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Conserved domains on  [gi|1021589312|ref|NP_001310865|]
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DIS3-like exonuclease 1 isoform 2 [Homo sapiens]

Protein Classification

RRP44/DIS3 family exonuclease( domain architecture ID 13212596)

RRP44/DIS3 family exonuclease 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; the exosome is a conserved macromolecular complex responsible for many RNA-processing and RNA-degradation reactions

EC:  3.1.-.-
Gene Ontology:  GO:0004540|GO:0003723|GO:0000175

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
VacB super family cl43181
Exoribonuclease R [Transcription];
155-783 2.77e-106

Exoribonuclease R [Transcription];


The actual alignment was detected with superfamily member COG0557:

Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 346.32  E-value: 2.77e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 155 IKSGRY--------IQGILNVNKHRaqiEAFVRLQgasskdsDLVSDILIHGmKARNRSIHGDVVVVELLPKNEwKGRtv 226
Cdd:COG0557    56 TRRGRYrlpekldlVEGRVRGHRDG---FGFVIPD-------DGEEDIFIPP-RELNGALHGDRVLVRVTKEDR-RGR-- 121
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 227 alcendcddkasgespsepmPTGRVVGILQKNWRDYVVTFpskeeVQSQGKNaqkiLVTPWDYRIPK-IRISTQQAETLQ 305
Cdd:COG0557   122 --------------------PEGRVVEILERANTRVVGRF-----EKEKGFG----FVVPDDKRLLQdIFIPPDDLNGAK 172
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 306 D-FRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSISVIpFSEAQMCEmpvnTPESPWKVSPEEEQKRKD 384
Cdd:COG0557   173 DgDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAE----AEALPDEVPEADLKGRRD 247
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 385 LRKSHLVfSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLSADL 464
Cdd:COG0557   248 LRDLPLV-TIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGL 326
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 465 CSLLGGVDRYAVSIMWELDKASyEIKKVWYGRTIIRSAYKLFYEAAQELLDGNlsvvddipefkdldEKSRQAKLEELVW 544
Cdd:COG0557   327 CSLNPGEDRLAMSCEMEIDAKG-EVVSYEFYRSVIRSDARLTYEEVQAILDGK--------------DEELREEYADLVP 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 545 AIGKLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKI-WESFPhqALL 623
Cdd:COG0557   392 MLEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLeKLKLP--FLY 469
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 624 RQHPPPHQEFFSELRECAKAKGFFI---DTRSNKTLADSLDNAND-PHDPIVNR-LLRSMAtQAMsnalYfstgscAEEE 698
Cdd:COG0557   470 RVHEEPDPEKLEALREFLANLGLKLkggDEPTPKDLQKLLEQVKGrPEEELLNTlLLRSMK-QAV----Y------SPEN 538
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 699 FHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKGNLfsNKDLEELCRHINNRNQAAQHSQKQSTELFQCM 778
Cdd:COG0557   539 IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKRSPGLQEYL--EEELEEIAEHCSETERRADEAERDVVDLKKAE 616

                  ....*
gi 1021589312 779 YFKDK 783
Cdd:COG0557   617 YMKDR 621
PIN_SF super family cl28905
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
1-105 1.49e-32

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN 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 while some others lack several of these key catalytic residues. 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. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


The actual alignment was detected with superfamily member cd09862:

Pssm-ID: 475124  Cd Length: 178  Bit Score: 124.62  E-value: 1.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312   1 MQTACQAVQHqRGRRQYNKLRNLLKDARHDCILFANEFQQCCYLPRERGESMEKWQTRSIYNAAVWYYHHCQD-RMPIVM 79
Cdd:cd09862    76 LQTVLEEVRH-RSLPLYNRLRALLKDPRKRFYVFSNEFHRETYVEREPGESPNDRNDRAIRKAAKWYQNHLAKlGIPVVL 154
                          90       100
                  ....*....|....*....|....*.
gi 1021589312  80 VTEDEEAIQQYgsETEGVFVITFKNY 105
Cdd:cd09862   155 LTDDADNREKA--EEEGILALTVREY 178
Rrp44_S1 super family cl25439
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ...
798-873 1.45e-05

S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44.


The actual alignment was detected with superfamily member pfam17215:

Pssm-ID: 435792  Cd Length: 87  Bit Score: 44.06  E-value: 1.45e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1021589312 798 YSIRT--NGVLLFIPRFGIKGAAYLKNKDGLVIScgpdscSEWKPgslQRFQNKITSTTTdGESVTFHLFDHVTVRIS 873
Cdd:pfam17215   6 YVIKVfnNGIVVFVPKFGIEGLIRLEDLTGDEPE------AEFDA---DEYSLTFPDKGS-GKKRTVGVFDKVRVRVK 73
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
155-783 2.77e-106

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 346.32  E-value: 2.77e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 155 IKSGRY--------IQGILNVNKHRaqiEAFVRLQgasskdsDLVSDILIHGmKARNRSIHGDVVVVELLPKNEwKGRtv 226
Cdd:COG0557    56 TRRGRYrlpekldlVEGRVRGHRDG---FGFVIPD-------DGEEDIFIPP-RELNGALHGDRVLVRVTKEDR-RGR-- 121
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 227 alcendcddkasgespsepmPTGRVVGILQKNWRDYVVTFpskeeVQSQGKNaqkiLVTPWDYRIPK-IRISTQQAETLQ 305
Cdd:COG0557   122 --------------------PEGRVVEILERANTRVVGRF-----EKEKGFG----FVVPDDKRLLQdIFIPPDDLNGAK 172
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 306 D-FRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSISVIpFSEAQMCEmpvnTPESPWKVSPEEEQKRKD 384
Cdd:COG0557   173 DgDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAE----AEALPDEVPEADLKGRRD 247
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 385 LRKSHLVfSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLSADL 464
Cdd:COG0557   248 LRDLPLV-TIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGL 326
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 465 CSLLGGVDRYAVSIMWELDKASyEIKKVWYGRTIIRSAYKLFYEAAQELLDGNlsvvddipefkdldEKSRQAKLEELVW 544
Cdd:COG0557   327 CSLNPGEDRLAMSCEMEIDAKG-EVVSYEFYRSVIRSDARLTYEEVQAILDGK--------------DEELREEYADLVP 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 545 AIGKLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKI-WESFPhqALL 623
Cdd:COG0557   392 MLEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLeKLKLP--FLY 469
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 624 RQHPPPHQEFFSELRECAKAKGFFI---DTRSNKTLADSLDNAND-PHDPIVNR-LLRSMAtQAMsnalYfstgscAEEE 698
Cdd:COG0557   470 RVHEEPDPEKLEALREFLANLGLKLkggDEPTPKDLQKLLEQVKGrPEEELLNTlLLRSMK-QAV----Y------SPEN 538
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 699 FHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKGNLfsNKDLEELCRHINNRNQAAQHSQKQSTELFQCM 778
Cdd:COG0557   539 IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKRSPGLQEYL--EEELEEIAEHCSETERRADEAERDVVDLKKAE 616

                  ....*
gi 1021589312 779 YFKDK 783
Cdd:COG0557   617 YMKDR 621
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
382-732 3.71e-102

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 321.93  E-value: 3.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 382 RKDLRKShLVFSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLS 461
Cdd:pfam00773   1 RKDLRDL-PFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLS 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 462 ADLCSLLGGVDRYAVSIMWELDKaSYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNLSVVDDIPEFKDLDEksrqaklee 541
Cdd:pfam00773  80 NDLCSLNPGEDRLALSVEITIDA-DGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKPDLAEDLRL--------- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 542 lvwaigkLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIhDLIPKQPLEVHETVAECMILANHWVAKKIwESFPHQA 621
Cdd:pfam00773 150 -------LYELAKILRAKRLQRGALDLDTPENKLILDEEGVI-DILIQERTDAHSLIEEFMLLANEAVARHL-QELGIPA 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 622 LLRQHPPPHQEFFSELRECAKAKgffidtRSNKTLADSLDNANDPhdpivNRLLRSMATQAMSNALYFStgscaeEEFHH 701
Cdd:pfam00773 221 LYRVHPEPDLEKLNSLIKLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYSP------EPLGH 283
                         330       340       350
                  ....*....|....*....|....*....|.
gi 1021589312 702 YGLALDKYTHFTSPIRRYSDIVVHRLLMAAI 732
Cdd:pfam00773 284 FGLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
382-734 3.51e-97

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 307.66  E-value: 3.51e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  382 RKDLRkSHLVFSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLS 461
Cdd:smart00955   1 RVDLR-DLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELS 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  462 ADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYGRTIIRSAYKLFYEAAQELLDGnlsvvddipefkdldeksrqaklee 541
Cdd:smart00955  80 NGLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSKARLTYEEVDAILEK------------------------- 134
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  542 lvwaigkltdiarhvrakrdgcgalelegvevcVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKIWESFPhQA 621
Cdd:smart00955 135 ---------------------------------IVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGI-PG 180
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  622 LLRQHPPPHQEFFSE-LRECAKAKGFFI-DTRSNKTLADSLDNANDPHDpivNRLLRSMATQAMSNALYFSTGScaeeef 699
Cdd:smart00955 181 LYRVHEGPDPEKLAElLKEFLALLGLLLlGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNS------ 251
                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1021589312  700 HHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISK 734
Cdd:smart00955 252 GHFGLALDAYTHFTSPIRRYPDLIVHRQLKAALRG 286
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
202-816 1.75e-92

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: 309.20  E-value: 1.75e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 202 RNRSIHGDVVVVELLPKNEWKGRtvalcendcddkasgespsepmPTGRVVGILQKNWRDYVVTFpsKEEvqsqgkNAQK 281
Cdd:TIGR02063 100 MNGAMHGDRVLVRITGKPDGGDR----------------------FEARVIKILERANDQIVGTF--YIE------NGIG 149
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 282 ILVtPWDYRIP-KIRISTQQAETLQD-FRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSIsVIPFSEAQ 359
Cdd:TIGR02063 150 FVI-PDDKRIYlDIFIPPEQILGAEEgDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGI-PYEFPEEV 227
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 360 MCEmpvnTPESPWKVSPEEEQKRKDLRKShLVFSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEA 439
Cdd:TIGR02063 228 LDE----AAKIPEEVPEEEIKGRKDLRDL-PFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEA 302
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 440 RTRATTYYLADRRYDMLPSVLSADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYgRTIIRSAYKLFYEAAQELLDGNls 519
Cdd:TIGR02063 303 LKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFY-EAVINSHARLTYNQVNDIIEGK-- 379
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 520 vvddipefKDLDEKsrQAKLEELVWAIGKLTDIARHVRAKRdgcGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVA 599
Cdd:TIGR02063 380 --------DALDKK--EPPLKEMLKNLFELYKILRKKRKKR---GAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIE 446
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 600 ECMILANHWVAKKIwESFPHQALLRQHPPPHQE----FFSELRECA-KAKGFFIDTRSNKTLADSL-DNANDPHDPIVNR 673
Cdd:TIGR02063 447 EFMIAANETVAEHL-EKAKLPFIYRVHERPSEEklqnLREFLKTLGiTLKGGTSDKPQPKDFQKLLeKVKGRPEEELINT 525
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 674 -LLRSMAtQAMsnalyFSTgscaeEEFHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKK-MEIKGNLFSNKDLE 751
Cdd:TIGR02063 526 vLLRSMQ-QAK-----YSP-----ENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENtTTEKEREYLEAKLE 594
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1021589312 752 ELCRHINNRNQAAQHSQKQSTELFQCMYFKDKdpateERCISDGVIYSIRTNGVLLFIPRFGIKG 816
Cdd:TIGR02063 595 EIAEHSSKTERRADEAERDVNDWKKAEYMSEK-----IGEEFEGVISGVTSFGLFVELENNTIEG 654
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
1-105 1.49e-32

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: 124.62  E-value: 1.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312   1 MQTACQAVQHqRGRRQYNKLRNLLKDARHDCILFANEFQQCCYLPRERGESMEKWQTRSIYNAAVWYYHHCQD-RMPIVM 79
Cdd:cd09862    76 LQTVLEEVRH-RSLPLYNRLRALLKDPRKRFYVFSNEFHRETYVEREPGESPNDRNDRAIRKAAKWYQNHLAKlGIPVVL 154
                          90       100
                  ....*....|....*....|....*.
gi 1021589312  80 VTEDEEAIQQYgsETEGVFVITFKNY 105
Cdd:cd09862   155 LTDDADNREKA--EEEGILALTVREY 178
PRK11642 PRK11642
ribonuclease R;
339-736 5.34e-32

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 134.49  E-value: 5.34e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 339 GEIATILVEN---SISV--------IPFS-----EAQMCEMPVNTPEspwkvspEEEQKRKDLRKSHLVfSIDPKGCEDV 402
Cdd:PRK11642  208 GKIVEVLGDNmgtGMAVdialrtheIPYIwpqavEQQVAGLKEEVPE-------EAKAGRVDLRDLPLV-TIDGEDARDF 279
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 403 DDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLSADLCSLLGGVDR------YAV 476
Cdd:PRK11642  280 DDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRlcmvceMTI 359
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 477 SIMWELdkASYEikkvwYGRTIIRSAYKLFYEAAQELLDGNLSVVDDI-PEFKDLDEksrqakLEELVwaigKLTDIARH 555
Cdd:PRK11642  360 SSKGRL--TGYK-----FYEAVMSSHARLTYTKVWHILQGDQDLREQYaPLVKHLEE------LHNLY----KVLDKARE 422
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 556 VRakrdgcGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKIwESFPHQALLRQHPPPHQEFFS 635
Cdd:PRK11642  423 ER------GGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEAIT 495
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 636 ELRECAKAKGFFI---DTRSNKTLADSLDNANDPHDpivNRLLRSMATQAMSNALYfstgscAEEEFHHYGLALDKYTHF 712
Cdd:PRK11642  496 SFRSVLAELGLELpggNKPEPRDYAELLESVADRPD---AEMLQTMLLRSMKQAIY------DPENRGHFGLALQSYAHF 566
                         410       420
                  ....*....|....*....|....
gi 1021589312 713 TSPIRRYSDIVVHRLLMAAISKDK 736
Cdd:PRK11642  567 TSPIRRYPDLSLHRAIKYLLAKEQ 590
Rrp44_S1 pfam17215
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ...
798-873 1.45e-05

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: 44.06  E-value: 1.45e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1021589312 798 YSIRT--NGVLLFIPRFGIKGAAYLKNKDGLVIScgpdscSEWKPgslQRFQNKITSTTTdGESVTFHLFDHVTVRIS 873
Cdd:pfam17215   6 YVIKVfnNGIVVFVPKFGIEGLIRLEDLTGDEPE------AEFDA---DEYSLTFPDKGS-GKKRTVGVFDKVRVRVK 73
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
155-783 2.77e-106

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 346.32  E-value: 2.77e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 155 IKSGRY--------IQGILNVNKHRaqiEAFVRLQgasskdsDLVSDILIHGmKARNRSIHGDVVVVELLPKNEwKGRtv 226
Cdd:COG0557    56 TRRGRYrlpekldlVEGRVRGHRDG---FGFVIPD-------DGEEDIFIPP-RELNGALHGDRVLVRVTKEDR-RGR-- 121
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 227 alcendcddkasgespsepmPTGRVVGILQKNWRDYVVTFpskeeVQSQGKNaqkiLVTPWDYRIPK-IRISTQQAETLQ 305
Cdd:COG0557   122 --------------------PEGRVVEILERANTRVVGRF-----EKEKGFG----FVVPDDKRLLQdIFIPPDDLNGAK 172
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 306 D-FRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSISVIpFSEAQMCEmpvnTPESPWKVSPEEEQKRKD 384
Cdd:COG0557   173 DgDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAE----AEALPDEVPEADLKGRRD 247
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 385 LRKSHLVfSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLSADL 464
Cdd:COG0557   248 LRDLPLV-TIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGL 326
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 465 CSLLGGVDRYAVSIMWELDKASyEIKKVWYGRTIIRSAYKLFYEAAQELLDGNlsvvddipefkdldEKSRQAKLEELVW 544
Cdd:COG0557   327 CSLNPGEDRLAMSCEMEIDAKG-EVVSYEFYRSVIRSDARLTYEEVQAILDGK--------------DEELREEYADLVP 391
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 545 AIGKLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKI-WESFPhqALL 623
Cdd:COG0557   392 MLEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLeKLKLP--FLY 469
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 624 RQHPPPHQEFFSELRECAKAKGFFI---DTRSNKTLADSLDNAND-PHDPIVNR-LLRSMAtQAMsnalYfstgscAEEE 698
Cdd:COG0557   470 RVHEEPDPEKLEALREFLANLGLKLkggDEPTPKDLQKLLEQVKGrPEEELLNTlLLRSMK-QAV----Y------SPEN 538
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 699 FHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKGNLfsNKDLEELCRHINNRNQAAQHSQKQSTELFQCM 778
Cdd:COG0557   539 IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKRSPGLQEYL--EEELEEIAEHCSETERRADEAERDVVDLKKAE 616

                  ....*
gi 1021589312 779 YFKDK 783
Cdd:COG0557   617 YMKDR 621
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
382-732 3.71e-102

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 321.93  E-value: 3.71e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 382 RKDLRKShLVFSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLS 461
Cdd:pfam00773   1 RKDLRDL-PFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLS 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 462 ADLCSLLGGVDRYAVSIMWELDKaSYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNLSVVDDIPEFKDLDEksrqaklee 541
Cdd:pfam00773  80 NDLCSLNPGEDRLALSVEITIDA-DGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDKPDLAEDLRL--------- 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 542 lvwaigkLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIhDLIPKQPLEVHETVAECMILANHWVAKKIwESFPHQA 621
Cdd:pfam00773 150 -------LYELAKILRAKRLQRGALDLDTPENKLILDEEGVI-DILIQERTDAHSLIEEFMLLANEAVARHL-QELGIPA 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 622 LLRQHPPPHQEFFSELRECAKAKgffidtRSNKTLADSLDNANDPhdpivNRLLRSMATQAMSNALYFStgscaeEEFHH 701
Cdd:pfam00773 221 LYRVHPEPDLEKLNSLIKLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYSP------EPLGH 283
                         330       340       350
                  ....*....|....*....|....*....|.
gi 1021589312 702 YGLALDKYTHFTSPIRRYSDIVVHRLLMAAI 732
Cdd:pfam00773 284 FGLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
382-734 3.51e-97

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 307.66  E-value: 3.51e-97
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  382 RKDLRkSHLVFSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLS 461
Cdd:smart00955   1 RVDLR-DLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELS 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  462 ADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYGRTIIRSAYKLFYEAAQELLDGnlsvvddipefkdldeksrqaklee 541
Cdd:smart00955  80 NGLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSKARLTYEEVDAILEK------------------------- 134
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  542 lvwaigkltdiarhvrakrdgcgalelegvevcVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKIWESFPhQA 621
Cdd:smart00955 135 ---------------------------------IVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGI-PG 180
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312  622 LLRQHPPPHQEFFSE-LRECAKAKGFFI-DTRSNKTLADSLDNANDPHDpivNRLLRSMATQAMSNALYFSTGScaeeef 699
Cdd:smart00955 181 LYRVHEGPDPEKLAElLKEFLALLGLLLlGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNS------ 251
                          330       340       350
                   ....*....|....*....|....*....|....*
gi 1021589312  700 HHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISK 734
Cdd:smart00955 252 GHFGLALDAYTHFTSPIRRYPDLIVHRQLKAALRG 286
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
202-816 1.75e-92

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: 309.20  E-value: 1.75e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 202 RNRSIHGDVVVVELLPKNEWKGRtvalcendcddkasgespsepmPTGRVVGILQKNWRDYVVTFpsKEEvqsqgkNAQK 281
Cdd:TIGR02063 100 MNGAMHGDRVLVRITGKPDGGDR----------------------FEARVIKILERANDQIVGTF--YIE------NGIG 149
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 282 ILVtPWDYRIP-KIRISTQQAETLQD-FRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSIsVIPFSEAQ 359
Cdd:TIGR02063 150 FVI-PDDKRIYlDIFIPPEQILGAEEgDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGI-PYEFPEEV 227
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 360 MCEmpvnTPESPWKVSPEEEQKRKDLRKShLVFSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEA 439
Cdd:TIGR02063 228 LDE----AAKIPEEVPEEEIKGRKDLRDL-PFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEA 302
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 440 RTRATTYYLADRRYDMLPSVLSADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYgRTIIRSAYKLFYEAAQELLDGNls 519
Cdd:TIGR02063 303 LKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFY-EAVINSHARLTYNQVNDIIEGK-- 379
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 520 vvddipefKDLDEKsrQAKLEELVWAIGKLTDIARHVRAKRdgcGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVA 599
Cdd:TIGR02063 380 --------DALDKK--EPPLKEMLKNLFELYKILRKKRKKR---GAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIE 446
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 600 ECMILANHWVAKKIwESFPHQALLRQHPPPHQE----FFSELRECA-KAKGFFIDTRSNKTLADSL-DNANDPHDPIVNR 673
Cdd:TIGR02063 447 EFMIAANETVAEHL-EKAKLPFIYRVHERPSEEklqnLREFLKTLGiTLKGGTSDKPQPKDFQKLLeKVKGRPEEELINT 525
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 674 -LLRSMAtQAMsnalyFSTgscaeEEFHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKK-MEIKGNLFSNKDLE 751
Cdd:TIGR02063 526 vLLRSMQ-QAK-----YSP-----ENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENtTTEKEREYLEAKLE 594
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1021589312 752 ELCRHINNRNQAAQHSQKQSTELFQCMYFKDKdpateERCISDGVIYSIRTNGVLLFIPRFGIKG 816
Cdd:TIGR02063 595 EIAEHSSKTERRADEAERDVNDWKKAEYMSEK-----IGEEFEGVISGVTSFGLFVELENNTIEG 654
3_prime_RNase TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
203-828 7.88e-60

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: 216.89  E-value: 7.88e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 203 NRSIHGDVVVVellpknewkgrtvalCENDCDDKASGEspsepmptGRVVGILQKNWRDYVVTFPSKeevqsqgKNAQKI 282
Cdd:TIGR00358  49 KKVMHGDLVEA---------------CPLSQPQRGRFE--------AEVERILEPALTRFVGKFLGE-------NDFGFV 98
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 283 LV-TPWDYRIPKIRISTQQAETLQDFRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENSISVIPFS--EAQ 359
Cdd:TIGR00358  99 VPdDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFEFPDgvEQQ 178
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 360 MCEMPVNTPESPWKVspeeeqkRKDLRKSHLVfSIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEA 439
Cdd:TIGR00358 179 AAKLQFDVDEQAKKY-------REDLTDLAFV-TIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEA 250
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 440 RTRATTYYLADRRYDMLPSVLSADLCSLLGGVDRYAVSIMWELD-KASYEIKKVwYGRTIIRSAyKLFYeaaqelldgnl 518
Cdd:TIGR00358 251 KHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISaQGRITDNEF-YPATIESKA-RLTY----------- 317
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 519 SVVDDIPEFKDlDEKSRQAKLEELVWAIGKLTDIARHVRAKRdgcGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETV 598
Cdd:TIGR00358 318 DKVNDWLENDD-ELQPEYETLVEQLKALHQLSQALGEWRHKR---GLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKII 393
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 599 AECMILANHWVAKKIWESFPHqALLRQHPPPHQEFFSELRECAKAKG-----FFIDTRSNKTLADSLDNAND--PHDPIV 671
Cdd:TIGR00358 394 EEAMIVANICAARFLHNHKVP-GIYRVHPGPSKKKLQSLLEFLAELGltlpgGNAENVTTLDGACWLREVKDrpEYEILV 472
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 672 NRLLRSmatqaMSNALYFStgscaeEEFHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEikGNLFSNKDLE 751
Cdd:TIGR00358 473 TRLLRS-----LSQAEYSP------EPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDT--ERYQPQDELL 539
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 752 ELCRHINNRNQAAQHSQKQSTELFQCMYFKDKDPATEERCISD----GVIYSIRTNGVLLFIPRFGIKGAAYLKNKDGLV 827
Cdd:TIGR00358 540 QIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSvtrfGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMA 619

                  .
gi 1021589312 828 I 828
Cdd:TIGR00358 620 L 620
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
1-105 1.49e-32

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: 124.62  E-value: 1.49e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312   1 MQTACQAVQHqRGRRQYNKLRNLLKDARHDCILFANEFQQCCYLPRERGESMEKWQTRSIYNAAVWYYHHCQD-RMPIVM 79
Cdd:cd09862    76 LQTVLEEVRH-RSLPLYNRLRALLKDPRKRFYVFSNEFHRETYVEREPGESPNDRNDRAIRKAAKWYQNHLAKlGIPVVL 154
                          90       100
                  ....*....|....*....|....*.
gi 1021589312  80 VTEDEEAIQQYgsETEGVFVITFKNY 105
Cdd:cd09862   155 LTDDADNREKA--EEEGILALTVREY 178
PRK11642 PRK11642
ribonuclease R;
339-736 5.34e-32

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 134.49  E-value: 5.34e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 339 GEIATILVEN---SISV--------IPFS-----EAQMCEMPVNTPEspwkvspEEEQKRKDLRKSHLVfSIDPKGCEDV 402
Cdd:PRK11642  208 GKIVEVLGDNmgtGMAVdialrtheIPYIwpqavEQQVAGLKEEVPE-------EAKAGRVDLRDLPLV-TIDGEDARDF 279
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 403 DDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVLSADLCSLLGGVDR------YAV 476
Cdd:PRK11642  280 DDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRlcmvceMTI 359
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 477 SIMWELdkASYEikkvwYGRTIIRSAYKLFYEAAQELLDGNLSVVDDI-PEFKDLDEksrqakLEELVwaigKLTDIARH 555
Cdd:PRK11642  360 SSKGRL--TGYK-----FYEAVMSSHARLTYTKVWHILQGDQDLREQYaPLVKHLEE------LHNLY----KVLDKARE 422
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 556 VRakrdgcGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAKKIwESFPHQALLRQHPPPHQEFFS 635
Cdd:PRK11642  423 ER------GGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEAIT 495
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 636 ELRECAKAKGFFI---DTRSNKTLADSLDNANDPHDpivNRLLRSMATQAMSNALYfstgscAEEEFHHYGLALDKYTHF 712
Cdd:PRK11642  496 SFRSVLAELGLELpggNKPEPRDYAELLESVADRPD---AEMLQTMLLRSMKQAIY------DPENRGHFGLALQSYAHF 566
                         410       420
                  ....*....|....*....|....
gi 1021589312 713 TSPIRRYSDIVVHRLLMAAISKDK 736
Cdd:PRK11642  567 TSPIRRYPDLSLHRAIKYLLAKEQ 590
Rnb COG4776
Exoribonuclease II [Transcription];
377-873 1.21e-31

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 132.28  E-value: 1.21e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 377 EEEQKRKDLrkSHLVF-SIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDM 455
Cdd:COG4776   185 DEGLEREDL--TALPFvTIDSESTEDMDDALYIEKLENGGWKLTVAIADPTAYIPEGSELDKEARQRAFTNYLPGFNIPM 262
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 456 LPSVLSADLCSLLGGVDRYAVSIMWELDK-----ASYEIKKVWygrtiIRSAYKLFYEAAQELLDGnlsVVDDIPEFKDL 530
Cdd:COG4776   263 LPRELSDDLCSLKENEKRPALVCRVTIDAdgsigDDIEFFAAW-----IRSKAKLAYDNVSDWLEG---KGEWQPENEEI 334
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 531 DEKSRQakleelvwaigkLTDIARHVRAKRDGCGALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVA 610
Cdd:COG4776   335 AEQIRL------------LHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAA 402
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 611 KkiwesfphqaLLRQHP-----PPHQEFFSELRECAKA-----------------KGF-----FIDTRSNKTLaDSldna 663
Cdd:COG4776   403 R----------VLREHLgfgifNVHSGFDPEKLEQAVEllaehgiefdpeqlltlEGFcalrrELDAQPTSYL-DS---- 467
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 664 ndphdpivnRLLRSMATQAMSNalyfstgscaeEEFHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKkmeikgn 743
Cdd:COG4776   468 ---------RLRRFQTFAEIST-----------EPGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQP------- 520
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 744 lfSNKDLEELCRHINNRNQAAQHSQKQSTELFQCMYFKDKdpATEERCISDGVIYSIRT--------NGVLLFIPrfgik 815
Cdd:COG4776   521 --AEKPDEELTERLAERRRLNRMAERDVADWLYARYLKPK--VGSGQVFTAEIIDINRGglrvrlleNGAVAFIP----- 591
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1021589312 816 gAAYL-KNKDGLVIScgpdscseWKPGSLQrfqnkitsttTDGEsVTFHLFDHVTVRIS 873
Cdd:COG4776   592 -ASFIhSVRDELVCS--------QEEGTVY----------IKGE-VRYKLGDTIQVTLA 630
PRK05054 PRK05054
exoribonuclease II; Provisional
377-829 4.95e-24

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 108.43  E-value: 4.95e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 377 EEEQKRKDLrkSHLVF-SIDPKGCEDVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDM 455
Cdd:PRK05054  185 DEGLEREDL--TALDFvTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPM 262
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 456 LPSVLSADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNLSVVDDIPEFK----DLD 531
Cdd:PRK05054  263 LPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAeqirLLH 342
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 532 EKSrQAKLEelvWaigkltdiaRHVRAkrdgcgALELEGVEVCVQLDDKKNIHDLIPKQPLEVHETVAECMILANHWVAK 611
Cdd:PRK05054  343 QFC-LARSE---W---------RKQHA------LVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAANICAAR 403
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 612 kiwesfphqaLLRQHppphqeffselrecakaKGFFI-------DTRSNKTLADSLDNANDPHDP----------IVNRL 674
Cdd:PRK05054  404 ----------VLRDK-----------------LGFGIynvhsgfDPANAEQAVALLKEHGLHFDAeelltlegfcKLRRE 456
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 675 LRSMATQAMSNAL--YFSTGSCAEEEFHHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKgnlfsnkdlEE 752
Cdd:PRK05054  457 LDAQPTGYLDSRIrrFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ---------DE 527
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 753 LCRHINNRNQAAQHSQKQSTELFQCMYFKDKdPATEERC---ISD----GVIYSIRTNGVLLFIPrfgikgAAYL-KNKD 824
Cdd:PRK05054  528 ITVQLAERRRLNRMAERDVGDWLYARYLKDK-AGTDTRFaaeIIDisrgGMRVRLLENGAVAFIP------ASFLhAVRD 600

                  ....*
gi 1021589312 825 GLVIS 829
Cdd:PRK05054  601 ELVCN 605
OB_Dis3 pfam17849
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ...
282-349 6.06e-24

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: 96.14  E-value: 6.06e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1021589312 282 ILVTPWDYRIPKIRISTQQA--------ETLQDFRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIATILVENS 349
Cdd:pfam17849   2 VLFVPRDKRIPRIRIPTKSApeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
Rrp44_CSD1 pfam17216
Rrp44-like cold shock domain;
142-223 1.97e-06

Rrp44-like cold shock domain;


Pssm-ID: 375054  Cd Length: 148  Bit Score: 48.61  E-value: 1.97e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1021589312 142 YPEHLPLEVLEAGIKSGRYIQGILnvnkhraQIEAFVRLQGASSKDSdLVSDILIHGMKARNRSIHGDVVVVELLPKNEW 221
Cdd:pfam17216   4 FPEYYSTARVMGGLKNGVLYQGNI-------QISEYNFLEGSVSLPR-FSKPVLIVGQKNLNRAFNGDQVIVELLPQSEW 75

                  ..
gi 1021589312 222 KG 223
Cdd:pfam17216  76 KA 77
Rrp44_S1 pfam17215
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ...
798-873 1.45e-05

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: 44.06  E-value: 1.45e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1021589312 798 YSIRT--NGVLLFIPRFGIKGAAYLKNKDGLVIScgpdscSEWKPgslQRFQNKITSTTTdGESVTFHLFDHVTVRIS 873
Cdd:pfam17215   6 YVIKVfnNGIVVFVPKFGIEGLIRLEDLTGDEPE------AEFDA---DEYSLTFPDKGS-GKKRTVGVFDKVRVRVK 73
 
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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