|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
112-835 |
2.55e-138 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 427.60 E-value: 2.55e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 112 ELIDRLaylsDEMneIESGKIIFsehlplsklqqgIKSGSYLqgtfRASRENYLEATVWIHGD-------KEEEKEILIQ 184
Cdd:COG0557 39 ALKRRL----RAL--EREGQLVK------------TRRGRYR----LPEKLDLVEGRVRGHRDgfgfvipDDGEEDIFIP 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 185 GiKHLNRAVHEDIVAVELLPRsqwvapssvvlDDEGqneddvekdeerelllktavsekmlRPTGRVVGIIKRNWRPYCG 264
Cdd:COG0557 97 P-RELNGALHGDRVLVRVTKE-----------DRRG-------------------------RPEGRVVEILERANTRVVG 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 265 MLSKSDikesRRHLFTPADKRIPR-IRI-ETRQASALEGRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETEVLLLE 342
Cdd:COG0557 140 RFEKEK----GFGFVVPDDKRLLQdIFIpPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRK 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 343 HDVPHQpFSQAVLSFLPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPG 422
Cdd:COG0557 216 HGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPG 294
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 423 NALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMR 502
Cdd:COG0557 295 SALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAI 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 503 IDS-----AAMNDDITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDsETHDPIDLQTKELRETNSMVEEFMLLAN 577
Cdd:COG0557 375 LDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLAN 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 578 ISVAkkihEEFSEH---ALLRKHPAPPPSNYDILVKAAKSKNLQIKTD---TAKSLADSLDRAE-SPDFPYLNTLLRila 650
Cdd:COG0557 454 EAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL--- 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 651 tRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADIIVHRLLAVAIGADcTYPELT--DKHKLSDICKNLNFRHK 728
Cdd:COG0557 527 -RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETER 600
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 729 MAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpkprlaYD 794
Cdd:COG0557 601 RADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YD 664
|
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 1334928335 795 DEIPSLRIE--GTVFHVFDKVKVKitLDSSNLQHQKIRMALVE 835
Cdd:COG0557 665 ERRQALVGErtGKRYRLGDRVEVR--VVRVDLDRRQIDFELVE 705
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
373-697 |
5.18e-120 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 365.84 E-value: 5.18e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 373 REDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 452
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 453 NLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRID---SAAMNDDITTSLRGLNQLAKILKKG 529
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEgkdAEKDKPDLAEDLRLLYELAKILRAK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 530 RIEKGALTLSSPEIRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYDILV 609
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 610 KAAKSKnlqiktDTAKSLADSLDRAESPdfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 689
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302
|
....*...
gi 1334928335 690 DIIVHRLL 697
Cdd:pfam00773 303 DLIVHRQL 310
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
113-834 |
2.07e-112 |
|
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: 359.66 E-value: 2.07e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 113 LIDRLAYLSDE--MNEIESGKIIFSEHLPLsklqqgiksgsyLQGTFRASRENYLEatvwIHGDKEEEKEILIQGiKHLN 190
Cdd:TIGR02063 39 LRKRLRALEDDglVKKNRRGLYALPESLKL------------VKGTVIAHRDGFGF----LRPEDDDEDDIFIPP-RQMN 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 191 RAVHEDIVAVELLprsqwvapssvvlddegQNEDdvEKDeerelllktavsekmlRPTGRVVGIIKRNWRPYCGMLSKSD 270
Cdd:TIGR02063 102 GAMHGDRVLVRIT-----------------GKPD--GGD----------------RFEARVIKILERANDQIVGTFYIEN 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 271 -IKEsrrhlFTPADKRIP-RIRIETRQASALE-GRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETEVLLLEHDVPH 347
Cdd:TIGR02063 147 gIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 348 QpFSQAVLSFLPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQ 427
Cdd:TIGR02063 222 E-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDK 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 428 ESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRI---- 503
Cdd:TIGR02063 301 EALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIegkd 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 504 DSAAMNDDITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKK 583
Cdd:TIGR02063 381 ALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIVPRERGDAHKLIEEFMIAANETVAEH 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 584 IhEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIK-----TDTAKSLADSLDR-AESPDFPYLNTLLrilaTRCMMQA 657
Cdd:TIGR02063 460 L-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEKvKGRPEEELINTVL----LRSMQQA 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 658 VYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADIIVHRLLAVAIGADCTYPELTDKH----KLSDICKNLNFRHKMAQYA 733
Cdd:TIGR02063 535 KY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREyleaKLEEIAEHSSKTERRADEA 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 734 QRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTV--------FFEekdkpkprlaYDDEIP 798
Cdd:TIGR02063 611 ERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVhistlkddYYV----------FDEKGL 673
|
730 740 750
....*....|....*....|....*....|....*...
gi 1334928335 799 SLRIE--GTVFHVFDKVKVKITldSSNLQHQKIRMALV 834
Cdd:TIGR02063 674 ALVGErtGKVFRLGDRVKVRVV--KADLDTGKIDFELV 709
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
373-702 |
1.12e-104 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 324.99 E-value: 1.12e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 373 REDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 452
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 453 NLCSLRSNVDRLAFSCIWEMNHNA-EILKTRFTKSVINSKASLTYAEAQMRIDsaamnddittslrglnqlakilkkgri 531
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 532 ekgaltlsspeiRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYDILVK- 610
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 611 -AAKSKNLQIKTDTAKSLADSLDRAESPDFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 689
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
|
330
....*....|...
gi 1334928335 690 DIIVHRLLAVAIG 702
Cdd:smart00955 273 DLIVHRQLKAALR 285
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
320-695 |
6.24e-47 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 180.32 E-value: 6.24e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 320 GHFVKNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCR 399
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 400 ELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCiwEMNHNAE-- 477
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 478 ILKTRFTKSVINSKASLTY--------AEAQMRIDSAAmnddITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDS 549
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYAP----LVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 550 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIKTDTA---K 625
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKpepR 517
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1334928335 626 SLADSLDR-AESPDFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADIIVHR 695
Cdd:PRK11642 518 DYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
|
|
| PIN_Rrp44-like |
cd09862 |
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ... |
1-103 |
2.68e-46 |
|
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic homologs; PIN (PilT N terminus) domain of the Saccharomyces cerevisiae exosome subunit Rrp44 (Ribosomal RNA-processing protein 44 or Protein Dis3 homolog) and other similar eukaryotic homologs are included in this family. The eukaryotic exosome is a conserved macromolecular complex responsible for many RNA-processing and RNA-degradation reactions. It is composed of nine core subunits that directly binds Rrp44. The Rrp44 nuclease is the catalytic subunit of the exosome and has endonuclease activity in the PIN domain and an exoribonuclease activity in its RNase II-like region. Rrp44 binding to the exosome is mediated mainly by the PIN domain and by subunits Rrp41-Rrp45, and binding predictions indicate that the PIN domain active site is positioned on the outer surface of the exosome. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these residues which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Recombinant Rrp44 was shown to possess manganese-dependent endonuclease activity in vitro that was abolished by point mutations in these putative metal binding residues of its PIN domain. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.
Pssm-ID: 350211 Cd Length: 178 Bit Score: 163.53 E-value: 2.68e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 1 MQEVRNRSAPIYKRIRDVTNNQEKHFYTFTNEHHKETYIEQEQGENANDRNDRAIRVAAKWYNEHLKRvaadSQLQVILI 80
Cdd:cd09862 80 LEEVRHRSLPLYNRLRALLKDPRKRFYVFSNEFHRETYVEREPGESPNDRNDRAIRKAAKWYQNHLAK----LGIPVVLL 155
|
90 100
....*....|....*....|...
gi 1334928335 81 TNDRKNKEKAVQEGIPAFTCEEY 103
Cdd:cd09862 156 TDDADNREKAEEEGILALTVREY 178
|
|
| PINc |
smart00670 |
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ... |
1-88 |
3.57e-08 |
|
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Pssm-ID: 214771 [Multi-domain] Cd Length: 111 Bit Score: 52.43 E-value: 3.57e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 1 MQEVRNRSAPIYKRIRDVTNNQEKHFYTFTNEHHKETYIEQEQGENANDRNDRAIRVAAKWYNEhlkrvaadsqlqVILI 80
Cdd:smart00670 36 LEELEYLALRSLKKLEELALEGKIILKVLKEERIEEEILERLSLKLELLPNDALILATAKELGN------------VVLV 103
|
....*...
gi 1334928335 81 TNDRKNKE 88
Cdd:smart00670 104 TNDRDLRR 111
|
|
| PIN_4 |
pfam13638 |
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ... |
1-99 |
7.89e-08 |
|
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).
Pssm-ID: 433369 Cd Length: 131 Bit Score: 51.85 E-value: 7.89e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 1 MQEVR---NRSAPIYKRIRDVTNNQEKHFY-TFTNEHHKETYIEQEQGENAN--DRNDRAIRVAAKWYNEHLKRVaadsq 74
Cdd:pfam13638 31 LEELDglkKGSDESGRELARLARQANRWLDeLLENNGGRLRGQTLDERLPPDpfDKNDNRILAVALYLKEELPDR----- 105
|
90 100
....*....|....*....|....*
gi 1334928335 75 lQVILITNDRKNKEKAVQEGIPAFT 99
Cdd:pfam13638 106 -PVILVSKDINLRIKADALGIPAED 129
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
112-835 |
2.55e-138 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 427.60 E-value: 2.55e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 112 ELIDRLaylsDEMneIESGKIIFsehlplsklqqgIKSGSYLqgtfRASRENYLEATVWIHGD-------KEEEKEILIQ 184
Cdd:COG0557 39 ALKRRL----RAL--EREGQLVK------------TRRGRYR----LPEKLDLVEGRVRGHRDgfgfvipDDGEEDIFIP 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 185 GiKHLNRAVHEDIVAVELLPRsqwvapssvvlDDEGqneddvekdeerelllktavsekmlRPTGRVVGIIKRNWRPYCG 264
Cdd:COG0557 97 P-RELNGALHGDRVLVRVTKE-----------DRRG-------------------------RPEGRVVEILERANTRVVG 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 265 MLSKSDikesRRHLFTPADKRIPR-IRI-ETRQASALEGRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETEVLLLE 342
Cdd:COG0557 140 RFEKEK----GFGFVVPDDKRLLQdIFIpPDDLNGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRK 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 343 HDVPHQpFSQAVLSFLPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPG 422
Cdd:COG0557 216 HGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPG 294
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 423 NALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMR 502
Cdd:COG0557 295 SALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAI 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 503 IDS-----AAMNDDITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDsETHDPIDLQTKELRETNSMVEEFMLLAN 577
Cdd:COG0557 375 LDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLAN 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 578 ISVAkkihEEFSEH---ALLRKHPAPPPSNYDILVKAAKSKNLQIKTD---TAKSLADSLDRAE-SPDFPYLNTLLRila 650
Cdd:COG0557 454 EAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL--- 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 651 tRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADIIVHRLLAVAIGADcTYPELT--DKHKLSDICKNLNFRHK 728
Cdd:COG0557 527 -RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETER 600
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 729 MAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpkprlaYD 794
Cdd:COG0557 601 RADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YD 664
|
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 1334928335 795 DEIPSLRIE--GTVFHVFDKVKVKitLDSSNLQHQKIRMALVE 835
Cdd:COG0557 665 ERRQALVGErtGKRYRLGDRVEVR--VVRVDLDRRQIDFELVE 705
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
373-697 |
5.18e-120 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 365.84 E-value: 5.18e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 373 REDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 452
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 453 NLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRID---SAAMNDDITTSLRGLNQLAKILKKG 529
Cdd:pfam00773 81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEgkdAEKDKPDLAEDLRLLYELAKILRAK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 530 RIEKGALTLSSPEIRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYDILV 609
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 610 KAAKSKnlqiktDTAKSLADSLDRAESPdfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 689
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302
|
....*...
gi 1334928335 690 DIIVHRLL 697
Cdd:pfam00773 303 DLIVHRQL 310
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
113-834 |
2.07e-112 |
|
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: 359.66 E-value: 2.07e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 113 LIDRLAYLSDE--MNEIESGKIIFSEHLPLsklqqgiksgsyLQGTFRASRENYLEatvwIHGDKEEEKEILIQGiKHLN 190
Cdd:TIGR02063 39 LRKRLRALEDDglVKKNRRGLYALPESLKL------------VKGTVIAHRDGFGF----LRPEDDDEDDIFIPP-RQMN 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 191 RAVHEDIVAVELLprsqwvapssvvlddegQNEDdvEKDeerelllktavsekmlRPTGRVVGIIKRNWRPYCGMLSKSD 270
Cdd:TIGR02063 102 GAMHGDRVLVRIT-----------------GKPD--GGD----------------RFEARVIKILERANDQIVGTFYIEN 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 271 -IKEsrrhlFTPADKRIP-RIRIETRQASALE-GRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETEVLLLEHDVPH 347
Cdd:TIGR02063 147 gIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 348 QpFSQAVLSFLPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQ 427
Cdd:TIGR02063 222 E-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDK 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 428 ESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRI---- 503
Cdd:TIGR02063 301 EALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIegkd 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 504 DSAAMNDDITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKK 583
Cdd:TIGR02063 381 ALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIVPRERGDAHKLIEEFMIAANETVAEH 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 584 IhEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIK-----TDTAKSLADSLDR-AESPDFPYLNTLLrilaTRCMMQA 657
Cdd:TIGR02063 460 L-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEKvKGRPEEELINTVL----LRSMQQA 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 658 VYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADIIVHRLLAVAIGADCTYPELTDKH----KLSDICKNLNFRHKMAQYA 733
Cdd:TIGR02063 535 KY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREyleaKLEEIAEHSSKTERRADEA 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 734 QRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTV--------FFEekdkpkprlaYDDEIP 798
Cdd:TIGR02063 611 ERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVhistlkddYYV----------FDEKGL 673
|
730 740 750
....*....|....*....|....*....|....*...
gi 1334928335 799 SLRIE--GTVFHVFDKVKVKITldSSNLQHQKIRMALV 834
Cdd:TIGR02063 674 ALVGErtGKVFRLGDRVKVRVV--KADLDTGKIDFELV 709
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
373-702 |
1.12e-104 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 324.99 E-value: 1.12e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 373 REDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 452
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 453 NLCSLRSNVDRLAFSCIWEMNHNA-EILKTRFTKSVINSKASLTYAEAQMRIDsaamnddittslrglnqlakilkkgri 531
Cdd:smart00955 81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 532 ekgaltlsspeiRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYDILVK- 610
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 611 -AAKSKNLQIKTDTAKSLADSLDRAESPDFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 689
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
|
330
....*....|...
gi 1334928335 690 DIIVHRLLAVAIG 702
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 ... |
281-818 |
5.35e-79 |
|
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: 268.89 E-value: 5.35e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 281 PADKRIPR---IRIETRQASALEGRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSF 357
Cdd:TIGR00358 100 PDDPRIYLdiiVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFE-FPDGVEQQ 178
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 358 LPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVY 437
Cdd:TIGR00358 179 AAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVY 258
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 438 LCEKRIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAE-AQMRIDSAAMNDDITT-- 514
Cdd:TIGR00358 259 LPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKvNDWLENDDELQPEYETlv 338
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 515 -SLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEfSEHAL 593
Cdd:TIGR00358 339 eQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVD-EEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGI 416
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 594 LRKHPAPPPSNYDILVKAAKSKNLQIK-----TDTAKSLADSLDR-AESPDFPYLNTLLRilatRCMMQAVYfcsgMDND 667
Cdd:TIGR00358 417 YRVHPGPSKKKLQSLLEFLAELGLTLPggnaeNVTTLDGACWLREvKDRPEYEILVTRLL----RSLSQAEY----SPEP 488
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 668 FHHYGLASPIYTHFTSPIRRYADIIVHRLLAVAIGADCTYPELTD-KHKLSDICKNLNFRHKMAQYAQRASVAFHTQLFF 746
Cdd:TIGR00358 489 LGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQpQDELLQIAEHCSDTERRARDAERDVADWLKCRYL 568
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 747 KSKG-------IVSEEAYILFVR--KNAIVVLIPKYGLEGTVFFEEKDKpkprlayddeiPSLRIEGT--VFHVFDKVKV 815
Cdd:TIGR00358 569 LDKVgtefsgeISSVTRFGMFVRldDNGIDGLIHISTLHNDYYVFDQEK-----------MALIGKGTgkVYRIGDRVTV 637
|
...
gi 1334928335 816 KIT 818
Cdd:TIGR00358 638 KLT 640
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
320-695 |
6.24e-47 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 180.32 E-value: 6.24e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 320 GHFVKNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPRMPWSITEEDMKNREDLRHLCVCSVDPPGCTDIDDALHCR 399
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 400 ELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCiwEMNHNAE-- 477
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 478 ILKTRFTKSVINSKASLTY--------AEAQMRIDSAAmnddITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDS 549
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYAP----LVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 550 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIKTDTA---K 625
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKpepR 517
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1334928335 626 SLADSLDR-AESPDFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADIIVHR 695
Cdd:PRK11642 518 DYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
|
|
| PIN_Rrp44-like |
cd09862 |
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ... |
1-103 |
2.68e-46 |
|
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic homologs; PIN (PilT N terminus) domain of the Saccharomyces cerevisiae exosome subunit Rrp44 (Ribosomal RNA-processing protein 44 or Protein Dis3 homolog) and other similar eukaryotic homologs are included in this family. The eukaryotic exosome is a conserved macromolecular complex responsible for many RNA-processing and RNA-degradation reactions. It is composed of nine core subunits that directly binds Rrp44. The Rrp44 nuclease is the catalytic subunit of the exosome and has endonuclease activity in the PIN domain and an exoribonuclease activity in its RNase II-like region. Rrp44 binding to the exosome is mediated mainly by the PIN domain and by subunits Rrp41-Rrp45, and binding predictions indicate that the PIN domain active site is positioned on the outer surface of the exosome. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these residues which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Recombinant Rrp44 was shown to possess manganese-dependent endonuclease activity in vitro that was abolished by point mutations in these putative metal binding residues of its PIN domain. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.
Pssm-ID: 350211 Cd Length: 178 Bit Score: 163.53 E-value: 2.68e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 1 MQEVRNRSAPIYKRIRDVTNNQEKHFYTFTNEHHKETYIEQEQGENANDRNDRAIRVAAKWYNEHLKRvaadSQLQVILI 80
Cdd:cd09862 80 LEEVRHRSLPLYNRLRALLKDPRKRFYVFSNEFHRETYVEREPGESPNDRNDRAIRKAAKWYQNHLAK----LGIPVVLL 155
|
90 100
....*....|....*....|...
gi 1334928335 81 TNDRKNKEKAVQEGIPAFTCEEY 103
Cdd:cd09862 156 TDDADNREKAEEEGILALTVREY 178
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
362-818 |
1.08e-41 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 162.71 E-value: 1.08e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 362 PWSITEEDMkNREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEK 441
Cdd:COG4776 180 EWELLDEGL-EREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKEARQRAFTNYLPGF 258
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 442 RIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEIL-KTRFTKSVINSKASLTYAEAQMRIDSAA----MNDDITTSL 516
Cdd:COG4776 259 NIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGdDIEFFAAWIRSKAKLAYDNVSDWLEGKGewqpENEEIAEQI 338
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 517 RGLNQLAKILKKGRIEKGALTLSSPEIRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEE-----FSEH 591
Cdd:COG4776 339 RLLHQFALARSQWRQQHALVFKDRPDYRFELD-EKGNVLDIHAEPRRIANRIVEEAMIAANICAARVLREHlgfgiFNVH 417
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 592 ALLRkhpappPSNYDILVKAAKSKNLQIKTDTAKSLAD--SLDR--AESPDfPYLNTLLRILATRCMMQAVyfcSGmdnd 667
Cdd:COG4776 418 SGFD------PEKLEQAVELLAEHGIEFDPEQLLTLEGfcALRRelDAQPT-SYLDSRLRRFQTFAEISTE---PG---- 483
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 668 fHHYGLASPIYTHFTSPIRRYADIIVHRLL-AVAIGADCTYPELTDKHKLSDiCKNLNfrhKMAQ-------YAQrasva 739
Cdd:COG4776 484 -PHFGLGLDAYATWTSPIRKYGDMVNHRLIkAVILGQPAEKPDEELTERLAE-RRRLN---RMAErdvadwlYAR----- 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 740 fhtqlFFKSKgIVSEEAYilfvrkNAIVVLIPKYGLE------GTVFF-------EEKDkpkpRLAYDDEIPSLRIEG-T 805
Cdd:COG4776 554 -----YLKPK-VGSGQVF------TAEIIDINRGGLRvrllenGAVAFipasfihSVRD----ELVCSQEEGTVYIKGeV 617
|
490
....*....|...
gi 1334928335 806 VFHVFDKVKVKIT 818
Cdd:COG4776 618 RYKLGDTIQVTLA 630
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
338-730 |
6.38e-39 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 154.26 E-value: 6.38e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 338 VLLLEHDVPHQPFSQAVlsflprmPWSITEEDMKnREDLRHLCVCSVDPPGCTDIDDALHCRELSNGNLEVGVHIADVSH 417
Cdd:PRK05054 163 VTLARHNLEREAPAGGV-------AWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTA 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 418 FIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLRSNVDRLAFSCIWEMNHNAEIL-KTRFTKSVINSKASLTY 496
Cdd:PRK05054 235 YIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEdDIRFFAAWIESKAKLAY 314
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 497 AE----AQMRIDSAAMNDDITTSLRGLNQLAKILKKGRIEKGALTLSSPEIRFHMdSETHDPIDLQTKELRETNSMVEEF 572
Cdd:PRK05054 315 DNvsdwLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFEL-GEKGEVLDIVAEPRRIANRIVEES 393
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 573 MLLANISVAKKIHEEFsEHALLRKHPAPPPSNYDILVKAAKSKNLQIktdTAKSLAdSLD-----RAESPDFP--YLNTL 645
Cdd:PRK05054 394 MIAANICAARVLRDKL-GFGIYNVHSGFDPANAEQAVALLKEHGLHF---DAEELL-TLEgfcklRRELDAQPtgYLDSR 468
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 646 LRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADIIVHRLL-AVAIGADCTYPEltdkhklSDICKNLN 724
Cdd:PRK05054 469 IRRFQSFAEISTE---PG-----PHFGLGLEAYATWTSPIRKYGDMINHRLLkAVIKGETAERPQ-------DEITVQLA 533
|
....*....
gi 1334928335 725 FR---HKMA 730
Cdd:PRK05054 534 ERrrlNRMA 542
|
|
| OB_Dis3 |
pfam17849 |
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ... |
278-344 |
7.16e-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: 101.53 E-value: 7.16e-26
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1334928335 278 LFTPADKRIPRIRIETRQA--------SALEGRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETEVLLLEHD 344
Cdd:pfam17849 3 LFVPRDKRIPRIRIPTKSApeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
|
|
| Rrp44_CSD1 |
pfam17216 |
Rrp44-like cold shock domain; |
134-258 |
6.60e-19 |
|
Rrp44-like cold shock domain;
Pssm-ID: 375054 Cd Length: 148 Bit Score: 84.05 E-value: 6.60e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 134 FSEHLPLSKLQQGIKSGSYLQGTFRASRENYLEATVWIhgdKEEEKEILIQGIKHLNRAVHEDIVAVELLPRSQWVAPSS 213
Cdd:pfam17216 4 FPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSL---PRFSKPVLIVGQKNLNRAFNGDQVIVELLPQSEWKAPSS 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1334928335 214 VVLDDE------------GQNEDDVE--------KDEERELLLKTAV---SEKMLRPTGRVVGIIKRN 258
Cdd:pfam17216 81 IVLDSEhfdvndnpdieaGDDDDNNEsssnttviSDKQRRLLAKDAMiaqRSKKIQPTAKVVYIQRRS 148
|
|
| Rrp44_S1 |
pfam17215 |
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ... |
752-831 |
1.16e-14 |
|
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: 69.87 E-value: 1.16e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 752 VSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPKPRLAYDDEIPSLRIEGTV------FHVFDKVKVKIT--LDSSN 823
Cdd:pfam17215 1 SEEEGYVIKVFNNGIVVFVPKFGIEGLIRLEDLTGDEPEAEFDADEYSLTFPDKGsgkkrtVGVFDKVRVRVKsvKDENT 80
|
....*...
gi 1334928335 824 lQHQKIRM 831
Cdd:pfam17215 81 -GKRKVKL 87
|
|
| PINc |
smart00670 |
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, ... |
1-88 |
3.57e-08 |
|
Large family of predicted nucleotide-binding domains; From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Pssm-ID: 214771 [Multi-domain] Cd Length: 111 Bit Score: 52.43 E-value: 3.57e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 1 MQEVRNRSAPIYKRIRDVTNNQEKHFYTFTNEHHKETYIEQEQGENANDRNDRAIRVAAKWYNEhlkrvaadsqlqVILI 80
Cdd:smart00670 36 LEELEYLALRSLKKLEELALEGKIILKVLKEERIEEEILERLSLKLELLPNDALILATAKELGN------------VVLV 103
|
....*...
gi 1334928335 81 TNDRKNKE 88
Cdd:smart00670 104 TNDRDLRR 111
|
|
| PIN_4 |
pfam13638 |
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ... |
1-99 |
7.89e-08 |
|
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).
Pssm-ID: 433369 Cd Length: 131 Bit Score: 51.85 E-value: 7.89e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 1 MQEVR---NRSAPIYKRIRDVTNNQEKHFY-TFTNEHHKETYIEQEQGENAN--DRNDRAIRVAAKWYNEHLKRVaadsq 74
Cdd:pfam13638 31 LEELDglkKGSDESGRELARLARQANRWLDeLLENNGGRLRGQTLDERLPPDpfDKNDNRILAVALYLKEELPDR----- 105
|
90 100
....*....|....*....|....*
gi 1334928335 75 lQVILITNDRKNKEKAVQEGIPAFT 99
Cdd:pfam13638 106 -PVILVSKDINLRIKADALGIPAED 129
|
|
| CSD2 |
pfam17876 |
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ... |
280-347 |
2.26e-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: 45.84 E-value: 2.26e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1334928335 280 TPADKRIPR-IRIETRQAS-ALEGRRIIVAIDGWPrNSRYPNGHFVKNLGDVGEKETETEVLLLEHDVPH 347
Cdd:pfam17876 3 VPDDKRIPQdIFIPKEDLKgAKDGDKVVVEITEYP-DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLPH 71
|
|
| |
