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Conserved domains on  [gi|190014625|ref|NP_001121698|]
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exosome complex exonuclease RRP44 isoform b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VacB super family cl43181
Exoribonuclease R [Transcription];
176-899 7.96e-139

Exoribonuclease R [Transcription];


The actual alignment was detected with superfamily member COG0557:

Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 430.68  E-value: 7.96e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 176 ELIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEATVwihgdnEENKEIILQGLKHL 253
Cdd:COG0557   39 ALKRRLRALEREGqlVKTRRGRYRLPEKLDL------------VEGRVRGHRDGFGFVIP------DDGEEDIFIPPREL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 254 NRAVHEDIVAVELLPKsqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKS 333
Cdd:COG0557  101 NGALHGDRVLVRVTKE------------DRRG------------------------RPEGRVVEILERANTRVVGRFEKE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 334 DikesRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 411
Cdd:COG0557  145 K----GFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 412 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 491
Cdd:COG0557  221 E-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDR 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 492 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDS-- 569
Cdd:COG0557  300 EARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkd 379

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 570 ---ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAk 646
Cdd:COG0557  380 eelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLANEAVA- 457

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 647 kihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLDQAE-SPTFPYLNTLLRilatRCMM 719
Cdd:COG0557  458 ---EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL----RSMK 530

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 720 QAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT--DKHKLADICKNLNFRHKMAQYA 797
Cdd:COG0557  531 QAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETERRADEA 605

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 798 QRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpnpqliYDDEIPS 863
Cdd:COG0557  606 ERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YDERRQA 669

                        730       740       750
                 ....*....|....*....|....*....|....*...
gi 190014625 864 LKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 899
Cdd:COG0557  670 LVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
 9-167 3.43e-53

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: 183.18  E-value: 3.43e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   9 KKTRAGGVMKIVREHYLRDDIGCGAPGCAACGGAHEGPAlepqpqdPASSVCPQPHYLLPDTNVLLHQI----VSAWR-- 82
Cdd:cd09862    1 KKTRRGKVVKVVREHYLRDDIPCGSELCPLCPQTNPKLL-------LLSLLSDAKHYLIPDTNVVLHQIdlleDPEITnv 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  83 --PGT-WASV-ASSLRLPGSL--------------------ETYVEQEQGENANDRNDRAIRVAAKWYNEHLKKmsadNQ 138
Cdd:cd09862   74 iiLQTvLEEVrHRSLPLYNRLrallkdprkrfyvfsnefhrETYVEREPGESPNDRNDRAIRKAAKWYQNHLAK----LG 149

                        170       180
                 ....*....|....*....|....*....
gi 190014625 139 LQVIFITNDRRNKEKAIEEGIPAFTCEEY 167
Cdd:cd09862  150 IPVVLLTDDADNREKAEEEGILALTVREY 178
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
176-899 7.96e-139

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 430.68  E-value: 7.96e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 176 ELIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEATVwihgdnEENKEIILQGLKHL 253
Cdd:COG0557   39 ALKRRLRALEREGqlVKTRRGRYRLPEKLDL------------VEGRVRGHRDGFGFVIP------DDGEEDIFIPPREL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 254 NRAVHEDIVAVELLPKsqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKS 333
Cdd:COG0557  101 NGALHGDRVLVRVTKE------------DRRG------------------------RPEGRVVEILERANTRVVGRFEKE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 334 DikesRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 411
Cdd:COG0557  145 K----GFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 412 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 491
Cdd:COG0557  221 E-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDR 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 492 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDS-- 569
Cdd:COG0557  300 EARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkd 379

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 570 ---ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAk 646
Cdd:COG0557  380 eelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLANEAVA- 457

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 647 kihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLDQAE-SPTFPYLNTLLRilatRCMM 719
Cdd:COG0557  458 ---EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL----RSMK 530

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 720 QAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT--DKHKLADICKNLNFRHKMAQYA 797
Cdd:COG0557  531 QAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETERRADEA 605

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 798 QRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpnpqliYDDEIPS 863
Cdd:COG0557  606 ERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YDERRQA 669

                        730       740       750
                 ....*....|....*....|....*....|....*...
gi 190014625 864 LKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 899
Cdd:COG0557  670 LVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
 437-761 7.15e-122

RNB domain; This domain is the catalytic domain of ribonuclease II.


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 372.39  E-value: 7.15e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  437 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 516
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  517 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 593
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  594 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 673
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  674 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 753
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302


                  ....*...
gi 190014625  754 DVIVHRLL 761
Cdd:pfam00773 303 DLIVHRQL 310
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
 177-898 3.16e-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: 358.12  E-value: 3.16e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  177 LIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEatvwIHGDNEENKEIILQGlKHLN 254
Cdd:TIGR02063  39 LRKRLRALEDDGlvKKNRRGLYALPESLKL------------VKGTVIAHRDGFGF----LRPEDDDEDDIFIPP-RQMN 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  255 RAVHEDIVAVELLPKSqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKSD 334
Cdd:TIGR02063 102 GAMHGDRVLVRITGKP-----------DGGD------------------------RFEARVIKILERANDQIVGTFYIEN 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  335 -IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 411
Cdd:TIGR02063 147 gIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  412 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 491
Cdd:TIGR02063 222 E-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDK 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  492 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQ----LRI 567
Cdd:TIGR02063 301 EALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNdiieGKD 380

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  568 DSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKK 647
Cdd:TIGR02063 381 ALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIVPRERGDAHKLIEEFMIAANETVAEH 459

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  648 IhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQA 721
Cdd:TIGR02063 460 L-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEKvKGRPEEELINTVL----LRSMQQA 534

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  722 VYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTDKH----KLADICKNLNFRHKMAQYA 797
Cdd:TIGR02063 535 KY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREyleaKLEEIAEHSSKTERRADEA 610

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  798 QRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFFeeKDKPNPQLIYDDEIPSLKIEDT- 869
Cdd:TIGR02063 611 ERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI--STLKDDYYVFDEKGLALVGERTg 681

                         730       740       750
                  ....*....|....*....|....*....|
gi 190014625  870 -VFHVFDKVKVKIMldSSNLQHQKIRMSLV 898
Cdd:TIGR02063 682 kVFRLGDRVKVRVV--KADLDTGKIDFELV 709
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
437-766 1.93e-104

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 325.76  E-value: 1.93e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   437 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 516
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   517 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 595
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   596 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 674
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   675 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 753
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272

                          330
                   ....*....|...
gi 190014625   754 DVIVHRLLAVAIG 766
Cdd:smart00955 273 DLIVHRQLKAALR 285
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
 9-167 3.43e-53

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: 183.18  E-value: 3.43e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   9 KKTRAGGVMKIVREHYLRDDIGCGAPGCAACGGAHEGPAlepqpqdPASSVCPQPHYLLPDTNVLLHQI----VSAWR-- 82
Cdd:cd09862    1 KKTRRGKVVKVVREHYLRDDIPCGSELCPLCPQTNPKLL-------LLSLLSDAKHYLIPDTNVVLHQIdlleDPEITnv 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  83 --PGT-WASV-ASSLRLPGSL--------------------ETYVEQEQGENANDRNDRAIRVAAKWYNEHLKKmsadNQ 138
Cdd:cd09862   74 iiLQTvLEEVrHRSLPLYNRLrallkdprkrfyvfsnefhrETYVEREPGESPNDRNDRAIRKAAKWYQNHLAK----LG 149

                        170       180
                 ....*....|....*....|....*....
gi 190014625 139 LQVIFITNDRRNKEKAIEEGIPAFTCEEY 167
Cdd:cd09862  150 IPVVLLTDDADNREKAEEEGILALTVREY 178
PRK11642 PRK11642
ribonuclease R;
384-759 1.98e-48

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 185.33  E-value: 1.98e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 384 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 463
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 464 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 541
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 542 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 613
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 614 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 688
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 190014625 689 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 759
Cdd:PRK11642 514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 103-163 1.33e-07

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: 51.47  E-value: 1.33e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 190014625  103 VEQEQGENANDRNDRAIRVAAKWYNEHLKKMsadnqlQVIFITNDRRNKEKAIEEGIPAFT 163
Cdd:pfam13638  75 LDERLPPDPFDKNDNRILAVALYLKEELPDR------PVILVSKDINLRIKADALGIPAED 129
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
176-899 7.96e-139

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 430.68  E-value: 7.96e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 176 ELIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEATVwihgdnEENKEIILQGLKHL 253
Cdd:COG0557   39 ALKRRLRALEREGqlVKTRRGRYRLPEKLDL------------VEGRVRGHRDGFGFVIP------DDGEEDIFIPPREL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 254 NRAVHEDIVAVELLPKsqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKS 333
Cdd:COG0557  101 NGALHGDRVLVRVTKE------------DRRG------------------------RPEGRVVEILERANTRVVGRFEKE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 334 DikesRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 411
Cdd:COG0557  145 K----GFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 412 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 491
Cdd:COG0557  221 E-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDR 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 492 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDS-- 569
Cdd:COG0557  300 EARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkd 379

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 570 ---ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAk 646
Cdd:COG0557  380 eelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLANEAVA- 457

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 647 kihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLDQAE-SPTFPYLNTLLRilatRCMM 719
Cdd:COG0557  458 ---EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL----RSMK 530

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 720 QAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT--DKHKLADICKNLNFRHKMAQYA 797
Cdd:COG0557  531 QAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETERRADEA 605

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 798 QRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpnpqliYDDEIPS 863
Cdd:COG0557  606 ERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YDERRQA 669

                        730       740       750
                 ....*....|....*....|....*....|....*...
gi 190014625 864 LKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 899
Cdd:COG0557  670 LVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
 437-761 7.15e-122

RNB domain; This domain is the catalytic domain of ribonuclease II.


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 372.39  E-value: 7.15e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  437 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 516
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  517 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 593
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  594 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 673
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  674 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 753
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302


                  ....*...
gi 190014625  754 DVIVHRLL 761
Cdd:pfam00773 303 DLIVHRQL 310
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
 177-898 3.16e-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: 358.12  E-value: 3.16e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  177 LIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEatvwIHGDNEENKEIILQGlKHLN 254
Cdd:TIGR02063  39 LRKRLRALEDDGlvKKNRRGLYALPESLKL------------VKGTVIAHRDGFGF----LRPEDDDEDDIFIPP-RQMN 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  255 RAVHEDIVAVELLPKSqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKSD 334
Cdd:TIGR02063 102 GAMHGDRVLVRITGKP-----------DGGD------------------------RFEARVIKILERANDQIVGTFYIEN 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  335 -IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 411
Cdd:TIGR02063 147 gIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY 221

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  412 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 491
Cdd:TIGR02063 222 E-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDK 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  492 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQ----LRI 567
Cdd:TIGR02063 301 EALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNdiieGKD 380

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  568 DSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKK 647
Cdd:TIGR02063 381 ALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIVPRERGDAHKLIEEFMIAANETVAEH 459

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  648 IhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQA 721
Cdd:TIGR02063 460 L-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEKvKGRPEEELINTVL----LRSMQQA 534

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  722 VYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTDKH----KLADICKNLNFRHKMAQYA 797
Cdd:TIGR02063 535 KY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREyleaKLEEIAEHSSKTERRADEA 610

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  798 QRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFFeeKDKPNPQLIYDDEIPSLKIEDT- 869
Cdd:TIGR02063 611 ERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI--STLKDDYYVFDEKGLALVGERTg 681

                         730       740       750
                  ....*....|....*....|....*....|
gi 190014625  870 -VFHVFDKVKVKIMldSSNLQHQKIRMSLV 898
Cdd:TIGR02063 682 kVFRLGDRVKVRVV--KADLDTGKIDFELV 709
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
437-766 1.93e-104

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 325.76  E-value: 1.93e-104
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   437 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 516
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   517 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 595
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   596 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 674
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   675 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 753
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272

                          330
                   ....*....|...
gi 190014625   754 DVIVHRLLAVAIG 766
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 ...
 364-881 6.12e-76

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: 261.57  E-value: 6.12e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  364 EGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHL 443
Cdd:TIGR00358 122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFE-FPDGVEQQAAKLQFDVDEQAKKYREDLTDL 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  444 CICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKC 523
Cdd:TIGR00358 201 AFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNP 280

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  524 DVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAE-AQLRIDSANMNDDITT---SLRGLNKLAKILKKRRIEKGA 599
Cdd:TIGR00358 281 NEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKvNDWLENDDELQPEYETlveQLKALHQLSQALGEWRHKRGL 360

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  600 LTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEfSEHALLRKHPAPPPSNYEILVKAARSR 679
Cdd:TIGR00358 361 IDFEHPETKFIVD-EEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAEL 438

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  680 NLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLRilatRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYA 753
Cdd:TIGR00358 439 GLTLPggnaeNVTTLDGACWLREvKDRPEYEILVTRLL----RSLSQAEY----SPEPLGHFGLGLEHYAHFTSPIRRYP 510

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  754 DVIVHRLLAVAIGADCTYPELTD-KHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKG-------IVSEEAYILFV 825
Cdd:TIGR00358 511 DLTNHRLIKAVLAKEQTDTERYQpQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVgtefsgeISSVTRFGMFV 590

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  826 R--KNAIVVLIPKYGLegtvffeekdkPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKI 881
Cdd:TIGR00358 591 RldDNGIDGLIHISTL-----------HNDYYVFDQEKMALIGKGTgkVYRIGDRVTVKL 639
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
 9-167 3.43e-53

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: 183.18  E-value: 3.43e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625   9 KKTRAGGVMKIVREHYLRDDIGCGAPGCAACGGAHEGPAlepqpqdPASSVCPQPHYLLPDTNVLLHQI----VSAWR-- 82
Cdd:cd09862    1 KKTRRGKVVKVVREHYLRDDIPCGSELCPLCPQTNPKLL-------LLSLLSDAKHYLIPDTNVVLHQIdlleDPEITnv 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  83 --PGT-WASV-ASSLRLPGSL--------------------ETYVEQEQGENANDRNDRAIRVAAKWYNEHLKKmsadNQ 138
Cdd:cd09862   74 iiLQTvLEEVrHRSLPLYNRLrallkdprkrfyvfsnefhrETYVEREPGESPNDRNDRAIRKAAKWYQNHLAK----LG 149

                        170       180
                 ....*....|....*....|....*....
gi 190014625 139 LQVIFITNDRRNKEKAIEEGIPAFTCEEY 167
Cdd:cd09862  150 IPVVLLTDDADNREKAEEEGILALTVREY 178
PRK11642 PRK11642
ribonuclease R;
384-759 1.98e-48

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 185.33  E-value: 1.98e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 384 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 463
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 464 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 541
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 542 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 613
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 614 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 688
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 190014625 689 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 759
Cdd:PRK11642 514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
Rnb COG4776
Exoribonuclease II [Transcription];
402-799 3.22e-39

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 155.40  E-value: 3.22e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 402 VLLLEHDVPHQPfsqavlsflPKMP--WSItEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 479
Cdd:COG4776  163 VTLARHNLEREA---------PEGDdeWEL-LDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADP 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 480 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 558
Cdd:COG4776  233 TAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGdDIEFFAAWIRSKAKL 312

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 559 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVE 634
Cdd:COG4776  313 AYDNVSDWLEGKGewqpENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELD-EKGNVLDIHAEPRRIANRIVE 391

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 635 EFMLLANISVAKKIHEE-----FSEHALLRkhpappPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESPtf 703
Cdd:COG4776  392 EAMIAANICAARVLREHlgfgiFNVHSGFD------PEKLEQAVELLAEHGIEFDPEQLLTLEgfcalrRELDAQPTS-- 463

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 704 pYLNTLLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklAD 782
Cdd:COG4776  464 -YLDSRLRRFQTFAEISTE---PG-----PHFGLGLDAYATWTSPIRKYGDMVNHRLIkAVILGQPAEKPD-------EE 527

                        410
                 ....*....|....*..
gi 190014625 783 ICKNLNFRHKMAQYAQR 799
Cdd:COG4776  528 LTERLAERRRLNRMAER 544
PRK05054 PRK05054
exoribonuclease II; Provisional
 402-794 2.34e-37

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 149.64  E-value: 2.34e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 402 VLLLEHDVPHQPfsqavlsflPKM--PWSITEKDMKnREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 479
Cdd:PRK05054 163 VTLARHNLEREA---------PAGgvAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADP 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 480 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 558
Cdd:PRK05054 233 TAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEdDIRFFAAWIESKAKL 312

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 559 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMdSETHDPIDLQTKELRETNSMVE 634
Cdd:PRK05054 313 AYDNVSDWLENGGdwqpESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFEL-GEKGEVLDIVAEPRRIANRIVE 391

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 635 EFMLLANISVAKKIHEEFsEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESptfPYLNT 708
Cdd:PRK05054 392 ESMIAANICAARVLRDKL-GFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEgfcklrRELDAQPT---GYLDS 467

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625 709 LLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklADICKNL 787
Cdd:PRK05054 468 RIRRFQSFAEISTE---PG-----PHFGLGLEAYATWTSPIRKYGDMINHRLLkAVIKGETAERPQ-------DEITVQL 532

                        410
                 ....*....|
gi 190014625 788 NFR---HKMA 794
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 ...
 342-408 3.06e-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: 102.69  E-value: 3.06e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 190014625  342 LFTPADKRIPRIRIETRQA--------STLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHD 408
Cdd:pfam17849   3 LFVPRDKRIPRIRIPTKSApeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
Rrp44_S1 pfam17215
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ...
 816-895 3.17e-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: 71.79  E-value: 3.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  816 VSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTV------FHVFDKVKVKIM--LDSSN 887
Cdd:pfam17215   1 SEEEGYVIKVFNNGIVVFVPKFGIEGLIRLEDLTGDEPEAEFDADEYSLTFPDKGsgkkrtVGVFDKVRVRVKsvKDENT 80


                  ....*...
gi 190014625  888 lQHQKIRM 895
Cdd:pfam17215  81 -GKRKVKL 87
Rrp44_CSD1 pfam17216
Rrp44-like cold shock domain;
198-283 1.89e-13

Rrp44-like cold shock domain;


Pssm-ID: 375054  Cd Length: 148  Bit Score: 68.64  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  198 FSEHLPLSKLQQGIKSGTYLQGTFRASRENYLEATVWIhgdNEENKEIILQGLKHLNRAVHEDIVAVELLPKSQWVAPSS 277
Cdd:pfam17216   4 FPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSL---PRFSKPVLIVGQKNLNRAFNGDQVIVELLPQSEWKAPSS 80


                  ....*.
gi 190014625  278 VVLHDE 283
Cdd:pfam17216  81 IVLDSE 86
PIN_4 pfam13638
PIN domain; Members of this family of bacterial domains are predicted to be RNases (from ...
 103-163 1.33e-07

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: 51.47  E-value: 1.33e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 190014625  103 VEQEQGENANDRNDRAIRVAAKWYNEHLKKMsadnqlQVIFITNDRRNKEKAIEEGIPAFT 163
Cdd:pfam13638  75 LDERLPPDPFDKNDNRILAVALYLKEELPDR------PVILVSKDINLRIKADALGIPAED 129
CSD2 pfam17876
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ...
 344-411 7.20e-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: 44.69  E-value: 7.20e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190014625  344 TPADKRIPR-IRIETRQASTL-EGRRIIVAIDGWPrNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 411
Cdd:pfam17876   3 VPDDKRIPQdIFIPKEDLKGAkDGDKVVVEITEYP-DGKNPEGKIVEVLGDPGDPGVEILSIIRKHGLPH 71
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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