|
Name |
Accession |
Description |
Interval |
E-value |
| PRK11642 |
PRK11642 |
ribonuclease R; |
1-813 |
0e+00 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 1750.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASRDELAVELHIEGEEQLEGLRRRLRAMERDGQLVFTRRQCYALPE 80
Cdd:PRK11642 1 MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYALPE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 81 RLDLVKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTEA 160
Cdd:PRK11642 81 RLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTDA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 161 GVGFVVPDDSRLSFDILIPPDQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
Cdd:PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRG 320
Cdd:PRK11642 241 VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 321 TSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
Cdd:PRK11642 321 TSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
Cdd:PRK11642 401 APLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
Cdd:PRK11642 481 ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLAL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 561 QSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFML 640
Cdd:PRK11642 561 QSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFML 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK11642 641 DQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKI 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 721 DFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKPKPKAAKKDVRKAKKPSAKTQKIAAA 800
Cdd:PRK11642 721 DFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKTQKIAAA 800
|
810
....*....|...
gi 1353173508 801 TKAKRAAKKKVAE 813
Cdd:PRK11642 801 TKAKRAAKKKVAE 813
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
20-732 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 1160.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 20 SREFILEHLTK-REKPASRDELAVELHIEGEEQLEGLRRRLRAMERDGQLVFTRRQCYALPERLDLVKGTVIGHRDGYGF 98
Cdd:COG0557 4 SRETILAFLKEdAYKPLSKKELAKALGLKDEESREALKRRLRALEREGQLVKTRRGRYRLPEKLDLVEGRVRGHRDGFGF 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 99 LRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTEAGVGFVVPDDSRLSFDILI 178
Cdd:COG0557 84 VIPDDGEEDIFIPPRELNGALHGDRVLVRVTKEDRRGRPEGRVVEILERANTRVVGRFEKEKGFGFVVPDDKRLLQDIFI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 179 PPDQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKA 258
Cdd:COG0557 164 PPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEEVLAEAEALPDEVPEADLK 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 259 GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLS 338
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLS 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 339 NGLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQG-DQDLREQYAPLVKHLEELHNLYKVL 417
Cdd:COG0557 324 NGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkDEELREEYADLVPMLEELYELAKIL 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 418 DKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSF 497
Cdd:COG0557 404 RKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLKLPFLYRVHEEPDPEKLEAL 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 498 RSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLT 577
Cdd:COG0557 484 REFLANLGLKLKGGDEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHFGLALEAYTHFTSPIRRYPDLL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 578 LHRAIKYLLAKEQGhqgntteTGGYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGF 657
Cdd:COG0557 564 VHRALKAYLEGKRS-------PGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRVGEEFEGVISGVTSF 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1353173508 658 GFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLISSERAPR 732
Cdd:COG0557 637 GLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQIDFELVEGGSEAP 711
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
18-725 |
0e+00 |
|
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA]
Pssm-ID: 273947 [Multi-domain] Cd Length: 709 Bit Score: 1085.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 18 IPSREFILEHLTK-REKPASRDELAVELHIEGEEQLEGLRRRLRAMERDGQLVFTRRQCYALPERLDLVKGTVIGHRDGY 96
Cdd:TIGR02063 1 SPLRELILEFLKSkKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALPESLKLVKGTVIAHRDGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 97 GFLRVEGRK-DDLYLSSEQMKTCIHGDQVLAQPLG-ADRKGRREARIVRVLVPKTSQIVGRYFTEAGVGFVVPDDSRLSF 174
Cdd:TIGR02063 81 GFLRPEDDDeDDIFIPPRQMNGAMHGDRVLVRITGkPDGGDRFEARVIKILERANDQIVGTFYIENGIGFVIPDDKRIYL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 175 DILIPPDQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPE 254
Cdd:TIGR02063 161 DIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEVLDEAAKIPEEVPE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 255 EAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLP 334
Cdd:TIGR02063 241 EEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLP 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 335 EVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLY 414
Cdd:TIGR02063 321 ERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELY 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 415 KVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAI 494
Cdd:TIGR02063 401 KILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 495 TSFRSVLAELGLELPGG--NKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRR 572
Cdd:TIGR02063 481 QNLREFLKTLGITLKGGtsDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 573 YPDLTLHRAIKYLLAKEQghqgNTTETGGYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVIS 652
Cdd:TIGR02063 561 YPDLIVHRLIKKALFGGE----NTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVIS 636
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1353173508 653 SVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLI 725
Cdd:TIGR02063 637 GVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
67-725 |
0e+00 |
|
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA]
Pssm-ID: 273033 [Multi-domain] Cd Length: 654 Bit Score: 1029.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 67 QLVFTrrQCYALPERLDLVKGTVIGHRDGYGFLR-VEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRVL 145
Cdd:TIGR00358 1 QLLAT--LKYALPEKDDLVKGVVKAHNKGFGFLRpDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGRFEAEVERIL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 146 VPKTSQIVGRYFTEAGVGFVVPDDSRLSFDILIPPD-QIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAV 224
Cdd:TIGR00358 79 EPALTRFVGKFLGENDFGFVVPDDPRIYLDIIVPKAsVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPW 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 225 DIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSY 304
Cdd:TIGR00358 159 WVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 305 YVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYT 384
Cdd:TIGR00358 239 YVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 385 KVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMI 464
Cdd:TIGR00358 319 KVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMI 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 465 LANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPE--PRDYAELLESVADRPDAEMLQTMLLRS 542
Cdd:TIGR00358 399 VANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENvtTLDGACWLREVKDRPEYEILVTRLLRS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 543 MKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQghqgntTETGGYhYSMEEMLQLGQHCSMAERR 622
Cdd:TIGR00358 479 LSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ------TDTERY-QPQDELLQIAEHCSDTERR 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 623 ADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRL 702
Cdd:TIGR00358 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRI 631
|
650 660
....*....|....*....|...
gi 1353173508 703 GDRVEVRVEAVNMDERKIDFSLI 725
Cdd:TIGR00358 632 GDRVTVKLTEVNMETRSIIFELV 654
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
260-588 |
5.69e-139 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 412.43 E-value: 5.69e-139
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 260 RVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSN 339
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 340 GLCSLNPQVDRLCMVCEMTVSSKG-RLTGYKFYEAVMSSHARLTYTKVWHILQgdqdlreqyaplvkhleelhnlykvld 418
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 419 kareerggisfeseeaKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAIT-SF 497
Cdd:smart00955 134 ----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAeLL 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 498 RSVLAELGLELPGGnkPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLT 577
Cdd:smart00955 198 KEFLALLGLLLLGG--DGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPDLI 275
|
330
....*....|.
gi 1353173508 578 LHRAIKYLLAK 588
Cdd:smart00955 276 VHRQLKAALRG 286
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
260-586 |
6.55e-137 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 408.21 E-value: 6.55e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 260 RVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSN 339
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 340 GLCSLNPQVDRLCMVCEMTVSSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQyAPLVKHLEELHNLYKVLDK 419
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILRA 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 420 AREERGGISFESEEAKFIFNAERRIErIEQTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRS 499
Cdd:pfam00773 160 KRLQRGALDLDTPENKLILDEEGVID-ILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLIK 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 500 VLAELglelpggnkPEPRDYAELLESVADRPDAemLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLH 579
Cdd:pfam00773 239 LLQLL---------PDDKGLSKSLEKIKDDERL--LSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDLIVH 307
|
....*..
gi 1353173508 580 RAIKYLL 586
Cdd:pfam00773 308 RQLKALL 314
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
80-720 |
3.97e-91 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 300.23 E-value: 3.97e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 80 ERLDLVKGTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAQPLGAdrKGRREARIVRVLVPKTSQIVGRYFTE 159
Cdd:COG4776 17 EQTPRVEGVVKATDKGFGFLEVDDQKS-YFIPPPQMKKVMHGDRIKAVIRTE--KDKESAEPETLIEPFLTRFVGRVQKK 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 160 AGVGFVVPDDSRLSFDILIPPDQIMGA--RMGFVVVVELTQRPTRRTK-AVGKIVEVLGDNMGTGMAVDIALRTHEIPYI 236
Cdd:COG4776 94 DGRLFVVPDHPLIKDAIKARPKKGLEEglKEGDWVVAELKRHPLKGDRgFFAEITEFIADADDPFAPWWVTLARHNLERE 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 237 WPQAvEQQVAGLKEEVPeeakagRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPSTPLDREA 316
Cdd:COG4776 174 APEG-DDEWELLDEGLE------REDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKEA 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 317 RNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTG-YKFYEAVMSSHARLTYTKVWHILQGDQD 395
Cdd:COG4776 247 RQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGDdIEFFAAWIRSKAKLAYDNVSDWLEGKGE 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 396 LREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVE 475
Cdd:COG4776 327 WQPENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVLR 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 476 KAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMlqTMLLRSMKQ-AIYDPENRG 554
Cdd:COG4776 407 EHLGFGIFNVHSGFDPEKLEQAVELLAEHGIEFDPEQLLTLEGFCALRRELDAQPTSYL--DSRLRRFQTfAEISTEPGP 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 555 HFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNttetggyhysmEEMLQLGQHCSMAERRADeatRDVADWL 634
Cdd:COG4776 485 HFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQPAEKPD-----------EELTERLAERRRLNRMAE---RDVADWL 550
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 635 KCDFMLDQVGN--VFKGVISSVTGFGFFVRLDD----LFIDGlvhvSSLDNDYYRFdQVGQR-----LMGEssgQTYRLG 703
Cdd:COG4776 551 YARYLKPKVGSgqVFTAEIIDINRGGLRVRLLEngavAFIPA----SFIHSVRDEL-VCSQEegtvyIKGE---VRYKLG 622
|
650
....*....|....*..
gi 1353173508 704 DRVEVRVEAVNMDERKI 720
Cdd:COG4776 623 DTIQVTLAEVREETRSI 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
85-720 |
6.70e-76 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 259.04 E-value: 6.70e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 85 VKGTVIGHRDGYGFLRVEGRKDdLYLSSEQMKTCIHGDQVLAqpLGADRKGRREARIVRVLVPKTSQIVGRyfteagvgf 164
Cdd:PRK05054 22 VEGVVKATEKGFGFLEVDAQKS-YFIPPPQMKKVMHGDRIIA--VIHTEKDREIAEPEELIEPFLTRFVGR--------- 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 165 VVPDDSRLSfdilIPPD-----QIMGARM----------GFVVVVELTQRPTR-----RTKAVGKIVEvlGDNmgtgmav 224
Cdd:PRK05054 90 VQKKDDRLS----IVPDhpllkDAIPCRAakglnhefkeGDWVVAELRRHPLKgdrgfYAEITQFITD--ADD------- 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 225 DIA-----LRTHEIPYIWPQaVEQQVAGLKEEVPeeakagRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAI 299
Cdd:PRK05054 157 HFApwwvtLARHNLEREAPA-GGVAWEMLDEGLE------REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAI 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 300 ADVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVSSKGRLTG-YKFYEAVMSSH 378
Cdd:PRK05054 230 ADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDdIRFFAAWIESK 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 379 ARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKL 458
Cdd:PRK05054 310 AKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRI 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 459 IEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLE--------LPGgnkpeprdYAELLESVADRP 530
Cdd:PRK05054 390 VEESMIAANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLKEHGLHfdaeelltLEG--------FCKLRRELDAQP 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 531 DaEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNttetggyhysmEEML 610
Cdd:PRK05054 462 T-GYLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ-----------DEIT 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 611 QLgqhcsMAERRADE--ATRDVADWLKCDFMLDQVGN--VFKGVISSVTGFGFFVRLDD----LFIDG-LVHvsslDN-D 680
Cdd:PRK05054 530 VQ-----LAERRRLNrmAERDVGDWLYARYLKDKAGTdtRFAAEIIDISRGGMRVRLLEngavAFIPAsFLH----AVrD 600
|
650 660 670 680
....*....|....*....|....*....|....*....|..
gi 1353173508 681 YYRFDQVGQRLM--GEssgQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK05054 601 ELVCNQENGTVQikGE---TVYKLGDVIDVTLAEVRMETRSI 639
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
643-725 |
2.70e-40 |
|
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Pssm-ID: 239917 [Multi-domain] Cd Length: 83 Bit Score: 142.54 E-value: 2.70e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 1353173508 723 SLI 725
Cdd:cd04471 81 ELV 83
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
164-238 |
2.12e-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: 111.33 E-value: 2.12e-29
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1353173508 164 FVVPDDSRLSFDILIPPDQIMGARMGFVVVVELTQRPTRRtKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWP 238
Cdd:pfam17876 1 FVVPDDKRIPQDIFIPKEDLKGAKDGDKVVVEITEYPDGK-NPEGKIVEVLGDPGDPGVEILSIIRKHGLPHEFP 74
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
87-144 |
4.20e-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: 4.20e-23
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1353173508 87 GTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIHGDQVLAQPLGADRKGRREARIVRV 144
Cdd:pfam08206 1 GTVRGHKKGFGFLIPDDEEDDIFIPPNQMKKAMHGDRVLVRITKGDRRGRREGRIVRI 58
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
646-720 |
8.84e-15 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 73.32 E-value: 8.84e-15
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1353173508 646 VFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:PRK08563 84 VVEGEVVEVVEFGAFVRIGP--VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
641-724 |
1.77e-14 |
|
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 68.85 E-value: 1.77e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 641 DQVGNVFKGVISSVTGFGFFVRLdDLFIDGLVHVSSLDNDYYrfdqvgqrlmgESSGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:pfam00575 1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHV-----------EDPDEVIKVGDEVKVKVLKVDKDRRRI 68
|
....
gi 1353173508 721 DFSL 724
Cdd:pfam00575 69 ILSI 72
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
646-725 |
1.57e-13 |
|
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Pssm-ID: 239907 [Multi-domain] Cd Length: 99 Bit Score: 66.93 E-value: 1.57e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 646 VFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLI 725
Cdd:cd04460 2 VVEGEVVEVVDFGAFVRIGP--VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKI 79
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
86-145 |
4.02e-13 |
|
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 64.54 E-value: 4.02e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1353173508 86 KGTVIGHRDGYGFLRVEGRKDDLYLSSEQ----MKTCIHGDQVLAQPLGADRKGRREARIVRVL 145
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQiqggLKSLREGDEVEFKVVSPEGGEKPEAENVVKL 64
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
642-724 |
6.10e-13 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 64.55 E-value: 6.10e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYyrfdqvgqrlmGESSGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKR-----------VKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
...
gi 1353173508 722 FSL 724
Cdd:smart00316 69 LSL 71
|
|
| HTH_12 |
pfam08461 |
Ribonuclease R winged-helix domain; This domain is found at the amino terminus of Ribonuclease ... |
22-81 |
4.87e-09 |
|
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: 53.17 E-value: 4.87e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1353173508 22 EFILEHLTKREKPASRDELAVELHIEGEE-QLEGLRRRLRAMERDGqlvFTRRQCYA---LPER 81
Cdd:pfam08461 1 EEILSILAESDAPIGAKIIAEELNLRGYDiGERAVRYHLRKLEERG---LTRRVGYAgreITEK 61
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
647-723 |
7.05e-09 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 52.77 E-value: 7.05e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1353173508 647 FKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYrfdqvgqrlmgESSGQTYRLGDRVEVRVEAVNMDERKIDFS 723
Cdd:cd00164 1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
643-727 |
9.56e-09 |
|
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 52.72 E-value: 9.56e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDyyrfdqvgqrLMGESSGQtYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN----------RVADASKL-FRVGDKVRAKVLKIDAEKKRISL 70
|
....*
gi 1353173508 723 SLISS 727
Cdd:cd05708 71 GLKAS 75
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
5.76e-08 |
|
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit
Pssm-ID: 440305 [Multi-domain] Cd Length: 348 Bit Score: 55.44 E-value: 5.76e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDyyrfdqvgQRLmgESSGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:COG0539 273 PVGDVVKGKVTRLTDFGAFVELEP-GVEGLVHISEMSWT--------KRV--AHPSDVVKVGDEVEVKVLDIDPEERRIS 341
|
...
gi 1353173508 722 FSL 724
Cdd:COG0539 342 LSI 344
|
|
| S1_RPS1_repeat_ec5 |
cd05690 |
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-720 |
5.94e-08 |
|
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240195 [Multi-domain] Cd Length: 69 Bit Score: 50.18 E-value: 5.94e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1353173508 644 GNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLdndyyrfdQVGQRlmGESSGQTYRLGDRVEVRVEAVNMDERKI 720
Cdd:cd05690 1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDI--------SWTQR--VRHPSEIYKKGQEVEAVVLNIDVERERI 66
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
642-724 |
6.25e-08 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 56.33 E-value: 6.25e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDndyyrFDQVgqrlmGESSGQTYRLGDRVEVRVEAVNMDERKId 721
Cdd:PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDIS-----WDKK-----GEEAVELYKKGDEVEAVVLKVDVEKERI- 439
|
...
gi 1353173508 722 fSL 724
Cdd:PRK06299 440 -SL 441
|
|
| S1_Tex |
cd05685 |
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ... |
644-723 |
1.69e-07 |
|
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Pssm-ID: 240190 [Multi-domain] Cd Length: 68 Bit Score: 48.77 E-value: 1.69e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 644 GNVFKGVISSVTGFGFFVrldDLFI--DGLVHVSSLDNDYY--RFDQVGqrlmgessgqtyrLGDRVEVRVEAVNMDERK 719
Cdd:cd05685 1 GMVLEGVVTNVTDFGAFV---DIGVkqDGLIHISKMADRFVshPSDVVS-------------VGDIVEVKVISIDEERGR 64
|
....
gi 1353173508 720 IDFS 723
Cdd:cd05685 65 ISLS 68
|
|
| S1_DHX8_helicase |
cd05684 |
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ... |
644-680 |
6.27e-07 |
|
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: 47.62 E-value: 6.27e-07
10 20 30
....*....|....*....|....*....|....*....
gi 1353173508 644 GNVFKGVISSVTGFGFFVRLDDL--FIDGLVHVSSLDND 680
Cdd:cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFE 39
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
643-724 |
2.41e-06 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 50.89 E-value: 2.41e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNdyyrfDQVGQRLmgessgQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSE-----NRDEDKT------DEIKVGDEVEAKVVDIDKKNRKVSL 513
|
..
gi 1353173508 723 SL 724
Cdd:TIGR00717 514 SV 515
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
3.42e-06 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 50.72 E-value: 3.42e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLdnDYYRFDQVGQRLmgessgqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGG--VDGLLHVSEI--SWGRVEKPSDVL---------KVGDEIKVYILDIDKENKKLS 542
|
...
gi 1353173508 722 FSL 724
Cdd:PRK00087 543 LSL 545
|
|
| RpsA |
COG0539 |
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ... |
642-724 |
4.69e-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: 49.66 E-value: 4.69e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLdnDYYRFDQVGQRLmgessgqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:COG0539 188 EEGDVVEGTVKNITDFGAFVDLGG--VDGLLHISEI--SWGRVKHPSEVL---------KVGDEVEVKVLKIDREKERIS 254
|
...
gi 1353173508 722 FSL 724
Cdd:COG0539 255 LSL 257
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-731 |
5.30e-06 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 49.66 E-value: 5.30e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLdnDYYRFDQvgqrlmgesSGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLGG--VDGLVHVSEL--SWKHIDH---------PSEVVEVGQEVTVEVLDVDMDRERVS 273
|
90
....*....|
gi 1353173508 722 FSLISSERAP 731
Cdd:PRK07899 274 LSLKATQEDP 283
|
|
| YabR |
COG1098 |
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ... |
642-724 |
5.64e-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: 5.64e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlfiD--GLVHVSSLDNDY----YRFDQVGQrlmgessgqtyrlgdrvEVRVEAVNM 715
Cdd:COG1098 4 EVGDIVEGKVTGITPFGAFVELPE---GttGLVHISEIADGYvkdiNDYLKVGD-----------------EVKVKVLSI 63
|
90
....*....|
gi 1353173508 716 DER-KIDFSL 724
Cdd:COG1098 64 DEDgKISLSI 73
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
642-724 |
1.01e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 48.72 E-value: 1.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLdnDYYRFDQVGQRLmgessgqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK06676 191 KEGDVVEGTVARLTDFGAFVDIGG--VDGLVHISEL--SHERVEKPSEVV---------SVGQEVEVKVLSIDWETERIS 257
|
...
gi 1353173508 722 FSL 724
Cdd:PRK06676 258 LSL 260
|
|
| S1_RecJ_like |
cd04473 |
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ... |
643-723 |
1.47e-05 |
|
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Pssm-ID: 239919 [Multi-domain] Cd Length: 77 Bit Score: 43.75 E-value: 1.47e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDyyrfdqvgqrlmgessgqtYRLGDRVEVRVEAVNmDERKIDF 722
Cdd:cd04473 16 VGKLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLLRD-------------------YEVGDEVIVQVTDIP-ENGNIDL 74
|
.
gi 1353173508 723 S 723
Cdd:cd04473 75 I 75
|
|
| Tex |
COG2183 |
Transcriptional accessory protein Tex/SPT6 [Transcription]; |
642-733 |
1.51e-05 |
|
Transcriptional accessory protein Tex/SPT6 [Transcription];
Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 48.48 E-value: 1.51e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVrldDLFI--DGLVHVSSLDNDYYR--FDQVgqrlmgessgqtyRLGDRVEVRVEAVNMDE 717
Cdd:COG2183 640 KPGMILEGTVTNVTDFGAFV---DIGVhqDGLVHISQLSDRFVKdpREVV-------------KVGDIVKVKVLEVDLKR 703
|
90
....*....|....*.
gi 1353173508 718 RKIDFSLISSERAPRN 733
Cdd:COG2183 704 KRISLSMKLDDEAGAA 719
|
|
| S1_pNO40 |
cd05686 |
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ... |
642-724 |
2.33e-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: 42.85 E-value: 2.33e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDyyRFDQVGQRLmgessgqtyRLGDRVEVRVEAVNMDErKID 721
Cdd:cd05686 2 ALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RVDDPSEVV---------DVGEKVWVKVIGREMKD-KMK 69
|
...
gi 1353173508 722 FSL 724
Cdd:cd05686 70 LSL 72
|
|
| rpsA |
PRK06676 |
30S ribosomal protein S1; Reviewed |
643-731 |
2.64e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 47.18 E-value: 2.64e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNdyyrfdqvgQRLmgESSGQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQISH---------KHI--ATPSEVLEEGQEVKVKVLEVNEEEKRISL 344
|
....*....
gi 1353173508 723 SLISSERAP 731
Cdd:PRK06676 345 SIKALEEAP 353
|
|
| rpsA |
PRK07899 |
30S ribosomal protein S1; Reviewed |
642-724 |
3.03e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 47.35 E-value: 3.03e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYrfdqvgqrlmgESSGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAERHV-----------EVPEQVVQVGDEVFVKVIDIDLERRRIS 359
|
...
gi 1353173508 722 FSL 724
Cdd:PRK07899 360 LSL 362
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
643-723 |
3.28e-05 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 42.62 E-value: 3.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDlfIDGLVHVSSLdnDYYRFDQVGQRLmgessgqtyRLGDRVEVRVEAVNMDERKIDF 722
Cdd:cd05688 1 EGDVVEGTVKSITDFGAFVDLGG--VDGLLHISDM--SWGRVKHPSEVV---------NVGDEVEVKVLKIDKERKRISL 67
|
.
gi 1353173508 723 S 723
Cdd:cd05688 68 G 68
|
|
| PRK11824 |
PRK11824 |
polynucleotide phosphorylase/polyadenylase; Provisional |
642-724 |
4.16e-05 |
|
polynucleotide phosphorylase/polyadenylase; Provisional
Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 46.97 E-value: 4.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVrldDLF--IDGLVHVSSLDNDyyRFDQVGQRLmgessgqtyRLGDRVEVRVeaVNMDER- 718
Cdd:PRK11824 620 EVGEIYEGKVVRIVDFGAFV---EILpgKDGLVHISEIADE--RVEKVEDVL---------KEGDEVKVKV--LEIDKRg 683
|
....*.
gi 1353173508 719 KIDFSL 724
Cdd:PRK11824 684 RIRLSR 689
|
|
| PRK00087 |
PRK00087 |
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1; |
642-724 |
6.07e-05 |
|
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 46.48 E-value: 6.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNdyYRFDQVGQRLmgessgqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISW--KRIDKPEDVL---------SEGEEVKAKILEVDPEEKRIR 628
|
...
gi 1353173508 722 FSL 724
Cdd:PRK00087 629 LSI 631
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
642-724 |
1.41e-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: 45.11 E-value: 1.41e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDyyrfdqvgqrLMGESSGQTYRLGDRVEVRVEAVNMDERKID 721
Cdd:TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWD----------KDGREADHLYKKGDEIEAVVLAVDKEKKRIS 426
|
...
gi 1353173508 722 FSL 724
Cdd:TIGR00717 427 LGV 429
|
|
| PRK08059 |
PRK08059 |
general stress protein 13; Validated |
642-731 |
2.38e-04 |
|
general stress protein 13; Validated
Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 41.57 E-value: 2.38e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 642 QVGNVFKGVISSVTGFGFFVRLDDLfIDGLVHVSSLDNDYYRfdQVGQRLmgessgqtyRLGDRVEVRVEAVNMDERKID 721
Cdd:PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDEE-TQGLVHISEITHGFVK--DIHDFL---------SVGDEVKVKVLSVDEEKGKIS 73
|
90
....*....|
gi 1353173508 722 FSLISSERAP 731
Cdd:PRK08059 74 LSIRATEEAP 83
|
|
| OB_RNB |
pfam08206 |
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease ... |
158-213 |
4.45e-04 |
|
Ribonuclease B OB domain; This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Pssm-ID: 429863 [Multi-domain] Cd Length: 58 Bit Score: 39.06 E-value: 4.45e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1353173508 158 TEAGVGFVVPDDSrlSFDILIPPDQIMGARMGFVVVVELTQrPTRRTKAVGKIVEV 213
Cdd:pfam08206 6 HKKGFGFLIPDDE--EDDIFIPPNQMKKAMHGDRVLVRITK-GDRRGRREGRIVRI 58
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
643-724 |
9.44e-04 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 42.84 E-value: 9.44e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDyyrfdqvgQRLMgeSSGQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:PRK06299 286 VGSKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWT--------KKNK--HPSKVVSVGQEVEVMVLEIDEEKRRISL 354
|
..
gi 1353173508 723 SL 724
Cdd:PRK06299 355 GL 356
|
|
| PRK12269 |
PRK12269 |
bifunctional cytidylate kinase/ribosomal protein S1; Provisional |
643-729 |
1.28e-03 |
|
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 42.39 E-value: 1.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 643 VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDyyRFDQVGQRLmgessgQTYRLGDRVEVRVEAVNMDERKIDF 722
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVEN--RDGDPGEAL------RKYAVGDRVKAVIVDMNVKDRKVAF 822
|
....*..
gi 1353173508 723 SLISSER 729
Cdd:PRK12269 823 SVRDYQR 829
|
|
| S1_RPS1_repeat_hs4 |
cd05692 |
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-723 |
2.32e-03 |
|
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: 37.26 E-value: 2.32e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 644 GNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYRfdqvgqrlmgeSSGQTYRLGDRVEVRVeaVNMDER-KIDF 722
Cdd:cd05692 1 GSVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVK-----------DVKDVLKEGDKVKVKV--LSIDARgRISL 66
|
.
gi 1353173508 723 S 723
Cdd:cd05692 67 S 67
|
|
| S1_PNPase |
cd04472 |
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ... |
644-723 |
2.52e-03 |
|
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Pssm-ID: 239918 [Multi-domain] Cd Length: 68 Bit Score: 37.14 E-value: 2.52e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 644 GNVFKGVISSVTGFGFFVRlddlFI---DGLVHVSSLDNDyyRFDQVGQRLmgessgqtyRLGDRVEVRVeaVNMDER-K 719
Cdd:cd04472 1 GKIYEGKVVKIKDFGAFVE----ILpgkDGLVHISELSDE--RVEKVEDVL---------KVGDEVKVKV--IEVDDRgR 63
|
....
gi 1353173508 720 IDFS 723
Cdd:cd04472 64 ISLS 67
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
607-724 |
3.80e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 40.49 E-value: 3.80e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 607 EEMLQLGQHCSMAERRADEATRDVADWLKcdfMLDQ-----------VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVS 675
Cdd:TIGR00717 228 SEYVKVGQEVKVKVIKFDKEKGRISLSLK---QLGEdpweaiekkfpVGDKITGRVTNLTDYGVFVEIEE-GIEGLVHVS 303
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1353173508 676 SLDNDYyrfdqvgqrlMGESSGQTYRLGDRVEVRVEAVNMDERKIDFSL 724
Cdd:TIGR00717 304 EMSWVK----------KNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
|
|
| PRK08582 |
PRK08582 |
RNA-binding protein S1; |
639-724 |
6.63e-03 |
|
RNA-binding protein S1;
Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 37.70 E-value: 6.63e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1353173508 639 MLDQVGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYRfdQVGQRLmgessgqtyRLGDRVEVRVEAVNmDER 718
Cdd:PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVK--DINDHL---------KVGDEVEVKVLNVE-DDG 67
|
....*.
gi 1353173508 719 KIDFSL 724
Cdd:PRK08582 68 KIGLSI 73
|
|
| |
