLRKA 728
Cdd:PRK05807 68 ISL----SIKQA 75
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-721 |
1.55e-04 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 45.32 E-value: 1.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNEllIDGLVHISTLDNGYYHFDSDrqrlvgengvMYRLGDPVRVKVIGVNLDDKKIDFAL 721
Cdd:PRK00087 478 GDVVEGEVKRLTDFGAFVDIGG--VDGLLHVSEISWGRVEKPSD----------VLKVGDEIKVYILDIDKENKKLSLSL 545
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
635-717 |
1.55e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 45.16 E-value: 1.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 635 EYMQDH-IGEVFDGVISSVTGFGLFVKLNElLIDGLVHIStldngyyHFDSDRQRLVGEngvMYRLGDPVRVKVIGVNLD 713
Cdd:PRK06299 453 EFAKKHkKGSIVTGTVTEVKDKGAFVELED-GVEGLIRAS-------ELSRDRVEDATE---VLKVGDEVEAKVINIDRK 521
|
....
gi 1800573186 714 DKKI 717
Cdd:PRK06299 522 NRRI 525
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
642-718 |
2.17e-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: 2.17e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNELlIDGLVHISTLDNgyyhfdsdrQRLVGENGVMyRLGDPVRVKVIGVNlDDKKID 718
Cdd:cd05692 1 GSVVEGTVTRLKPFGAFVELGGG-ISGLVHISQIAH---------KRVKDVKDVL-KEGDKVKVKVLSID-ARGRIS 65
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
641-717 |
2.83e-04 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 44.34 E-value: 2.83e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLnELLIDGLVHISTLdngyyhFDSDRQRlvgENGVMYRLGDPVRVKVIGVNLDDKKI 717
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVEL-EGGIDGLIHLSDI------SWDKDGR---EADHLYKKGDEIEAVVLAVDKEKKRI 425
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
634-720 |
4.76e-04 |
|
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: 39.51 E-value: 4.76e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 634 CEYMQDHIGEVFDGVISSVTGFGLFVKLNElLIDGLVHISTLDNGyyhfdsdrqrlvgengvmYRLGDPVRVKVIGVnLD 713
Cdd:cd04473 9 CTMEDLEVGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLLRD------------------YEVGDEVIVQVTDI-PE 68
|
....*..
gi 1800573186 714 DKKIDFA 720
Cdd:cd04473 69 NGNIDLI 75
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
641-729 |
1.27e-03 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 42.39 E-value: 1.27e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNELlIDGLVHIStldngyyHFDSDRQRLVGENGVMYRLGDPVRVKVIGVNLDDKKIDFA 720
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGG-VEGLVRKQ-------HLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFS 823
|
....*....
gi 1800573186 721 LVTSLRKAR 729
Cdd:PRK12269 824 VRDYQRKVQ 832
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
640-721 |
1.84e-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: 41.64 E-value: 1.84e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 640 HIGEVFDGVISSVTGFGLFVKLNEllIDGLVHISTLDNGYYHFDSDrqrlvgengvMYRLGDPVRVKVIGVNLDDKKIDF 719
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDLGG--VDGLLHITDMSWKRVKHPSE----------YVKVGQEVKVKVIKFDKEKGRISL 253
|
..
gi 1800573186 720 AL 721
Cdd:TIGR00717 254 SL 255
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
641-721 |
1.97e-03 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 38.87 E-value: 1.97e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 641 IGEVFDGVISSVTGFGLFVKLNELLiDGLVHISTLDNGYyhfdsdrqrlVGENGVMYRLGDPVRVKVIGVNLDDKKIDFA 720
Cdd:PRK08059 7 VGSVVTGKVTGIQPYGAFVALDEET-QGLVHISEITHGF----------VKDIHDFLSVGDEVKVKVLSVDEEKGKISLS 75
|
.
gi 1800573186 721 L 721
Cdd:PRK08059 76 I 76
|
|
| RNase_II_C_S1 |
pfam18614 |
RNase II-type exonuclease C-terminal S1 domain; This entry describes the C-terminal S1 domain ... |
643-722 |
3.44e-03 |
|
RNase II-type exonuclease C-terminal S1 domain; This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interacts with a flexible loop that connects two beta-strands from the conserved C-terminal S1 domain, forming a beta-wing fold common in wHTH domains.
Pssm-ID: 436621 [Multi-domain] Cd Length: 59 Bit Score: 36.38 E-value: 3.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 643 EVFDGVISSVTGFGLFVKLNELLIDGlvhistldngyyhfdsdrqRLVGENGVmyRLGDPVRVKVIGVNLDDKKIDFALV 722
Cdd:pfam18614 1 ETFDAVVVDADERGATVQLADPAVEA-------------------RCVGGDGL--PLGDRVRVRLVEADVATGTVRFAVV 59
|
|
| rpsA |
PRK13806 |
30S ribosomal protein S1; Provisional |
642-731 |
5.10e-03 |
|
30S ribosomal protein S1; Provisional
Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 40.09 E-value: 5.10e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1800573186 642 GEVFDGVISSVTGFGLFVKLNELLiDGLVHISTLDngyyhfdsdrQRLVGENGVMYRLGDPVRVKVIGVNLDDKKIDFAL 721
Cdd:PRK13806 203 GDVVEGTVTRLAPFGAFVELAPGV-EGMVHISELS----------WSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRI 271
|
90
....*....|
gi 1800573186 722 VTSLRKARGE 731
Cdd:PRK13806 272 SLSIKQAGGD 281
|
|
| |
