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Conserved domains on  [gi|5262619|emb|CAB45749|]
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hypothetical protein, partial [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];
14-603 6.88e-140

Exoribonuclease R [Transcription];


The actual alignment was detected with superfamily member COG0557:

Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 424.13  E-value: 6.88e-140
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   14 KPTGRVVGIIKRNWRPYCGMLsksdIKESRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFV 91
Cdd:COG0557 121 RPEGRVVEILERANTRVVGRF----EKEKGFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVV 196
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   92 RNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELEN 171
Cdd:COG0557 197 EVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN 275
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  172 GNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKF 251
Cdd:COG0557 276 GGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEF 355
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  252 TKSVINSKASLTYAEAQLRIDS-----ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQ 326
Cdd:COG0557 356 YRSVIRSDARLTYEEVQAILDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIV 434
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  327 TKELRETNSMVEEFMLLANISVAkkihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLD 400
Cdd:COG0557 435 PRERNDAHKLIEEFMLLANEAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLE 510
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  401 QAE-SPTFPYLNTLLRilatRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT 479
Cdd:COG0557 511 QVKgRPEEELLNTLLL----RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQ 581
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  480 --DKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV---- 547
Cdd:COG0557 582 eyLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvss 655
                       570       580       590       600       610       620
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 5262619  548 ----FFEekdkpnpqliYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 603
Cdd:COG0557 656 lgddYYE----------YDERRQALVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
14-603 6.88e-140

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 424.13  E-value: 6.88e-140
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   14 KPTGRVVGIIKRNWRPYCGMLsksdIKESRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFV 91
Cdd:COG0557 121 RPEGRVVEILERANTRVVGRF----EKEKGFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVV 196
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   92 RNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELEN 171
Cdd:COG0557 197 EVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN 275
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  172 GNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKF 251
Cdd:COG0557 276 GGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEF 355
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  252 TKSVINSKASLTYAEAQLRIDS-----ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQ 326
Cdd:COG0557 356 YRSVIRSDARLTYEEVQAILDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIV 434
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  327 TKELRETNSMVEEFMLLANISVAkkihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLD 400
Cdd:COG0557 435 PRERNDAHKLIEEFMLLANEAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLE 510
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  401 QAE-SPTFPYLNTLLRilatRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT 479
Cdd:COG0557 511 QVKgRPEEELLNTLLL----RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQ 581
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  480 --DKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV---- 547
Cdd:COG0557 582 eyLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvss 655
                       570       580       590       600       610       620
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 5262619  548 ----FFEekdkpnpqliYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 603
Cdd:COG0557 656 lgddYYE----------YDERRQALVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
141-465 1.53e-123

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 368.15  E-value: 1.53e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    221 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 297
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    298 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 377
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    378 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 457
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302

                  ....*...
gi 5262619    458 DVIVHRLL 465
Cdd:pfam00773 303 DLIVHRQL 310
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
14-602 6.92e-111

ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA]


Pssm-ID: 273947 [Multi-domain]  Cd Length: 709  Bit Score: 348.88  E-value: 6.92e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     14 KPTGRVVGIIKRNWRPYCGMLSKSD-IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHF 90
Cdd:TIGR02063 122 RFEARVIKILERANDQIVGTFYIENgIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKV 196
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     91 VRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELE 170
Cdd:TIGR02063 197 VEILGHADDPGIDILIIIRKHGIPYE-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLK 275
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    171 NGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTK 250
Cdd:TIGR02063 276 DGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYE 355
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    251 FTKSVINSKASLTYAEAQ----LRIDSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQ 326
Cdd:TIGR02063 356 FYEAVINSHARLTYNQVNdiieGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIV 434
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    327 TKELRETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ 401
Cdd:TIGR02063 435 PRERGDAHKLIEEFMIAANETVAEHL-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEK 513
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    402 -AESPTFPYLNTLLrilaTRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTD 480
Cdd:TIGR02063 514 vKGRPEEELINTVL----LRSMQQAKY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKE 585
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    481 KH----KLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFF 549
Cdd:TIGR02063 586 REyleaKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI 658
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 5262619    550 eeKDKPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLV 602
Cdd:TIGR02063 659 --STLKDDYYVFDEKGLALVGERTgkVFRLGDRVKVRVV--KADLDTGKIDFELV 709
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
141-470 5.68e-106

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 321.91  E-value: 5.68e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     221 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 299
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     300 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 378
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     379 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 457
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
                          330
                   ....*....|...
gi 5262619     458 DVIVHRLLAVAIG 470
Cdd:smart00955 273 DLIVHRQLKAALR 285
PRK11642 PRK11642
ribonuclease R;
88-463 1.95e-49

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 184.56  E-value: 1.95e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    88 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 167
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   168 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 245
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   246 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 317
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   318 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 392
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5262619   393 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 463
Cdd:PRK11642 514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
 
Name Accession Description Interval E-value
VacB COG0557
Exoribonuclease R [Transcription];
14-603 6.88e-140

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 424.13  E-value: 6.88e-140
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   14 KPTGRVVGIIKRNWRPYCGMLsksdIKESRRHLFTPADKRIPR-IRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHFV 91
Cdd:COG0557 121 RPEGRVVEILERANTRVVGRF----EKEKGFGFVVPDDKRLLQdIFIPPDDLNGAKdGDLVVVEITRYPERRGPPEGRVV 196
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   92 RNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELEN 171
Cdd:COG0557 197 EVLGSPGDPGAEILIAIRKHGLPHE-FPEEVLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDN 275
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  172 GNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTKF 251
Cdd:COG0557 276 GGWRLGVHIADVSHYVRPGSALDREARKRGTSVYLPDRVIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEF 355
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  252 TKSVINSKASLTYAEAQLRIDS-----ANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQ 326
Cdd:COG0557 356 YRSVIRSDARLTYEEVQAILDGkdeelREEYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILD-EEGKPEDIV 434
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  327 TKELRETNSMVEEFMLLANISVAkkihEEFSEH---ALLRKHPAPPPSNYEILVKAARSRNLEIKTD---TAKSLAESLD 400
Cdd:COG0557 435 PRERNDAHKLIEEFMLLANEAVA----EFLEKLklpFLYRVHEEPDPEKLEALREFLANLGLKLKGGdepTPKDLQKLLE 510
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  401 QAE-SPTFPYLNTLLRilatRCMMQAVYfcsGMDNdFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADcTYPELT 479
Cdd:COG0557 511 QVKgRPEEELLNTLLL----RSMKQAVY---SPEN-IGHFGLALEAYTHFTSPIRRYPDLLVHRALKAYLEGK-RSPGLQ 581
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  480 --DKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSEeayilfVRKNAIVVLIPKYGLEGTV---- 547
Cdd:COG0557 582 eyLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKDRvgeefeGVISG------VTSFGLFVELDELGVEGLVhvss 655
                       570       580       590       600       610       620
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 5262619  548 ----FFEekdkpnpqliYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLVE 603
Cdd:COG0557 656 lgddYYE----------YDERRQALVGERTgkRYRLGDRVEVRVV--RVDLDRRQIDFELVE 705
RNB pfam00773
RNB domain; This domain is the catalytic domain of ribonuclease II.
141-465 1.53e-123

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


Pssm-ID: 459934 [Multi-domain]  Cd Length: 314  Bit Score: 368.15  E-value: 1.53e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:pfam00773   1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGGYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDRVIPMLPEKLSN 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    221 NLCSLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDD---ITTSLRGLNKLAKILKKR 297
Cdd:pfam00773  81 DLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDkpdLAEDLRLLYELAKILRAK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    298 RIEKGALTLSSPEVRFHMDSEThdPIDLQTKELRETNSMVEEFMLLANISVAKKIHeEFSEHALLRKHPAPPPSNYEILV 377
Cdd:pfam00773 161 RLQRGALDLDTPENKLILDEEG--VIDILIQERTDAHSLIEEFMLLANEAVARHLQ-ELGIPALYRVHPEPDLEKLNSLI 237
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    378 KAARSRnleiktDTAKSLAESLDQAESPtfpylNTLLRILATRCMMQAVYFcsgmDNDFHHYGLASPIYTHFTSPIRRYA 457
Cdd:pfam00773 238 KLLQLL------PDDKGLSKSLEKIKDD-----ERLLSILLLRTMPRAEYS----PEPLGHFGLGLDIYTHFTSPIRRYP 302

                  ....*...
gi 5262619    458 DVIVHRLL 465
Cdd:pfam00773 303 DLIVHRQL 310
RNase_R TIGR02063
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ...
14-602 6.92e-111

ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA]


Pssm-ID: 273947 [Multi-domain]  Cd Length: 709  Bit Score: 348.88  E-value: 6.92e-111
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     14 KPTGRVVGIIKRNWRPYCGMLSKSD-IKEsrrhlFTPADKRIP-RIRIETRQASTLE-GRRIIVAIDGWPRNSRYPNGHF 90
Cdd:TIGR02063 122 RFEARVIKILERANDQIVGTFYIENgIGF-----VIPDDKRIYlDIFIPPEQILGAEeGDKVLVEITKYPDRNRPAIGKV 196
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     91 VRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELE 170
Cdd:TIGR02063 197 VEILGHADDPGIDILIIIRKHGIPYE-FPEEVLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLK 275
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    171 NGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEILKTK 250
Cdd:TIGR02063 276 DGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYE 355
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    251 FTKSVINSKASLTYAEAQ----LRIDSANMNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHdPIDLQ 326
Cdd:TIGR02063 356 FYEAVINSHARLTYNQVNdiieGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGK-PIDIV 434
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    327 TKELRETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIK-----TDTAKSLAESLDQ 401
Cdd:TIGR02063 435 PRERGDAHKLIEEFMIAANETVAEHL-EKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKggtsdKPQPKDFQKLLEK 513
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    402 -AESPTFPYLNTLLrilaTRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTD 480
Cdd:TIGR02063 514 vKGRPEEELINTVL----LRSMQQAKY----SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKE 585
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    481 KH----KLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSK------GIVSE-EAYILFVRknaivvlIPKYGLEGTVFF 549
Cdd:TIGR02063 586 REyleaKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKigeefeGVISGvTSFGLFVE-------LENNTIEGLVHI 658
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 5262619    550 eeKDKPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKIMldSSNLQHQKIRMSLV 602
Cdd:TIGR02063 659 --STLKDDYYVFDEKGLALVGERTgkVFRLGDRVKVRVV--KADLDTGKIDFELV 709
RNB smart00955
This domain is the catalytic domain of ribonuclease II;
141-470 5.68e-106

This domain is the catalytic domain of ribonuclease II;


Pssm-ID: 214935 [Multi-domain]  Cd Length: 286  Bit Score: 321.91  E-value: 5.68e-106
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     141 REDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSS 220
Cdd:smart00955   1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDRVIPMLPEELSN 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     221 NLCSLKCDVDRLAFSCIWEMNHNA-EILKTKFTKSVINSKASLTYAEAQLRIDsanmnddittslrglnklakilkkrri 299
Cdd:smart00955  81 GLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE--------------------------- 133
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     300 ekgaltlsspevRFHMDSETHdPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEFSEhALLRKHPAPPPSNYEILVK- 378
Cdd:smart00955 134 ------------KIVLDEEGK-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIP-GLYRVHEGPDPEKLAELLKe 199
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     379 -AARSRNLEIKTDTAKSLAESLDQAESPTFpylNTLLRILATRCMMQAVYFCSGMDndfhHYGLASPIYTHFTSPIRRYA 457
Cdd:smart00955 200 fLALLGLLLLGGDGPKALAKLLEKIRDSPE---ERLLELLLLRSMPHAEYSVDNSG----HFGLALDAYTHFTSPIRRYP 272
                          330
                   ....*....|...
gi 5262619     458 DVIVHRLLAVAIG 470
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 ...
68-585 1.89e-77

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: 1.89e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     68 EGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHL 147
Cdd:TIGR00358 122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFE-FPDGVEQQAAKLQFDVDEQAKKYREDLTDL 200
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    148 CICSVDPPGCTDIDDALHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKC 227
Cdd:TIGR00358 201 AFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNP 280
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    228 DVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAE-AQLRIDSANMNDDITT---SLRGLNKLAKILKKRRIEKGA 303
Cdd:TIGR00358 281 NEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKvNDWLENDDELQPEYETlveQLKALHQLSQALGEWRHKRGL 360
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    304 LTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVEEFMLLANISVAKKIHEEfSEHALLRKHPAPPPSNYEILVKAARSR 383
Cdd:TIGR00358 361 IDFEHPETKFIVD-EEGRVIDIVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAEL 438
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    384 NLEIK-----TDTAKSLAESLDQ-AESPTFPYLNTLLRilatRCMMQAVYfcsgMDNDFHHYGLASPIYTHFTSPIRRYA 457
Cdd:TIGR00358 439 GLTLPggnaeNVTTLDGACWLREvKDRPEYEILVTRLL----RSLSQAEY----SPEPLGHFGLGLEHYAHFTSPIRRYP 510
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    458 DVIVHRLLAVAIGADCTYPELTD-KHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKG-------IVSEEAYILFV 529
Cdd:TIGR00358 511 DLTNHRLIKAVLAKEQTDTERYQpQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVgtefsgeISSVTRFGMFV 590
                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    530 R--KNAIVVLIPKYGLegtvffeekdkPNPQLIYDDEIPSLKIEDT--VFHVFDKVKVKI 585
Cdd:TIGR00358 591 RldDNGIDGLIHISTL-----------HNDYYVFDQEKMALIGKGTgkVYRIGDRVTVKL 639
PRK11642 PRK11642
ribonuclease R;
88-463 1.95e-49

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 184.56  E-value: 1.95e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    88 GHFVRNLGDVGEKETETEVLLLEHDVPHQpFSQAVLSFLPKMPWSITEKDMKNREDLRHLCICSVDPPGCTDIDDALHCR 167
Cdd:PRK11642 208 GKIVEVLGDNMGTGMAVDIALRTHEIPYI-WPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCE 286
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   168 ELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCiwEMNHNAE-- 245
Cdd:PRK11642 287 KKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVC--EMTISSKgr 364
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   246 ILKTKFTKSVINSKASLTY--------AEAQLRIDSAnmndDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDS 317
Cdd:PRK11642 365 LTGYKFYEAVMSSHARLTYtkvwhilqGDQDLREQYA----PLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNA 440
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   318 ETHdpIDLQTKELR-ETNSMVEEFMLLANISVAKKIhEEFSEHALLRKHPAPPPSNyeilVKAARS----RNLEIKTDTA 392
Cdd:PRK11642 441 ERR--IERIEQTQRnDAHKLIEECMILANISAARFV-EKAKEPALFRIHDKPSTEA----ITSFRSvlaeLGLELPGGNK 513
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 5262619   393 ---KSLAESLDQ-AESPTFPYLNTLLrilaTRCMMQAVYfcsgmDNDFH-HYGLASPIYTHFTSPIRRYADVIVHR 463
Cdd:PRK11642 514 pepRDYAELLESvADRPDAEMLQTML----LRSMKQAIY-----DPENRgHFGLALQSYAHFTSPIRRYPDLSLHR 580
Rnb COG4776
Exoribonuclease II [Transcription];
106-503 8.66e-40

Exoribonuclease II [Transcription];


Pssm-ID: 443808 [Multi-domain]  Cd Length: 644  Bit Score: 154.63  E-value: 8.66e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  106 VLLLEHDVPHQPfsqavlsflPKMP--WSItEKDMKNREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 183
Cdd:COG4776 163 VTLARHNLEREA---------PEGDdeWEL-LDEGLEREDLTALPFVTIDSESTEDMDDALYIEKLENGGWKLTVAIADP 232
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  184 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 262
Cdd:COG4776 233 TAYIPEGSELDKEARQRAFTNYLPGFNIPMLPRELSDDLCSLKENEKRPALVCRVTIDADGSIGdDIEFFAAWIRSKAKL 312
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  263 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDsETHDPIDLQTKELRETNSMVE 338
Cdd:COG4776 313 AYDNVSDWLEGKGewqpENEEIAEQIRLLHQFALARSQWRQQHALVFKDRPDYRFELD-EKGNVLDIHAEPRRIANRIVE 391
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  339 EFMLLANISVAKKIHEE-----FSEHALLRkhpappPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESPtf 407
Cdd:COG4776 392 EAMIAANICAARVLREHlgfgiFNVHSGFD------PEKLEQAVELLAEHGIEFDPEQLLTLEgfcalrRELDAQPTS-- 463
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619  408 pYLNTLLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklAD 486
Cdd:COG4776 464 -YLDSRLRRFQTFAEISTE---PG-----PHFGLGLDAYATWTSPIRKYGDMVNHRLIkAVILGQPAEKPD-------EE 527
                       410
                ....*....|....*..
gi 5262619  487 ICKNLNFRHKMAQYAQR 503
Cdd:COG4776 528 LTERLAERRRLNRMAER 544
PRK05054 PRK05054
exoribonuclease II; Provisional
106-498 9.64e-38

exoribonuclease II; Provisional


Pssm-ID: 179920 [Multi-domain]  Cd Length: 644  Bit Score: 148.87  E-value: 9.64e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   106 VLLLEHDVPHQPfsqavlsflPKM--PWSITEKDMKnREDLRHLCICSVDPPGCTDIDDALHCRELENGNLEVGVHIADV 183
Cdd:PRK05054 163 VTLARHNLEREA---------PAGgvAWEMLDEGLE-REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADP 232
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   184 SHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSCIWEMNHNAEIL-KTKFTKSVINSKASL 262
Cdd:PRK05054 233 TAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEdDIRFFAAWIESKAKL 312
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   263 TYAEAQLRIDSAN----MNDDITTSLRGLNKLAKILKKRRIEKGALTLSSPEVRFHMdSETHDPIDLQTKELRETNSMVE 338
Cdd:PRK05054 313 AYDNVSDWLENGGdwqpESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFEL-GEKGEVLDIVAEPRRIANRIVE 391
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   339 EFMLLANISVAKKIHEEFsEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLA------ESLDQAESptfPYLNT 412
Cdd:PRK05054 392 ESMIAANICAARVLRDKL-GFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEgfcklrRELDAQPT---GYLDS 467
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619   413 LLRILATRCMMQAVyfcSGmdndfHHYGLASPIYTHFTSPIRRYADVIVHRLL-AVAIGADCTYPEltdkhklADICKNL 491
Cdd:PRK05054 468 RIRRFQSFAEISTE---PG-----PHFGLGLEAYATWTSPIRKYGDMINHRLLkAVIKGETAERPQ-------DEITVQL 532
                        410
                 ....*....|
gi 5262619   492 NFR---HKMA 498
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 ...
46-112 3.56e-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: 3.56e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 5262619     46 LFTPADKRIPRIRIETRQA--------STLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETEVLLLEHD 112
Cdd:pfam17849   3 LFVPRDKRIPRIRIPTKSApeeflenpEDLEGKLFVVKIDDWPENSRYPLGHIVKVLGEIGDIETETEAILLENG 77
Rrp44_S1 pfam17215
S1 domain; This domain corresponds to the S1 domain found at the C-terminus of ribonucleases ...
520-599 2.89e-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: 71.41  E-value: 2.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619    520 VSEEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTV------FHVFDKVKVKIM--LDSSN 591
Cdd:pfam17215   1 SEEEGYVIKVFNNGIVVFVPKFGIEGLIRLEDLTGDEPEAEFDADEYSLTFPDKGsgkkrtVGVFDKVRVRVKsvKDENT 80

                  ....*...
gi 5262619    592 lQHQKIRM 599
Cdd:pfam17215  81 -GKRKVKL 87
CSD2 pfam17876
Cold shock domain; Crystallographic structure analysis of E. coli wild-type RNase II revealed ...
48-115 6.18e-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: 6.18e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5262619     48 TPADKRIPR-IRIETRQASTL-EGRRIIVAIDGWPrNSRYPNGHFVRNLGDVGEKETETEVLLLEHDVPH 115
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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