|
Name |
Accession |
Description |
Interval |
E-value |
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
66-726 |
0e+00 |
|
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: 1015.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 66 QLLINYELADPVLDQKFQGILNLGNKNTGFVRPLDDDKTVYYIHFSNLAGALDGDLVEFCPLDKPQVGDkFDAAVLKIVK 145
Cdd:TIGR00358 1 QLLATLKYALPEKDDLVKGVVKAHNKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGR-FEAEVERILE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 146 RSRVLYAGNFLIEYsDFGQefrIVADNPRFYLTPIVNKASVPAELESNTKVAFQIDEYDPANNLCKVSIQQILGNNDEPL 225
Cdd:TIGR00358 80 PALTRFVGKFLGEN-DFGF---VVPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 226 INLKAIMLDHSIVFEDNDVVEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYVKR-TDKGFVLYVAIAD 304
Cdd:TIGR00358 156 IPWWVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKlPDGGWKLYVAIAD 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 305 VAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRR 384
Cdd:TIGR00358 236 VSYYVAENSPLDKEAKHRGFSVYLPGF-VIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKAR 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 385 FAYSEVNDWLEDSDALKDESATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIE 464
Cdd:TIGR00358 315 LTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIE 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 465 NLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQMLLENIVELKITQPNFVLDTVTSTQIAAWLKENKDNPSYDIFVIL 544
Cdd:TIGR00358 395 EAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTR 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 545 LLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYADLTVHRLLWMNLFTPErfTDTEREQLNAELEQICETINDTEIKI 624
Cdd:TIGR00358 475 LLRSLSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ--TDTERYQPQDELLQIAEHCSDTERRA 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 625 NGCERTANDYLTTLYLSKQVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIG 704
Cdd:TIGR00358 553 RDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIG 632
|
650 660
....*....|....*....|..
gi 1802581771 705 DRLTAKLTEIDTVQKRAILTLV 726
Cdd:TIGR00358 633 DRVTVKLTEVNMETRSIIFELV 654
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
6-726 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 613.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 6 DLQKRIFAIVKKENGKPIPPGIVVRMMeNQAGFPGKQQVYRAIDDLL-EWHIFRKSGGAtnqllinYELADPvlDQKFQG 84
Cdd:COG0557 3 NSRETILAFLKEDAYKPLSKKELAKAL-GLKDEESREALKRRLRALErEGQLVKTRRGR-------YRLPEK--LDLVEG 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 85 ILNLGNKNTGFVRPlDDDKTVYYIHFSNLAGALDGDLVEFCpLDKPQVGDKFDAAVLKIVKRSRVLYAGNFLIEySDFGq 164
Cdd:COG0557 73 RVRGHRDGFGFVIP-DDGEEDIFIPPRELNGALHGDRVLVR-VTKEDRRGRPEGRVVEILERANTRVVGRFEKE-KGFG- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 165 efRIVADNPRFYLTPIVNKASVpAELESNTKVAFQIDEYDPANNLCKVSIQQILGNNDEPLINLKAIMLDHSIVFEDNDV 244
Cdd:COG0557 149 --FVVPDDKRLLQDIFIPPDDL-NGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEE 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 245 VEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKT 323
Cdd:COG0557 226 VLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGgWRLGVHIADVSHYVRPGSALDREARKRG 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 324 SSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRRFAYSEVNDWLEDSD-ALKD 402
Cdd:COG0557 306 TSVYLPDR-VIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDeELRE 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 403 ESATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHK 482
Cdd:COG0557 385 EYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLK 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 483 VHLPYRVHPRPSKKKLQMLLENIVELKITQPNFvlDTVTSTQIAAWLKENKDNPSYDIFVILLLRTLGKAFYIVNPLIHF 562
Cdd:COG0557 465 LPFLYRVHEEPDPEKLEALREFLANLGLKLKGG--DEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHF 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 563 SIGSHHYTHFTSPIRRYADLTVHRLLWMNLFtpERFTDTEREQLNAELEQICETINDTEIKINGCERTANDYLTTLYLSK 642
Cdd:COG0557 543 GLALEAYTHFTSPIRRYPDLLVHRALKAYLE--GKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKD 620
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:COG0557 621 RVGEEFEGVISGVTSFGLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQID 700
|
....
gi 1802581771 723 LTLV 726
Cdd:COG0557 701 FELV 704
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
264-592 |
3.99e-105 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 323.47 E-value: 3.99e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 264 RKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLS 342
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGgYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDR-VIPMLPEKLS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 343 NELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRRFAYSEVNDWLEDSDALKDEsATVLESLKAGFTLSELIA 422
Cdd:pfam00773 80 NDLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 423 EQRKKKGTIDLSHSETEVVVDQNyYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQMLL 502
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEE-GVIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 503 ENIVELkitqpnfvldtVTSTQIAAWLKENKDNpsYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYADL 582
Cdd:pfam00773 238 KLLQLL-----------PDDKGLSKSLEKIKDD--ERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDL 304
|
330
....*....|
gi 1802581771 583 TVHRLLWMNL 592
Cdd:pfam00773 305 IVHRQLKALL 314
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
264-592 |
1.41e-98 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 305.35 E-value: 1.41e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 264 RKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLS 342
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGgYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDR-VIPMLPEELS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 343 NELCSLNPNEKRYVVVCELNFDHEA-RLNFSEVYPATIVSQRRFAYSEVNDWLEdsdalkdesatvleslkagftlseli 421
Cdd:smart00955 80 NGLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE-------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 422 aeqrkkkgtidlshsetEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQML 501
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 502 LENIVELKitqPNFVLDTVTSTQIAAWLKENKDNPSYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYAD 581
Cdd:smart00955 197 LKEFLALL---GLLLLGGDGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273
|
330
....*....|.
gi 1802581771 582 LTVHRLLWMNL 592
Cdd:smart00955 274 LIVHRQLKAAL 284
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
214-711 |
4.14e-75 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 258.90 E-value: 4.14e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 214 IQQILGNNDEPLINLKAIMLDHSIVFEDNDVVEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYV-KRT 292
Cdd:PRK11642 210 IVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCeKKR 289
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 293 DKGFVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFS 372
Cdd:PRK11642 290 GGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQ-VVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGY 368
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 373 EVYPATIVSQRRFAYSEVNDWLEDSDALKDESATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIR 452
Cdd:PRK11642 369 KFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIE 448
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 453 FLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQMLLENIVELKITQPNFvlDTVTSTQIAAWLKEN 532
Cdd:PRK11642 449 QTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGG--NKPEPRDYAELLESV 526
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 533 KDNPSYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYADLTVHR----LLWMNLFTPERFTDT-----ER 603
Cdd:PRK11642 527 ADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRaikyLLAKEQGHKGNTTETggyhySM 606
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 604 EQLnAELEQICETindTEIKINGCERTANDYLTTLYLSKQVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFF 683
Cdd:PRK11642 607 EEM-LQLGQHCSM---TERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYY 682
|
490 500
....*....|....*....|....*...
gi 1802581771 684 VFEKDRMVLRGKRTNKVFRIGDRLTAKL 711
Cdd:PRK11642 683 RFDQVGQRLIGESSGQTYRLGDRVEVRV 710
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
644-726 |
4.19e-23 |
|
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Pssm-ID: 239917 [Multi-domain] Cd Length: 83 Bit Score: 93.62 E-value: 4.19e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 644 VGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLTEIDTVQKRAIL 723
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 1802581771 724 TLV 726
Cdd:cd04471 81 ELV 83
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| 3_prime_RNase |
TIGR00358 |
VacB and RNase II family 3'-5' exoribonucleases; This model is defined to identify a pair of ... |
66-726 |
0e+00 |
|
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: 1015.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 66 QLLINYELADPVLDQKFQGILNLGNKNTGFVRPLDDDKTVYYIHFSNLAGALDGDLVEFCPLDKPQVGDkFDAAVLKIVK 145
Cdd:TIGR00358 1 QLLATLKYALPEKDDLVKGVVKAHNKGFGFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPLSQPQRGR-FEAEVERILE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 146 RSRVLYAGNFLIEYsDFGQefrIVADNPRFYLTPIVNKASVPAELESNTKVAFQIDEYDPANNLCKVSIQQILGNNDEPL 225
Cdd:TIGR00358 80 PALTRFVGKFLGEN-DFGF---VVPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 226 INLKAIMLDHSIVFEDNDVVEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYVKR-TDKGFVLYVAIAD 304
Cdd:TIGR00358 156 IPWWVTLARHEIPFEFPDGVEQQAAKLQFDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKlPDGGWKLYVAIAD 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 305 VAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRR 384
Cdd:TIGR00358 236 VSYYVAENSPLDKEAKHRGFSVYLPGF-VIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKAR 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 385 FAYSEVNDWLEDSDALKDESATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIE 464
Cdd:TIGR00358 315 LTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEEGRVIDIVAEVRRIAEKIIE 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 465 NLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQMLLENIVELKITQPNFVLDTVTSTQIAAWLKENKDNPSYDIFVIL 544
Cdd:TIGR00358 395 EAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTR 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 545 LLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYADLTVHRLLWMNLFTPErfTDTEREQLNAELEQICETINDTEIKI 624
Cdd:TIGR00358 475 LLRSLSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQ--TDTERYQPQDELLQIAEHCSDTERRA 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 625 NGCERTANDYLTTLYLSKQVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIG 704
Cdd:TIGR00358 553 RDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIG 632
|
650 660
....*....|....*....|..
gi 1802581771 705 DRLTAKLTEIDTVQKRAILTLV 726
Cdd:TIGR00358 633 DRVTVKLTEVNMETRSIIFELV 654
|
|
| RNase_R |
TIGR02063 |
ribonuclease R; This family consists of an exoribonuclease, ribonuclease R, also called VacB. ... |
5-726 |
0e+00 |
|
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: 907.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 5 TDLQKRIFAIVKKENGKPIPPGIVVRMMEnQAGFPGKQQVYRAIDDLLEWHIFRKSggaTNQLLINYELADpvldqKFQG 84
Cdd:TIGR02063 1 SPLRELILEFLKSKKGKPISLKELAKAFH-LKGADEKKALRKRLRALEDDGLVKKN---RRGLYALPESLK-----LVKG 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 85 ILNLGNKNTGFVRPLDDDKTVYYIHFSNLAGALDGDLVEFCPLDKPQVGDKFDAAVLKIVKRSRVLYAGNFLIEYsdfGQ 164
Cdd:TIGR02063 72 TVIAHRDGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPDGGDRFEARVIKILERANDQIVGTFYIEN---GI 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 165 EFRIVaDNPRFYLTPIVNKAsVPAELESNTKVAFQIDEYDPANNLCKVSIQQILGNNDEPLINLKAIMLDHSIVFEDNDV 244
Cdd:TIGR02063 149 GFVIP-DDKRIYLDIFIPPE-QILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEE 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 245 VEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKT 323
Cdd:TIGR02063 227 VLDEAAKIPEEVPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGnYKLGVAIADVSHYVREGSALDKEALKRG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 324 SSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRRFAYSEVNDWLEDSDALKDE 403
Cdd:TIGR02063 307 TSVYLPDR-VIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKK 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 404 SATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKV 483
Cdd:TIGR02063 386 EPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDENGKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEKAKL 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 484 HLPYRVHPRPSKKKLQMLLENIVELKITQPNFVLDTVTSTQIAAWLKENKDNPSYDIFVILLLRTLGKAFYIVNPLIHFS 563
Cdd:TIGR02063 466 PFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSPENIGHFG 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 564 IGSHHYTHFTSPIRRYADLTVHRLLWMNLFTPERFT-DTEREQLNAELEQICETINDTEIKINGCERTANDYLTTLYLSK 642
Cdd:TIGR02063 546 LALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTtEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSE 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:TIGR02063 626 KIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKID 705
|
....
gi 1802581771 723 LTLV 726
Cdd:TIGR02063 706 FELV 709
|
|
| VacB |
COG0557 |
Exoribonuclease R [Transcription]; |
6-726 |
0e+00 |
|
Exoribonuclease R [Transcription];
Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 613.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 6 DLQKRIFAIVKKENGKPIPPGIVVRMMeNQAGFPGKQQVYRAIDDLL-EWHIFRKSGGAtnqllinYELADPvlDQKFQG 84
Cdd:COG0557 3 NSRETILAFLKEDAYKPLSKKELAKAL-GLKDEESREALKRRLRALErEGQLVKTRRGR-------YRLPEK--LDLVEG 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 85 ILNLGNKNTGFVRPlDDDKTVYYIHFSNLAGALDGDLVEFCpLDKPQVGDKFDAAVLKIVKRSRVLYAGNFLIEySDFGq 164
Cdd:COG0557 73 RVRGHRDGFGFVIP-DDGEEDIFIPPRELNGALHGDRVLVR-VTKEDRRGRPEGRVVEILERANTRVVGRFEKE-KGFG- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 165 efRIVADNPRFYLTPIVNKASVpAELESNTKVAFQIDEYDPANNLCKVSIQQILGNNDEPLINLKAIMLDHSIVFEDNDV 244
Cdd:COG0557 149 --FVVPDDKRLLQDIFIPPDDL-NGAKDGDLVVVEITRYPERRGPPEGRVVEVLGSPGDPGAEILIAIRKHGLPHEFPEE 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 245 VEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKT 323
Cdd:COG0557 226 VLAEAEALPDEVPEADLKGRRDLRDLPLVTIDGEDAKDFDDAVSAEKLDNGgWRLGVHIADVSHYVRPGSALDREARKRG 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 324 SSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRRFAYSEVNDWLEDSD-ALKD 402
Cdd:COG0557 306 TSVYLPDR-VIPMLPERLSNGLCSLNPGEDRLAMSCEMEIDAKGEVVSYEFYRSVIRSDARLTYEEVQAILDGKDeELRE 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 403 ESATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHK 482
Cdd:COG0557 385 EYADLVPMLEELYELAKILRKAREKRGAIDFDLPETKIILDEEGKPEDIVPRERNDAHKLIEEFMLLANEAVAEFLEKLK 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 483 VHLPYRVHPRPSKKKLQMLLENIVELKITQPNFvlDTVTSTQIAAWLKENKDNPSYDIFVILLLRTLGKAFYIVNPLIHF 562
Cdd:COG0557 465 LPFLYRVHEEPDPEKLEALREFLANLGLKLKGG--DEPTPKDLQKLLEQVKGRPEEELLNTLLLRSMKQAVYSPENIGHF 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 563 SIGSHHYTHFTSPIRRYADLTVHRLLWMNLFtpERFTDTEREQLNAELEQICETINDTEIKINGCERTANDYLTTLYLSK 642
Cdd:COG0557 543 GLALEAYTHFTSPIRRYPDLLVHRALKAYLE--GKRSPGLQEYLEEELEEIAEHCSETERRADEAERDVVDLKKAEYMKD 620
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:COG0557 621 RVGEEFEGVISGVTSFGLFVELDELGVEGLVHVSSLGDDYYEYDERRQALVGERTGKRYRLGDRVEVRVVRVDLDRRQID 700
|
....
gi 1802581771 723 LTLV 726
Cdd:COG0557 701 FELV 704
|
|
| RNB |
pfam00773 |
RNB domain; This domain is the catalytic domain of ribonuclease II. |
264-592 |
3.99e-105 |
|
RNB domain; This domain is the catalytic domain of ribonuclease II.
Pssm-ID: 459934 [Multi-domain] Cd Length: 314 Bit Score: 323.47 E-value: 3.99e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 264 RKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLS 342
Cdd:pfam00773 1 RKDLRDLPFITIDPADAKDLDDAISVEKLPNGgYRLGVHIADVSHYVPPGSPLDREARKRGTSVYLPDR-VIPMLPEKLS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 343 NELCSLNPNEKRYVVVCELNFDHEARLNFSEVYPATIVSQRRFAYSEVNDWLEDSDALKDEsATVLESLKAGFTLSELIA 422
Cdd:pfam00773 80 NDLCSLNPGEDRLALSVEITIDADGEVTSYEIYPSVIRSKARLTYEEVDDLLEGKDAEKDK-PDLAEDLRLLYELAKILR 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 423 EQRKKKGTIDLSHSETEVVVDQNyYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQMLL 502
Cdd:pfam00773 159 AKRLQRGALDLDTPENKLILDEE-GVIDILIQERTDAHSLIEEFMLLANEAVARHLQELGIPALYRVHPEPDLEKLNSLI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 503 ENIVELkitqpnfvldtVTSTQIAAWLKENKDNpsYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYADL 582
Cdd:pfam00773 238 KLLQLL-----------PDDKGLSKSLEKIKDD--ERLLSILLLRTMPRAEYSPEPLGHFGLGLDIYTHFTSPIRRYPDL 304
|
330
....*....|
gi 1802581771 583 TVHRLLWMNL 592
Cdd:pfam00773 305 IVHRQLKALL 314
|
|
| RNB |
smart00955 |
This domain is the catalytic domain of ribonuclease II; |
264-592 |
1.41e-98 |
|
This domain is the catalytic domain of ribonuclease II;
Pssm-ID: 214935 [Multi-domain] Cd Length: 286 Bit Score: 305.35 E-value: 1.41e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 264 RKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLS 342
Cdd:smart00955 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGgYRLGVHIADVSHYVKPGSALDREARKRGTSVYLPDR-VIPMLPEELS 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 343 NELCSLNPNEKRYVVVCELNFDHEA-RLNFSEVYPATIVSQRRFAYSEVNDWLEdsdalkdesatvleslkagftlseli 421
Cdd:smart00955 80 NGLCSLNPGEDRLALSVEMTLDADGgEILDYEFYRSVIRSKARLTYEEVDAILE-------------------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 422 aeqrkkkgtidlshsetEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQML 501
Cdd:smart00955 134 -----------------KIVLDEEGKIEDIVPRERNDAHSLVEEFMILANEAVARFLAKNGIPGLYRVHEGPDPEKLAEL 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 502 LENIVELKitqPNFVLDTVTSTQIAAWLKENKDNPSYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYAD 581
Cdd:smart00955 197 LKEFLALL---GLLLLGGDGPKALAKLLEKIRDSPEERLLELLLLRSMPHAEYSVDNSGHFGLALDAYTHFTSPIRRYPD 273
|
330
....*....|.
gi 1802581771 582 LTVHRLLWMNL 592
Cdd:smart00955 274 LIVHRQLKAAL 284
|
|
| PRK11642 |
PRK11642 |
ribonuclease R; |
214-711 |
4.14e-75 |
|
ribonuclease R;
Pssm-ID: 236944 [Multi-domain] Cd Length: 813 Bit Score: 258.90 E-value: 4.14e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 214 IQQILGNNDEPLINLKAIMLDHSIVFEDNDVVEQQAAKLQFDEKEQSKPYRKDLTELAFVTIDPATSKDLDDAIYV-KRT 292
Cdd:PRK11642 210 IVEVLGDNMGTGMAVDIALRTHEIPYIWPQAVEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCeKKR 289
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 293 DKGFVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYyVVPMLPERLSNELCSLNPNEKRYVVVCELNFDHEARLNFS 372
Cdd:PRK11642 290 GGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQ-VVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGY 368
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 373 EVYPATIVSQRRFAYSEVNDWLEDSDALKDESATVLESLKAGFTLSELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIR 452
Cdd:PRK11642 369 KFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERRIERIE 448
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 453 FLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKLQMLLENIVELKITQPNFvlDTVTSTQIAAWLKEN 532
Cdd:PRK11642 449 QTQRNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSVLAELGLELPGG--NKPEPRDYAELLESV 526
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 533 KDNPSYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFTSPIRRYADLTVHR----LLWMNLFTPERFTDT-----ER 603
Cdd:PRK11642 527 ADRPDAEMLQTMLLRSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLSLHRaikyLLAKEQGHKGNTTETggyhySM 606
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 604 EQLnAELEQICETindTEIKINGCERTANDYLTTLYLSKQVGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFF 683
Cdd:PRK11642 607 EEM-LQLGQHCSM---TERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYY 682
|
490 500
....*....|....*....|....*...
gi 1802581771 684 VFEKDRMVLRGKRTNKVFRIGDRLTAKL 711
Cdd:PRK11642 683 RFDQVGQRLIGESSGQTYRLGDRVEVRV 710
|
|
| Rnb |
COG4776 |
Exoribonuclease II [Transcription]; |
264-722 |
1.52e-59 |
|
Exoribonuclease II [Transcription];
Pssm-ID: 443808 [Multi-domain] Cd Length: 644 Bit Score: 212.41 E-value: 1.52e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 264 RKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYYVvPMLPERLS 342
Cdd:COG4776 190 REDLTALPFVTIDSESTEDMDDALYIEKLENGgWKLTVAIADPTAYIPEGSELDKEARQRAFTNYLPGFNI-PMLPRELS 268
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 343 NELCSLNPNEKRYVVVCELNFDHEARL-NFSEVYPATIVSQRRFAYSEVNDWLEDSDALKDESATVLESLKAGFTLSELI 421
Cdd:COG4776 269 DDLCSLKENEKRPALVCRVTIDADGSIgDDIEFFAAWIRSKAKLAYDNVSDWLEGKGEWQPENEEIAEQIRLLHQFALAR 348
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 422 AEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKL--- 498
Cdd:COG4776 349 SQWRQQHALVFKDRPDYRFELDEKGNVLDIHAEPRRIANRIVEEAMIAANICAARVLREHLGFGIFNVHSGFDPEKLeqa 428
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 499 -QMLLENIVELKITQpnfvLDTVTS-TQIAAWLKENKDNpsydiFVILLLRT-LGKAFYIVNPLIHFSIGSHHYTHFTSP 575
Cdd:COG4776 429 vELLAEHGIEFDPEQ----LLTLEGfCALRRELDAQPTS-----YLDSRLRRfQTFAEISTEPGPHFGLGLDAYATWTSP 499
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 576 IRRYADLTVHRLLWMNLF--TPERFTDTEREQLNAELEQicetindteikiNG-CERTANDYLTTLYLSKQVG--QTFHG 650
Cdd:COG4776 500 IRKYGDMVNHRLIKAVILgqPAEKPDEELTERLAERRRL------------NRmAERDVADWLYARYLKPKVGsgQVFTA 567
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 651 FISAITSFGIFMRMDENN---FdglikitsIPEDFFVFEKDRMVLRGKR------TNKVFRIGDRLTAKLTEIDtVQKRA 721
Cdd:COG4776 568 EIIDINRGGLRVRLLENGavaF--------IPASFIHSVRDELVCSQEEgtvyikGEVRYKLGDTIQVTLAEVR-EETRS 638
|
.
gi 1802581771 722 I 722
Cdd:COG4776 639 I 639
|
|
| PRK05054 |
PRK05054 |
exoribonuclease II; Provisional |
264-714 |
2.01e-54 |
|
exoribonuclease II; Provisional
Pssm-ID: 179920 [Multi-domain] Cd Length: 644 Bit Score: 198.18 E-value: 2.01e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 264 RKDLTELAFVTIDPATSKDLDDAIYVKRTDKG-FVLYVAIADVAYYVQRNSELDIEARHKTSSIYLPGYYvVPMLPERLS 342
Cdd:PRK05054 190 REDLTALDFVTIDSASTEDMDDALYVEKLPDGgLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFN-IPMLPRELS 268
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 343 NELCSLNPNEKRYVVVCELNFDHEARL----NFsevYPATIVSQRRFAYSEVNDWLEDSDALKDESATVLESLKAGFTLS 418
Cdd:PRK05054 269 DDLCSLRPNERRPALACRVTIDADGTIeddiRF---FAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFC 345
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 419 ELIAEQRKKKGTIDLSHSETEVVVDQNYYPIEIRFLTHGKAETMIENLMVVANEAVAWTLTNHKVHLPYRVHPRPSKKKl 498
Cdd:PRK05054 346 LARSEWRKQHALVFKDRPDYRFELGEKGEVLDIVAEPRRIANRIVEESMIAANICAARVLRDKLGFGIYNVHSGFDPAN- 424
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 499 qmlLENIVE-LKITQPNFVLDTVTS----TQIAAWLkenkDNPSYDIFVILLLRTLGKAFYIVNPLIHFSIGSHHYTHFT 573
Cdd:PRK05054 425 ---AEQAVAlLKEHGLHFDAEELLTlegfCKLRREL----DAQPTGYLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWT 497
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 574 SPIRRYADLTVHRLLWMNLFTperfTDTEREQlnaelEQICETINDTEIKINGCERTANDYLTTLYLSKQVG--QTFHGF 651
Cdd:PRK05054 498 SPIRKYGDMINHRLLKAVIKG----ETAERPQ-----DEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGtdTRFAAE 568
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1802581771 652 ISAITSFGIFMRMDENNfdgliKITSIPEDFFVFEKDRMVLRGK------RTNKVFRIGDRLTAKLTEI 714
Cdd:PRK05054 569 IIDISRGGMRVRLLENG-----AVAFIPASFLHAVRDELVCNQEngtvqiKGETVYKLGDVIDVTLAEV 632
|
|
| S1_RNase_R |
cd04471 |
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ... |
644-726 |
4.19e-23 |
|
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Pssm-ID: 239917 [Multi-domain] Cd Length: 83 Bit Score: 93.62 E-value: 4.19e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 644 VGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLTEIDTVQKRAIL 723
Cdd:cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDF 80
|
...
gi 1802581771 724 TLV 726
Cdd:cd04471 81 ELV 83
|
|
| S1 |
smart00316 |
Ribosomal protein S1-like RNA-binding domain; |
643-725 |
8.08e-10 |
|
Ribosomal protein S1-like RNA-binding domain;
Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 55.30 E-value: 8.08e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMdENNFDGLIKITSIPEDffvfekdrmvlRGKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:smart00316 1 EVGDVVEGTVTEITPGGAFVDL-GNGVEGLIPISELSDK-----------RVKDPEEVLKVGDEVKVKVLSVDEEKGRII 68
|
...
gi 1802581771 723 LTL 725
Cdd:smart00316 69 LSL 71
|
|
| CSP |
smart00357 |
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ... |
83-144 |
3.46e-09 |
|
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Pssm-ID: 214633 [Multi-domain] Cd Length: 64 Bit Score: 53.37 E-value: 3.46e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1802581771 83 QGILNLGNKNTGFVRPLDDDKTVYyIHFS----NLAGALDGDLVEFCPLdKPQVGDKFDAAVLKIV 144
Cdd:smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVF-VHPSqiqgGLKSLREGDEVEFKVV-SPEGGEKPEAENVVKL 64
|
|
| S1_RpoE |
cd04460 |
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ... |
650-712 |
1.00e-06 |
|
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Pssm-ID: 239907 [Multi-domain] Cd Length: 99 Bit Score: 47.67 E-value: 1.00e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1802581771 650 GFISAITSFGIFMRMdeNNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLT 712
Cdd:cd04460 5 GEVVEVVDFGAFVRI--GPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIV 65
|
|
| S1_Rrp5_repeat_sc12 |
cd05708 |
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ... |
644-725 |
2.08e-06 |
|
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 240213 [Multi-domain] Cd Length: 77 Bit Score: 45.78 E-value: 2.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 644 VGQTFHGFISAITSFGIFMRMDENNFDGLIKITSIPEDffvfekdrmvlRGKRTNKVFRIGDRLTAKLTEIDTVQKRAIL 723
Cdd:cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN-----------RVADASKLFRVGDKVRAKVLKIDAEKKRISL 70
|
..
gi 1802581771 724 TL 725
Cdd:cd05708 71 GL 72
|
|
| S1_Rrp5_repeat_hs8_sc7 |
cd04461 |
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ... |
643-725 |
5.34e-06 |
|
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Pssm-ID: 239908 [Multi-domain] Cd Length: 83 Bit Score: 44.89 E-value: 5.34e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMDeNNFDGLIKITSIPEDFFvfekdrmvlrgKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:cd04461 13 KPGMVVHGYVRNITPYGVFVEFL-GGLTGLAPKSYISDEFV-----------TDPSFGFKKGQSVTAKVTSVDEEKQRFL 80
|
...
gi 1802581771 723 LTL 725
Cdd:cd04461 81 LSL 83
|
|
| PRK08563 |
PRK08563 |
DNA-directed RNA polymerase subunit E'; Provisional |
650-714 |
6.87e-06 |
|
DNA-directed RNA polymerase subunit E'; Provisional
Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 47.13 E-value: 6.87e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1802581771 650 GFISAITSFGIFMRMdeNNFDGLIKITSIPEDFFVFEKDRMVLRGKRTNKVFRIGDRLTAKLTEI 714
Cdd:PRK08563 87 GEVVEVVEFGAFVRI--GPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAV 149
|
|
| rpsA |
PRK06299 |
30S ribosomal protein S1; Reviewed |
643-724 |
6.01e-05 |
|
30S ribosomal protein S1; Reviewed
Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 46.31 E-value: 6.01e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMdENNFDGLIKITSIPEDffvfekdrmvlRGKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVEL-EDGVEGLIRASELSRD-----------RVEDATEVLKVGDEVEAKVINIDRKNRRIS 526
|
..
gi 1802581771 723 LT 724
Cdd:PRK06299 527 LS 528
|
|
| S1 |
pfam00575 |
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ... |
643-725 |
2.06e-04 |
|
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Pssm-ID: 425760 [Multi-domain] Cd Length: 72 Bit Score: 40.35 E-value: 2.06e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802581771 643 QVGQTFHGFISAITSFGIFMRMDeNNFDGLIKITSIPEDffvfekdrmvlRGKRTNKVFRIGDRLTAKLTEIDTVQKRAI 722
Cdd:pfam00575 2 EKGDVVEGEVTRVTKGGAFVDLG-NGVEGFIPISELSDD-----------HVEDPDEVIKVGDEVKVKVLKVDKDRRRII 69
|
...
gi 1802581771 723 LTL 725
Cdd:pfam00575 70 LSI 72
|
|
| S1_RPS1_repeat_ec3 |
cd05688 |
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ... |
644-720 |
2.82e-04 |
|
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Pssm-ID: 240193 [Multi-domain] Cd Length: 68 Bit Score: 39.53 E-value: 2.82e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1802581771 644 VGQTFHGFISAITSFGIFmrMDENNFDGLIKITSIPEDffvfekdrmvlRGKRTNKVFRIGDRLTAKLTEIDTVQKR 720
Cdd:cd05688 1 EGDVVEGTVKSITDFGAF--VDLGGVDGLLHISDMSWG-----------RVKHPSEVVNVGDEVEVKVLKIDKERKR 64
|
|
| S1_like |
cd00164 |
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ... |
648-724 |
8.21e-04 |
|
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Pssm-ID: 238094 [Multi-domain] Cd Length: 65 Bit Score: 38.13 E-value: 8.21e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1802581771 648 FHGFISAITSFGIFMrMDENNFDGLIKITSIPEDFFvfekdrmvlrgKRTNKVFRIGDRLTAKLTEIDTVQKRAILT 724
Cdd:cd00164 1 VTGKVVSITKFGVFV-ELEDGVEGLVHISELSDKFV-----------KDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
|
|
| rpsA |
TIGR00717 |
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ... |
644-715 |
4.70e-03 |
|
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]
Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 40.10 E-value: 4.70e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1802581771 644 VGQTFHGFISAITSFGIFMRMDeNNFDGLIKITSIPEDFFVFEKDRmvlrgkrtnkvFRIGDRLTAKLTEID 715
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELP-GGVEGLIRNSELSENRDEDKTDE-----------IKVGDEVEAKVVDID 505
|
|
| |
