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Conserved domains on  [gi|1016563101|ref|NP_001309278|]
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exosome complex exonuclease RRP44 isoform d [Homo sapiens]

Protein Classification

ribonuclease R family protein( domain architecture ID 1904260)

ribonuclease R (RNaseR or RNR) family protein similar to RNR, a 3'-5' exoribonuclease that releases 5'-nucleoside monophosphates and is involved in maturation of structured RNAs

EC:  3.1.-.-
Gene Ontology:  GO:0003723|GO:0004527
PubMed:  25542646
SCOP:  3000135

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
VacB super family cl43181
Exoribonuclease R [Transcription];
44-767 2.98e-139

Exoribonuclease R [Transcription];


The actual alignment was detected with superfamily member COG0557:

Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 427.99  E-value: 2.98e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  44 ELIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEATVwihgdnEENKEIILQGLKHL 121
Cdd:COG0557    39 ALKRRLRALEREGqlVKTRRGRYRLPEKLDL------------VEGRVRGHRDGFGFVIP------DDGEEDIFIPPREL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 122 NRAVHEDIVAVELLPKsqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKS 201
Cdd:COG0557   101 NGALHGDRVLVRVTKE------------DRRG------------------------RPEGRVVEILERANTRVVGRFEKE 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 202 DikesRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 279
Cdd:COG0557   145 K----GFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 280 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 359
Cdd:COG0557   221 E-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDR 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 360 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDS-- 437
Cdd:COG0557   300 EARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkd 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 438 ---ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAk 514
Cdd:COG0557   380 eelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLANEAVA- 457
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 515 kihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLDQAE-SPTFPYLNTLLRilatRCMM 587
Cdd:COG0557   458 ---EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL----RSMK 530
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 588 QAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT--DKHKLADICKNLNFRHKMAQYA 665
Cdd:COG0557   531 QAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETERRADEA 605
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 666 QRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpnpqliYDDEIPS 731
Cdd:COG0557   606 ERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YDERRQA 669
                         730       740       750
                  ....*....|....*....|....*....|....*...
gi 1016563101 732 LKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 767
Cdd:COG0557   670 LVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
PIN_SF super family cl28905
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
3-35 2.39e-06

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: 48.74  E-value: 2.39e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1016563101   3 ADNQLQVIFITNDRRNKEKAIEEGIPAFTCEEY 35
Cdd:cd09862   146 AKLGIPVVLLTDDADNREKAEEEGILALTVREY 178
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
44-767 2.98e-139

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 427.99  E-value: 2.98e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  44 ELIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEATVwihgdnEENKEIILQGLKHL 121
Cdd:COG0557    39 ALKRRLRALEREGqlVKTRRGRYRLPEKLDL------------VEGRVRGHRDGFGFVIP------DDGEEDIFIPPREL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 122 NRAVHEDIVAVELLPKsqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKS 201
Cdd:COG0557   101 NGALHGDRVLVRVTKE------------DRRG------------------------RPEGRVVEILERANTRVVGRFEKE 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 202 DikesRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 279
Cdd:COG0557   145 K----GFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 280 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 359
Cdd:COG0557   221 E-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDR 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 360 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDS-- 437
Cdd:COG0557   300 EARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkd 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 438 ---ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAk 514
Cdd:COG0557   380 eelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLANEAVA- 457
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 515 kihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLDQAE-SPTFPYLNTLLRilatRCMM 587
Cdd:COG0557   458 ---EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL----RSMK 530
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 588 QAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT--DKHKLADICKNLNFRHKMAQYA 665
Cdd:COG0557   531 QAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETERRADEA 605
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 666 QRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpnpqliYDDEIPS 731
Cdd:COG0557   606 ERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YDERRQA 669
                         730       740       750
                  ....*....|....*....|....*....|....*...
gi 1016563101 732 LKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 767
Cdd:COG0557   670 LVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
305-629 5.10e-122

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 369.31  E-value: 5.10e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 305 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 384
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 385 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 461
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 462 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 541
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 542 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 621
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302

                  ....*...
gi 1016563101 622 DVIVHRLL 629
Cdd:pfam00773 303 DLIVHRQL 310
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
45-766 1.53e-110

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: 353.11  E-value: 1.53e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  45 LIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEatvwIHGDNEENKEIILQGlKHLN 122
Cdd:TIGR02063  39 LRKRLRALEDDGlvKKNRRGLYALPESLKL------------VKGTVIAHRDGFGF----LRPEDDDEDDIFIPP-RQMN 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 123 RAVHEDIVAVELLPKSqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKSD 202
Cdd:TIGR02063 102 GAMHGDRVLVRITGKP-----------DGGD------------------------RFEARVIKILERANDQIVGTFYIEN 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 203 -IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 279
Cdd:TIGR02063 147 gIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY 221
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 280 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 359
Cdd:TIGR02063 222 E-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDK 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 360 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQ----LRI 435
Cdd:TIGR02063 301 EALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNdiieGKD 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 436 DSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKK 515
Cdd:TIGR02063 381 ALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIVPRERGDAHKLIEEFMIAANETVAEH 459
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 516 IhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQA 589
Cdd:TIGR02063 460 L-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEKvKGRPEEELINTVL----LRSMQQA 534
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 590 VYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTDKH----KLADICKNLNFRHKMAQYA 665
Cdd:TIGR02063 535 KY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREyleaKLEEIAEHSSKTERRADEA 610
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 666 QRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFFeeKDKPNPQLIYDDEIPSLKIEDT- 737
Cdd:TIGR02063 611 ERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI--STLKDDYYVFDEKGLALVGERTg 681
                         730       740       750
                  ....*....|....*....|....*....|
gi 1016563101 738 -VFHVFDKVKVKIMldSSNLQHQKIRMSLV 766
Cdd:TIGR02063 682 kVFRLGDRVKVRVV--KADLDTGKIDFELV 709
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
305-634 9.64e-105

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 323.45  E-value: 9.64e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  305 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 384
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  385 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 463
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  464 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 542
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  543 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 621
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
                          330
                   ....*....|...
gi 1016563101  622 DVIVHRLLAVAIG 634
Cdd:smart00955 273 DLIVHRQLKAALR 285
PRK11642 PRK11642
ribonuclease R;
252-627 1.00e-48

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 184.95  E-value: 1.00e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 252 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 331
Cdd:PRK11642  208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 332 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 409
Cdd:PRK11642  287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 410 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 481
Cdd:PRK11642  365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 482 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 556
Cdd:PRK11642  441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1016563101 557 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 627
Cdd:PRK11642  514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
3-35 2.39e-06

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: 48.74  E-value: 2.39e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1016563101   3 ADNQLQVIFITNDRRNKEKAIEEGIPAFTCEEY 35
Cdd:cd09862   146 AKLGIPVVLLTDDADNREKAEEEGILALTVREY 178
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
44-767 2.98e-139

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 427.99  E-value: 2.98e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  44 ELIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEATVwihgdnEENKEIILQGLKHL 121
Cdd:COG0557    39 ALKRRLRALEREGqlVKTRRGRYRLPEKLDL------------VEGRVRGHRDGFGFVIP------DDGEEDIFIPPREL 100
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 122 NRAVHEDIVAVELLPKsqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKS 201
Cdd:COG0557   101 NGALHGDRVLVRVTKE------------DRRG------------------------RPEGRVVEILERANTRVVGRFEKE 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 202 DikesRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 279
Cdd:COG0557   145 K----GFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH 220
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 280 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 359
Cdd:COG0557   221 E-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGGWRLGVHIADVSHYVRPGSALDR 299
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 360 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDS-- 437
Cdd:COG0557   300 EARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGkd 379
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 438 ---ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAk 514
Cdd:COG0557   380 eelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIVPRERNDAHKLIEEFMLLANEAVA- 457
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 515 kihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLDQAE-SPTFPYLNTLLRilatRCMM 587
Cdd:COG0557   458 ---EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKgRPEEELLNTLLL----RSMK 530
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 588 QAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT--DKHKLADICKNLNFRHKMAQYA 665
Cdd:COG0557   531 QAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQeyLEEELEEIAEHCSETERRADEA 605
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 666 QRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV--------FFEekdkpnpqliYDDEIPS 731
Cdd:COG0557   606 ERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvsslgddYYE----------YDERRQA 669
                         730       740       750
                  ....*....|....*....|....*....|....*...
gi 1016563101 732 LKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 767
Cdd:COG0557   670 LVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
305-629 5.10e-122

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 369.31  E-value: 5.10e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 305 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 384
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 385 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 461
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 462 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 541
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 542 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 621
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302

                  ....*...
gi 1016563101 622 DVIVHRLL 629
Cdd:pfam00773 303 DLIVHRQL 310
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
45-766 1.53e-110

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: 353.11  E-value: 1.53e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  45 LIDRLACLSEEG--NEIESGKIIFSEHLPLsklqqgiksgtyLQGTFRASRENYLEatvwIHGDNEENKEIILQGlKHLN 122
Cdd:TIGR02063  39 LRKRLRALEDDGlvKKNRRGLYALPESLKL------------VKGTVIAHRDGFGF----LRPEDDDEDDIFIPP-RQMN 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 123 RAVHEDIVAVELLPKSqwvapssvvlhDEGQneedvekeeetermlktavsekmlKPTGRVVGIIKRNWRPYCGMLSKSD 202
Cdd:TIGR02063 102 GAMHGDRVLVRITGKP-----------DGGD------------------------RFEARVIKILERANDQIVGTFYIEN 146
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 203 -IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 279
Cdd:TIGR02063 147 gIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY 221
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 280 QpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQ 359
Cdd:TIGR02063 222 E-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDK 300
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 360 ESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQ----LRI 435
Cdd:TIGR02063 301 EALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNdiieGKD 380
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 436 DSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKK 515
Cdd:TIGR02063 381 ALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIVPRERGDAHKLIEEFMIAANETVAEH 459
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 516 IhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQA 589
Cdd:TIGR02063 460 L-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEKvKGRPEEELINTVL----LRSMQQA 534
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 590 VYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTDKH----KLADICKNLNFRHKMAQYA 665
Cdd:TIGR02063 535 KY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREyleaKLEEIAEHSSKTERRADEA 610
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 666 QRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFFeeKDKPNPQLIYDDEIPSLKIEDT- 737
Cdd:TIGR02063 611 ERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI--STLKDDYYVFDEKGLALVGERTg 681
                         730       740       750
                  ....*....|....*....|....*....|
gi 1016563101 738 -VFHVFDKVKVKIMldSSNLQHQKIRMSLV 766
Cdd:TIGR02063 682 kVFRLGDRVKVRVV--KADLDTGKIDFELV 709
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
305-634 9.64e-105

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 323.45  E-value: 9.64e-105
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  305 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 384
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  385 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 463
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  464 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 542
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  543 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 621
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
                          330
                   ....*....|...
gi 1016563101  622 DVIVHRLLAVAIG 634
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 ...
232-749 5.43e-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: 259.26  E-value: 5.43e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 232 EGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHL 311
Cdd:TIGR00358 122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFE-FPDGVEQQAAKLQFDVDEQAKKYREDLTDL 200
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 312 CICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKC 391
Cdd:TIGR00358 201 AFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNP 280
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 392 DVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAE-AQLRIDSANMNDDITT---SLRGLNKLAKILKKRRIEKGA 467
Cdd:TIGR00358 281 NEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKvNDWLENDDELQPEYETlveQLKALHQLSQALGEWRHKRGL 360
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 468 LTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEfSEHALLRKHPAPPPSNYEILVKAARSR 547
Cdd:TIGR00358 361 IDFEHPETKFIVD-EEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAEL 438
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 548 NLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLRilatRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYA 621
Cdd:TIGR00358 439 GLTLPggnaeNVTTLDGACWLREvKDRPEYEILVTRLL----RSLSQAEY----SPEPLGHFGLGLEHYAHFTSPIRRYP 510
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 622 DVIVHRLLAVAIGADCTYPELTD-KHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKG-------IVSEEAYILFV 693
Cdd:TIGR00358 511 DLTNHRLIKAVLAKEQTDTERYQpQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVgtefsgeISSVTRFGMFV 590
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 694 R--KNAIVVLIPKYGLegtvffeekdkPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKI 749
Cdd:TIGR00358 591 RldDNGIDGLIHISTL-----------HNDYYVFDQEKMALIGKGTgkVYRIGDRVTVKL 639
PRK11642 PRK11642
ribonuclease R;
252-627 1.00e-48

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 184.95  E-value: 1.00e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 252 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 331
Cdd:PRK11642  208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 332 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 409
Cdd:PRK11642  287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 410 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 481
Cdd:PRK11642  365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 482 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 556
Cdd:PRK11642  441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1016563101 557 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 627
Cdd:PRK11642  514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
Rnb COG4776
Exoribonuclease II [Transcription];
270-667 3.33e-39

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 154.63  E-value: 3.33e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 270 VLLLEHDVPHQPfsqavlsflPKMP--WSItEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 347
Cdd:COG4776   163 VTLARHNLEREA---------PEGDdeWEL-LDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADP 232
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 348 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 426
Cdd:COG4776   233 TAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGdDIEFFAAWIRSKAKL 312
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 427 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVE 502
Cdd:COG4776   313 AYDNVSDWLEGKGewqpENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELD-EKGNVLDIHAEPRRIANRIVE 391
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 503 EFMLLANISVAKKIHEE-----FSEHALLRkhpappPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESPtf 571
Cdd:COG4776   392 EAMIAANICAARVLREHlgfgiFNVHSGFD------PEKLEQAVELLAEHGIEFDPEQLLTLEgfcalrRELDAQPTS-- 463
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 572 pYLNTLLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklAD 650
Cdd:COG4776   464 -YLDSRLRRFQTFAEISTE---PG-----PHFGLGLDAYATWTSPIRKYGDMVNHRLIkAVILGQPAEKPD-------EE 527
                         410
                  ....*....|....*..
gi 1016563101 651 ICKNLNFRHKMAQYAQR 667
Cdd:COG4776   528 LTERLAERRRLNRMAER 544
PRK05054 PRK05054
exoribonuclease II; Provisional
270-662 3.07e-37

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 148.87  E-value: 3.07e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 270 VLLLEHDVPHQPfsqavlsflPKM--PWSITEKDMKnREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 347
Cdd:PRK05054  163 VTLARHNLEREA---------PAGgvAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADP 232
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 348 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 426
Cdd:PRK05054  233 TAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEdDIRFFAAWIESKAKL 312
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 427 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMdSETHDPIDLQTKELRETNSMVE 502
Cdd:PRK05054  313 AYDNVSDWLENGGdwqpESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFEL-GEKGEVLDIVAEPRRIANRIVE 391
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 503 EFMLLANISVAKKIHEEFsEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESptfPYLNT 576
Cdd:PRK05054  392 ESMIAANICAARVLRDKL-GFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEgfcklrRELDAQPT---GYLDS 467
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 577 LLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklADICKNL 655
Cdd:PRK05054  468 RIRRFQSFAEISTE---PG-----PHFGLGLEAYATWTSPIRKYGDMINHRLLkAVIKGETAERPQ-------DEITVQL 532
                         410
                  ....*....|
gi 1016563101 656 NFR---HKMA 662
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 ...
210-276 4.59e-26

Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA.


Pssm-ID: 436091 [Multi-domain]  Cd Length: 77  Bit Score: 101.92  E-value: 4.59e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1016563101 210 LFTPADKRIPRIRIETRQA--------STLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHD 276
Cdd:pfam17849   3 LFVPRDKRIPRIRIPTKSApeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
Rrp44_S1 pfam17215
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ...
684-763 4.39e-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: 71.02  E-value: 4.39e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 684 VSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTV------FHVFDKVKVKIM--LDSSN 755
Cdd:pfam17215   1 SEEEGYVIKVFNNGIVVFVPKFGIEGLIRLEDLTGDEPEAEFDADEYSLTFPDKGsgkkrtVGVFDKVRVRVKsvKDENT 80

                  ....*...
gi 1016563101 756 lQHQKIRM 763
Cdd:pfam17215  81 -GKRKVKL 87
Rrp44_CSD1 pfam17216
Rrp44-like cold shock domain;
66-151 1.59e-13

Rrp44-like cold shock domain;


Pssm-ID: 375054  Cd Length: 148  Bit Score: 68.64  E-value: 1.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101  66 FSEHLPLSKLQQGIKSGTYLQGTFRASRENYLEATVWIhgdNEENKEIILQGLKHLNRAVHEDIVAVELLPKSQWVAPSS 145
Cdd:pfam17216   4 FPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSL---PRFSKPVLIVGQKNLNRAFNGDQVIVELLPQSEWKAPSS 80

                  ....*.
gi 1016563101 146 VVLHDE 151
Cdd:pfam17216  81 IVLDSE 86
PIN_Rrp44-like cd09862
VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic ...
3-35 2.39e-06

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: 48.74  E-value: 2.39e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1016563101   3 ADNQLQVIFITNDRRNKEKAIEEGIPAFTCEEY 35
Cdd:cd09862   146 AKLGIPVVLLTDDADNREKAEEEGILALTVREY 178
CSD2 pfam17876
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ...
212-279 7.70e-06

Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding.


Pssm-ID: 465546 [Multi-domain]  Cd Length: 74  Bit Score: 44.30  E-value: 7.70e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016563101 212 TPADKRIPR-IRIETRQASTL-EGRRIIVAIDGWPrNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 279
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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