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Conserved domains on  [gi|6323943|ref|NP_014014|]
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exoribonuclease II [Saccharomyces cerevisiae S288C]

Protein Classification

ribonuclease catalytic domain-containing protein( domain architecture ID 10466333)

ribonuclease catalytic domain-containing protein may function as a 3'-5'exoribonuclease

EC:  3.1.13.-
Gene Ontology:  GO:0016896|GO:0006401|GO:0003723
PubMed:  16806266

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
522-852 2.06e-73

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


:

Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 244.50  E-value: 2.06e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    522 RYDFGDLRVFCIDSETAHEIDDGVSVKNYGrDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTV 601
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLP-NGGYRLGVHIADVSHYVPPGSPLDRE---------ARKRGTSVYLPDRV 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    602 VPMLPQS----ICHLsdlgKQGQRTKTISFSVDVKITSKCSgksieimydSFKIRKGIVSNFPKATYEDVDRILGTPNSE 677
Cdd:pfam00773  71 IPMLPEKlsndLCSL----NPGEDRLALSVEITIDADGEVT---------SYEIYPSVIRSKARLTYEEVDDLLEGKDAE 137
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    678 ASP--VKKDLESLSMISKLLREQRIKNSNAVifgegFNKGLVMLNADSEGELTEVTfsdQEETLSTILVSEMMILANTLT 755
Cdd:pfam00773 138 KDKpdLAEDLRLLYELAKILRAKRLQRGALD-----LDTPENKLILDEEGVIDILI---QERTDAHSLIEEFMLLANEAV 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    756 GRYFAENKIGGVFRCYKqlplgEVAQQQYDSMITSTKKGIFPK--LKDIVKLSS-----------LLNSSFYTGRPFRHE 822
Cdd:pfam00773 210 ARHLQELGIPALYRVHP-----EPDLEKLNSLIKLLQLLPDDKglSKSLEKIKDderllsilllrTMPRAEYSPEPLGHF 284
                         330       340       350
                  ....*....|....*....|....*....|
gi 6323943    823 MIGAKQYLTVTSPLRRFPDLINHLQIHRHL 852
Cdd:pfam00773 285 GLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
 
Name Accession Description Interval E-value
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
522-852 2.06e-73

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 244.50  E-value: 2.06e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    522 RYDFGDLRVFCIDSETAHEIDDGVSVKNYGrDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTV 601
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLP-NGGYRLGVHIADVSHYVPPGSPLDRE---------ARKRGTSVYLPDRV 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    602 VPMLPQS----ICHLsdlgKQGQRTKTISFSVDVKITSKCSgksieimydSFKIRKGIVSNFPKATYEDVDRILGTPNSE 677
Cdd:pfam00773  71 IPMLPEKlsndLCSL----NPGEDRLALSVEITIDADGEVT---------SYEIYPSVIRSKARLTYEEVDDLLEGKDAE 137
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    678 ASP--VKKDLESLSMISKLLREQRIKNSNAVifgegFNKGLVMLNADSEGELTEVTfsdQEETLSTILVSEMMILANTLT 755
Cdd:pfam00773 138 KDKpdLAEDLRLLYELAKILRAKRLQRGALD-----LDTPENKLILDEEGVIDILI---QERTDAHSLIEEFMLLANEAV 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    756 GRYFAENKIGGVFRCYKqlplgEVAQQQYDSMITSTKKGIFPK--LKDIVKLSS-----------LLNSSFYTGRPFRHE 822
Cdd:pfam00773 210 ARHLQELGIPALYRVHP-----EPDLEKLNSLIKLLQLLPDDKglSKSLEKIKDderllsilllrTMPRAEYSPEPLGHF 284
                         330       340       350
                  ....*....|....*....|....*....|
gi 6323943    823 MIGAKQYLTVTSPLRRFPDLINHLQIHRHL 852
Cdd:pfam00773 285 GLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
522-854 2.48e-53

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 187.86  E-value: 2.48e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     522 RYDFGDLRVFCIDSETAHEIDDGVSVKNYGrDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTV 601
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLD-NGGYRLGVHIADVSHYVKPGSALDRE---------ARKRGTSVYLPDRV 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     602 VPMLPQSICHlsDLGKQGQRTKTISFSVDVKITSKcsGKSIEimydSFKIRKGIVSNFPKATYEDVDRILgtpnseaspv 681
Cdd:smart00955  71 IPMLPEELSN--GLCSLNPGEDRLALSVEMTLDAD--GGEIL----DYEFYRSVIRSKARLTYEEVDAIL---------- 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     682 kkdleslsmiskllreqriknsNAVIFgegfnkglvmlnaDSEGELTEVTFsdQEETLSTILVSEMMILANTLTGRYFAE 761
Cdd:smart00955 133 ----------------------EKIVL-------------DEEGKIEDIVP--RERNDAHSLVEEFMILANEAVARFLAK 175
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     762 NKIGGVFRCYKQLPLGEVAQQQYDSMitSTKKGIFPKLKDIVKLSSLLNSSFYT----------GRPFRHEMIG------ 825
Cdd:smart00955 176 NGIPGLYRVHEGPDPEKLAELLKEFL--ALLGLLLLGGDGPKALAKLLEKIRDSpeerllelllLRSMPHAEYSvdnsgh 253
                          330       340       350
                   ....*....|....*....|....*....|...
gi 6323943     826 ----AKQYLTVTSPLRRFPDLINHLQIHRHLQK 854
Cdd:smart00955 254 fglaLDAYTHFTSPIRRYPDLIVHRQLKAALRG 286
3_prime_RNase TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
387-967 3.23e-31

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: 130.99  E-value: 3.23e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    387 AQVIEKLE------ANSYREVNKFVKLV--NERKYRDIsalypsviqllkdFAAGNFHNNGIivALISKIFRKIERYkdc 458
Cdd:TIGR00358  72 AEVERILEpaltrfVGKFLGENDFGFVVpdDPRIYLDI-------------IVPKASVKNEL--AEGDKVVVELTEY--- 133
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    459 DITRDICQDLINEITPNSipNPLLLNMDLALPASSKLVKW----QQKLYDLTNIEELQWKKsgtddDRYDFGDLRVFCID 534
Cdd:TIGR00358 134 PLRRNLFYGEITQILGNN--DDPLIPWWVTLARHEIPFEFpdgvEQQAAKLQFDVDEQAKK-----YREDLTDLAFVTID 206
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    535 SETAHEIDDGVSVKNYgRDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTVVPMLPQ----SIC 610
Cdd:TIGR00358 207 GADAKDLDDAVYVKKL-PDGGWKLYVAIADVSYYVAENSPLDKE---------AKHRGFSVYLPGFVIPMLPEelsnGLC 276
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    611 HLSDLGKQGQRTKTISFSVDVKITSKcsgksieimydsfKIRKGIVSNFPKATYEDVDRIL---GTPNSEASPVKKDLES 687
Cdd:TIGR00358 277 SLNPNEDRLVLVCEMTISAQGRITDN-------------EFYPATIESKARLTYDKVNDWLendDELQPEYETLVEQLKA 343
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    688 LSMISKLLREQRiKNSNAVIFGEGFNKGLVmlnaDSEGELTEVTFsdQEETLSTILVSEMMILANTLTGRYFAENKIGGV 767
Cdd:TIGR00358 344 LHQLSQALGEWR-HKRGLIDFEHPETKFIV----DEEGRVIDIVA--EVRRIAEKIIEEAMIVANICAARFLHNHKVPGI 416
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    768 FRCYK-------------------QLP---LGEVAQQQYDSMITSTKKGIFPKLKDIVKLSSLlNSSFYTGRPFRHEMIG 825
Cdd:TIGR00358 417 YRVHPgpskkklqslleflaelglTLPggnAENVTTLDGACWLREVKDRPEYEILVTRLLRSL-SQAEYSPEPLGHFGLG 495
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    826 AKQYLTVTSPLRRFPDLINHLQIHRHLqKKPLCFNQTQI--DSLIWPIQSRADILKR---ASRNSSTYWTLNYLKKltkl 900
Cdd:TIGR00358 496 LEHYAHFTSPIRRYPDLTNHRLIKAVL-AKEQTDTERYQpqDELLQIAEHCSDTERRardAERDVADWLKCRYLLD---- 570
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    901 EPERTFDVMVTSV---------PQNGFTGCV--------FPDLSFARGTLKLHPSSMHYpMIGDIVKnCKISKIDCLEGM 963
Cdd:TIGR00358 571 KVGTEFSGEISSVtrfgmfvrlDDNGIDGLIhistlhndYYVFDQEKMALIGKGTGKVY-RIGDRVT-VKLTEVNMETRS 648

                  ....
gi 6323943    964 LELE 967
Cdd:TIGR00358 649 IIFE 652
VacB COG0557
Exoribonuclease R [Transcription];
521-856 2.15e-29

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 125.60  E-value: 2.15e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  521 DRYDFGDLRVFCIDSETAHEIDDGVSVKnYGRDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDT 600
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAE-KLDNGGWRLGVHIADVSHYVRPGSALDRE---------ARKRGTSVYLPDR 313
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  601 VVPMLPQS----ICHLsdlgKQGQ-RtktISFSVDVKITSKcsGKSIeimydSFKIRKGIV-SnfpKA--TYEDVDRILG 672
Cdd:COG0557 314 VIPMLPERlsngLCSL----NPGEdR---LAMSCEMEIDAK--GEVV-----SYEFYRSVIrS---DArlTYEEVQAILD 376
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  673 TPNSEAS----PVKKDLESLSMISKLLREQRiknsnavifgegFNKGLVMLNA-------DSEGELTEVTFSdqEETLST 741
Cdd:COG0557 377 GKDEELReeyaDLVPMLEELYELAKILRKAR------------EKRGAIDFDLpetkiilDEEGKPEDIVPR--ERNDAH 442
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  742 ILVSEMMILANTLTGRYFAENKIGGVFRC--------------------YKqLPLGEVAQ-QQYDSMITSTKKGIFPKLk 800
Cdd:COG0557 443 KLIEEFMLLANEAVAEFLEKLKLPFLYRVheepdpeklealreflanlgLK-LKGGDEPTpKDLQKLLEQVKGRPEEEL- 520
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  801 divkLSSLLNSS----FYTGRPFRHEMIGAKQYLTVTSPLRRFPDLINHLQIHRHLQKKP 856
Cdd:COG0557 521 ----LNTLLLRSmkqaVYSPENIGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKR 576
PRK05054 PRK05054
exoribonuclease II; Provisional
491-856 1.90e-14

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 77.61  E-value: 1.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   491 ASSKLVKWQQKL--YDLTNIE---ELQWKKSGTDDDRYDFGDLRVFCIDSETAHEIDDGVSVKNYGRDGLyTLYIHIADP 565
Cdd:PRK05054 154 ADDHFAPWWVTLarHNLEREApagGVAWEMLDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGL-QLTVAIADP 232
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   566 TSMFPESTNVDiegistdilNVALKRSFTTYLPDTVVPMLPQsicHLSD-------------------LGKQGQRTKTIS 626
Cdd:PRK05054 233 TAYIAEGSKLD---------KAARQRAFTNYLPGFNIPMLPR---ELSDdlcslrpnerrpalacrvtIDADGTIEDDIR 300
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   627 FsVDVKITSKcsGKsieIMYDSfkirkgiVSNFpkatYEDVDRilGTPNSEAspVKKDLESLSMISKLLREQRIKnsNAV 706
Cdd:PRK05054 301 F-FAAWIESK--AK---LAYDN-------VSDW----LENGGD--WQPESEA--IAEQIRLLHQFCLARSEWRKQ--HAL 357
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   707 IFGEGFNKGLVmLNADseGELTEVtFSDQEETLSTIlVSEMMILANTLTGRYFAENKIGGVFRC---YKQLPLGEVAQ-- 781
Cdd:PRK05054 358 VFKDRPDYRFE-LGEK--GEVLDI-VAEPRRIANRI-VEESMIAANICAARVLRDKLGFGIYNVhsgFDPANAEQAVAll 432
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   782 QQYDsmITSTKKGI-----FPKLK-DIVKLSsllnSSFYTGR-------------PFRHEMIGAKQYLTVTSPLRRFPDL 842
Cdd:PRK05054 433 KEHG--LHFDAEELltlegFCKLRrELDAQP----TGYLDSRirrfqsfaeistePGPHFGLGLEAYATWTSPIRKYGDM 506
                        410
                 ....*....|....
gi 6323943   843 INHLQIHRHLQKKP 856
Cdd:PRK05054 507 INHRLLKAVIKGET 520
 
Name Accession Description Interval E-value
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
522-852 2.06e-73

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 244.50  E-value: 2.06e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    522 RYDFGDLRVFCIDSETAHEIDDGVSVKNYGrDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTV 601
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLP-NGGYRLGVHIADVSHYVPPGSPLDRE---------ARKRGTSVYLPDRV 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    602 VPMLPQS----ICHLsdlgKQGQRTKTISFSVDVKITSKCSgksieimydSFKIRKGIVSNFPKATYEDVDRILGTPNSE 677
Cdd:pfam00773  71 IPMLPEKlsndLCSL----NPGEDRLALSVEITIDADGEVT---------SYEIYPSVIRSKARLTYEEVDDLLEGKDAE 137
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    678 ASP--VKKDLESLSMISKLLREQRIKNSNAVifgegFNKGLVMLNADSEGELTEVTfsdQEETLSTILVSEMMILANTLT 755
Cdd:pfam00773 138 KDKpdLAEDLRLLYELAKILRAKRLQRGALD-----LDTPENKLILDEEGVIDILI---QERTDAHSLIEEFMLLANEAV 209
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    756 GRYFAENKIGGVFRCYKqlplgEVAQQQYDSMITSTKKGIFPK--LKDIVKLSS-----------LLNSSFYTGRPFRHE 822
Cdd:pfam00773 210 ARHLQELGIPALYRVHP-----EPDLEKLNSLIKLLQLLPDDKglSKSLEKIKDderllsilllrTMPRAEYSPEPLGHF 284
                         330       340       350
                  ....*....|....*....|....*....|
gi 6323943    823 MIGAKQYLTVTSPLRRFPDLINHLQIHRHL 852
Cdd:pfam00773 285 GLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
522-854 2.48e-53

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 187.86  E-value: 2.48e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     522 RYDFGDLRVFCIDSETAHEIDDGVSVKNYGrDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTV 601
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLD-NGGYRLGVHIADVSHYVKPGSALDRE---------ARKRGTSVYLPDRV 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     602 VPMLPQSICHlsDLGKQGQRTKTISFSVDVKITSKcsGKSIEimydSFKIRKGIVSNFPKATYEDVDRILgtpnseaspv 681
Cdd:smart00955  71 IPMLPEELSN--GLCSLNPGEDRLALSVEMTLDAD--GGEIL----DYEFYRSVIRSKARLTYEEVDAIL---------- 132
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     682 kkdleslsmiskllreqriknsNAVIFgegfnkglvmlnaDSEGELTEVTFsdQEETLSTILVSEMMILANTLTGRYFAE 761
Cdd:smart00955 133 ----------------------EKIVL-------------DEEGKIEDIVP--RERNDAHSLVEEFMILANEAVARFLAK 175
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943     762 NKIGGVFRCYKQLPLGEVAQQQYDSMitSTKKGIFPKLKDIVKLSSLLNSSFYT----------GRPFRHEMIG------ 825
Cdd:smart00955 176 NGIPGLYRVHEGPDPEKLAELLKEFL--ALLGLLLLGGDGPKALAKLLEKIRDSpeerllelllLRSMPHAEYSvdnsgh 253
                          330       340       350
                   ....*....|....*....|....*....|...
gi 6323943     826 ----AKQYLTVTSPLRRFPDLINHLQIHRHLQK 854
Cdd:smart00955 254 fglaLDAYTHFTSPIRRYPDLIVHRQLKAALRG 286
3_prime_RNase TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
387-967 3.23e-31

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: 130.99  E-value: 3.23e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    387 AQVIEKLE------ANSYREVNKFVKLV--NERKYRDIsalypsviqllkdFAAGNFHNNGIivALISKIFRKIERYkdc 458
Cdd:TIGR00358  72 AEVERILEpaltrfVGKFLGENDFGFVVpdDPRIYLDI-------------IVPKASVKNEL--AEGDKVVVELTEY--- 133
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    459 DITRDICQDLINEITPNSipNPLLLNMDLALPASSKLVKW----QQKLYDLTNIEELQWKKsgtddDRYDFGDLRVFCID 534
Cdd:TIGR00358 134 PLRRNLFYGEITQILGNN--DDPLIPWWVTLARHEIPFEFpdgvEQQAAKLQFDVDEQAKK-----YREDLTDLAFVTID 206
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    535 SETAHEIDDGVSVKNYgRDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTVVPMLPQ----SIC 610
Cdd:TIGR00358 207 GADAKDLDDAVYVKKL-PDGGWKLYVAIADVSYYVAENSPLDKE---------AKHRGFSVYLPGFVIPMLPEelsnGLC 276
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    611 HLSDLGKQGQRTKTISFSVDVKITSKcsgksieimydsfKIRKGIVSNFPKATYEDVDRIL---GTPNSEASPVKKDLES 687
Cdd:TIGR00358 277 SLNPNEDRLVLVCEMTISAQGRITDN-------------EFYPATIESKARLTYDKVNDWLendDELQPEYETLVEQLKA 343
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    688 LSMISKLLREQRiKNSNAVIFGEGFNKGLVmlnaDSEGELTEVTFsdQEETLSTILVSEMMILANTLTGRYFAENKIGGV 767
Cdd:TIGR00358 344 LHQLSQALGEWR-HKRGLIDFEHPETKFIV----DEEGRVIDIVA--EVRRIAEKIIEEAMIVANICAARFLHNHKVPGI 416
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    768 FRCYK-------------------QLP---LGEVAQQQYDSMITSTKKGIFPKLKDIVKLSSLlNSSFYTGRPFRHEMIG 825
Cdd:TIGR00358 417 YRVHPgpskkklqslleflaelglTLPggnAENVTTLDGACWLREVKDRPEYEILVTRLLRSL-SQAEYSPEPLGHFGLG 495
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    826 AKQYLTVTSPLRRFPDLINHLQIHRHLqKKPLCFNQTQI--DSLIWPIQSRADILKR---ASRNSSTYWTLNYLKKltkl 900
Cdd:TIGR00358 496 LEHYAHFTSPIRRYPDLTNHRLIKAVL-AKEQTDTERYQpqDELLQIAEHCSDTERRardAERDVADWLKCRYLLD---- 570
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943    901 EPERTFDVMVTSV---------PQNGFTGCV--------FPDLSFARGTLKLHPSSMHYpMIGDIVKnCKISKIDCLEGM 963
Cdd:TIGR00358 571 KVGTEFSGEISSVtrfgmfvrlDDNGIDGLIhistlhndYYVFDQEKMALIGKGTGKVY-RIGDRVT-VKLTEVNMETRS 648

                  ....
gi 6323943    964 LELE 967
Cdd:TIGR00358 649 IIFE 652
VacB COG0557
Exoribonuclease R [Transcription];
521-856 2.15e-29

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 125.60  E-value: 2.15e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  521 DRYDFGDLRVFCIDSETAHEIDDGVSVKnYGRDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDT 600
Cdd:COG0557 244 GRRDLRDLPLVTIDGEDAKDFDDAVSAE-KLDNGGWRLGVHIADVSHYVRPGSALDRE---------ARKRGTSVYLPDR 313
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  601 VVPMLPQS----ICHLsdlgKQGQ-RtktISFSVDVKITSKcsGKSIeimydSFKIRKGIV-SnfpKA--TYEDVDRILG 672
Cdd:COG0557 314 VIPMLPERlsngLCSL----NPGEdR---LAMSCEMEIDAK--GEVV-----SYEFYRSVIrS---DArlTYEEVQAILD 376
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  673 TPNSEAS----PVKKDLESLSMISKLLREQRiknsnavifgegFNKGLVMLNA-------DSEGELTEVTFSdqEETLST 741
Cdd:COG0557 377 GKDEELReeyaDLVPMLEELYELAKILRKAR------------EKRGAIDFDLpetkiilDEEGKPEDIVPR--ERNDAH 442
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  742 ILVSEMMILANTLTGRYFAENKIGGVFRC--------------------YKqLPLGEVAQ-QQYDSMITSTKKGIFPKLk 800
Cdd:COG0557 443 KLIEEFMLLANEAVAEFLEKLKLPFLYRVheepdpeklealreflanlgLK-LKGGDEPTpKDLQKLLEQVKGRPEEEL- 520
                       330       340       350       360       370       380
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  801 divkLSSLLNSS----FYTGRPFRHEMIGAKQYLTVTSPLRRFPDLINHLQIHRHLQKKP 856
Cdd:COG0557 521 ----LNTLLLRSmkqaVYSPENIGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGKR 576
Rnb COG4776
Exoribonuclease II [Transcription];
521-856 8.15e-17

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 85.29  E-value: 8.15e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  521 DRYDFGDLRVFCIDSETAHEIDDGVSVKnYGRDGLYTLYIHIADPTSMFPESTNVDiegistdilNVALKRSFTTYLPDT 600
Cdd:COG4776 189 EREDLTALPFVTIDSESTEDMDDALYIE-KLENGGWKLTVAIADPTAYIPEGSELD---------KEARQRAFTNYLPGF 258
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  601 VVPMLPQsicHLSD-------------------LGKQGQRTKTISFSVDVkITSKcsGKsieIMYDSfkirkgiVSNFpk 661
Cdd:COG4776 259 NIPMLPR---ELSDdlcslkenekrpalvcrvtIDADGSIGDDIEFFAAW-IRSK--AK---LAYDN-------VSDW-- 320
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  662 atYEDVDRilGTPNSEAspVKKDLESLSMISKLLREQRIKnsNAVIFGEGFNKGLVMlnaDSEGELTEVtFSDQEETLST 741
Cdd:COG4776 321 --LEGKGE--WQPENEE--IAEQIRLLHQFALARSQWRQQ--HALVFKDRPDYRFEL---DEKGNVLDI-HAEPRRIANR 388
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943  742 IlVSEMMILANTLTGRYFAENKIGGVFRCY---KQLPLGEVAQ--QQYDsmITSTKKGIFpKLKDIVKLSSLLN---SSF 813
Cdd:COG4776 389 I-VEEAMIAANICAARVLREHLGFGIFNVHsgfDPEKLEQAVEllAEHG--IEFDPEQLL-TLEGFCALRRELDaqpTSY 464
                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 6323943  814 YTGR-------------PFRHEMIGAKQYLTVTSPLRRFPDLINHLQIHRHLQKKP 856
Cdd:COG4776 465 LDSRlrrfqtfaeistePGPHFGLGLDAYATWTSPIRKYGDMVNHRLIKAVILGQP 520
PRK05054 PRK05054
exoribonuclease II; Provisional
491-856 1.90e-14

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 77.61  E-value: 1.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   491 ASSKLVKWQQKL--YDLTNIE---ELQWKKSGTDDDRYDFGDLRVFCIDSETAHEIDDGVSVKNYGRDGLyTLYIHIADP 565
Cdd:PRK05054 154 ADDHFAPWWVTLarHNLEREApagGVAWEMLDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGL-QLTVAIADP 232
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   566 TSMFPESTNVDiegistdilNVALKRSFTTYLPDTVVPMLPQsicHLSD-------------------LGKQGQRTKTIS 626
Cdd:PRK05054 233 TAYIAEGSKLD---------KAARQRAFTNYLPGFNIPMLPR---ELSDdlcslrpnerrpalacrvtIDADGTIEDDIR 300
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   627 FsVDVKITSKcsGKsieIMYDSfkirkgiVSNFpkatYEDVDRilGTPNSEAspVKKDLESLSMISKLLREQRIKnsNAV 706
Cdd:PRK05054 301 F-FAAWIESK--AK---LAYDN-------VSDW----LENGGD--WQPESEA--IAEQIRLLHQFCLARSEWRKQ--HAL 357
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   707 IFGEGFNKGLVmLNADseGELTEVtFSDQEETLSTIlVSEMMILANTLTGRYFAENKIGGVFRC---YKQLPLGEVAQ-- 781
Cdd:PRK05054 358 VFKDRPDYRFE-LGEK--GEVLDI-VAEPRRIANRI-VEESMIAANICAARVLRDKLGFGIYNVhsgFDPANAEQAVAll 432
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   782 QQYDsmITSTKKGI-----FPKLK-DIVKLSsllnSSFYTGR-------------PFRHEMIGAKQYLTVTSPLRRFPDL 842
Cdd:PRK05054 433 KEHG--LHFDAEELltlegFCKLRrELDAQP----TGYLDSRirrfqsfaeistePGPHFGLGLEAYATWTSPIRKYGDM 506
                        410
                 ....*....|....
gi 6323943   843 INHLQIHRHLQKKP 856
Cdd:PRK05054 507 INHRLLKAVIKGET 520
PRK11642 PRK11642
ribonuclease R;
522-855 2.05e-13

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 74.39  E-value: 2.05e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   522 RYDFGDLRVFCIDSETAHEIDDGVSVKNyGRDGLYTLYIHIADPTSMFPESTNVDIEgistdilnvALKRSFTTYLPDTV 601
Cdd:PRK11642 260 RVDLRDLPLVTIDGEDARDFDDAVYCEK-KRGGGWRLWVAIADVSYYVRPPTPLDRE---------ARNRGTSVYFPSQV 329
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   602 VPMLPQSICH-LSDLGKQGQRtktISFSVDVKITSKcsGKsieimYDSFKIRKGIVSNFPKATYEDVDRIL-GTPN--SE 677
Cdd:PRK11642 330 VPMLPEVLSNgLCSLNPQVDR---LCMVCEMTISSK--GR-----LTGYKFYEAVMSSHARLTYTKVWHILqGDQDlrEQ 399
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   678 ASPVKKDLESLSMISKLL---REQRiknsNAVIFGEGFNKglVMLNADSEGELTEVTFSDQEETlstiLVSEMMILANTL 754
Cdd:PRK11642 400 YAPLVKHLEELHNLYKVLdkaREER----GGISFESEEAK--FIFNAERRIERIEQTQRNDAHK----LIEECMILANIS 469
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323943   755 TGRYFAENKIGGVFRCYKQlPlGEVAQQQYDSMIT----STKKGIFPKLKDivkLSSLLNSsfYTGRPfRHEMI------ 824
Cdd:PRK11642 470 AARFVEKAKEPALFRIHDK-P-STEAITSFRSVLAelglELPGGNKPEPRD---YAELLES--VADRP-DAEMLqtmllr 541
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 6323943   825 GAKQ-----------------YLTVTSPLRRFPDLINHLQIHRHLQKK 855
Cdd:PRK11642 542 SMKQaiydpenrghfglalqsYAHFTSPIRRYPDLSLHRAIKYLLAKE 589
 
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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