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Conserved domains on  [gi|392894994|ref|NP_498160|]
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DIS3-like exonuclease 2 [Caenorhabditis elegans]

Protein Classification

ribonuclease R family protein( domain architecture ID 11426128)

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];
78-723 2.23e-129

Exoribonuclease R [Transcription];


The actual alignment was detected with superfamily member COG0557:

Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 403.72  E-value: 2.23e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  78 IEDGSMFKGVLRINPKNYqeCFLdHPKGtNHPDVLVLGQDRNRAMQGDVVAVKIKPKedwlvnyveyvkwwaehKKGDRN 157
Cdd:COG0557   64 PEKLDLVEGRVRGHRDGF--GFV-IPDD-GEEDIFIPPRELNGALHGDRVLVRVTKE-----------------DRRGRP 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 158 SGKtdnnspnktekrclrneiqdngvtsdevpdsclitigaIVHILEKKHFRVAaGKLQlmpnsANPNVLFV-ATDSRVP 236
Cdd:COG0557  123 EGR--------------------------------------VVEILERANTRVV-GRFE-----KEKGFGFVvPDDKRLL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 237 R-ILIPKSDVDKEffsRPKDferfLYTAKITDWRAESVYADGRLVKLLGMSGEIDTETERIVYEHQIDHrEFSDECL--- 312
Cdd:COG0557  159 QdIFIPPDDLNGA---KDGD----LVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH-EFPEEVLaea 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 313 ESLPITtaenwkVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkGtpGLEIGVHIADVTFFLKEGTELD 392
Cdd:COG0557  231 EALPDE------VPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN----G--GWRLGVHIADVSHYVRPGSALD 298

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 393 KWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIENP 472
Cdd:COG0557  299 REARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGK 378

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 473 EKDfTCDELPDISDgntpfEIKEktlmLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKLVEEF 552
Cdd:COG0557  379 DEE-LREEYADLVP-----MLEE----LYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEF 448

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 553 MLLANMEVAKKIAENfPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDGR---TSGLLSTSLRKYQGKSRldmciRQVIS 629
Cdd:COG0557  449 MLLANEAVAEFLEKL-KLPFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKGRPE-----EELLN 522

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 630 SLTIKPMQQAKYFctfemPLSFyHHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALG---YNERSERVPEEIQEICTRCN 706
Cdd:COG0557  523 TLLLRSMKQAVYS-----PENI-GHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEgkrSPGLQEYLEEELEEIAEHCS 596

                        650
                 ....*....|....*..
gi 392894994 707 DTKLASKEASDESAMLY 723
Cdd:COG0557  597 ETERRADEAERDVVDLK 613
Dis3l2_C_term pfam17877
DIS3-like exonuclease 2 C terminal; This is the C-terminal S1 domain found in Dis3L2 proteins. ...
 732-802 1.48e-20

DIS3-like exonuclease 2 C terminal; This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans.


:

Pssm-ID: 465547  Cd Length: 87  Bit Score: 86.55  E-value: 1.48e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392894994  732 GPMKCQAVVLGVMDLSFDVLIVEYGVVKRVYVDKM---KRDFNKsTEKLTIYW-PADPNAESGNREEFSSSIQMC 802
Cdd:pfam17877   1 GPLETEAVVLGVLDSSFDVLIPEYGIEKRVYLDQLplkKFEFDK-TGVLTLYWkKGVPSSAYVPEDERFSSLVVV 74
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
78-723 2.23e-129

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 403.72  E-value: 2.23e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  78 IEDGSMFKGVLRINPKNYqeCFLdHPKGtNHPDVLVLGQDRNRAMQGDVVAVKIKPKedwlvnyveyvkwwaehKKGDRN 157
Cdd:COG0557   64 PEKLDLVEGRVRGHRDGF--GFV-IPDD-GEEDIFIPPRELNGALHGDRVLVRVTKE-----------------DRRGRP 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 158 SGKtdnnspnktekrclrneiqdngvtsdevpdsclitigaIVHILEKKHFRVAaGKLQlmpnsANPNVLFV-ATDSRVP 236
Cdd:COG0557  123 EGR--------------------------------------VVEILERANTRVV-GRFE-----KEKGFGFVvPDDKRLL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 237 R-ILIPKSDVDKEffsRPKDferfLYTAKITDWRAESVYADGRLVKLLGMSGEIDTETERIVYEHQIDHrEFSDECL--- 312
Cdd:COG0557  159 QdIFIPPDDLNGA---KDGD----LVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH-EFPEEVLaea 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 313 ESLPITtaenwkVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkGtpGLEIGVHIADVTFFLKEGTELD 392
Cdd:COG0557  231 EALPDE------VPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN----G--GWRLGVHIADVSHYVRPGSALD 298

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 393 KWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIENP 472
Cdd:COG0557  299 REARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGK 378

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 473 EKDfTCDELPDISDgntpfEIKEktlmLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKLVEEF 552
Cdd:COG0557  379 DEE-LREEYADLVP-----MLEE----LYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEF 448

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 553 MLLANMEVAKKIAENfPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDGR---TSGLLSTSLRKYQGKSRldmciRQVIS 629
Cdd:COG0557  449 MLLANEAVAEFLEKL-KLPFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKGRPE-----EELLN 522

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 630 SLTIKPMQQAKYFctfemPLSFyHHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALG---YNERSERVPEEIQEICTRCN 706
Cdd:COG0557  523 TLLLRSMKQAVYS-----PENI-GHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEgkrSPGLQEYLEEELEEIAEHCS 596

                        650
                 ....*....|....*..
gi 392894994 707 DTKLASKEASDESAMLY 723
Cdd:COG0557  597 ETERRADEAERDVVDLK 613
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
 333-685 1.28e-107

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 333.10  E-value: 1.28e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  333 RRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKWASERGNSTYLSQTVIPML 412
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPN------GGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPML 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  413 PRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIEnpekdftcdelpDISDGNTPFE 492
Cdd:pfam00773  75 PEKLSNDLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLE------------GKDAEKDKPD 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  493 IKEKTLMLHRIAQVLRQKREDSGALRIELPRLKFALDEDkKPQGVSIYEIKDSNKLVEEFMLLANMEVAKKIAEnFPEHA 572
Cdd:pfam00773 143 LAEDLRLLYELAKILRAKRLQRGALDLDTPENKLILDEE-GVIDILIQERTDAHSLIEEFMLLANEAVARHLQE-LGIPA 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  573 LLRNHPPPKEKMIKDVAEQCARIGFPLDgrtsglLSTSLRKYQGKsrldmciRQVISSLTIKPMQQAKYFCTfemplsFY 652
Cdd:pfam00773 221 LYRVHPEPDLEKLNSLIKLLQLLPDDKG------LSKSLEKIKDD-------ERLLSILLLRTMPRAEYSPE------PL 281

                         330       340       350
                  ....*....|....*....|....*....|...
gi 392894994  653 HHFALNVDHYTHFTSPIRRYPDVIVHRQLAAAL 685
Cdd:pfam00773 282 GHFGLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
 76-728 1.34e-104

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: 338.48  E-value: 1.34e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   76 AGIEDGSMFKGVLRINPKNYQecFLdHPKGTNHPDVLVLGQDRNRAMQGDVVAVKIKPKEDwlvnyveyvkwwaehkKGD 155
Cdd:TIGR02063  61 ALPESLKLVKGTVIAHRDGFG--FL-RPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPD----------------GGD 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  156 RNSGktdnnspnktekrclrneiqdngvtsdevpdsclitigAIVHILEKKHFRVAaGKLQLMPNSAnpnvLFVATDSRV 235
Cdd:TIGR02063 122 RFEA--------------------------------------RVIKILERANDQIV-GTFYIENGIG----FVIPDDKRI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  236 P-RILIPKSDVDKeffsrPKDFERFLytAKITDWRAESVYADGRLVKLLGMSGEIDTETERIVYEHQIDHrEFSDECLES 314
Cdd:TIGR02063 159 YlDIFIPPEQILG-----AEEGDKVL--VEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY-EFPEEVLDE 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  315 LpiTTAENwKVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKW 394
Cdd:TIGR02063 231 A--AKIPE-EVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKD------GNYKLGVAIADVSHYVREGSALDKE 301

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  395 ASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIEnpEK 474
Cdd:TIGR02063 302 ALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIE--GK 379

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  475 DFTCDELPdisdgntpfEIKEKTLMLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKLVEEFML 554
Cdd:TIGR02063 380 DALDKKEP---------PLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMI 450

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  555 LANMEVAKKIaENFPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDGRT-----SGLLSTSLRKYQGKSRLDMcirqvIS 629
Cdd:TIGR02063 451 AANETVAEHL-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTsdkpqPKDFQKLLEKVKGRPEEEL-----IN 524

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  630 SLTIKPMQQAKYfctFEMPLSfyhHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALGYNER------SERVPEEIQEICT 703
Cdd:TIGR02063 525 TVLLRSMQQAKY---SPENIG---HFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENtttekeREYLEAKLEEIAE 598

                         650       660
                  ....*....|....*....|....*
gi 392894994  704 RCNDTKLASKEASDESAMLYFGVFI 728
Cdd:TIGR02063 599 HSSKTERRADEAERDVNDWKKAEYM 623
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
333-686 4.12e-101

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 315.36  E-value: 4.12e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   333 RRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKWASERGNSTYLSQTVIPML 412
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDN------GGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPML 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   413 PRILCEQLCSLNPGVDRLSFSTVFKMSYEA-ELYDVWFGRSVIRSRVKLAYEHAQDFIEnpekdftcdelpdisdgntpf 491
Cdd:smart00955  75 PEELSNGLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------- 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   492 eikektlmlhriaqvlrqkredsgalrielprlKFALDEDKKPQGVSIYEIKDSNKLVEEFMLLANMEVAKKIAENFPEh 571
Cdd:smart00955 134 ---------------------------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP- 179

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   572 ALLRNHPPP-KEKMIKDVAEQCARIGFPL-DGRTSGLLSTSLRKYQGKSRldmciRQVISSLTIKPMQQAKYFCTFEMpl 649
Cdd:smart00955 180 GLYRVHEGPdPEKLAELLKEFLALLGLLLlGGDGPKALAKLLEKIRDSPE-----ERLLELLLLRSMPHAEYSVDNSG-- 252

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 392894994   650 sfyhHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALG 686
Cdd:smart00955 253 ----HFGLALDAYTHFTSPIRRYPDLIVHRQLKAALR 285
PRK11642 PRK11642
ribonuclease R;
229-691 1.31e-44

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 173.00  E-value: 1.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 229 VATDSRVP-RILIPKSDVDKEFFSrpkdferFLYTAKITDWRAESVYADGRLVKLLG------MSGEIDTETerivyeHQ 301
Cdd:PRK11642 166 VPDDSRLSfDILIPPEQIMGARMG-------FVVVVELTQRPTRRTKAVGKIVEVLGdnmgtgMAVDIALRT------HE 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 302 IDHrEFSDECLESLPITTAEnwkVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHakhiddCDGKGTPGLEIGVHIADV 381
Cdd:PRK11642 233 IPY-IWPQAVEQQVAGLKEE---VPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVY------CEKKRGGGWRLWVAIADV 302

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 382 TFFLKEGTELDKWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLA 461
Cdd:PRK11642 303 SYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLT 382

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 462 YEHAQDFIENPEkdftcdelpDISDGNTPF--EIKEktlmLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSI 539
Cdd:PRK11642 383 YTKVWHILQGDQ---------DLREQYAPLvkHLEE----LHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQ 449

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 540 YEIKDSNKLVEEFMLLANMEVAKKIAENfPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDG------RTSGLLSTSLrk 613
Cdd:PRK11642 450 TQRNDAHKLIEECMILANISAARFVEKA-KEPALFRIHDKPSTEAITSFRSVLAELGLELPGgnkpepRDYAELLESV-- 526

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 614 yqgKSRLDmciRQVISSLTIKPMQQAKYfctfeMPLSfYHHFALNVDHYTHFTSPIRRYPDVIVHR----QLAAALGYNE 689
Cdd:PRK11642 527 ---ADRPD---AEMLQTMLLRSMKQAIY-----DPEN-RGHFGLALQSYAHFTSPIRRYPDLSLHRaikyLLAKEQGHKG 594


                 ..
gi 392894994 690 RS 691
Cdd:PRK11642 595 NT 596
Dis3l2_C_term pfam17877
DIS3-like exonuclease 2 C terminal; This is the C-terminal S1 domain found in Dis3L2 proteins. ...
 732-802 1.48e-20

DIS3-like exonuclease 2 C terminal; This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans.


Pssm-ID: 465547  Cd Length: 87  Bit Score: 86.55  E-value: 1.48e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392894994  732 GPMKCQAVVLGVMDLSFDVLIVEYGVVKRVYVDKM---KRDFNKsTEKLTIYW-PADPNAESGNREEFSSSIQMC 802
Cdd:pfam17877   1 GPLETEAVVLGVLDSSFDVLIPEYGIEKRVYLDQLplkKFEFDK-TGVLTLYWkKGVPSSAYVPEDERFSSLVVV 74
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
78-723 2.23e-129

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 403.72  E-value: 2.23e-129
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  78 IEDGSMFKGVLRINPKNYqeCFLdHPKGtNHPDVLVLGQDRNRAMQGDVVAVKIKPKedwlvnyveyvkwwaehKKGDRN 157
Cdd:COG0557   64 PEKLDLVEGRVRGHRDGF--GFV-IPDD-GEEDIFIPPRELNGALHGDRVLVRVTKE-----------------DRRGRP 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 158 SGKtdnnspnktekrclrneiqdngvtsdevpdsclitigaIVHILEKKHFRVAaGKLQlmpnsANPNVLFV-ATDSRVP 236
Cdd:COG0557  123 EGR--------------------------------------VVEILERANTRVV-GRFE-----KEKGFGFVvPDDKRLL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 237 R-ILIPKSDVDKEffsRPKDferfLYTAKITDWRAESVYADGRLVKLLGMSGEIDTETERIVYEHQIDHrEFSDECL--- 312
Cdd:COG0557  159 QdIFIPPDDLNGA---KDGD----LVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPH-EFPEEVLaea 230

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 313 ESLPITtaenwkVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkGtpGLEIGVHIADVTFFLKEGTELD 392
Cdd:COG0557  231 EALPDE------VPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN----G--GWRLGVHIADVSHYVRPGSALD 298

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 393 KWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIENP 472
Cdd:COG0557  299 REARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGK 378

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 473 EKDfTCDELPDISDgntpfEIKEktlmLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKLVEEF 552
Cdd:COG0557  379 DEE-LREEYADLVP-----MLEE----LYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEF 448

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 553 MLLANMEVAKKIAENfPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDGR---TSGLLSTSLRKYQGKSRldmciRQVIS 629
Cdd:COG0557  449 MLLANEAVAEFLEKL-KLPFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLEQVKGRPE-----EELLN 522

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 630 SLTIKPMQQAKYFctfemPLSFyHHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALG---YNERSERVPEEIQEICTRCN 706
Cdd:COG0557  523 TLLLRSMKQAVYS-----PENI-GHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEgkrSPGLQEYLEEELEEIAEHCS 596

                        650
                 ....*....|....*..
gi 392894994 707 DTKLASKEASDESAMLY 723
Cdd:COG0557  597 ETERRADEAERDVVDLK 613
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
 333-685 1.28e-107

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 333.10  E-value: 1.28e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  333 RRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKWASERGNSTYLSQTVIPML 412
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPN------GGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPML 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  413 PRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIEnpekdftcdelpDISDGNTPFE 492
Cdd:pfam00773  75 PEKLSNDLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLE------------GKDAEKDKPD 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  493 IKEKTLMLHRIAQVLRQKREDSGALRIELPRLKFALDEDkKPQGVSIYEIKDSNKLVEEFMLLANMEVAKKIAEnFPEHA 572
Cdd:pfam00773 143 LAEDLRLLYELAKILRAKRLQRGALDLDTPENKLILDEE-GVIDILIQERTDAHSLIEEFMLLANEAVARHLQE-LGIPA 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  573 LLRNHPPPKEKMIKDVAEQCARIGFPLDgrtsglLSTSLRKYQGKsrldmciRQVISSLTIKPMQQAKYFCTfemplsFY 652
Cdd:pfam00773 221 LYRVHPEPDLEKLNSLIKLLQLLPDDKG------LSKSLEKIKDD-------ERLLSILLLRTMPRAEYSPE------PL 281

                         330       340       350
                  ....*....|....*....|....*....|...
gi 392894994  653 HHFALNVDHYTHFTSPIRRYPDVIVHRQLAAAL 685
Cdd:pfam00773 282 GHFGLGLDIYTHFTSPIRRYPDLIVHRQLKALL 314
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
 76-728 1.34e-104

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: 338.48  E-value: 1.34e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   76 AGIEDGSMFKGVLRINPKNYQecFLdHPKGTNHPDVLVLGQDRNRAMQGDVVAVKIKPKEDwlvnyveyvkwwaehkKGD 155
Cdd:TIGR02063  61 ALPESLKLVKGTVIAHRDGFG--FL-RPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPD----------------GGD 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  156 RNSGktdnnspnktekrclrneiqdngvtsdevpdsclitigAIVHILEKKHFRVAaGKLQLMPNSAnpnvLFVATDSRV 235
Cdd:TIGR02063 122 RFEA--------------------------------------RVIKILERANDQIV-GTFYIENGIG----FVIPDDKRI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  236 P-RILIPKSDVDKeffsrPKDFERFLytAKITDWRAESVYADGRLVKLLGMSGEIDTETERIVYEHQIDHrEFSDECLES 314
Cdd:TIGR02063 159 YlDIFIPPEQILG-----AEEGDKVL--VEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY-EFPEEVLDE 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  315 LpiTTAENwKVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKW 394
Cdd:TIGR02063 231 A--AKIPE-EVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKD------GNYKLGVAIADVSHYVREGSALDKE 301

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  395 ASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIEnpEK 474
Cdd:TIGR02063 302 ALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIE--GK 379

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  475 DFTCDELPdisdgntpfEIKEKTLMLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKLVEEFML 554
Cdd:TIGR02063 380 DALDKKEP---------PLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMI 450

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  555 LANMEVAKKIaENFPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDGRT-----SGLLSTSLRKYQGKSRLDMcirqvIS 629
Cdd:TIGR02063 451 AANETVAEHL-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTsdkpqPKDFQKLLEKVKGRPEEEL-----IN 524

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  630 SLTIKPMQQAKYfctFEMPLSfyhHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALGYNER------SERVPEEIQEICT 703
Cdd:TIGR02063 525 TVLLRSMQQAKY---SPENIG---HFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENtttekeREYLEAKLEEIAE 598

                         650       660
                  ....*....|....*....|....*
gi 392894994  704 RCNDTKLASKEASDESAMLYFGVFI 728
Cdd:TIGR02063 599 HSSKTERRADEAERDVNDWKKAEYM 623
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
333-686 4.12e-101

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 315.36  E-value: 4.12e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   333 RRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKWASERGNSTYLSQTVIPML 412
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDN------GGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPML 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   413 PRILCEQLCSLNPGVDRLSFSTVFKMSYEA-ELYDVWFGRSVIRSRVKLAYEHAQDFIEnpekdftcdelpdisdgntpf 491
Cdd:smart00955  75 PEELSNGLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------- 133

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   492 eikektlmlhriaqvlrqkredsgalrielprlKFALDEDKKPQGVSIYEIKDSNKLVEEFMLLANMEVAKKIAENFPEh 571
Cdd:smart00955 134 ---------------------------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP- 179

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994   572 ALLRNHPPP-KEKMIKDVAEQCARIGFPL-DGRTSGLLSTSLRKYQGKSRldmciRQVISSLTIKPMQQAKYFCTFEMpl 649
Cdd:smart00955 180 GLYRVHEGPdPEKLAELLKEFLALLGLLLlGGDGPKALAKLLEKIRDSPE-----ERLLELLLLRSMPHAEYSVDNSG-- 252

                          330       340       350
                   ....*....|....*....|....*....|....*..
gi 392894994   650 sfyhHFALNVDHYTHFTSPIRRYPDVIVHRQLAAALG 686
Cdd:smart00955 253 ----HFGLALDAYTHFTSPIRRYPDLIVHRQLKAALR 285
3_prime_RNase TIGR00358
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ...
 197-717 8.73e-71

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: 246.16  E-value: 8.73e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  197 GAIVHILEKKHFRVAaGKLQLmpnsaNPNVLF-VATDSRVPR-ILIPKSDVDKEFFsrpkdfERFLYTAKITDWRAESVY 274
Cdd:TIGR00358  72 AEVERILEPALTRFV-GKFLG-----ENDFGFvVPDDPRIYLdIIVPKASVKNELA------EGDKVVVELTEYPLRRNL 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  275 ADGRLVKLLGMSGEIDTETERIVYEHQIDHrEFSDECLE---SLPITTAENWKvpdaefEYRRDFRSDIVFTIDPKTARD 351
Cdd:TIGR00358 140 FYGEITQILGNNDDPLIPWWVTLARHEIPF-EFPDGVEQqaaKLQFDVDEQAK------KYREDLTDLAFVTIDGADAKD 212

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  352 LDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLS 431
Cdd:TIGR00358 213 LDDAVYVKKLPD------GGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLV 286

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  432 FSTVFKMSYEAELYDVWFGRSVIRSRVKLAYEHAQDFIENPekdftcDELPDISDgntpfEIKEKTLMLHRIAQVLRQKR 511
Cdd:TIGR00358 287 LVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLEND------DELQPEYE-----TLVEQLKALHQLSQALGEWR 355

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  512 EDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKLVEEFMLLANMEVAKKIaENFPEHALLRNHPPPKEKMIKDVAEQ 591
Cdd:TIGR00358 356 HKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFL-HNHKVPGIYRVHPGPSKKKLQSLLEF 434

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994  592 CARIGFPLDGRTSGLLSTSLRKYQGKSRLDMCIRQVISSLTIKPMQQAKYFCTFEMplsfyhHFALNVDHYTHFTSPIRR 671
Cdd:TIGR00358 435 LAELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYSPEPLG------HFGLGLEHYAHFTSPIRR 508

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 392894994  672 YPDVIVHRQLAAAL---GYNERSERVPEEIQEICTRCNDTK----LASKEASD 717
Cdd:TIGR00358 509 YPDLTNHRLIKAVLakeQTDTERYQPQDELLQIAEHCSDTErrarDAERDVAD 561
PRK11642 PRK11642
ribonuclease R;
229-691 1.31e-44

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 173.00  E-value: 1.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 229 VATDSRVP-RILIPKSDVDKEFFSrpkdferFLYTAKITDWRAESVYADGRLVKLLG------MSGEIDTETerivyeHQ 301
Cdd:PRK11642 166 VPDDSRLSfDILIPPEQIMGARMG-------FVVVVELTQRPTRRTKAVGKIVEVLGdnmgtgMAVDIALRT------HE 232

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 302 IDHrEFSDECLESLPITTAEnwkVPDAEFEYRRDFRSDIVFTIDPKTARDLDDALHakhiddCDGKGTPGLEIGVHIADV 381
Cdd:PRK11642 233 IPY-IWPQAVEQQVAGLKEE---VPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVY------CEKKRGGGWRLWVAIADV 302

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 382 TFFLKEGTELDKWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFSTVFKMSYEAELYDVWFGRSVIRSRVKLA 461
Cdd:PRK11642 303 SYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLT 382

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 462 YEHAQDFIENPEkdftcdelpDISDGNTPF--EIKEktlmLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSI 539
Cdd:PRK11642 383 YTKVWHILQGDQ---------DLREQYAPLvkHLEE----LHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIEQ 449

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 540 YEIKDSNKLVEEFMLLANMEVAKKIAENfPEHALLRNHPPPKEKMIKDVAEQCARIGFPLDG------RTSGLLSTSLrk 613
Cdd:PRK11642 450 TQRNDAHKLIEECMILANISAARFVEKA-KEPALFRIHDKPSTEAITSFRSVLAELGLELPGgnkpepRDYAELLESV-- 526

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 614 yqgKSRLDmciRQVISSLTIKPMQQAKYfctfeMPLSfYHHFALNVDHYTHFTSPIRRYPDVIVHR----QLAAALGYNE 689
Cdd:PRK11642 527 ---ADRPD---AEMLQTMLLRSMKQAIY-----DPEN-RGHFGLALQSYAHFTSPIRRYPDLSLHRaikyLLAKEQGHKG 594


                 ..
gi 392894994 690 RS 691
Cdd:PRK11642 595 NT 596
PRK05054 PRK05054
exoribonuclease II; Provisional
 312-698 3.97e-40

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 157.73  E-value: 3.97e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 312 LESLPITTAENWKVPDAEFEyRRDFRSDIVFTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTEL 391
Cdd:PRK05054 170 LEREAPAGGVAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPD------GGLQLTVAIADPTAYIAEGSKL 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 392 DKWASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDRLSFstVFKMSYEAE---LYDVWFGRSVIRSRVKLAYEHAQDF 468
Cdd:PRK05054 243 DKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPAL--ACRVTIDADgtiEDDIRFFAAWIESKAKLAYDNVSDW 320

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 469 IENPEkdftcDELPDiSDgntpfEIKEKTLMLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKL 548
Cdd:PRK05054 321 LENGG-----DWQPE-SE-----AIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRI 389

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 549 VEEFMLLANMEVAKKIAENF------------PE-----HALLRNHPPPKEkmikdvAEQCARI-GF-----PLDGRTSG 605
Cdd:PRK05054 390 VEESMIAANICAARVLRDKLgfgiynvhsgfdPAnaeqaVALLKEHGLHFD------AEELLTLeGFcklrrELDAQPTG 463

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 606 LLSTSLRKYQGKSRLdmcirqvisSLTIKPmqqakyfctfemplsfyhHFALNVDHYTHFTSPIRRYPDVIVHRQLAAAL 685
Cdd:PRK05054 464 YLDSRIRRFQSFAEI---------STEPGP------------------HFGLGLEAYATWTSPIRKYGDMINHRLLKAVI 516

                        410
                 ....*....|...
gi 392894994 686 GyNERSERVPEEI 698
Cdd:PRK05054 517 K-GETAERPQDEI 528
Rnb COG4776
Exoribonuclease II [Transcription];
323-700 5.91e-38

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 151.16  E-value: 5.91e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 323 WKVPDAEFEY-RRDF---RSDIV----FTIDPKTARDLDDALHAKHIDDcdgkgtPGLEIGVHIADVTFFLKEGTELDKW 394
Cdd:COG4776  172 REAPEGDDEWeLLDEgleREDLTalpfVTIDSESTEDMDDALYIEKLEN------GGWKLTVAIADPTAYIPEGSELDKE 245

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 395 ASERGNSTYLSQTVIPMLPRILCEQLCSLNPGVDR---LSFSTVFK---MSYEAELYDVWfgrsvIRSRVKLAYEHAQDF 468
Cdd:COG4776  246 ARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRpalVCRVTIDAdgsIGDDIEFFAAW-----IRSKAKLAYDNVSDW 320

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 469 IENpekdfTCDELPDiSDgntpfEIKEKTLMLHRIAQVLRQKREDSGALRIELPRLKFALDEDKKPQGVSIYEIKDSNKL 548
Cdd:COG4776  321 LEG-----KGEWQPE-NE-----EIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRI 389

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 549 VEEFMLLANMEVAKKIAENF------------PE-----HALLRNHPPPKEKmikdvaEQCARI-GF-----PLDGRTSG 605
Cdd:COG4776  390 VEEAMIAANICAARVLREHLgfgifnvhsgfdPEkleqaVELLAEHGIEFDP------EQLLTLeGFcalrrELDAQPTS 463

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392894994 606 LLSTSLRKYQGKSRLdmcirqvisSLTIKPmqqakyfctfemplsfyhHFALNVDHYTHFTSPIRRYPDVIVHRQLAAAL 685
Cdd:COG4776  464 YLDSRLRRFQTFAEI---------STEPGP------------------HFGLGLDAYATWTSPIRKYGDMVNHRLIKAVI 516

                        410
                 ....*....|....*
gi 392894994 686 GyNERSERVPEEIQE 700
Cdd:COG4776  517 L-GQPAEKPDEELTE 530
OB_Dis3 pfam17849
Dis3-like cold-shock domain 2 (CSD2); This domain has an OB fold and is found in the Dis3l2 ...
 225-301 6.75e-27

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: 104.23  E-value: 6.75e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392894994  225 NVLFVATDSRVPRILIPKSDVDKEFFSRPKDFERFLYTAKITDWRAESVYADGRLVKLLGMSGEIDTETERIVYEHQ 301
Cdd:pfam17849   1 YVLFVPRDKRIPRIRIPTKSAPEEFLENPEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
Dis3l2_C_term pfam17877
DIS3-like exonuclease 2 C terminal; This is the C-terminal S1 domain found in Dis3L2 proteins. ...
 732-802 1.48e-20

DIS3-like exonuclease 2 C terminal; This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans.


Pssm-ID: 465547  Cd Length: 87  Bit Score: 86.55  E-value: 1.48e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392894994  732 GPMKCQAVVLGVMDLSFDVLIVEYGVVKRVYVDKM---KRDFNKsTEKLTIYW-PADPNAESGNREEFSSSIQMC 802
Cdd:pfam17877   1 GPLETEAVVLGVLDSSFDVLIPEYGIEKRVYLDQLplkKFEFDK-TGVLTLYWkKGVPSSAYVPEDERFSSLVVV 74
Rrp44_CSD1 pfam17216
Rrp44-like cold shock domain;
65-137 6.18e-06

Rrp44-like cold shock domain;


Pssm-ID: 375054  Cd Length: 148  Bit Score: 46.69  E-value: 6.18e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392894994   65 FTEYISKEETDAGIEDGSMFKGVLRINPKNYQECFLDHPKGTNhpDVLVLGQ-DRNRAMQGDVVAVKIKPKEDW 137
Cdd:pfam17216   4 FPEYYSTARVMGGLKNGVLYQGNIQISEYNFLEGSVSLPRFSK--PVLIVGQkNLNRAFNGDQVIVELLPQSEW 75
 
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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