|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
14-603 |
6.88e-140 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 424.13 E-value: 6.88e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 14 KPTGRVVGIIKRNWRPYCGMLsksdIKESRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFV 91
Cdd:COG0557 121 RPEGRVVEILERANTRVVGRF----EKEKGFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVV 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 92 RNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELEN 171
Cdd:COG0557 197 EVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 172 GNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKF 251
Cdd:COG0557 276 GGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEF 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 252 TKSVINSKASLTYAEAQLRIDS-----ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQ 326
Cdd:COG0557 356 YRSVIRSDARLTYEEVQAILDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIV 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 327 TKELRETNSMVEEFMLLANISVAkkihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLD 400
Cdd:COG0557 435 PRERNDAHKLIEEFMLLANEAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLE 510
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 401 QAE-SPTFPYLNTLLRilatRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT 479
Cdd:COG0557 511 QVKgRPEEELLNTLLL----RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQ 581
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 480 --DKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV---- 547
Cdd:COG0557 582 eyLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvss 655
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 5262619 548 ----FFEekdkpnpqliYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 603
Cdd:COG0557 656 lgddYYE----------YDERRQALVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
141-465 |
1.53e-123 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 368.15 E-value: 1.53e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 221 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 297
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 298 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 377
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 378 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 457
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302
|
....*...
gi 5262619 458 DVIVHRLL 465
Cdd:pfam00773 303 DLIVHRQL 310
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
14-602 |
6.92e-111 |
|
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: 348.88 E-value: 6.92e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 14 KPTGRVVGIIKRNWRPYCGMLSKSD-IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHF 90
Cdd:TIGR02063 122 RFEARVIKILERANDQIVGTFYIENgIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKV 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 91 VRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELE 170
Cdd:TIGR02063 197 VEILGHADDPGIDILIIIRKHGIPYE-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLK 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 171 NGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTK 250
Cdd:TIGR02063 276 DGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYE 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 251 FTKSVINSKASLTYAEAQ----LRIDSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQ 326
Cdd:TIGR02063 356 FYEAVINSHARLTYNQVNdiieGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIV 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 327 TKELRETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ 401
Cdd:TIGR02063 435 PRERGDAHKLIEEFMIAANETVAEHL-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEK 513
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 402 -AESPTFPYLNTLLrilaTRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTD 480
Cdd:TIGR02063 514 vKGRPEEELINTVL----LRSMQQAKY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKE 585
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 481 KH----KLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFF 549
Cdd:TIGR02063 586 REyleaKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI 658
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 5262619 550 eeKDKPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLV 602
Cdd:TIGR02063 659 --STLKDDYYVFDEKGLALVGERTgkVFRLGDRVKVRVV--KADLDTGKIDFELV 709
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
141-470 |
5.68e-106 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 321.91 E-value: 5.68e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 221 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 299
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 300 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 378
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 379 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 457
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
|
330
....*....|...
gi 5262619 458 DVIVHRLLAVAIG 470
Cdd:smart00955 273 DLIVHRQLKAALR 285
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
88-463 |
1.95e-49 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 184.56 E-value: 1.95e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 88 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 167
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 168 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 245
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 246 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 317
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 318 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 392
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5262619 393 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 463
Cdd:PRK11642 514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
|
|
|
|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
14-603 |
6.88e-140 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 424.13 E-value: 6.88e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 14 KPTGRVVGIIKRNWRPYCGMLsksdIKESRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFV 91
Cdd:COG0557 121 RPEGRVVEILERANTRVVGRF----EKEKGFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVV 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 92 RNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELEN 171
Cdd:COG0557 197 EVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 172 GNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKF 251
Cdd:COG0557 276 GGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEF 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 252 TKSVINSKASLTYAEAQLRIDS-----ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQ 326
Cdd:COG0557 356 YRSVIRSDARLTYEEVQAILDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIV 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 327 TKELRETNSMVEEFMLLANISVAkkihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLD 400
Cdd:COG0557 435 PRERNDAHKLIEEFMLLANEAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLE 510
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 401 QAE-SPTFPYLNTLLRilatRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT 479
Cdd:COG0557 511 QVKgRPEEELLNTLLL----RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQ 581
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 480 --DKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV---- 547
Cdd:COG0557 582 eyLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvss 655
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 5262619 548 ----FFEekdkpnpqliYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 603
Cdd:COG0557 656 lgddYYE----------YDERRQALVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
141-465 |
1.53e-123 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 368.15 E-value: 1.53e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 221 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 297
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 298 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 377
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 378 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 457
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302
|
....*...
gi 5262619 458 DVIVHRLL 465
Cdd:pfam00773 303 DLIVHRQL 310
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
14-602 |
6.92e-111 |
|
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: 348.88 E-value: 6.92e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 14 KPTGRVVGIIKRNWRPYCGMLSKSD-IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHF 90
Cdd:TIGR02063 122 RFEARVIKILERANDQIVGTFYIENgIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKV 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 91 VRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELE 170
Cdd:TIGR02063 197 VEILGHADDPGIDILIIIRKHGIPYE-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLK 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 171 NGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTK 250
Cdd:TIGR02063 276 DGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYE 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 251 FTKSVINSKASLTYAEAQ----LRIDSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQ 326
Cdd:TIGR02063 356 FYEAVINSHARLTYNQVNdiieGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIV 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 327 TKELRETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ 401
Cdd:TIGR02063 435 PRERGDAHKLIEEFMIAANETVAEHL-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEK 513
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 402 -AESPTFPYLNTLLrilaTRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTD 480
Cdd:TIGR02063 514 vKGRPEEELINTVL----LRSMQQAKY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKE 585
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 481 KH----KLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFF 549
Cdd:TIGR02063 586 REyleaKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI 658
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 5262619 550 eeKDKPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLV 602
Cdd:TIGR02063 659 --STLKDDYYVFDEKGLALVGERTgkVFRLGDRVKVRVV--KADLDTGKIDFELV 709
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
141-470 |
5.68e-106 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 321.91 E-value: 5.68e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 221 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 299
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 300 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 378
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 379 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 457
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
|
330
....*....|...
gi 5262619 458 DVIVHRLLAVAIG 470
Cdd:smart00955 273 DLIVHRQLKAALR 285
|
|
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
68-585 |
1.89e-77 |
|
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: 259.26 E-value: 1.89e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 68 EGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHL 147
Cdd:TIGR00358 122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFE-FPDGVEQQAAKLQFDVDEQAKKYREDLTDL 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 148 CICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKC 227
Cdd:TIGR00358 201 AFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNP 280
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 228 DVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAE-AQLRIDSANMNDDITT---SLRGLNKLAKILKKRRIEKGA 303
Cdd:TIGR00358 281 NEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKvNDWLENDDELQPEYETlveQLKALHQLSQALGEWRHKRGL 360
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 304 LTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEfSEHALLRKHPAPPPSNYEILVKAARSR 383
Cdd:TIGR00358 361 IDFEHPETKFIVD-EEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAEL 438
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 384 NLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLRilatRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYA 457
Cdd:TIGR00358 439 GLTLPggnaeNVTTLDGACWLREvKDRPEYEILVTRLL----RSLSQAEY----SPEPLGHFGLGLEHYAHFTSPIRRYP 510
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 458 DVIVHRLLAVAIGADCTYPELTD-KHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKG-------IVSEEAYILFV 529
Cdd:TIGR00358 511 DLTNHRLIKAVLAKEQTDTERYQpQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVgtefsgeISSVTRFGMFV 590
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 530 R--KNAIVVLIPKYGLegtvffeekdkPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKI 585
Cdd:TIGR00358 591 RldDNGIDGLIHISTL-----------HNDYYVFDQEKMALIGKGTgkVYRIGDRVTVKL 639
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
88-463 |
1.95e-49 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 184.56 E-value: 1.95e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 88 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 167
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 168 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 245
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 246 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 317
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 318 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 392
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5262619 393 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 463
Cdd:PRK11642 514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
106-503 |
8.66e-40 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 154.63 E-value: 8.66e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 106 VLLLEHDVPHQPfsqavlsflPKMP--WSItEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 183
Cdd:COG4776 163 VTLARHNLEREA---------PEGDdeWEL-LDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADP 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 184 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 262
Cdd:COG4776 233 TAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGdDIEFFAAWIRSKAKL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 263 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVE 338
Cdd:COG4776 313 AYDNVSDWLEGKGewqpENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELD-EKGNVLDIHAEPRRIANRIVE 391
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 339 EFMLLANISVAKKIHEE-----FSEHALLRkhpappPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESPtf 407
Cdd:COG4776 392 EAMIAANICAARVLREHlgfgiFNVHSGFD------PEKLEQAVELLAEHGIEFDPEQLLTLEgfcalrRELDAQPTS-- 463
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 408 pYLNTLLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklAD 486
Cdd:COG4776 464 -YLDSRLRRFQTFAEISTE---PG-----PHFGLGLDAYATWTSPIRKYGDMVNHRLIkAVILGQPAEKPD-------EE 527
|
410
....*....|....*..
gi 5262619 487 ICKNLNFRHKMAQYAQR 503
Cdd:COG4776 528 LTERLAERRRLNRMAER 544
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
106-498 |
9.64e-38 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 148.87 E-value: 9.64e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 106 VLLLEHDVPHQPfsqavlsflPKM--PWSITEKDMKnREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 183
Cdd:PRK05054 163 VTLARHNLEREA---------PAGgvAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADP 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 184 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 262
Cdd:PRK05054 233 TAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEdDIRFFAAWIESKAKL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 263 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMdSETHDPIDLQTKELRETNSMVE 338
Cdd:PRK05054 313 AYDNVSDWLENGGdwqpESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFEL-GEKGEVLDIVAEPRRIANRIVE 391
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 339 EFMLLANISVAKKIHEEFsEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESptfPYLNT 412
Cdd:PRK05054 392 ESMIAANICAARVLRDKL-GFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEgfcklrRELDAQPT---GYLDS 467
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 413 LLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklADICKNL 491
Cdd:PRK05054 468 RIRRFQSFAEISTE---PG-----PHFGLGLEAYATWTSPIRKYGDMINHRLLkAVIKGETAERPQ-------DEITVQL 532
|
410
....*....|
gi 5262619 492 NFR---HKMA 498
Cdd:PRK05054 533 AERrrlNRMA 542
|
|
| OB_Dis3 |
pfam17849 |
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ... |
46-112 |
3.56e-26 |
|
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA.
Pssm-ID: 436091 [Multi-domain] Cd Length: 77 Bit Score: 101.92 E-value: 3.56e-26
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 5262619 46 LFTPADKRIPRIRIETRQA--------STLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHD 112
Cdd:pfam17849 3 LFVPRDKRIPRIRIPTKSApeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
|
|
| Rrp44_S1 |
pfam17215 |
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ... |
520-599 |
2.89e-15 |
|
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44.
Pssm-ID: 435792 Cd Length: 87 Bit Score: 71.41 E-value: 2.89e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 520 VSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTV------FHVFDKVKVKIM--LDSSN 591
Cdd:pfam17215 1 SEEEGYVIKVFNNGIVVFVPKFGIEGLIRLEDLTGDEPEAEFDADEYSLTFPDKGsgkkrtVGVFDKVRVRVKsvKDENT 80
|
....*...
gi 5262619 592 lQHQKIRM 599
Cdd:pfam17215 81 -GKRKVKL 87
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
48-115 |
6.18e-06 |
|
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: 44.30 E-value: 6.18e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619 48 TPADKRIPR-IRIETRQASTL-EGRRIIVAIDGWPrNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 115
Cdd:pfam17876 3 VPDDKRIPQdIFIPKEDLKGAkDGDKVVVEITEYP-DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLPH 71
|
|
|