Citrus Sinensis ID: 008167

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-----
Protein Sequence
MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
Secondary Structure (PSIPRED)
cccccccccccEEEEEEcccccccEEEcccccccccccEEEEEEcEEccccccccEEEEEcccccccHHHHHHHHHHHcccccccccHHHHHccccccccccccccccccccccccccEEEEccccccccccEEEEEEcccccEEEEEEEcccccccccccHHHHHHHHccccEEEccccccccccccccccccccccccEEEEEEEEEEccccEEEEEEEEEcEEEccccccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccccEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEcccccccHHHHHHHHHHHHHcccEEcccccHHHHHHHHHHHccccHHHHHHHHHHHHcccccEEcccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEccEEEEEEEcccEEEEEEcccccccccccEEEccccEEEEEEcccEEEEEccEEEEEEEEEccccccccEEEEEc
Secondary Structure Prediction (SSPRO)
cccccccccccEEEEEccccccccEEEccHHcccccccEEEEEEEcccccccccccEEEEEEccccccccHHHHHHHHcccccccccHHHHHHHHcccccccHHHHHccccccHccccEEEEccccccccccEEEEEEcccccEEEEEEEEEEEEEEccccHHHHHHHHcccEEEccccEcccccHHHccccccccccccEEEEEEEEEEcccccEEcEEEEHHHHccHHHccHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccEEEEEEccccccccEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEEcccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHEEcccccccccccccccccHHHHccccHHcccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHccccccEEEEEEcccEEEEEEccccEEEEEEEEEcccccccEEEEcccccEEEEccccEEEEEccEEEEEEEEEcccccccEEEEEEc
Coil and Loop (DISEMBL)
mpmpagsgsvahalfvpkdrripkirIQTRQLGNLLDKRIIVAVdswdcqsrypfghyVRVIGeigdrdtesemvlidndidarpfstqvlaclpplpwsvssedlanpirldlrdlrvfsvdppgckdiddalhctalssgnfevGVHIAdvtnfvhpgtplddeaskrgtsVYLVERRidmlpkpltediCSLRADVERLAFSVIWeltpeaeiisTRYTKSVIKSCAALSYVEAQArmddsrlmdpltTDLRNMNSLAKKMRQRRIERGALTLASAEVKFqidtethdpldigmYQIREANQMVEEFMLAANVSVAEQILRQfplcsllrrhpsptkemLEPLLRTAAAVGLNLDVSSSKALADSldravgddpyfNKLIRILATRCMTQAvyfcsgdltppefhhyglaaplythftspirRYADVVVHRLLSASlgiyklpsvfqdrpqltsiadnlnyrhrnaqmasrgsvELHTLIYfrkrptdteARIVKIRsngfivfvpkfgiegpvyltprgqkgsgdwyvdEQQQKIVkmdgnlsySVLQTVNIHMevvepqpnrpklqltli
Flexible Loop (DISEMBL)
mpmpagsgsvahalfvpkdrripkiriqtrqlgnlldkRIIVAVdswdcqsrypfGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVhpgtplddeaskrgTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIweltpeaeiistrytkSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADsldravgddpYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAqmasrgsvelhtliyfrkrptdteariVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHmevvepqpnrpklqltli
Low Complexity Region (SEG)
MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
Disordered region (IsUnstruct)
***********HALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPL*******GTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQ*********************************GALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRR********LEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV**************
Disordered Region (DISOPRED)
*************LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS********DRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
Disordered Region (DISEMBL)
*********VAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
Disordered Region (DISPRO)
*********VAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	575	2.2.26 [Sep-21-2011]
Q9CSH3	958	Exosome complex exonuclea	yes	no	0.951	0.570	0.508	1e-166
Q9Y2L1	958	Exosome complex exonuclea	yes	no	0.951	0.570	0.508	1e-165
Q17632	961	Probable exosome complex	yes	no	0.993	0.594	0.480	1e-155
P37202	970	Exosome complex exonuclea	yes	no	0.987	0.585	0.466	1e-150
Q08162	1001	Exosome complex exonuclea	yes	no	0.886	0.509	0.483	1e-141
A0JN80	1053	DIS3-like exonuclease 1 O	no	no	0.893	0.488	0.415	1e-111
Q5U2P0	1054	DIS3-like exonuclease 1 O	no	no	0.953	0.519	0.395	1e-111
Q8C0S1	1053	DIS3-like exonuclease 1 O	no	no	0.972	0.530	0.385	1e-110
A2RV18	1057	DIS3-like exonuclease 1 O	no	no	0.991	0.539	0.389	1e-110
Q5R5N8	1054	DIS3-like exonuclease 1 O	yes	no	0.878	0.479	0.412	1e-107

>sp|Q9CSH3|RRP44_MOUSE Exosome complex exonuclease RRP44 OS=Mus musculus GN=Dis3 PE=2 SV=4

 Score =  586 bits (1511), Expect = e-166,   Method: Compositional matrix adjust.
 Identities = 287/564 (50%), Positives = 397/564 (70%), Gaps = 17/564 (3%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
           LF P D+RIP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+V+ +G++G+++TE+E
Sbjct: 372 LFTPADKRIPRIRIETRQASALEGRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETE 431

Query: 74  MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
           ++L+++D+  +PFS  VL+ LP +PWS++ ED+ N  R DLR L V SVDPPGC DIDDA
Sbjct: 432 VLLLEHDVPHQPFSQAVLSFLPRMPWSITEEDMKN--REDLRHLCVCSVDPPGCTDIDDA 489

Query: 134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
           LHC  LS+GN EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct: 490 LHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 549

Query: 194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
           SLR++V+RLAFS IWE+   AEI+ TR+TKSVI S A+L+Y EAQ R+D + + D +TT 
Sbjct: 550 SLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRIDSAAMNDDITTS 609

Query: 254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
           LR +N LAK +++ RIE+GALTL+S E++F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct: 610 LRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 669

Query: 314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
           AN+SVA++I  +F   +LLR+HP+P     + L++ A +  L +   ++K+LADSLDRA 
Sbjct: 670 ANISVAKKIHEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIKTDTAKSLADSLDRAE 729

Query: 374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
             D PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++V
Sbjct: 730 SPDFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADIIV 787

Query: 433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
           HRLL+ ++G         D+ +L+ I  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct: 788 HRLLAVAIGADCTYPELTDKHKLSDICKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 847

Query: 492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE-----------QQQKIV 540
            EA I+ +R N  +V +PK+G+EG V+   + +      Y DE                V
Sbjct: 848 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPKPRLAYDDEIPSLRIEGTVFHVFDKV 907

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
           K+   L  S LQ   I M +VEPQ
Sbjct: 908 KVKITLDSSNLQHQKIRMALVEPQ 931

Putative catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. DIS3 has both 3'-5' exonuclease and endonuclease activities.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 1EC: .EC: 2EC: 6EC: .EC: -

>sp|Q9Y2L1|RRP44_HUMAN Exosome complex exonuclease RRP44 OS=Homo sapiens GN=DIS3 PE=1 SV=2

 Score =  583 bits (1503), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 287/564 (50%), Positives = 396/564 (70%), Gaps = 17/564 (3%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
           LF P D+RIP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+VR +G++G+++TE+E
Sbjct: 372 LFTPADKRIPRIRIETRQASTLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETE 431

Query: 74  MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
           ++L+++D+  +PFS  VL+ LP +PWS++ +D+ N  R DLR L + SVDPPGC DIDDA
Sbjct: 432 VLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKN--REDLRHLCICSVDPPGCTDIDDA 489

Query: 134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
           LHC  L +GN EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct: 490 LHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 549

Query: 194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
           SL+ DV+RLAFS IWE+   AEI+ T++TKSVI S A+L+Y EAQ R+D + + D +TT 
Sbjct: 550 SLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDDITTS 609

Query: 254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
           LR +N LAK +++RRIE+GALTL+S EV+F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct: 610 LRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 669

Query: 314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
           AN+SVA++I  +F   +LLR+HP+P     E L++ A +  L +   ++K+LA+SLD+A 
Sbjct: 670 ANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLAESLDQAE 729

Query: 374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
               PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYADV+V
Sbjct: 730 SPTFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADVIV 787

Query: 433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
           HRLL+ ++G         D+ +L  I  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct: 788 HRLLAVAIGADCTYPELTDKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 847

Query: 492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE-QQQKI----------V 540
            EA I+ +R N  +V +PK+G+EG V+   + +      Y DE    KI          V
Sbjct: 848 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTVFHVFDKV 907

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
           K+   L  S LQ   I M +VEPQ
Sbjct: 908 KVKIMLDSSNLQHQKIRMSLVEPQ 931

Putative catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. DIS3 has both 3'-5' exonuclease and endonuclease activities.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: -

>sp|Q17632|RRP44_CAEEL Probable exosome complex exonuclease RRP44 OS=Caenorhabditis elegans GN=dis-3 PE=3 SV=2

 Score =  550 bits (1416), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 277/577 (48%), Positives = 383/577 (66%), Gaps = 6/577 (1%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           M +P+        LF P +R IP+IRI+T Q   L  +RI+VA+D W   S+YP GHYVR
Sbjct: 368 MLLPSTVKGARRHLFCPAERLIPRIRIETEQAETLSQQRIVVAIDHWPRDSKYPLGHYVR 427

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPI-RLDLRDLRV 119
            IGE+G R+TE+E++L+++DI   PFS  VL CLP   W     +   P+ R+DLRDL +
Sbjct: 428 SIGEMGSRETENEVLLLEHDIPHAPFSESVLDCLPREEWEPDLTENRGPLPRVDLRDLTI 487

Query: 120 FSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVER 179
            SVDP GC DIDDALHC  +    FEVGVHIADVT+FV PGT +DDEA+ RGT+VYL +R
Sbjct: 488 CSVDPLGCTDIDDALHCKQIGEDLFEVGVHIADVTHFVRPGTAIDDEAALRGTTVYLCDR 547

Query: 180 RIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQA 239
           RIDMLP  L+ ++CSLR + ER AFS IW +T  A+I S +Y KS+IKS AAL+Y +AQ 
Sbjct: 548 RIDMLPCLLSSNLCSLRGEEERYAFSCIWTMTSSADIQSVKYHKSLIKSKAALTYEKAQE 607

Query: 240 RMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQ 299
            +DD +  + +   LR +  L+K +  RR   GALTLAS+EV+F +D E+  P  +   Q
Sbjct: 608 IIDDPKEQNDVALGLRGLMKLSKVLNARRTGNGALTLASSEVRFDMDWESRTPKKVMEKQ 667

Query: 300 IREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDV 359
             + + MVEEFML AN+SVAE+IL ++P C+LLRRHP P KE  +PL+  A   G  + V
Sbjct: 668 HLDTHSMVEEFMLLANISVAEKILEEYPDCALLRRHPVPLKESYKPLVEAARHRGFEIIV 727

Query: 360 SSSKALADSLDRAV-GDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYT 418
            S K LADSL+R V   +P  N+L+R+L TRCMTQAVYF +G +  P++ H+GLA  +YT
Sbjct: 728 ESGKGLADSLNRCVDKKNPMLNRLLRMLTTRCMTQAVYFSAGTVPVPQYQHFGLACAIYT 787

Query: 419 HFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVE 478
           HFTSPIRRYADV+VHRLL+A++G   + S   ++ + T I  N+NYRH+ AQ A R SV+
Sbjct: 788 HFTSPIRRYADVIVHRLLAAAIGADDIQSGLLNQARCTKICTNINYRHKQAQYAGRASVQ 847

Query: 479 LHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQK 538
           L+ + YF+ +    E  ++ +R+NG  VFVPK+G+E  + L      G+    +D ++  
Sbjct: 848 LNVVRYFKGKVETCEGFVMGVRNNGIQVFVPKYGLESIIVLQTSAASGTT---IDVEEMS 904

Query: 539 IVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
            VK++G++    L+ V + + V E    RP+++L LI
Sbjct: 905 -VKVNGDVVIKELEPVTVRISVNEKNQQRPRVELQLI 940

Putative catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. dis-3 has both 3'-5' exonuclease and endonuclease activities.

Caenorhabditis elegans (taxid: 6239)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|P37202|DIS3_SCHPO Exosome complex exonuclease dis3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=dis3 PE=1 SV=1

 Score =  533 bits (1374), Expect = e-150,   Method: Compositional matrix adjust.
 Identities = 274/587 (46%), Positives = 379/587 (64%), Gaps = 19/587 (3%)

Query: 5   AGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGE 64
           +  GS    L  P DRR+PKIR +TRQ   L+ +RI+VA+D WD  SRYP GH+VR +GE
Sbjct: 386 SKGGSQQTVLLTPMDRRVPKIRFRTRQAPRLVGRRIVVAIDLWDASSRYPEGHFVRDLGE 445

Query: 65  IGDRDTESEMVLIDNDIDARPFSTQVLACLPP--LPWSVSSEDLANPI---RLDLRDLRV 119
           +  ++ E+E +L++ D+  RPF   VL CLP     W V + D  +P+   R D RD  +
Sbjct: 446 METKEAETEALLLEYDVQHRPFPKAVLDCLPEEGHNWKVPA-DKTHPLWKNRKDFRDKLI 504

Query: 120 FSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVER 179
            S+DPPGC+DIDDALH   L +GN+EVGVHIADVT+FV P T +D EA+ RGT+VYLV++
Sbjct: 505 CSIDPPGCQDIDDALHACVLPNGNYEVGVHIADVTHFVKPNTSMDSEAASRGTTVYLVDK 564

Query: 180 RIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQA 239
           RIDMLP  L  D+CSLR  VER AFS IWE+   A II   +TKSVI S  A SY +AQA
Sbjct: 565 RIDMLPMLLGTDLCSLRPYVERFAFSCIWEMDENANIIKVHFTKSVIASKEAFSYADAQA 624

Query: 240 RMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQ 299
           R+DD ++ DPLT  +R +  L+K ++Q+R++ GAL LAS EV+ Q D ET DP+D+ + Q
Sbjct: 625 RIDDQKMQDPLTQGMRVLLKLSKILKQKRMDEGALNLASPEVRIQTDNETSDPMDVEIKQ 684

Query: 300 IREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSP---TKEMLEPLLRTAAAVGLN 356
           + E N +VEEFML AN+SVA++I   FP  ++LRRH +P     + L+ +LR     G++
Sbjct: 685 LLETNSLVEEFMLLANISVAQKIYDAFPQTAVLRRHAAPPLTNFDSLQDILRVCK--GMH 742

Query: 357 LDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAP 415
           L   +SK+LA SLD  V   +PYFN L+RIL TRCM  A YFCSG   PP+F HYGLA+P
Sbjct: 743 LKCDTSKSLAKSLDECVDPKEPYFNTLLRILTTRCMLSAEYFCSGTFAPPDFRHYGLASP 802

Query: 416 LYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRG 475
           +YTHFTSPIRRYADV+ HR L+A++    +     D+ +L  I + +NYRHR AQMA R 
Sbjct: 803 IYTHFTSPIRRYADVLAHRQLAAAIDYETINPSLSDKSRLIEICNGINYRHRMAQMAGRA 862

Query: 476 SVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQ--KGSGDWYVD 533
           S+E +     +    + +A ++K+  NGF+VF+ +FG+EG VY        + + ++  D
Sbjct: 863 SIEYYVGQALKGGVAEEDAYVIKVFKNGFVVFIARFGLEGIVYTKSLSSVLEPNVEYVED 922

Query: 534 EQQQKIVKMD----GNLSYSVLQTVNIHMEVV-EPQPNRPKLQLTLI 575
           E +  I   D      +   + Q V + +  V +    + K+Q+TL+
Sbjct: 923 EYKLNIEIRDQPKPQTVQIQMFQQVRVRVTTVRDEHSGKQKVQITLV 969

Catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. DIS3 has both 3'-5' exonuclease and endonuclease activities. The exonuclease activity of DIS3 is down-regulated upon association with Exo-9 possibly involving a conformational change in the catalytic domain and threading of the RNA substrate through the complex central channel. Structured substrates can be degraded if they have a 3' single-stranded extension sufficiently long (such as 35 nt poly(A)) to span the proposed complex inner RNA-binding path and to reach the exonuclease site provided by dis3 (By similarity). Implicated in mitotic control. Essential for cell division and spore germination. May be involved in regulating protein dephosphorylation during mitosis.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: -

>sp|Q08162|RRP44_YEAST Exosome complex exonuclease DIS3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DIS3 PE=1 SV=1

 Score =  501 bits (1289), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 256/529 (48%), Positives = 348/529 (65%), Gaps = 19/529 (3%)

Query: 7   SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
           S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR +G I 
Sbjct: 416 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 475

Query: 67  DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
               E+E +L+++D++ RPFS +VL CLP              P +VS + L    R DL
Sbjct: 476 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 534

Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
           RD  + S+DPPGC DIDDALH   L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 535 RDKLICSIDPPGCVDIDDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 594

Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
           YLV++RIDMLP  L  D+CSL+  V+R AFSVIWEL   A I++  + KSVI+S  A SY
Sbjct: 595 YLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSY 654

Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
            +AQ R+DD    D LT  +R +  L+ K++Q+R+E GAL LAS EVK  +D+ET DP +
Sbjct: 655 EQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNE 714

Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
           + + ++   N +VEEFML AN+SVA +I   FP  ++LRRH   PS   E+L  +L T  
Sbjct: 715 VEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRK 774

Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
            + ++L+  SSKALADSLDR V  +DPYFN L+RI++TRCM  A YF SG  + P+F HY
Sbjct: 775 NMSISLE--SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHY 832

Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
           GLA  +YTHFTSPIRRY DVV HR L+ ++G   L    +D+ ++  I  N+N +HRNAQ
Sbjct: 833 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQ 892

Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
            A R S+E +     R   +     ++K+ +NG +V VPKFG+EG + L
Sbjct: 893 FAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 941

Catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. DIS3 has both 3'-5' exonuclease and endonuclease activities. The exonuclease activity of DIS3 is down-regulated upon association with Exo-9 possibly involving a conformational change in the catalytic domain and threading of the RNA substrate through the complex central channel. Structured substrates can be degraded if they have a 3' single-stranded extension sufficiently long (such as 35 nt poly(A)) to span the proposed complex inner RNA-binding path and to reach the exonuclease site provided by DIS3. Plays a role in mitotic control.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 1

EC: .

EC: 2

EC: 6

EC: .

EC: -

>sp|A0JN80|DI3L1_BOVIN DIS3-like exonuclease 1 OS=Bos taurus GN=DIS3L PE=2 SV=2

 Score =  404 bits (1037), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 232/559 (41%), Positives = 321/559 (57%), Gaps = 45/559 (8%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
           L  P D RIPKIRI T+Q   L D R++V +DSW+  S YP GH+VRV+G IGD + E  
Sbjct: 366 LVTPWDYRIPKIRISTQQAEALQDFRVVVRIDSWESTSMYPNGHFVRVLGRIGDLEGEIA 425

Query: 74  MVLIDNDIDARPFSTQVLACLP----PLPWSVSSEDLANPIRLDLRDLR-VFSVDPPGCK 128
            +L++N I   PFS   +  +P      PW VSS++     R DLR    VFS+DP GC+
Sbjct: 426 TILVENSISVVPFSEAQMCEMPVNTPENPWKVSSQEERE--REDLRKTHLVFSIDPSGCE 483

Query: 129 DIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPL 188
           D+DD L   AL +GN E+GVHIADVT+FV P + +D EA  R T+ YL +RR DMLP  L
Sbjct: 484 DVDDTLSVRALDNGNLELGVHIADVTHFVAPHSYIDIEARTRATTYYLADRRYDMLPAIL 543

Query: 189 TEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSCAALSYVEAQARMDDS--- 244
           + D+CSL   V+R A SV+WEL   + EI    Y +++I+S   L Y  AQ  +D +   
Sbjct: 544 SADVCSLLGGVDRYAVSVMWELDKTSYEIKKVWYGRTIIRSAYKLFYEAAQDLLDGNFSV 603

Query: 245 ----------------RLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTE 288
                             ++ L   +R +  +A+ +R +R   GAL L   EV+ Q+D E
Sbjct: 604 VKDIPEFKDLDEKSRQAKLEELVWAIRKLTDIARHIRAKRDSCGALELEGVEVRIQLD-E 662

Query: 289 THDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLR 348
             +  D+   Q  E ++ V E M+ AN  VA++I   FP  +LLRRHP P +E    L  
Sbjct: 663 KKNIHDLIPKQPLEVHETVAECMILANHWVAKKIWESFPHQALLRRHPPPHQEFFSELRE 722

Query: 349 TAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
            A A G  +D  S+KALADSLD A   +DP  NKL+R +AT+ M+ A+YF +G     EF
Sbjct: 723 CAKAKGFFIDTRSNKALADSLDNANDPNDPIVNKLLRSMATQAMSNALYFSTGSCAEEEF 782

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQD---RPQLTSIADNLNY 464
           HHYGLA   YTHFTSPIRRY+D++VHRLL A++   K   + ++      L  +  ++N 
Sbjct: 783 HHYGLALDKYTHFTSPIRRYSDIIVHRLLMAAISKDKKMEIQENLFSNKDLEELCRHINN 842

Query: 465 RHRNAQMASRGSVELHTLIYFRKRPTDTEAR------IVKIRSNGFIVFVPKFGIEGPVY 518
           R+R AQ + + S EL   +YF+ +  +TE R      I  IR+NG +VF+P+FGI+G  Y
Sbjct: 843 RNRAAQHSQKQSTELFQCMYFKDKDPETEERCISDGVIYSIRTNGVLVFIPRFGIKGAAY 902

Query: 519 LTPR-------GQKGSGDW 530
           L  +       G  G  +W
Sbjct: 903 LRNKDGLVVSCGPDGHSEW 921

Putative cytoplasm-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q5U2P0|DI3L1_RAT DIS3-like exonuclease 1 OS=Rattus norvegicus GN=Dis3l PE=2 SV=2

 Score =  401 bits (1030), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 238/602 (39%), Positives = 339/602 (56%), Gaps = 54/602 (8%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
           L  P D RIPKIRI T+Q   L D R++V +DSW+  S YP GH+VRV+G IGD + E  
Sbjct: 366 LVTPWDYRIPKIRISTQQAEALQDFRVVVRIDSWETTSVYPNGHFVRVLGRIGDLEGEIA 425

Query: 74  MVLIDNDIDARPFSTQVLACLP----PLPWSVSSEDLANPIRLDLRDLR-VFSVDPPGCK 128
            +L++N I+  PFS   +  +P      PW VS ++     R DLR    VFS+DP GC+
Sbjct: 426 TILVENSINVVPFSEAQMCEMPVNTAENPWKVSPKEEQE--RRDLRSTHLVFSIDPKGCE 483

Query: 129 DIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPL 188
           D+DDAL    L++GN E+GVHIADVT+FV P + +D EA  R T+ YL +RR DMLP  L
Sbjct: 484 DVDDALSVRTLNNGNLELGVHIADVTHFVAPNSYIDVEARTRATTYYLADRRYDMLPSIL 543

Query: 189 TEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSCAALSYVEAQARMDDS--- 244
           + D+CSL   V+R A SV+WEL   + EI    Y +++I+S   L Y  AQ  +D +   
Sbjct: 544 SADLCSLLGGVDRYAVSVMWELDKTSYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNFSI 603

Query: 245 ----------------RLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTE 288
                             ++ L   +  +  +A+ +R +R   GAL L   EV+ Q+D +
Sbjct: 604 VDDIPEFKTLEEQNRQAKLEELVWAIGKLTDIARHIRAKRDRCGALELEGVEVRVQLD-D 662

Query: 289 THDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLR 348
             +  D+   Q  E ++ V E M+ AN  VA++I   FP  +LLR+HP P +E    L  
Sbjct: 663 KKNIHDLIPKQPLEVHETVAECMILANHWVAKKIWESFPHQALLRQHPPPHQEFFSELRE 722

Query: 349 TAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
            A A G  +D  S+K LADSLD A    DP  NKL+R +AT+ M+ A+YF +G     EF
Sbjct: 723 CAKAKGFFIDTRSNKTLADSLDSANDPSDPLVNKLLRSMATQAMSNALYFSTGSCAEEEF 782

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQD---RPQLTSIADNLNY 464
           HHYGLA   YTHFTSPIRRY+D+VVHRLL A++   K   + ++      L  +  ++N 
Sbjct: 783 HHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKVEIKENLFSNKNLEELCRHINN 842

Query: 465 RHRNAQMASRGSVELHTLIYFRKRPTDTEARIV------KIRSNGFIVFVPKFGIEGPVY 518
           R+R AQ + + S EL   +YF+ R  +TE R V       IR+NG +VF+P+FGI+G  Y
Sbjct: 843 RNRAAQRSQKQSTELFQCMYFKDRDPETEERCVVDGIIYSIRTNGVLVFIPRFGIKGAAY 902

Query: 519 LTPR-------GQKGSGDWY---VDEQQQKIVKMDG---NLSYSVLQTVNIHMEVVEPQP 565
           L  +       G +GS +W    +   Q KI+       ++++ +   V + + V   QP
Sbjct: 903 LKNKDGLVISCGPEGSSEWKPGSLQRSQNKIISTTAGGQSVTFHLFDHVTVRISV---QP 959

Query: 566 NR 567
           +R
Sbjct: 960 SR 961

Putative cytoplasm-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q8C0S1|DI3L1_MOUSE DIS3-like exonuclease 1 OS=Mus musculus GN=Dis3l PE=2 SV=2

 Score =  398 bits (1023), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 235/610 (38%), Positives = 340/610 (55%), Gaps = 51/610 (8%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
           L  P D RIPKIRI T+Q   L D R++V +DSW+  S YP GH+VRV+G IGD + E  
Sbjct: 366 LVTPWDYRIPKIRISTQQAEALQDFRVVVRIDSWEATSVYPNGHFVRVLGRIGDLEGEIA 425

Query: 74  MVLIDNDIDARPFSTQVLACLP----PLPWSVSSEDLANPIRLDLRDLR-VFSVDPPGCK 128
            +L++N I   PFS   +  +P      PW VS ++     R DLR    VFS+DP GC+
Sbjct: 426 TILVENSISVVPFSEAQMCEMPVNTPENPWKVSPKEEQE--RKDLRTTHLVFSIDPKGCE 483

Query: 129 DIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPL 188
           D+DD L    L++GN E+GVHIADVT+FV P + +D EA  R T+ YL +RR DMLP  L
Sbjct: 484 DVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDVEARTRATTYYLADRRYDMLPSIL 543

Query: 189 TEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSCAALSYVEAQARMDDS--- 244
           + D+CSL   V+R A SV+WEL   + EI    Y +++I+S   L Y  AQ  +D +   
Sbjct: 544 SADLCSLLGGVDRYAVSVMWELDKTSYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNFSI 603

Query: 245 ----------------RLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTE 288
                             ++ L   +  +  +A+ +R +R   GAL L   EV+ Q+D +
Sbjct: 604 VDDIPELKALDKQSQQAKLEELVWAIGKLTDIARHIRAKRDRCGALELEGVEVRVQLD-D 662

Query: 289 THDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLR 348
             +  D+   Q  E ++ V E M+ AN  VA++I   FP  +LLR+HP P +E    L  
Sbjct: 663 KKNIRDLIPKQPLEVHETVAECMILANHWVAKKIWESFPHQALLRQHPPPHQEFFSELRE 722

Query: 349 TAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
            A A G  +D  S+K LADSLD A    DP  NKL+R +AT+ M+ A+YF +G     EF
Sbjct: 723 CAKAKGFFIDTRSNKTLADSLDSANDPKDPLVNKLLRSMATQAMSNALYFSTGSCAEEEF 782

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQD---RPQLTSIADNLNY 464
           HHYGLA   YTHFTSPIRRY+D+VVHRLL A++   K   + ++      L  +  ++N 
Sbjct: 783 HHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKENLFSNKNLEELCRHINN 842

Query: 465 RHRNAQMASRGSVELHTLIYFRKRPTDTEAR------IVKIRSNGFIVFVPKFGIEGPVY 518
           R+R AQ + + S EL   +YF+ R  +TE R      I  IR+NG +VF+P+FGI+G  Y
Sbjct: 843 RNRAAQRSQKQSTELFQCMYFKDRDAETEERCIADGVIYSIRTNGVLVFIPRFGIKGAAY 902

Query: 519 LTPR-------GQKGSGDWY---VDEQQQKIVKMDG---NLSYSVLQTVNIHMEVVEPQP 565
           L  +       G +GS +W    +   Q KI+       ++++ +   V + + V   + 
Sbjct: 903 LKNKDSLVISCGPEGSSEWKPGSLQRSQNKIISTTAGGQSVTFHLFDHVTVRISVQASRC 962

Query: 566 NRPKLQLTLI 575
           +   ++L ++
Sbjct: 963 HSDTIRLEIV 972

Putative cytoplasm-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|A2RV18|DI3L1_DANRE DIS3-like exonuclease 1 OS=Danio rerio GN=dis3l PE=2 SV=1

 Score =  398 bits (1022), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 241/618 (38%), Positives = 353/618 (57%), Gaps = 48/618 (7%)

Query: 3   MPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVI 62
           M + S +    L VP D RIPKIRI T+Q   L D+R+IV +DSW+  S YP GH+VRV+
Sbjct: 349 MQSQSRNSQKILVVPWDYRIPKIRISTQQAEALQDQRVIVRLDSWESTSVYPNGHFVRVL 408

Query: 63  GEIGDRDTESEMVLIDNDIDARPFSTQVLACLP----PLPWSVSSEDLANPIRLDLRDLR 118
           G+ G+ +TE + +L++N I   PFS   L  +P      PW + S ++++  R DLRD  
Sbjct: 409 GKSGELETEIQTILVENCIHVPPFSEAQLREMPVNTEENPWQMDSNEVSS--RRDLRDSH 466

Query: 119 -VFSVDPPGCKDIDDALHCTALSSGN-FEVGVHIADVTNFVHPGTPLDDEASKRGTSVYL 176
            VFS+DP GC+D+DD L    L  G   E+GVHIADVT+FV  G+  D EA  R T+ YL
Sbjct: 467 LVFSIDPKGCEDVDDTLSVRTLPGGKRLELGVHIADVTHFVREGSLTDLEARSRATTYYL 526

Query: 177 VERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSCAALSYV 235
            +RR DMLP  L+ D+CSL   V+R A SV+WEL  E  E+ S  + +++I+S   L Y 
Sbjct: 527 ADRRYDMLPAVLSADLCSLLGGVDRYAMSVLWELDAETLEVCSVWFGRTLIRSSYQLHYE 586

Query: 236 EAQARMDDSRL----------------MDPLTTDLRNMNSLAKKMRQRRIERGALTLASA 279
            AQ+ ++   +                M  L   L  +  +A+ +R +R + GAL L   
Sbjct: 587 LAQSLLNGEEVEVPELNPLKGSQRDQKMSELLQALETLTRVARHLRAQRDKGGALELEGV 646

Query: 280 EVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPT 339
           EV+ Q+D E +    +   Q  E ++ V E M+ AN  VA +I   FP  +LLR HP P 
Sbjct: 647 EVRAQLDEEKNITALVPK-QPLEVHETVAECMIYANHWVARKIQESFPHHALLRHHPPPK 705

Query: 340 KEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFC 398
           +E    L+ +A A G ++D  S++ALADSL+RAV   DP  N+L+R++AT+ M+ A+YF 
Sbjct: 706 QEFFNHLIDSAKAHGFSIDTRSNRALADSLERAVDPRDPLVNRLLRMMATQAMSNALYFS 765

Query: 399 SGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPS---VFQDRPQL 455
           +G     +++HYGLA   YTHFTSPIRRYADV+VHRLL A++ + K  S         +L
Sbjct: 766 TGSCPEEQYYHYGLALARYTHFTSPIRRYADVIVHRLLMAAVQLEKDESPSKALACNKEL 825

Query: 456 TSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEAR------IVKIRSNGFIVFVP 509
             +A ++N ++R AQ + + S+EL   +YFR + + T+ R      I  +R+NGF+ FVP
Sbjct: 826 EELAQHINNKNRAAQHSQKQSIELFQCMYFRDKDSHTDERCVADAVIYAVRANGFLAFVP 885

Query: 510 KFGIEGPVYLTPR-GQ------KGSGDWYVDEQQQ---KIV--KMDGNLSYSVLQTVNIH 557
           ++G++G VYL  R GQ       G  +W     Q+   KI+     G  ++ +   V + 
Sbjct: 886 QYGLKGAVYLKDREGQVISVDGDGKCEWKPGTLQKYSDKIITSTSTGTHTFYLFNHVTVR 945

Query: 558 MEVVEPQPNRPKLQLTLI 575
           + V   + +   L L LI
Sbjct: 946 ISVEPSRCHADSLNLELI 963

Putative cytoplasm-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

>sp|Q5R5N8|DI3L1_PONAB DIS3-like exonuclease 1 OS=Pongo abelii GN=DIS3L PE=2 SV=1

 Score =  390 bits (1003), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 225/545 (41%), Positives = 315/545 (57%), Gaps = 40/545 (7%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
           L  P D RIPKIRI T+Q   L D R++V +DSW+  S YP GH+VRV+G IGD + E  
Sbjct: 366 LVTPWDYRIPKIRISTQQAETLQDFRVVVRIDSWESTSVYPNGHFVRVLGRIGDLEGEIA 425

Query: 74  MVLIDNDIDARPFSTQVLACLP----PLPWSVSSEDLANPIRLDLRDLR-VFSVDPPGCK 128
            +L++N I   PFS   +  +P      PW VS E+     R DLR    VFS+DP GC+
Sbjct: 426 TILVENSISVIPFSEAQMCEMPVNTPENPWKVSPEEEQK--RKDLRKSHLVFSIDPKGCE 483

Query: 129 DIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPL 188
           D+DD L    L++GN E+GVHIADVT+FV P + +D EA  R T+ YL +RR DMLP  L
Sbjct: 484 DVDDTLSVRTLNNGNLELGVHIADVTHFVAPNSYIDIEARTRATTYYLADRRYDMLPSVL 543

Query: 189 TEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSCAALSYVEAQARMDDS--- 244
           + D+CSL   V+R A S++WEL   + EI    Y +++I+S   L Y  AQ  +D +   
Sbjct: 544 SADLCSLLGGVDRYAVSIMWELDKASYEIKKVWYGRTIIRSAYKLFYEAAQELLDGNLSV 603

Query: 245 ----------------RLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTE 288
                             ++ L   +  +  +A+ +R +R   GAL L   EV+ Q+D +
Sbjct: 604 VDDIPEFKDLDEKSRQAKLEELVWAIGKLTDIARHVRAKRDGCGALELEGVEVRVQLD-D 662

Query: 289 THDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLR 348
             +  D+   Q  E ++ V E M+ AN  VA++I   FP  +LLR+HP P +E    L  
Sbjct: 663 KKNIHDLIPKQPLEVHETVAECMILANHWVAKKIWESFPHQALLRQHPPPHQEFFSELRE 722

Query: 349 TAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
            A A G  +D  S+K LADSLD A G  DP  N+L+R +AT+ M+ A+YF +G     EF
Sbjct: 723 CAKAKGFFIDTRSNKTLADSLDNANGPHDPIVNRLLRSMATQAMSNALYFSTGSCAEEEF 782

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYK----LPSVFQDRPQLTSIADNLN 463
           HHYGLA   YTHFTSPIRRY+D+VVHRLL A++   K      ++F ++  L  +  ++N
Sbjct: 783 HHYGLALDKYTHFTSPIRRYSDIVVHRLLMAAISKDKKMEIKGNLFSNK-DLEELCRHIN 841

Query: 464 YRHRNAQMASRGSVELHTLIYFRKRPTDTEAR------IVKIRSNGFIVFVPKFGIEGPV 517
            R+R AQ + + S EL   +YF+ +   TE R      I  IR+NG +VF+P+FGI+G  
Sbjct: 842 NRNRAAQHSQKQSTELFQCMYFKDKDPATEERCISDGVIYSIRANGVLVFIPRFGIKGAA 901

Query: 518 YLTPR 522
           YL  +
Sbjct: 902 YLKNK 906

Putative cytoplasm-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA.

Pongo abelii (taxid: 9601)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	575
225438438	937	PREDICTED: exosome complex exonuclease R	1.0	0.613	0.897	0.0
255561455	934	mitotic control protein dis3, putative [	1.0	0.615	0.890	0.0
297836470	933	ribonuclease II family protein [Arabidop	1.0	0.616	0.876	0.0
356509070	934	PREDICTED: exosome complex exonuclease R	0.998	0.614	0.888	0.0
356516247	934	PREDICTED: exosome complex exonuclease R	0.998	0.614	0.886	0.0
224071355	935	predicted protein [Populus trichocarpa]	1.0	0.614	0.873	0.0
449438436	934	PREDICTED: exosome complex exonuclease R	1.0	0.615	0.864	0.0
357517627	1045	Exosome complex exonuclease [Medicago tr	1.0	0.550	0.862	0.0
18398450	933	exosome complex exonuclease DIS3/RRP44 [	1.0	0.616	0.859	0.0
334184269	1012	exosome complex exonuclease DIS3/RRP44 [	1.0	0.568	0.809	0.0

>gi|225438438|ref|XP_002276939.1| PREDICTED: exosome complex exonuclease RRP44 isoform 2 [Vitis vinifera] gi|296082564|emb|CBI21569.3| unnamed protein product [Vitis vinifera]

 Score = 1090 bits (2818), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 516/575 (89%), Positives = 549/575 (95%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           MPMPAG+G +AHALFV KDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDC SRYP GHYVR
Sbjct: 361 MPMPAGNGGIAHALFVSKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCLSRYPSGHYVR 420

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IGEIGDRDTESE+VLI+NDI++RPFS QVLACLPPLPWSVSSEDLANP RLDLR + VF
Sbjct: 421 TIGEIGDRDTESEVVLIENDINSRPFSLQVLACLPPLPWSVSSEDLANPCRLDLRHVCVF 480

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHCT L +GNFEVGVHIADVTNFVHPGTPLDDEA++RGTSVYLVERR
Sbjct: 481 SVDPPGCKDIDDALHCTTLPNGNFEVGVHIADVTNFVHPGTPLDDEAAQRGTSVYLVERR 540

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLR+DVERLAFSVIWE+TP+AEIIST+YTKS+IKSCAALSY+EAQAR
Sbjct: 541 IDMLPKPLTEDICSLRSDVERLAFSVIWEMTPQAEIISTKYTKSIIKSCAALSYIEAQAR 600

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRLMDPLT DLRNMN+LAK MR RRIERGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 601 MDDSRLMDPLTMDLRNMNALAKVMRLRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 660

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVAE+IL+ FPLCSLLRRHPSPT+EMLEPLLRTAAAVGLNLDVS
Sbjct: 661 REANQMVEEFMLAANVSVAEKILKHFPLCSLLRRHPSPTREMLEPLLRTAAAVGLNLDVS 720

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLD AVGDDPYFNKLIRILATRCMTQAVYFCSGDL+PPEFHHYGLAAPLYTHF
Sbjct: 721 SSKALADSLDHAVGDDPYFNKLIRILATRCMTQAVYFCSGDLSPPEFHHYGLAAPLYTHF 780

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRYADV+VHRLL+ASLG+YKLP++FQD  QLTS ADNLNYRHRNAQMA R SVELH
Sbjct: 781 TSPIRRYADVIVHRLLAASLGLYKLPTIFQDNAQLTSTADNLNYRHRNAQMAGRASVELH 840

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           TLIYFRKRPTDTEARIVKIRSNGFIVFVPK+GIEGPVYLTPRG+KG G+W VDEQQQK+ 
Sbjct: 841 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKYGIEGPVYLTPRGEKGGGEWVVDEQQQKVK 900

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           KMDG++SYSVLQTV IHMEVVEPQPNRPKL+L LI
Sbjct: 901 KMDGSISYSVLQTVMIHMEVVEPQPNRPKLELALI 935

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255561455|ref|XP_002521738.1| mitotic control protein dis3, putative [Ricinus communis] gi|223539129|gb|EEF40725.1| mitotic control protein dis3, putative [Ricinus communis]

 Score = 1079 bits (2791), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/575 (89%), Positives = 547/575 (95%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           MP+PAGSG + +ALFV KDRR+PKIRIQTRQL NLLDKRIIVAVDSWD QSRYP GHYVR
Sbjct: 360 MPVPAGSGGLVYALFVSKDRRVPKIRIQTRQLQNLLDKRIIVAVDSWDRQSRYPSGHYVR 419

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IGEIGDRDTE+E+VLI+NDIDARPFS QVLACLPPLPWSVS EDLANPIR DLR L VF
Sbjct: 420 SIGEIGDRDTETEVVLIENDIDARPFSAQVLACLPPLPWSVSEEDLANPIRTDLRHLLVF 479

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHCT L  GNFEVGVHIADVTNFVHP TPLDDEA++RGTSVYLVERR
Sbjct: 480 SVDPPGCKDIDDALHCTMLPHGNFEVGVHIADVTNFVHPSTPLDDEATQRGTSVYLVERR 539

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLRADVERLAFSVIWE+TP+AEII+TRY KSVIKSCAALSY+EAQAR
Sbjct: 540 IDMLPKPLTEDICSLRADVERLAFSVIWEMTPQAEIITTRYAKSVIKSCAALSYIEAQAR 599

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRLMDP+T DLRNMN+LAK MRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 600 MDDSRLMDPVTKDLRNMNALAKIMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 659

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVAEQIL+QFP CSLLRRHP+PTK+MLEPLL+TAA+VGL LDVS
Sbjct: 660 REANQMVEEFMLAANVSVAEQILKQFPGCSLLRRHPTPTKDMLEPLLQTAASVGLTLDVS 719

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLDRAV DDPYFNKLIRI+ATRCMTQAVYFCSGDL+P EFHHYGLAAPLYTHF
Sbjct: 720 SSKALADSLDRAVSDDPYFNKLIRIMATRCMTQAVYFCSGDLSPLEFHHYGLAAPLYTHF 779

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRYADV+VHRLL+ASLGIYKLP++F+DRPQLTSIADNLNYRHRNAQMASRGSVELH
Sbjct: 780 TSPIRRYADVIVHRLLAASLGIYKLPTIFRDRPQLTSIADNLNYRHRNAQMASRGSVELH 839

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           TLIYFRKRPTDTEARIVKIRSNGFIVFVPK+GIEGPVYLTPRG+KG G+W+VDEQQQKI 
Sbjct: 840 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKYGIEGPVYLTPRGEKGGGEWFVDEQQQKIK 899

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           KMDG+LSY +LQ V IH+EVVEPQPNRPKLQLTL+
Sbjct: 900 KMDGSLSYGILQAVRIHLEVVEPQPNRPKLQLTLL 934

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297836470|ref|XP_002886117.1| ribonuclease II family protein [Arabidopsis lyrata subsp. lyrata] gi|297331957|gb|EFH62376.1| ribonuclease II family protein [Arabidopsis lyrata subsp. lyrata]

 Score = 1062 bits (2746), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 504/575 (87%), Positives = 544/575 (94%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           M +PAGSG  AHALFV KDRRIPKIRI TRQL NLLD RI+VAVDSWD QSRYP GHYVR
Sbjct: 359 MSLPAGSGGTAHALFVSKDRRIPKIRINTRQLQNLLDMRIVVAVDSWDRQSRYPSGHYVR 418

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IG+IGDR+TE+E+VLI+ND+D  PFS+QVLACLPPLPWSVS ED++NPIR DLR L VF
Sbjct: 419 PIGKIGDRETETEVVLIENDVDYSPFSSQVLACLPPLPWSVSPEDVSNPIRQDLRHLLVF 478

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHCT+L +GNFE+GVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR
Sbjct: 479 SVDPPGCKDIDDALHCTSLPNGNFELGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 538

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLRADVERLAFSVIWE++P+AEIISTR+TKS+IKS AALSYVEAQAR
Sbjct: 539 IDMLPKPLTEDICSLRADVERLAFSVIWEMSPDAEIISTRFTKSIIKSSAALSYVEAQAR 598

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRL D LTTDLRNMN+LAK MRQRRI+RGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 599 MDDSRLTDSLTTDLRNMNTLAKIMRQRRIDRGALTLASAEVKFQIDTETHDPLDIGMYQI 658

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVA QIL+ FP CSLLRRHP+PT+EMLEPLLRTAAA+GL LDVS
Sbjct: 659 REANQMVEEFMLAANVSVAGQILKLFPSCSLLRRHPTPTREMLEPLLRTAAAIGLTLDVS 718

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLDRAVG+DPYFNKLIRILATRCMTQAVYFCSGDLTPPE+HHYGLAAPLYTHF
Sbjct: 719 SSKALADSLDRAVGEDPYFNKLIRILATRCMTQAVYFCSGDLTPPEYHHYGLAAPLYTHF 778

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRYADV VHRLL+ASLGIYKLP+VFQDRPQLTS+ADNLNYRHRNAQMASR SVELH
Sbjct: 779 TSPIRRYADVFVHRLLAASLGIYKLPTVFQDRPQLTSVADNLNYRHRNAQMASRASVELH 838

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           TLIYFR RPTD EAR+VKIRSNGFIVFVPK+GIEGPVYLT +G+KG+GDWYVDE++QKIV
Sbjct: 839 TLIYFRNRPTDAEARVVKIRSNGFIVFVPKYGIEGPVYLTGKGEKGAGDWYVDEEKQKIV 898

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           KMDG+LSYSVLQTV IHMEVVEPQPNRPKLQL+L+
Sbjct: 899 KMDGSLSYSVLQTVKIHMEVVEPQPNRPKLQLSLL 933

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509070|ref|XP_003523275.1| PREDICTED: exosome complex exonuclease RRP44-like [Glycine max]

 Score = 1060 bits (2742), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 512/576 (88%), Positives = 542/576 (94%), Gaps = 2/576 (0%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           MPMPAGSG +AHALFV KDRRIPKIRIQTRQL NLLDKRIIVAVDSWD QSRYP GHYVR
Sbjct: 360 MPMPAGSGGIAHALFVSKDRRIPKIRIQTRQLENLLDKRIIVAVDSWDRQSRYPSGHYVR 419

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IGEIGDRDTESE+VLI+NDI+ RPFS+QVLACLPPLPW VSSEDL+NPIR DLR LRVF
Sbjct: 420 TIGEIGDRDTESEVVLIENDINTRPFSSQVLACLPPLPWVVSSEDLSNPIRKDLRHLRVF 479

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHC  L +GNFEVGVHIADVTNFV+PGTPLDDEA++RGTSVYLVERR
Sbjct: 480 SVDPPGCKDIDDALHCHVLPNGNFEVGVHIADVTNFVYPGTPLDDEAAQRGTSVYLVERR 539

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLR+DVERLAFSVIWE+TPEA+II+T YTKSVIKS AALSYVEAQAR
Sbjct: 540 IDMLPKPLTEDICSLRSDVERLAFSVIWEMTPEADIIATSYTKSVIKSSAALSYVEAQAR 599

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRLMDP+T DLRNMNSLAKKMR RRIERGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 600 MDDSRLMDPITADLRNMNSLAKKMRLRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 659

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVA+QIL+ FPLCSLLRRHP+PT+EMLEPLLRTAAAVGL+LDVS
Sbjct: 660 REANQMVEEFMLAANVSVAQQILKSFPLCSLLRRHPTPTREMLEPLLRTAAAVGLHLDVS 719

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLD AVGDDPYFNKLIRILATRCMTQAVYFCSGDL+PPE+HHYGLAA LYTHF
Sbjct: 720 SSKALADSLDHAVGDDPYFNKLIRILATRCMTQAVYFCSGDLSPPEYHHYGLAALLYTHF 779

Query: 421 TSPIRRYA-DVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVEL 479
           TSPIRRYA DV+VHRLL+ASLGI KLP VFQD  QLTSIADNLNYRHRNAQ A R SVEL
Sbjct: 780 TSPIRRYAVDVIVHRLLAASLGISKLPPVFQDSLQLTSIADNLNYRHRNAQYAGRASVEL 839

Query: 480 HTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKI 539
           HTLIYFRKRPTDTE RIVKIRSNGF VFVPK+GIEGPVYLT + +KGSG+WYVDEQQQKI
Sbjct: 840 HTLIYFRKRPTDTEGRIVKIRSNGFFVFVPKYGIEGPVYLT-KAEKGSGEWYVDEQQQKI 898

Query: 540 VKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
            KMDG+LSY+VLQTV IHMEVVEPQPNRPKLQLTLI
Sbjct: 899 KKMDGSLSYNVLQTVQIHMEVVEPQPNRPKLQLTLI 934

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516247|ref|XP_003526807.1| PREDICTED: exosome complex exonuclease RRP44-like [Glycine max]

 Score = 1058 bits (2737), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 510/575 (88%), Positives = 542/575 (94%), Gaps = 1/575 (0%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           MPMPAG+G +AHALFV KDRR PKIRIQTRQL NLLDKRIIVAVDSWD QSRYP GHYVR
Sbjct: 361 MPMPAGNGGIAHALFVSKDRRTPKIRIQTRQLENLLDKRIIVAVDSWDRQSRYPSGHYVR 420

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IG+I DRDTE+E+VLI+NDI+ RPFS+QVLACLPPLPW VSSEDL+NPIR DL  L VF
Sbjct: 421 TIGKIDDRDTETEVVLIENDINTRPFSSQVLACLPPLPWVVSSEDLSNPIRKDLCHLCVF 480

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHC +L +GNFEVGVHIADVTNFVHPGTPLDDEA++RGTSVYLVERR
Sbjct: 481 SVDPPGCKDIDDALHCHSLPNGNFEVGVHIADVTNFVHPGTPLDDEAAQRGTSVYLVERR 540

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLR+DVERLAFSVIWE+TPEA+IISTRYTKSVIKS AALSYVEAQAR
Sbjct: 541 IDMLPKPLTEDICSLRSDVERLAFSVIWEMTPEADIISTRYTKSVIKSSAALSYVEAQAR 600

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRLMDP+T DLRNMNSLAKKMR RRIERGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 601 MDDSRLMDPITADLRNMNSLAKKMRLRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 660

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVA+QIL  FPL SLLRRHP+PT+EMLEPLL+TAAAVGL+LDVS
Sbjct: 661 REANQMVEEFMLAANVSVAQQILNSFPLVSLLRRHPTPTREMLEPLLQTAAAVGLHLDVS 720

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLD AVGDDPYFNKLIRILATRCMTQAVYFCSGDL+PPE+HHYGLAAPLYTHF
Sbjct: 721 SSKALADSLDHAVGDDPYFNKLIRILATRCMTQAVYFCSGDLSPPEYHHYGLAAPLYTHF 780

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRYADV+VHRLL+ASLGI KLPSVFQDR QLTSIADNLNYRHRNAQ A R SVELH
Sbjct: 781 TSPIRRYADVIVHRLLAASLGISKLPSVFQDRLQLTSIADNLNYRHRNAQYAGRASVELH 840

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           TLIYFRKRPTDTEARIVKIRSNGF VFVPK+GIEGPVYLT + +KGSG+WYVD+QQQKI 
Sbjct: 841 TLIYFRKRPTDTEARIVKIRSNGFFVFVPKYGIEGPVYLT-KAEKGSGEWYVDDQQQKIK 899

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           KMDG+LSYSVLQTV IHMEVVEPQPNRPKLQLTLI
Sbjct: 900 KMDGSLSYSVLQTVQIHMEVVEPQPNRPKLQLTLI 934

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224071355|ref|XP_002303419.1| predicted protein [Populus trichocarpa] gi|222840851|gb|EEE78398.1| predicted protein [Populus trichocarpa]

 Score = 1058 bits (2735), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 502/575 (87%), Positives = 545/575 (94%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           MPMPAGSG + +ALFV KDRRIPKIRIQTRQL NLLDKRIIVAVDSWD QSR+P GHY+R
Sbjct: 361 MPMPAGSGGLVYALFVSKDRRIPKIRIQTRQLDNLLDKRIIVAVDSWDRQSRHPSGHYIR 420

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IG+IGDRDTE+E+VLI+NDIDARPFS QVLACLPPLPWSVSS+DL    R+DLR L VF
Sbjct: 421 SIGQIGDRDTETELVLIENDIDARPFSAQVLACLPPLPWSVSSKDLNESNRVDLRHLCVF 480

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHCT L +GNFEVGVHIADVTNFVHPGTPLDDEA++RGTSVYLVERR
Sbjct: 481 SVDPPGCKDIDDALHCTMLPTGNFEVGVHIADVTNFVHPGTPLDDEATQRGTSVYLVERR 540

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLRADVERLAFSVIWE+TPEAEIIST+YTKSVIKS AALSYVEAQAR
Sbjct: 541 IDMLPKPLTEDICSLRADVERLAFSVIWEMTPEAEIISTKYTKSVIKSRAALSYVEAQAR 600

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRL+DP+T DLRNMN+LAK MRQRRI RGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 601 MDDSRLVDPVTKDLRNMNALAKIMRQRRIHRGALTLASAEVKFQIDTETHDPLDIGMYQI 660

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVAE+IL++FP CSLLRRHP+PTKEML PLLRTAAAVGLNLDV+
Sbjct: 661 REANQMVEEFMLAANVSVAEKILKEFPECSLLRRHPTPTKEMLGPLLRTAAAVGLNLDVT 720

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLDRAVGDDPYFNKLIRI+ATRCMTQAVYFCSG+L+PPEF HYGLAAPLYTHF
Sbjct: 721 SSKALADSLDRAVGDDPYFNKLIRIMATRCMTQAVYFCSGELSPPEFLHYGLAAPLYTHF 780

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRY+DV+VHRLL+AS+GIYKLP++F+DRPQLTSIADNLNYRHRNAQMASRGSVELH
Sbjct: 781 TSPIRRYSDVIVHRLLAASIGIYKLPTIFRDRPQLTSIADNLNYRHRNAQMASRGSVELH 840

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           TLIYFR RPTDTEARIVK+RSNGFIVFVPKFGIEGPVYLT RG KG G+W+VDEQQQKI 
Sbjct: 841 TLIYFRNRPTDTEARIVKMRSNGFIVFVPKFGIEGPVYLTMRGDKGGGEWFVDEQQQKIR 900

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           KMDG++SYS+LQ V IH+EV+EP+PNRPKLQLTL+
Sbjct: 901 KMDGSVSYSILQAVKIHLEVLEPKPNRPKLQLTLL 935

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438436|ref|XP_004136994.1| PREDICTED: exosome complex exonuclease RRP44-like [Cucumis sativus]

 Score = 1049 bits (2712), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 497/575 (86%), Positives = 543/575 (94%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           MPMPAGSG +A+ALFV KDRRIPKIRIQTRQL NLLDKRIIVAVDSWD  SRYP GHYVR
Sbjct: 360 MPMPAGSGGIAYALFVSKDRRIPKIRIQTRQLENLLDKRIIVAVDSWDRLSRYPSGHYVR 419

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IGEIGDRDTESE+VLI+NDI++RPFS+QV+ CLPPLPWSVS  D+ANPIR DLR L VF
Sbjct: 420 SIGEIGDRDTESEVVLIENDINSRPFSSQVMTCLPPLPWSVSPVDIANPIRQDLRHLNVF 479

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHCTALS+GNFEVGVHIADVTNFVHPGT LDDEA++RGTSVYLVERR
Sbjct: 480 SVDPPGCKDIDDALHCTALSNGNFEVGVHIADVTNFVHPGTALDDEAAQRGTSVYLVERR 539

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLRADVERLAFSVIWE+TPEA+I+ST YTKS+IKS AALSYVEAQAR
Sbjct: 540 IDMLPKPLTEDICSLRADVERLAFSVIWEMTPEADIVSTSYTKSIIKSSAALSYVEAQAR 599

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRLMDP+T DLRNMN+LAKKMR RRIERGALTLASAEVKFQIDTETHDPLDIGMYQI
Sbjct: 600 MDDSRLMDPITRDLRNMNALAKKMRLRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 659

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
           REANQMVEEFMLAANVSVAE+IL+ FPLCSLLRRHP+PTKEMLEPL+RTA AVGL+LDVS
Sbjct: 660 REANQMVEEFMLAANVSVAEKILKHFPLCSLLRRHPTPTKEMLEPLIRTAVAVGLDLDVS 719

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLDRA+GDDPYFNKLIRILATRCMTQAVYF SGDL+PPE+ HYGLAA LYTHF
Sbjct: 720 SSKALADSLDRALGDDPYFNKLIRILATRCMTQAVYFYSGDLSPPEYQHYGLAARLYTHF 779

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRYADV+VHRLL+ASLGI+KLP++F DRP+LT+IADNLNYRHRNAQMA R SVELH
Sbjct: 780 TSPIRRYADVIVHRLLAASLGIFKLPTLFLDRPKLTTIADNLNYRHRNAQMAGRASVELH 839

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           TLIYF+KRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLT + +K SG+W+VDEQ+QKI 
Sbjct: 840 TLIYFKKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTGKSEKQSGEWFVDEQEQKIK 899

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           K+DG+++Y++LQ V IHMEVVEPQPNRPKLQLTL+
Sbjct: 900 KLDGSITYNILQAVRIHMEVVEPQPNRPKLQLTLL 934

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357517627|ref|XP_003629102.1| Exosome complex exonuclease [Medicago truncatula] gi|355523124|gb|AET03578.1| Exosome complex exonuclease [Medicago truncatula]

 Score = 1045 bits (2703), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 496/575 (86%), Positives = 539/575 (93%)

Query: 1    MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
            MP+P GS  VA+ALFV KDRR PKIRIQTRQL NLLDKRIIV+VDSWD QSRYP GHYVR
Sbjct: 471  MPIPGGSRGVAYALFVSKDRRFPKIRIQTRQLENLLDKRIIVSVDSWDRQSRYPSGHYVR 530

Query: 61   VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
             +G+IGD+DTE+E+VLI+NDI++RPFS QVLACLPPLPWSVSSEDL+ P R DLR LRVF
Sbjct: 531  TVGKIGDKDTETEVVLIENDINSRPFSAQVLACLPPLPWSVSSEDLSIPFRQDLRHLRVF 590

Query: 121  SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
            SVDPPGCKDIDDALHC AL +GNF+VGVHIADVTNFV PGTPLDDEAS+RGTSVYLVE+R
Sbjct: 591  SVDPPGCKDIDDALHCIALPNGNFDVGVHIADVTNFVFPGTPLDDEASQRGTSVYLVEKR 650

Query: 181  IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
            IDMLPKPLTED+CSLR+DVERLAFSVIWE+TPEA+IISTRYTKSVIKS AALSYVEAQAR
Sbjct: 651  IDMLPKPLTEDVCSLRSDVERLAFSVIWEMTPEADIISTRYTKSVIKSAAALSYVEAQAR 710

Query: 241  MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
            MDDSRLMDP+TTDLRNMNSLAKKMR RRIE GALTLASAEVKFQIDTETH+PLDIG+YQI
Sbjct: 711  MDDSRLMDPVTTDLRNMNSLAKKMRLRRIENGALTLASAEVKFQIDTETHNPLDIGIYQI 770

Query: 301  REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
            +EANQMVEEFMLAANVSVA+QIL+ FPLCSLLRRHP+PTKEMLEPLLR +AA+GLNLDVS
Sbjct: 771  KEANQMVEEFMLAANVSVAQQILKSFPLCSLLRRHPTPTKEMLEPLLRVSAAIGLNLDVS 830

Query: 361  SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
            SSKALADSLD AVGDDPYFNKLIRIL TRCM+QAVYFCSGDL+PPE+HHYGLA PLYTHF
Sbjct: 831  SSKALADSLDHAVGDDPYFNKLIRILTTRCMSQAVYFCSGDLSPPEYHHYGLATPLYTHF 890

Query: 421  TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
            TSPIRRYADV+VHRLL+AS+GI KLPSVFQDR QLTSIADNLNYRHRNAQMA R SVEL+
Sbjct: 891  TSPIRRYADVIVHRLLAASIGISKLPSVFQDRLQLTSIADNLNYRHRNAQMAGRASVELN 950

Query: 481  TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
            TLIYFR RPTDTEAR+VKIRSNGF VFVPKFGIEGPVYLT R +KGSG+WYVDEQ+QKI 
Sbjct: 951  TLIYFRTRPTDTEARVVKIRSNGFFVFVPKFGIEGPVYLTTRAEKGSGEWYVDEQEQKIK 1010

Query: 541  KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
            KMDG+ SYS+LQTV IH+EVVEPQPNRPKLQLTLI
Sbjct: 1011 KMDGSFSYSILQTVQIHLEVVEPQPNRPKLQLTLI 1045

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18398450|ref|NP_565418.1| exosome complex exonuclease DIS3/RRP44 [Arabidopsis thaliana] gi|15982745|gb|AAL09713.1| At2g17510/MJB20.7 [Arabidopsis thaliana] gi|19699186|gb|AAL90959.1| At2g17510/MJB20.7 [Arabidopsis thaliana] gi|20198264|gb|AAD32908.2| putative mitotic control protein dis3 [Arabidopsis thaliana] gi|330251544|gb|AEC06638.1| exosome complex exonuclease DIS3/RRP44 [Arabidopsis thaliana]

 Score = 1043 bits (2698), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 494/575 (85%), Positives = 539/575 (93%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
           M +PAGSG  AHALFV KDRRIPKIRI TRQL NLLD RI+VAVDSWD QSRYP GHYVR
Sbjct: 359 MSLPAGSGGTAHALFVSKDRRIPKIRINTRQLQNLLDMRIVVAVDSWDRQSRYPSGHYVR 418

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVF 120
            IG+IGD++TE+E+VLI+ND+D  PFS+QVLACLPPLPWSVSSED++NP+R DLR L VF
Sbjct: 419 PIGKIGDKETETEVVLIENDVDYSPFSSQVLACLPPLPWSVSSEDVSNPVRQDLRHLLVF 478

Query: 121 SVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 180
           SVDPPGCKDIDDALHCT+L +GNFE+GVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR
Sbjct: 479 SVDPPGCKDIDDALHCTSLPNGNFELGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERR 538

Query: 181 IDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQAR 240
           IDMLPKPLTEDICSLRADVERLAFSVIWE++P+AEIISTR+TKS+IKS AALSY+EAQAR
Sbjct: 539 IDMLPKPLTEDICSLRADVERLAFSVIWEMSPDAEIISTRFTKSIIKSSAALSYIEAQAR 598

Query: 241 MDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQI 300
           MDDSRL D LTTDLRNMN+LAK MRQRRI+RGALTLASAEVKF ID E HDPL+IGMYQI
Sbjct: 599 MDDSRLTDSLTTDLRNMNTLAKIMRQRRIDRGALTLASAEVKFDIDPENHDPLNIGMYQI 658

Query: 301 REANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS 360
            EANQMVEEFMLAANVSVA QIL+ FP CSLLRRHP+PT+EMLEPLLRTAAA+GL LDVS
Sbjct: 659 LEANQMVEEFMLAANVSVAGQILKLFPSCSLLRRHPTPTREMLEPLLRTAAAIGLTLDVS 718

Query: 361 SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHF 420
           SSKALADSLDRAVG+DPYFNKLIRILATRCMTQAVYFCSGDL+PPE+HHYGLAAPLYTHF
Sbjct: 719 SSKALADSLDRAVGEDPYFNKLIRILATRCMTQAVYFCSGDLSPPEYHHYGLAAPLYTHF 778

Query: 421 TSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELH 480
           TSPIRRYADV VHRLL+ASLGIYKLP+VFQDRPQLTS+ADNLNYRHRNAQMA R SVEL+
Sbjct: 779 TSPIRRYADVFVHRLLAASLGIYKLPTVFQDRPQLTSVADNLNYRHRNAQMAGRASVELY 838

Query: 481 TLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
            LIYFR RPTD EAR+VKIRSNGFIVFVPK+GIEGPVYLT +G+KG+GDWYVDE++QKIV
Sbjct: 839 VLIYFRTRPTDEEARVVKIRSNGFIVFVPKYGIEGPVYLTGKGEKGAGDWYVDEEKQKIV 898

Query: 541 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
           KMDG+LSYSVLQTV IHMEVVEPQPNRPKLQLTL+
Sbjct: 899 KMDGSLSYSVLQTVKIHMEVVEPQPNRPKLQLTLL 933

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334184269|ref|NP_001189541.1| exosome complex exonuclease DIS3/RRP44 [Arabidopsis thaliana] gi|330251545|gb|AEC06639.1| exosome complex exonuclease DIS3/RRP44 [Arabidopsis thaliana]

 Score = 1022 bits (2642), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 493/609 (80%), Positives = 539/609 (88%), Gaps = 34/609 (5%)

Query: 1    MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
            M +PAGSG  AHALFV KDRRIPKIRI TRQL NLLD RI+VAVDSWD QSRYP GHYVR
Sbjct: 404  MSLPAGSGGTAHALFVSKDRRIPKIRINTRQLQNLLDMRIVVAVDSWDRQSRYPSGHYVR 463

Query: 61   VIGEIGDRDTESEM----------------------VLIDNDIDARPFSTQVLACLPPLP 98
             IG+IGD++TE+E+                      VLI+ND+D  PFS+QVLACLPPLP
Sbjct: 464  PIGKIGDKETETEVRDHINLFDSILVGVRWARVGKVVLIENDVDYSPFSSQVLACLPPLP 523

Query: 99   WSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGV---------- 148
            WSVSSED++NP+R DLR L VFSVDPPGCKDIDDALHCT+L +GNFE+GV          
Sbjct: 524  WSVSSEDVSNPVRQDLRHLLVFSVDPPGCKDIDDALHCTSLPNGNFELGVRILESSDSHK 583

Query: 149  --HIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSV 206
              +IADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSV
Sbjct: 584  YDYIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSV 643

Query: 207  IWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQ 266
            IWE++P+AEIISTR+TKS+IKS AALSY+EAQARMDDSRL D LTTDLRNMN+LAK MRQ
Sbjct: 644  IWEMSPDAEIISTRFTKSIIKSSAALSYIEAQARMDDSRLTDSLTTDLRNMNTLAKIMRQ 703

Query: 267  RRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQF 326
            RRI+RGALTLASAEVKF ID E HDPL+IGMYQI EANQMVEEFMLAANVSVA QIL+ F
Sbjct: 704  RRIDRGALTLASAEVKFDIDPENHDPLNIGMYQILEANQMVEEFMLAANVSVAGQILKLF 763

Query: 327  PLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRIL 386
            P CSLLRRHP+PT+EMLEPLLRTAAA+GL LDVSSSKALADSLDRAVG+DPYFNKLIRIL
Sbjct: 764  PSCSLLRRHPTPTREMLEPLLRTAAAIGLTLDVSSSKALADSLDRAVGEDPYFNKLIRIL 823

Query: 387  ATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLP 446
            ATRCMTQAVYFCSGDL+PPE+HHYGLAAPLYTHFTSPIRRYADV VHRLL+ASLGIYKLP
Sbjct: 824  ATRCMTQAVYFCSGDLSPPEYHHYGLAAPLYTHFTSPIRRYADVFVHRLLAASLGIYKLP 883

Query: 447  SVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIV 506
            +VFQDRPQLTS+ADNLNYRHRNAQMA R SVEL+ LIYFR RPTD EAR+VKIRSNGFIV
Sbjct: 884  TVFQDRPQLTSVADNLNYRHRNAQMAGRASVELYVLIYFRTRPTDEEARVVKIRSNGFIV 943

Query: 507  FVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN 566
            FVPK+GIEGPVYLT +G+KG+GDWYVDE++QKIVKMDG+LSYSVLQTV IHMEVVEPQPN
Sbjct: 944  FVPKYGIEGPVYLTGKGEKGAGDWYVDEEKQKIVKMDGSLSYSVLQTVKIHMEVVEPQPN 1003

Query: 567  RPKLQLTLI 575
            RPKLQLTL+
Sbjct: 1004 RPKLQLTLL 1012

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	575
MGI|MGI:1919912	958	Dis3 "DIS3 mitotic control hom	0.951	0.570	0.510	1.1e-149
UNIPROTKB|E2RNY6	958	DIS3 "Uncharacterized protein"	0.951	0.570	0.512	2.3e-149
ZFIN|ZDB-GENE-080213-3	950	dis3 "DIS3 mitotic control hom	0.949	0.574	0.506	3.2e-149
UNIPROTKB|G3V1J5	796	DIS3 "Exosome complex exonucle	0.951	0.687	0.508	3.8e-149
UNIPROTKB|Q9Y2L1	958	DIS3 "Exosome complex exonucle	0.951	0.570	0.508	3.8e-149
UNIPROTKB|E1BXX6	963	DIS3 "Uncharacterized protein"	0.951	0.568	0.5	5.5e-148
UNIPROTKB|F1RHF7	752	DIS3 "Uncharacterized protein"	0.951	0.727	0.508	5.5e-148
FB|FBgn0039183	983	Dis3 "Dis3" [Drosophila melano	0.907	0.531	0.506	6.1e-142
DICTYBASE|DDB_G0293614	1006	DDB_G0293614 "putative exoribo	0.973	0.556	0.478	4.3e-141
WB|WBGene00001001	961	dis-3 [Caenorhabditis elegans	0.993	0.594	0.480	5.5e-141

MGI|MGI:1919912 Dis3 "DIS3 mitotic control homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 1461 (519.4 bits), Expect = 1.1e-149, P = 1.1e-149
 Identities = 288/564 (51%), Positives = 399/564 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF P D+RIP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+V+ +G++G+++TE+E
Sbjct:   372 LFTPADKRIPRIRIETRQASALEGRRIIVAIDGWPRNSRYPNGHFVKNLGDVGEKETETE 431

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PWS++ ED+ N  R DLR L V SVDPPGC DIDDA
Sbjct:   432 VLLLEHDVPHQPFSQAVLSFLPRMPWSITEEDMKN--REDLRHLCVCSVDPPGCTDIDDA 489

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  LS+GN EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct:   490 LHCRELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 549

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SLR++V+RLAFS IWE+   AEI+ TR+TKSVI S A+L+Y EAQ R+D + + D +TT 
Sbjct:   550 SLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRIDSAAMNDDITTS 609

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK +++ RIE+GALTL+S E++F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct:   610 LRGLNQLAKILKKGRIEKGALTLSSPEIRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 669

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             AN+SVA++I  +F   +LLR+HP+P     + L++ A +  L +   ++K+LADSLDRA 
Sbjct:   670 ANISVAKKIHEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIKTDTAKSLADSLDRAE 729

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
               D PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++V
Sbjct:   730 SPDFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADIIV 787

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
             HRLL+ ++G         D+ +L+ I  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct:   788 HRLLAVAIGADCTYPELTDKHKLSDICKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 847

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE-QQQKI----------V 540
              EA I+ +R N  +V +PK+G+EG V+   + +      Y DE    +I          V
Sbjct:   848 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPKPRLAYDDEIPSLRIEGTVFHVFDKV 907

Query:   541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
             K+   L  S LQ   I M +VEPQ
Sbjct:   908 KVKITLDSSNLQHQKIRMALVEPQ 931

GO:0000175 "3'-5'-exoribonuclease activity" evidence=ISO

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISO

GO:0000178 "exosome (RNase complex)" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=ISO

GO:0004527 "exonuclease activity" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=IEA

GO:0005085 "guanyl-nucleotide exchange factor activity" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005654 "nucleoplasm" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

GO:0016075 "rRNA catabolic process" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0071034 "CUT catabolic process" evidence=ISO

UNIPROTKB|E2RNY6 DIS3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1458 (518.3 bits), Expect = 2.3e-149, P = 2.3e-149
 Identities = 289/564 (51%), Positives = 396/564 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF P DRRIP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+V+ +GE+G+++TE+E
Sbjct:   372 LFTPADRRIPRIRIETRQASALEGRRIIVAIDGWPRNSRYPNGHFVKNLGEVGEKETETE 431

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PWS++ +D+ N  R DLR L V SVDPPGC DIDDA
Sbjct:   432 VLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKN--REDLRHLCVCSVDPPGCTDIDDA 489

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  L +GN EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct:   490 LHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 549

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SLR +V+RLAFS IWE+  +AEI+  R+TKSVI S A+L+Y EAQ R+D + + D +TT 
Sbjct:   550 SLRCNVDRLAFSCIWEMNHDAEILKVRFTKSVINSKASLTYAEAQMRIDSAAMNDDITTS 609

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK +++RRIE+GALTL+S EV+F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct:   610 LRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 669

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             AN+SVA++I  +F   +LLR+HP+P     E L++ A +  L +   ++K+LADSLDRA 
Sbjct:   670 ANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAAKSKNLEIKTDTAKSLADSLDRAD 729

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
                 PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++V
Sbjct:   730 SPTFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADIIV 787

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
             HRLL+ ++G         D+ +L  +  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct:   788 HRLLAVAIGADCTYPELTDKHKLADLCKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 847

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQ-KI----------V 540
              EA I+ +R N  +V +PK+G+EG V+   + +      Y DE    KI          V
Sbjct:   848 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPKPKLIYDDEVPSLKIEDTVFHIFDKV 907

Query:   541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
             K+   L  S LQ   I M +VEPQ
Sbjct:   908 KVKIMLDSSNLQHQKIRMSLVEPQ 931

GO:0071034 "CUT catabolic process" evidence=IEA

GO:0016075 "rRNA catabolic process" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005085 "guanyl-nucleotide exchange factor activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

ZFIN|ZDB-GENE-080213-3 dis3 "DIS3 mitotic control homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 1439 (511.6 bits), Expect = 3.2e-149, Sum P(2) = 3.2e-149
 Identities = 285/563 (50%), Positives = 395/563 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF P DRRIP+IRI+TRQ   L+ +RI+VA+D W   SRYP GH+V+ +G  GD++TE+E
Sbjct:   369 LFTPADRRIPRIRIETRQAATLIGQRIMVAIDGWPKNSRYPNGHFVKNLGTAGDKETETE 428

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PW ++ EDL   +R DLR L V SVDPPGC DIDDA
Sbjct:   429 VLLLEHDVPHQPFSQAVLSFLPKMPWGITEEDLK--VRADLRHLCVCSVDPPGCTDIDDA 486

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  L +GN EVGVHIADV++F+ PG  LD EA+ RGT+VYL  +RIDM+P+ L+ ++C
Sbjct:   487 LHCRELENGNLEVGVHIADVSHFIRPGNALDQEAANRGTTVYLCGKRIDMVPELLSSNLC 546

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SLR++VERLAFS IWE+  +AEII T +TKSVI S A+L+Y EAQ R+DD+ + D +T  
Sbjct:   547 SLRSNVERLAFSCIWEMNHKAEIIKTHFTKSVINSKASLTYAEAQMRIDDTTMNDDITKS 606

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK ++ +RI++GALTL+S EV+F ID+ETHDP+D+   ++ E N MVEEFML 
Sbjct:   607 LRGLNKLAKILKAQRIDKGALTLSSPEVRFHIDSETHDPIDLQTKELMETNSMVEEFMLL 666

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             AN+SVA++I  +F  C+LLR+HP+P     + L++ A +  L +   S+KALADSL+ A 
Sbjct:   667 ANISVAQKIYDEFSECALLRKHPAPPPSNYDILIKAAKSRDLEIHTDSAKALADSLNNAT 726

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
              ++  YFN L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++V
Sbjct:   727 IENFAYFNTLLRILATRCMMQAVYFCSG--MDSDFHHYGLASPIYTHFTSPIRRYADIIV 784

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPT-D 491
             HRLL+ ++          D+ + +++ +N+NYRH+ AQ A R SV  HT ++F+ +   +
Sbjct:   785 HRLLAVAINADSTYPDLMDKHKQSALCNNINYRHKMAQYAQRASVAFHTQLFFKNKGIIN 844

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYL------TPR-GQKGSGDWY-VDEQQQKI---V 540
              E  I+ +R N  I+ +PKFG+EG V+       +PR      G    V+E   +I   V
Sbjct:   845 EEGFILFVRKNAIIILIPKFGLEGTVFFENKDKPSPRLSFDTEGPTLKVEEHTFRIFDRV 904

Query:   541 KMDGNLSYSVLQTVNIHMEVVEP 563
             K+  +L  S LQ   I M + EP
Sbjct:   905 KVTISLDASNLQHQRIRMALTEP 927

GO:0003723 "RNA binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=IEA

UNIPROTKB|G3V1J5 DIS3 "Exosome complex exonuclease RRP44" [Homo sapiens (taxid:9606)]

 Score = 1456 (517.6 bits), Expect = 3.8e-149, P = 3.8e-149
 Identities = 287/564 (50%), Positives = 396/564 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF P D+RIP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+VR +G++G+++TE+E
Sbjct:   210 LFTPADKRIPRIRIETRQASTLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETE 269

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PWS++ +D+ N  R DLR L + SVDPPGC DIDDA
Sbjct:   270 VLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKN--REDLRHLCICSVDPPGCTDIDDA 327

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  L +GN EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct:   328 LHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 387

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SL+ DV+RLAFS IWE+   AEI+ T++TKSVI S A+L+Y EAQ R+D + + D +TT 
Sbjct:   388 SLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDDITTS 447

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK +++RRIE+GALTL+S EV+F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct:   448 LRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 507

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             AN+SVA++I  +F   +LLR+HP+P     E L++ A +  L +   ++K+LA+SLD+A 
Sbjct:   508 ANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLAESLDQAE 567

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
                 PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYADV+V
Sbjct:   568 SPTFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADVIV 625

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
             HRLL+ ++G         D+ +L  I  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct:   626 HRLLAVAIGADCTYPELTDKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 685

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE-QQQKI----------V 540
              EA I+ +R N  +V +PK+G+EG V+   + +      Y DE    KI          V
Sbjct:   686 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTVFHVFDKV 745

Query:   541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
             K+   L  S LQ   I M +VEPQ
Sbjct:   746 KVKIMLDSSNLQHQKIRMSLVEPQ 769

GO:0003723 "RNA binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=IEA

UNIPROTKB|Q9Y2L1 DIS3 "Exosome complex exonuclease RRP44" [Homo sapiens (taxid:9606)]

 Score = 1456 (517.6 bits), Expect = 3.8e-149, P = 3.8e-149
 Identities = 287/564 (50%), Positives = 396/564 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF P D+RIP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+VR +G++G+++TE+E
Sbjct:   372 LFTPADKRIPRIRIETRQASTLEGRRIIVAIDGWPRNSRYPNGHFVRNLGDVGEKETETE 431

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PWS++ +D+ N  R DLR L + SVDPPGC DIDDA
Sbjct:   432 VLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKN--REDLRHLCICSVDPPGCTDIDDA 489

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  L +GN EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct:   490 LHCRELENGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 549

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SL+ DV+RLAFS IWE+   AEI+ T++TKSVI S A+L+Y EAQ R+D + + D +TT 
Sbjct:   550 SLKCDVDRLAFSCIWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDDITTS 609

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK +++RRIE+GALTL+S EV+F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct:   610 LRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 669

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             AN+SVA++I  +F   +LLR+HP+P     E L++ A +  L +   ++K+LA+SLD+A 
Sbjct:   670 ANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAKSLAESLDQAE 729

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
                 PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYADV+V
Sbjct:   730 SPTFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADVIV 787

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
             HRLL+ ++G         D+ +L  I  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct:   788 HRLLAVAIGADCTYPELTDKHKLADICKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 847

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE-QQQKI----------V 540
              EA I+ +R N  +V +PK+G+EG V+   + +      Y DE    KI          V
Sbjct:   848 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPNPQLIYDDEIPSLKIEDTVFHVFDKV 907

Query:   541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
             K+   L  S LQ   I M +VEPQ
Sbjct:   908 KVKIMLDSSNLQHQKIRMSLVEPQ 931

GO:0003723 "RNA binding" evidence=IEA

GO:0005085 "guanyl-nucleotide exchange factor activity" evidence=IDA

GO:0006364 "rRNA processing" evidence=TAS

GO:0000178 "exosome (RNase complex)" evidence=TAS

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0000176 "nuclear exosome (RNase complex)" evidence=IDA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IMP

GO:0004519 "endonuclease activity" evidence=IMP

GO:0016075 "rRNA catabolic process" evidence=IMP

GO:0071034 "CUT catabolic process" evidence=IMP

GO:0000288 "nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0043928 "exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|E1BXX6 DIS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 1445 (513.7 bits), Expect = 5.5e-148, P = 5.5e-148
 Identities = 282/564 (50%), Positives = 397/564 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF+P DR IP+IRI+TRQ   L  +RIIVA+D W   SRYP GH+V+ +G  GD++TE+E
Sbjct:   375 LFIPADRSIPRIRIETRQADKLEGQRIIVAIDGWPRNSRYPNGHFVKNLGSAGDKETETE 434

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PWS++ +D+    R DLR L V SVDPPGC DIDDA
Sbjct:   435 VLLLEHDVPHQPFSQNVLSFLPKMPWSITEKDMK--YREDLRHLYVCSVDPPGCTDIDDA 492

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  + +GN EVGVHIADV++F+ PG  LD+E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct:   493 LHCREIENGNLEVGVHIADVSHFIRPGNALDEESARRGTTVYLCEKRIDMVPELLSSNLC 552

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SLR++V+RLAFS IWE+  +AEI+ TR+TKS+I S A+L+Y EAQ R+D + + D +T  
Sbjct:   553 SLRSNVDRLAFSCIWEMNQKAEILKTRFTKSIINSKASLTYAEAQMRIDSAAMNDDITVS 612

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK ++++RI+ GALTL+S EV+F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct:   613 LRGLNKLAKILKKKRIDNGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 672

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             ANVSVA++I  +FP  +LLR+HP+P     + L++ A +  L +   S+KALA+SLD+A 
Sbjct:   673 ANVSVAQKIYDEFPEFALLRKHPAPPPSNYDILVKAAKSKNLEIKTDSAKALAESLDKAE 732

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
               D PY N L+RIL TRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++V
Sbjct:   733 SPDFPYLNTLLRILTTRCMMQAVYFCSG--MDSDFHHYGLASPIYTHFTSPIRRYADIIV 790

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR-KRPTD 491
             HRLL+ ++G         D+ +L  +  NLNYRH+ AQ A R SV  HT ++F+ K   +
Sbjct:   791 HRLLAVAIGADSTYPELTDKHKLADLCKNLNYRHKMAQYAQRASVAFHTQLFFKTKGVVN 850

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYL------TPRGQKGSG--DWYVDEQQQKI---V 540
              +A I+ +R N  +V +PK+G+EG V+       TP+    S      V++    +   V
Sbjct:   851 EDAYILFVRRNAVVVLIPKYGLEGTVFFEEKDKPTPKLDYNSEVPSLTVEDTTLCVFDKV 910

Query:   541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
              +   L  S +Q   I ME+VEP+
Sbjct:   911 TVSVTLDASNIQHQKIRMELVEPK 934

GO:0003723 "RNA binding" evidence=IEA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IEA

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0005085 "guanyl-nucleotide exchange factor activity" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0016075 "rRNA catabolic process" evidence=IEA

GO:0071034 "CUT catabolic process" evidence=IEA

UNIPROTKB|F1RHF7 DIS3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1445 (513.7 bits), Expect = 5.5e-148, P = 5.5e-148
 Identities = 287/564 (50%), Positives = 395/564 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             LF P D+RIP+IRI+TRQ   L  +RIIV++D W   SRYP GH+V+ +GE+GD++TE+E
Sbjct:   166 LFTPADKRIPRIRIETRQASTLEGRRIIVSIDGWPRNSRYPNGHFVKNLGEVGDKETETE 225

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+  +PFS  VL+ LP +PWS++ +D+ N  R DLR L V SVDPPGC DIDDA
Sbjct:   226 VLLLEHDVPHQPFSQAVLSFLPKMPWSITEKDMKN--REDLRHLCVCSVDPPGCTDIDDA 283

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC 193
             LHC  L +G+ EVGVHIADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++C
Sbjct:   284 LHCRELENGDLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLC 343

Query:   194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD 253
             SLR++V+RLAFS IWE+   AEI+ TR+TKSVI S A+L+Y EAQ R+D + + D +T  
Sbjct:   344 SLRSNVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRIDSAAMNDSITAS 403

Query:   254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA 313
             LR +N LAK +++RRIE+GALTL+S EV+F +D+ETHDP+D+   ++RE N MVEEFML 
Sbjct:   404 LRGLNKLAKILKKRRIEKGALTLSSPEVRFHMDSETHDPIDLQTKELRETNSMVEEFMLL 463

Query:   314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV 373
             AN+SVA++I  +F   +LLR+HP+P     E L++ A +  L +   ++KALADSLDR  
Sbjct:   464 ANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAAKSKNLEIKTDTAKALADSLDRVD 523

Query:   374 GDD-PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
                 PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++V
Sbjct:   524 SPIFPYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADIIV 581

Query:   433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TD 491
             HRLL+ ++G         D+ +L  +  NLN+RH+ AQ A R SV  HT ++F+ +    
Sbjct:   582 HRLLAVAIGADCTYPELTDKHKLADLCKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVS 641

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQ-KI----------V 540
              EA I+ +R N  +V +PK+G+EG V+   + +      Y DE    KI          V
Sbjct:   642 EEAYILFVRKNAIVVLIPKYGLEGTVFFEEKDKPKPRLIYDDEVPSLKIEDTVFHIFDKV 701

Query:   541 KMDGNLSYSVLQTVNIHMEVVEPQ 564
             K+   L  S LQ   I M +VEPQ
Sbjct:   702 KVRIMLDSSNLQHQKIRMLLVEPQ 725

GO:0071034 "CUT catabolic process" evidence=IEA

GO:0016075 "rRNA catabolic process" evidence=IEA

GO:0005654 "nucleoplasm" evidence=IEA

GO:0005085 "guanyl-nucleotide exchange factor activity" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

GO:0000176 "nuclear exosome (RNase complex)" evidence=IEA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

FB|FBgn0039183 Dis3 "Dis3" [Drosophila melanogaster (taxid:7227)]

 Score = 1388 (493.7 bits), Expect = 6.1e-142, P = 6.1e-142
 Identities = 268/529 (50%), Positives = 372/529 (70%)

Query:    14 LFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESE 73
             +FVP DR+IP+IRI+TRQ   L ++RIIV +D+W   SRYP GH+VR +G +GD  TE+E
Sbjct:   379 IFVPADRKIPRIRIETRQAAMLQNQRIIVTIDTWPRNSRYPHGHFVRSLGPLGDMATENE 438

Query:    74 MVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDA 133
             ++L+++D+    FS +VL+ LP +PW+++ ED +   R+DLRDL + SVDPPGC DIDDA
Sbjct:   439 VILLEHDVPHCKFSDEVLSFLPKMPWTITDEDYSK--RVDLRDLYICSVDPPGCTDIDDA 496

Query:   134 LHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRG-TSVYLVERRIDMLPKPLTEDI 192
             LHC  L +GN EVGVHIADV++F+ PG       S  G T+VYLV +RIDM+P+ L+ ++
Sbjct:   497 LHCRELPNGNLEVGVHIADVSHFIRPGKRTGHGGSGPGETTVYLVGKRIDMVPELLSSNL 556

Query:   193 CSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTT 252
             CSL   VER AFS +WE+  EA ++S R+ KSVIKS  A++Y EAQ  +DD+   + +  
Sbjct:   557 CSLVGGVERFAFSCVWEVDNEANVLSKRFHKSVIKSKRAMTYEEAQNIIDDATQQNEIAK 616

Query:   253 DLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFML 312
              LRN+N LAK +++RR++ GAL LAS E++FQ+D+ETH+PL++ + Q+RE N MVEEFML
Sbjct:   617 SLRNLNRLAKILKKRRMDNGALVLASPEIRFQVDSETHEPLEVEVKQMRETNSMVEEFML 676

Query:   313 AANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRA 372
              AN++VAE I  +F  C++LRRHP P     +PL+++A   G  +D++S   L+ SLD+ 
Sbjct:   677 LANITVAEHIATEFSECAVLRRHPRPPPTNFDPLVKSARYQGFQVDINSGLELSHSLDKC 736

Query:   373 V-GDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVV 431
             V  D+PYFN +IRIL TRCM QAVYF SG L   EF HYGLAAP+YTHFTSPIRRY+D++
Sbjct:   737 VKADNPYFNTMIRILTTRCMMQAVYFISGSLQKEEFFHYGLAAPIYTHFTSPIRRYSDIM 796

Query:   432 VHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTD 491
             VHRLL+AS+G     +   DR     +  NLNYRH+ AQ A R SV L+T ++FR +  D
Sbjct:   797 VHRLLAASIGADSTYAQLLDRKSNEELCHNLNYRHKMAQYAGRASVALNTHLFFRGKEED 856

Query:   492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
              E  ++ +R N   V +PK+G+EG +YL  +  K   D  V+  + +IV
Sbjct:   857 EEGYVLFVRKNALQVLIPKYGLEGTLYL--KSDKDGKDG-VERVKSEIV 902

GO:0000177 "cytoplasmic exosome (RNase complex)" evidence=ISS

GO:0006397 "mRNA processing" evidence=ISS

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISS;IDA

GO:0000175 "3'-5'-exoribonuclease activity" evidence=ISS

GO:0003723 "RNA binding" evidence=IEA

GO:0005652 "nuclear lamina" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0071027 "nuclear RNA surveillance" evidence=IMP

GO:0010468 "regulation of gene expression" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

DICTYBASE|DDB_G0293614 DDB_G0293614 "putative exoribonuclease" [Dictyostelium discoideum (taxid:44689)]

 Score = 1380 (490.8 bits), Expect = 4.3e-141, P = 4.3e-141
 Identities = 276/577 (47%), Positives = 397/577 (68%)

Query:    12 HAL-FVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDT 70
             H L F+P D+RIPKIRI++RQ+ NL+ KRI+VA+D WD  S+YP GH+V+ +G +GD++T
Sbjct:   370 HFLYFMPIDKRIPKIRIKSRQVSNLIGKRIVVAIDQWDKNSKYPSGHFVKDLGPLGDKET 429

Query:    71 ESEMVLIDNDIDARPFSTQVLACLP-P-LPWSVSSEDLANPIRLDLRDLRVFSVDPPGCK 128
             ES+++L+  DI   PF   V+ CLP P +   V+S D+    R DLR   +FSVDPPGC 
Sbjct:   430 ESQVLLLQFDIPHHPFGAAVMKCLPSPDIMDRVTSADMVG--RKDLRKECIFSVDPPGCT 487

Query:   129 DIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPL 188
             DIDDALH   L  G  EVGVHIADV++FV  GT +D+EA+ R TSVYLV+RRIDMLP  L
Sbjct:   488 DIDDALHIKDLGKGIMEVGVHIADVSHFVQEGTAIDEEAANRSTSVYLVDRRIDMLPGEL 547

Query:   189 TEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSCAALSYVEAQARMDDSRLM 247
             + ++CSL ++V+R AFS IW++     EII+  YTKS+I+SCA+L+Y +AQ R+DD    
Sbjct:   548 SGNLCSLMSNVDRFAFSCIWKINQHTGEIIAVEYTKSIIRSCASLTYEQAQIRIDDKSQN 607

Query:   248 DPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMV 307
             D +T +LRN+NSLAK +R++R +RGAL LAS +VKF+ +    DP D+ +YQ+RE N M+
Sbjct:   608 DQITVNLRNLNSLAKILRKQRFDRGALYLASPQVKFKTEELGGDPSDVEIYQLRETNSMI 667

Query:   308 EEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALAD 367
             EEFML AN+ VA++I + FP C++LRRHP+P K   + L +     G     ++SK LAD
Sbjct:   668 EEFMLLANIWVAKKIYKHFPGCAMLRRHPTPNKAAFDLLTKLIENKGYKFSTTTSKDLAD 727

Query:   368 SLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRR 426
             SLD AV  +D YFN L RI+ TRCM+ A YF SG L   +F+HYGLA  +YTHFTSPIRR
Sbjct:   728 SLDSAVDKNDSYFNTLCRIMTTRCMSPAKYFSSGSLPYEDFNHYGLATDIYTHFTSPIRR 787

Query:   427 YADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR 486
             Y D++VHRLL++++GI  + S+  +   ++++ +N N+RH+ AQ ASRGS +LHTLI+F+
Sbjct:   788 YPDIIVHRLLASAIGIQSV-SLNLENKTISALTENNNFRHKMAQYASRGSTQLHTLIFFK 846

Query:   487 KRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL--------TPRGQKGSGDWYVDEQQQK 538
              R +  +A I+++++N F+V VP++G EG VY+        T  G  G+ + Y    + +
Sbjct:   847 GRKSVEDAYIIRVKANAFVVLVPRYGFEGTVYVSDPNSSTATTNGGGGTSNIYNYNHEDQ 906

Query:   539 IVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
              +  +G  ++ V   V + + V + + +  KL++  I
Sbjct:   907 TLG-NGIHTFRVFDKVTVEIYVDDSKAHDQKLKINCI 942

GO:0004540 "ribonuclease activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000176 "nuclear exosome (RNase complex)" evidence=ISS

WB|WBGene00001001 dis-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 1379 (490.5 bits), Expect = 5.5e-141, P = 5.5e-141
 Identities = 277/577 (48%), Positives = 383/577 (66%)

Query:     1 MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
             M +P+        LF P +R IP+IRI+T Q   L  +RI+VA+D W   S+YP GHYVR
Sbjct:   368 MLLPSTVKGARRHLFCPAERLIPRIRIETEQAETLSQQRIVVAIDHWPRDSKYPLGHYVR 427

Query:    61 VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPI-RLDLRDLRV 119
              IGE+G R+TE+E++L+++DI   PFS  VL CLP   W     +   P+ R+DLRDL +
Sbjct:   428 SIGEMGSRETENEVLLLEHDIPHAPFSESVLDCLPREEWEPDLTENRGPLPRVDLRDLTI 487

Query:   120 FSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVER 179
              SVDP GC DIDDALHC  +    FEVGVHIADVT+FV PGT +DDEA+ RGT+VYL +R
Sbjct:   488 CSVDPLGCTDIDDALHCKQIGEDLFEVGVHIADVTHFVRPGTAIDDEAALRGTTVYLCDR 547

Query:   180 RIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQA 239
             RIDMLP  L+ ++CSLR + ER AFS IW +T  A+I S +Y KS+IKS AAL+Y +AQ 
Sbjct:   548 RIDMLPCLLSSNLCSLRGEEERYAFSCIWTMTSSADIQSVKYHKSLIKSKAALTYEKAQE 607

Query:   240 RMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQ 299
              +DD +  + +   LR +  L+K +  RR   GALTLAS+EV+F +D E+  P  +   Q
Sbjct:   608 IIDDPKEQNDVALGLRGLMKLSKVLNARRTGNGALTLASSEVRFDMDWESRTPKKVMEKQ 667

Query:   300 IREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDV 359
               + + MVEEFML AN+SVAE+IL ++P C+LLRRHP P KE  +PL+  A   G  + V
Sbjct:   668 HLDTHSMVEEFMLLANISVAEKILEEYPDCALLRRHPVPLKESYKPLVEAARHRGFEIIV 727

Query:   360 SSSKALADSLDRAVGD-DPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYT 418
              S K LADSL+R V   +P  N+L+R+L TRCMTQAVYF +G +  P++ H+GLA  +YT
Sbjct:   728 ESGKGLADSLNRCVDKKNPMLNRLLRMLTTRCMTQAVYFSAGTVPVPQYQHFGLACAIYT 787

Query:   419 HFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVE 478
             HFTSPIRRYADV+VHRLL+A++G   + S   ++ + T I  N+NYRH+ AQ A R SV+
Sbjct:   788 HFTSPIRRYADVIVHRLLAAAIGADDIQSGLLNQARCTKICTNINYRHKQAQYAGRASVQ 847

Query:   479 LHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQK 538
             L+ + YF+ +    E  ++ +R+NG  VFVPK+G+E  + L      G+    +D ++  
Sbjct:   848 LNVVRYFKGKVETCEGFVMGVRNNGIQVFVPKYGLESIIVLQTSAASGTT---IDVEEMS 904

Query:   539 IVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
              VK++G++    L+ V + + V E    RP+++L LI
Sbjct:   905 -VKVNGDVVIKELEPVTVRISVNEKNQQRPRVELQLI 940

GO:0003723 "RNA binding" evidence=IEA

GO:0004540 "ribonuclease activity" evidence=IEA

GO:0051537 "2 iron, 2 sulfur cluster binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0040018 "positive regulation of multicellular organism growth" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040010 "positive regulation of growth rate" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.13	LOW CONFIDENCE prediction!
3rd Layer	3.1.13.1	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00019329001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (943 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00026977001	SubName- Full=Putative uncharacterized protein (Chromosome chr15 scaffold_40, whole genome shot [...] (241 aa)				•	•	•	•		0.943
	GSVIVG00023648001	SubName- Full=Chromosome chr7 scaffold_31, whole genome shotgun sequence; (320 aa)				•	•	•	•		0.903
	GSVIVG00031795001	SubName- Full=Chromosome chr18 scaffold_59, whole genome shotgun sequence; (431 aa)				•	•	•	•		0.870
	GSVIVG00026698001	SubName- Full=Chromosome chr4 scaffold_39, whole genome shotgun sequence; (200 aa)				•	•	•	•		0.862
	GSVIVG00016075001	SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (237 aa)				•	•	•	•		0.850
	GSVIVG00032741001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (287 aa)					•	•	•		0.819
	GSVIVG00032429001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (243 aa)					•	•	•		0.625
	GSVIVG00024436001	RecName- Full=DNA-directed RNA polymerase; EC=2.7.7.6; (1370 aa)				•	•				0.593
	GSVIVG00028763001	RecName- Full=DNA topoisomerase 2; EC=5.99.1.3;; Control of topological states of DNA by transi [...] (1489 aa)				•	•		•		0.581
	GSVIVG00021349001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (905 aa)				•					0.572

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	575
COG0557	706	COG0557, VacB, Exoribonuclease R [Transcription]	1e-147
pfam00773	322	pfam00773, RNB, RNB domain	1e-115
TIGR02063	709	TIGR02063, RNase_R, ribonuclease R	1e-110
smart00955	286	smart00955, RNB, This domain is the catalytic doma	1e-103
TIGR00358	654	TIGR00358, 3_prime_RNase, VacB and RNase II family	1e-67
PRK11642	813	PRK11642, PRK11642, exoribonuclease R; Provisional	1e-44
TIGR02062	639	TIGR02062, RNase_B, exoribonuclease II	3e-35
PRK05054	644	PRK05054, PRK05054, exoribonuclease II; Provisiona	3e-34
COG4776	645	COG4776, Rnb, Exoribonuclease II [Transcription]	1e-33

>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription]

 Score =  441 bits (1137), Expect = e-147
 Identities = 189/536 (35%), Positives = 280/536 (52%), Gaps = 22/536 (4%)

Query: 13  ALFVPKDRRIP-KIRIQTRQLGNL-LDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDT 70
              +P D+R+P  I I   Q         ++V +  W   SR PFG  V V+G++GD   
Sbjct: 151 GRVLPDDKRLPFLIAIPPEQAPGAEEGHLVVVEITRWPDTSRPPFGEVVEVLGDLGDPGA 210

Query: 71  ESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDI 130
           + E +L D+ I    F  +VL     LP  V  EDL    R+DLRDL +F++DP   KD+
Sbjct: 211 DIEAILRDHGIP-SEFPEKVLDEAAALPDEVPEEDLKG--RVDLRDLPIFTIDPEDAKDL 267

Query: 131 DDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTE 190
           DDA+    L +G + +GVHIADV+++V PG+ LD EA KRGTSVYL +R I MLP+ L+ 
Sbjct: 268 DDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEALSN 327

Query: 191 DICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL--MD 248
            +CSL   V+RLA S    L  E  +       SVIKS A L+Y E QA +D        
Sbjct: 328 GLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKYA 387

Query: 249 PLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVE 308
           PL   L  +  LAK ++++R+ RGA+   + E K  +D E   P++I + +  +A +++E
Sbjct: 388 PLLDSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLD-EEGRPVEIEIRERLDAEKLIE 446

Query: 309 EFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADS 368
           EFML AN +VAE + +      L R H  P+ E L+ L      +GL L +  SK     
Sbjct: 447 EFMLLANETVAEHLEKHKIP-LLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQD 505

Query: 369 LDRAV--GDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRR 426
               +          +++ L  R M QA Y      +P    H+GLA   YTHFTSPIRR
Sbjct: 506 YQILLETVKGRPLEAVLQTLLLRSMKQAEY------SPDNVGHFGLALDYYTHFTSPIRR 559

Query: 427 YADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR 486
           Y D++VHR L A L    +P       +L  +A +++   R AQ A R  ++L    Y +
Sbjct: 560 YPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMK 619

Query: 487 KRPTDT-EARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK 541
           KR  +  +  +  + S GF V +P+ G+EG V+++        D+Y  +++ + + 
Sbjct: 620 KRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHIS----SLPDDYYHFDERGQALV 671

Length = 706

>gnl|CDD|216112 pfam00773, RNB, RNB domain

 Score =  345 bits (886), Expect = e-115
 Identities = 137/333 (41%), Positives = 187/333 (56%), Gaps = 14/333 (4%)

Query: 111 RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKR 170
           R DLRDL  F++DP   KDIDDAL    L  G + +GVHIADV+++V PG+PLD EA KR
Sbjct: 1   RRDLRDLPFFTIDPETAKDIDDALSVEKLPDGGYRLGVHIADVSHYVPPGSPLDKEARKR 60

Query: 171 GTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCA 230
           GTSVYL E  I MLP+ L+ D+CSL    +RLA SV   +  + E++      SVI+S A
Sbjct: 61  GTSVYLPEGVIPMLPEELSNDLCSLLPGEDRLALSVEITIDKDGEVLDYEIYPSVIRSKA 120

Query: 231 ALSYVEAQARMDD--SRLMDPLTTDLRNMNSLAKKMRQRRIERGALTL-ASAEVKFQIDT 287
            L+Y E    ++   S    P+  DL  +  LAK +R++R++RGAL L    E K  +D 
Sbjct: 121 RLTYEEVDELLEGKPSEREAPVADDLELLYELAKALRKKRLKRGALELEDLPEAKIDLDE 180

Query: 288 ETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLL 347
           +      I +     A+ +VEEFM+ AN +VA   L +  +  + R HP P  E L+ LL
Sbjct: 181 DGEPVDIIRIEDRSPAHSLVEEFMILANEAVARF-LSENGIPGIYRVHPEPDLEKLQDLL 239

Query: 348 RTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
           ++A    L LD+      +         D    +L+ +L  R + +A Y      TP   
Sbjct: 240 KSA----LELDLDEEGLESLQKLLEELKDSPERRLLNLLLRRTLPRAEY----STTP--A 289

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASL 440
            H+GL   +YTHFTSPIRRYAD+VVHR L A L
Sbjct: 290 PHFGLGLEIYTHFTSPIRRYADLVVHRQLKALL 322

This domain is the catalytic domain of ribonuclease II. Length = 322

>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R

 Score =  345 bits (888), Expect = e-110
 Identities = 177/580 (30%), Positives = 285/580 (49%), Gaps = 36/580 (6%)

Query: 13  ALFVPKDRRIP-KIRIQTRQLGNLLDKRIIVA-VDSWDCQSRYPFGHYVRVIGEIGDRDT 70
              +P D+RI   I I   Q+    +   ++  +  +  ++R   G  V ++G   D   
Sbjct: 149 GFVIPDDKRIYLDIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGI 208

Query: 71  ESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDI 130
           +  +++  + I    F  +VL     +P  V  E++    R DLRDL   ++D    KD 
Sbjct: 209 DILIIIRKHGIPYE-FPEEVLDEAAKIPEEVPEEEIKG--RKDLRDLPFVTIDGEDAKDF 265

Query: 131 DDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTE 190
           DDA++   L  GN+++GV IADV+++V  G+ LD EA KRGTSVYL +R I MLP+ L+ 
Sbjct: 266 DDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSN 325

Query: 191 DICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMD-- 248
            ICSL  + +RL  S   E+  +  +    + ++VI S A L+Y +    ++    +D  
Sbjct: 326 GICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKK 385

Query: 249 --PLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQM 306
             PL   L+N+  L K +R++R +RGA+   S E K  +D E   P+DI   +  +A+++
Sbjct: 386 EPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILD-ENGKPIDIVPRERGDAHKL 444

Query: 307 VEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS-----S 361
           +EEFM+AAN +VAE  L +  L  + R H  P++E L+ L      +G+ L         
Sbjct: 445 IEEFMIAANETVAE-HLEKAKLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQ 503

Query: 362 SKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFT 421
            K     L++ V   P    LI  +  R M QA Y      +P    H+GLA   YTHFT
Sbjct: 504 PKDFQKLLEK-VKGRPEEE-LINTVLLRSMQQAKY------SPENIGHFGLALEYYTHFT 555

Query: 422 SPIRRYADVVVHRLLSASLGIYKLPSVFQDR----PQLTSIADNLNYRHRNAQMASRGSV 477
           SPIRRY D++VHRL+  +L   +  +  ++R     +L  IA++ +   R A  A R   
Sbjct: 556 SPIRRYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVN 615

Query: 478 ELHTLIYFRKRPTDT-EARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYV-DEQ 535
           +     Y  ++  +  E  I  + S G  V +    IEG V+++        D+YV DE+
Sbjct: 616 DWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKD----DYYVFDEK 671

Query: 536 QQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 575
              +V       + +   V +   VV+   +  K+   L+
Sbjct: 672 GLALVGERTGKVFRLGDRVKV--RVVKADLDTGKIDFELV 709

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]. Length = 709

>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of ribonuclease II

 Score =  313 bits (803), Expect = e-103
 Identities = 124/334 (37%), Positives = 170/334 (50%), Gaps = 52/334 (15%)

Query: 111 RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKR 170
           R+DLRDL +F++DP   KDIDDA+    L +G + +GVHIADV+++V PG+ LD EA KR
Sbjct: 1   RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRLGVHIADVSHYVKPGSALDREARKR 60

Query: 171 GTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEA-EIISTRYTKSVIKSC 229
           GTSVYL +R I MLP+ L+  +CSL    +RLA SV   L  +  EI+   + +SVI+S 
Sbjct: 61  GTSVYLPDRVIPMLPEELSNGLCSLNPGEDRLALSVEMTLDADGGEILDYEFYRSVIRSK 120

Query: 230 AALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTET 289
           A L+Y E  A ++                                       K  +D E 
Sbjct: 121 ARLTYEEVDAILE---------------------------------------KIVLDEEG 141

Query: 290 HDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRT 349
               DI   +  +A+ +VEEFM+ AN +VA  + +   +  L R H  P  E L  LL+ 
Sbjct: 142 K-IEDIVPRERNDAHSLVEEFMILANEAVARFLAKNG-IPGLYRVHEGPDPEKLAELLKE 199

Query: 350 AAAVG--LNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
             A+   L L     KALA  L++         +L+ +L  R M  A Y           
Sbjct: 200 FLALLGLLLLGGDGPKALAKLLEKIRDSPE--ERLLELLLLRSMPHAEYSVDN------S 251

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLG 441
            H+GLA   YTHFTSPIRRY D++VHR L A+L 
Sbjct: 252 GHFGLALDAYTHFTSPIRRYPDLIVHRQLKAALR 285

Length = 286

>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases

 Score =  231 bits (590), Expect = 1e-67
 Identities = 134/496 (27%), Positives = 226/496 (45%), Gaps = 32/496 (6%)

Query: 40  IIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDI---DARPFSTQVLACLPP 96
           ++V +  +  +    +G   +++G   D      + L  ++I          Q       
Sbjct: 126 VVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFEFPDGVEQQAAK---- 181

Query: 97  LPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNF 156
           L + V  +      R DL DL   ++D    KD+DDA++   L  G +++ V IADV+ +
Sbjct: 182 LQFDVDEQAK--KYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYY 239

Query: 157 VHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEI 216
           V   +PLD EA  RG SVYL    I MLP+ L+  +CSL  + +RL       ++ +  I
Sbjct: 240 VAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRI 299

Query: 217 ISTRYTKSVIKSCAALSYVEAQARM-DDSRL---MDPLTTDLRNMNSLAKKMRQRRIERG 272
               +  + I+S A L+Y +    + +D  L    + L   L+ ++ L++ + + R +RG
Sbjct: 300 TDNEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRG 359

Query: 273 ALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLL 332
            +     E KF +D E    +DI     R A +++EE M+ AN+  A + L    +  + 
Sbjct: 360 LIDFEHPETKFIVD-EEGRVIDIVAEVRRIAEKIIEEAMIVANICAA-RFLHNHKVPGIY 417

Query: 333 RRHPSPTKEMLEPLLRTAAAVGL-----NLDVSSSKALADSLDRAVGDDPYFNKLIRILA 387
           R HP P+K+ L+ LL   A +GL     N +  ++   A  L        Y  +++    
Sbjct: 418 RVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDRPEY--EILVTRL 475

Query: 388 TRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPS 447
            R ++QA Y  S +       H+GL    Y HFTSPIRRY D+  HRL+ A L   +   
Sbjct: 476 LRSLSQAEY--SPEPLG----HFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVL-AKEQTD 528

Query: 448 VFQDRPQ--LTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDT-EARIVKIRSNGF 504
             + +PQ  L  IA++ +   R A+ A R   +     Y   +        I  +   G 
Sbjct: 529 TERYQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGM 588

Query: 505 IVFVPKFGIEGPVYLT 520
            V +   GI+G ++++
Sbjct: 589 FVRLDDNGIDGLIHIS 604

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]. Length = 654

>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional

 Score =  169 bits (429), Expect = 1e-44
 Identities = 137/448 (30%), Positives = 221/448 (49%), Gaps = 41/448 (9%)

Query: 3   MPAGSGSVAHALFVPKDRR------IPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFG 56
             AG G V     VP D R      IP  +I   ++G +    ++V +     +     G
Sbjct: 158 TDAGVGFV-----VPDDSRLSFDILIPPEQIMGARMGFV----VVVELTQRPTRRTKAVG 208

Query: 57  HYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRD 116
             V V+G+        ++ L  ++I    +   V   +  L   V  E  A   R+DLRD
Sbjct: 209 KIVEVLGDNMGTGMAVDIALRTHEI-PYIWPQAVEQQVAGLKEEVPEE--AKAGRVDLRD 265

Query: 117 LRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYL 176
           L + ++D    +D DDA++C     G + + V IADV+ +V P TPLD EA  RGTSVY 
Sbjct: 266 LPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYF 325

Query: 177 VERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAE--IISTRYTKSVIKSCAALSY 234
             + + MLP+ L+  +CSL   V+RL   ++ E+T  ++  +   ++ ++V+ S A L+Y
Sbjct: 326 PSQVVPMLPEVLSNGLCSLNPQVDRL--CMVCEMTISSKGRLTGYKFYEAVMSSHARLTY 383

Query: 235 VEAQARMD-DSRLMD---PLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETH 290
            +    +  D  L +   PL   L  +++L K + + R ERG ++  S E KF  + E  
Sbjct: 384 TKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAERR 443

Query: 291 DPLDIGMYQIREANQMVEEFMLAANVSVAEQILR-QFPLCSLLRRHPSPTKEMLEPLLRT 349
               I   Q  +A++++EE M+ AN+S A  + + + P  +L R H  P+ E +      
Sbjct: 444 IE-RIEQTQRNDAHKLIEECMILANISAARFVEKAKEP--ALFRIHDKPSTEAITSFRSV 500

Query: 350 AAAVGLNL---DVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPE 406
            A +GL L   +    +  A+ L+ +V D P   ++++ +  R M QA+Y       P  
Sbjct: 501 LAELGLELPGGNKPEPRDYAELLE-SVADRPD-AEMLQTMLLRSMKQAIY------DPEN 552

Query: 407 FHHYGLAAPLYTHFTSPIRRYADVVVHR 434
             H+GLA   Y HFTSPIRRY D+ +HR
Sbjct: 553 RGHFGLALQSYAHFTSPIRRYPDLSLHR 580

Length = 813

>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II

 Score =  140 bits (354), Expect = 3e-35
 Identities = 115/425 (27%), Positives = 183/425 (43%), Gaps = 39/425 (9%)

Query: 106 LANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDD 165
           L   +R DL  L   ++D    KD+DDAL   AL +G  ++ V IAD T ++  G+ LD 
Sbjct: 181 LDGLVREDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDK 240

Query: 166 EASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIST-RYTKS 224
            A  RG + YL    I MLP+ L++D+CSLRA+  R   +    ++ +  I     +  +
Sbjct: 241 AAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAA 300

Query: 225 VIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE----RGALTLASAE 280
            IKS A L Y +    ++++    P + ++     L  +  Q RIE       +     +
Sbjct: 301 TIKSKAKLVYDQVSDWLENTSDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPD 360

Query: 281 VKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTK 340
            +F + +E  + LDI     R AN++VEE M+ AN+  A  +  +     +   H     
Sbjct: 361 YRFIL-SEKGEVLDIVAEPRRIANRIVEEAMIIANICAARFLRDKLGF-GIYNTHAGFDP 418

Query: 341 EMLEPLLRTAAAVGLNLDVSSSKAL----ADSLDRAVGDDPYFNKLIRILATRCMTQAVY 396
              E ++      GL++D      L        +    +  Y +  IR           Y
Sbjct: 419 ANAENVVALLKTNGLHVDAEELATLDGFCKLRRELDAQETGYLDSRIR----------RY 468

Query: 397 FCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLT 456
               +++     H+GL    Y  +TSPIR+Y D++ HRLL A   I    +    RPQ  
Sbjct: 469 QSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAV--IKGETAT---RPQED 523

Query: 457 SIADNLNYRHRNAQMASRGSVE-LHTLIYFRKRPTDT--EARI---------VKIRSNGF 504
            I   L  R R  ++A R   + L+      K   +T   A I         V++  NG 
Sbjct: 524 -ITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGA 582

Query: 505 IVFVP 509
           I F+P
Sbjct: 583 IAFIP 587

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing [Transcription, Degradation of RNA]. Length = 639

>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional

 Score =  137 bits (347), Expect = 3e-34
 Identities = 124/444 (27%), Positives = 185/444 (41%), Gaps = 47/444 (10%)

Query: 91  LACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHI 150
           L    P              R DL  L   ++D    +D+DDAL+   L  G  ++ V I
Sbjct: 170 LEREAPAGGVAWEMLDEGLEREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAI 229

Query: 151 ADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWEL 210
           AD T ++  G+ LD  A +R  + YL    I MLP+ L++D+CSLR +  R A +    +
Sbjct: 230 ADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTI 289

Query: 211 TPEAEIIS-TRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRI 269
             +  I    R+  + I+S A L+Y      +++     P +  +     L  +    R 
Sbjct: 290 DADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARS 349

Query: 270 E-RGALTLA---SAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQ 325
           E R    L      + +F++  E  + LDI     R AN++VEE M+AAN+  A ++LR 
Sbjct: 350 EWRKQHALVFKDRPDYRFELG-EKGEVLDIVAEPRRIANRIVEESMIAANICAA-RVLRD 407

Query: 326 FPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNK 381
                +   H        E  +      GL+ D      L     L R +   P  Y + 
Sbjct: 408 KLGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDS 467

Query: 382 LIRILATRCMTQAVYFCSGDLTP-PEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASL 440
            IR   +        F      P P   H+GL    Y  +TSPIR+Y D++ HRLL A  
Sbjct: 468 RIRRFQS--------FAEISTEPGP---HFGLGLEAYATWTSPIRKYGDMINHRLLKAV- 515

Query: 441 GIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--A 494
            I    +    RPQ   I   L  R R  +MA R   ++   +Y R    K  TDT   A
Sbjct: 516 -IKGETAE---RPQ-DEITVQLAERRRLNRMAER---DVGDWLYARYLKDKAGTDTRFAA 567

Query: 495 RI---------VKIRSNGFIVFVP 509
            I         V++  NG + F+P
Sbjct: 568 EIIDISRGGMRVRLLENGAVAFIP 591

Length = 644

>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription]

 Score =  135 bits (342), Expect = 1e-33
 Identities = 124/420 (29%), Positives = 187/420 (44%), Gaps = 39/420 (9%)

Query: 111 RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKR 170
           R DL  L   ++D    +D+DDAL+   L  G++++ V IAD T ++  G+ LD EA  R
Sbjct: 190 REDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSKLDKEAKIR 249

Query: 171 GTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIST-RYTKSVIKSC 229
             + YL    I MLP+ L++D+CSLRA+  R A +    +  +  I    R+  + I+S 
Sbjct: 250 AFTNYLPGFNIPMLPRELSDDLCSLRANEVRPALACRITIDKDGNITDKIRFFAATIESK 309

Query: 230 AALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RGALTLA-SAEVKFQI 285
           A L Y      ++++    P +  +     L  +  Q RIE     AL      + +F +
Sbjct: 310 AKLVYDHVSDWLENTGDWQPESEAIAQQIRLLHQFCQARIEWRKTHALVFKDRPDYRFIL 369

Query: 286 DTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEP 345
             E  + LDI     R AN++VEE M+AAN+  A ++LR+     +   H        E 
Sbjct: 370 -GEKGEVLDIVAEPRRIANRIVEESMIAANICAA-RVLREKLGFGIYNVHSGFDPANAEA 427

Query: 346 LLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILATRCMTQAVYFCSGD 401
                   GLN+D      L     L R +   P  Y +  IR    R  + A    S +
Sbjct: 428 AAALLKTNGLNVDAEELLTLEGFCKLRRELDAQPTGYLDSRIR----RFQSFAEI--STE 481

Query: 402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADN 461
             P    H+GL    Y  +TSPIR+Y D++ HRLL A   I    +    +PQ   I   
Sbjct: 482 PGP----HFGLGLEAYATWTSPIRKYGDMINHRLLKAV--IKGETAE---KPQED-ITVQ 531

Query: 462 LNYRHRNAQMASRGSVELHTLIYFRKRP-TDT--EARI---------VKIRSNGFIVFVP 509
           L  R R  +MA R   +     +   +  T+T   A I         V++  NG I F+P
Sbjct: 532 LAERRRLNRMAERDVADWLYARFLADKAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIP 591

Length = 645

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	575
TIGR00358	654	3_prime_RNase VacB and RNase II family 3'-5' exori	100.0
PRK11642	813	exoribonuclease R; Provisional	100.0
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	100.0
COG0557	706	VacB Exoribonuclease R [Transcription]	100.0
PRK05054	644	exoribonuclease II; Provisional	100.0
TIGR02062	639	RNase_B exoribonuclease II. This family consists o	100.0
KOG2102	941	consensus Exosomal 3'-5' exoribonuclease complex,	100.0
PF00773	325	RNB: RNB domain CAUTION: The Prosite pattern does	100.0
COG4776	645	Rnb Exoribonuclease II [Transcription]	100.0
cd04471	83	S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai	99.22
cd04460	99	S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain.	98.73
cd05686	73	S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom	98.72
cd05697	69	S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t	98.63
cd05706	73	S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a	98.53
cd05690	69	S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p	98.51
cd05689	72	S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p	98.47
cd05696	71	S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t	98.46
cd05703	73	S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R	98.46
cd05707	68	S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a	98.45
cd05708	77	S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a	98.44
cd05698	70	S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp	98.42
cd05705	74	S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a	98.42
TIGR00448	179	rpoE DNA-directed RNA polymerase (rpoE), archaeal	98.42
cd04461	83	S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp	98.4
COG1098	129	VacB Predicted RNA binding protein (contains ribos	98.39
PF00575	74	S1: S1 RNA binding domain; InterPro: IPR003029 Rib	98.38
PRK07252	120	hypothetical protein; Provisional	98.38
cd05684	79	S1_DHX8_helicase S1_DHX8_helicase: The N-terminal	98.37
PRK08582	139	hypothetical protein; Provisional	98.37
cd04452	76	S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr	98.34
COG1095	183	RPB7 DNA-directed RNA polymerase, subunit E' [Tran	98.28
cd05695	66	S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t	98.28
cd05685	68	S1_Tex S1_Tex: The C-terminal S1 domain of a trans	98.27
PTZ00248	319	eukaryotic translation initiation factor 2 subunit	98.26
cd05704	72	S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a	98.17
cd05691	73	S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p	98.16
PHA02945	88	interferon resistance protein; Provisional	98.15
PRK05807	136	hypothetical protein; Provisional	98.09
cd04472	68	S1_PNPase S1_PNPase: Polynucleotide phosphorylase	98.08
cd05692	69	S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p	98.07
cd05688	68	S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p	98.06
PRK08059	123	general stress protein 13; Validated	98.05
cd04473	77	S1_RecJ_like S1_RecJ_like: The S1 domain of the ar	98.03
PRK08563	187	DNA-directed RNA polymerase subunit E'; Provisiona	97.99
PLN00207	891	polyribonucleotide nucleotidyltransferase; Provisi	97.96
smart00316	72	S1 Ribosomal protein S1-like RNA-binding domain.	97.94
cd05694	74	S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp	97.93
PRK03987	262	translation initiation factor IF-2 subunit alpha;	97.92
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.92
COG0539	541	RpsA Ribosomal protein S1 [Translation, ribosomal	97.86
cd05687	70	S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib	97.86
cd00164	65	S1_like S1_like: Ribosomal protein S1-like RNA-bin	97.84
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.8
cd04465	67	S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib	97.68
cd05693	100	S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp	97.65
cd05702	70	S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R	97.59
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.58
PRK07400	318	30S ribosomal protein S1; Reviewed	97.58
PRK07899	486	rpsA 30S ribosomal protein S1; Reviewed	97.55
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.52
PRK11824	693	polynucleotide phosphorylase/polyadenylase; Provis	97.48
PRK13806	491	rpsA 30S ribosomal protein S1; Provisional	97.38
cd05789	86	S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain.	97.37
TIGR02696	719	pppGpp_PNP guanosine pentaphosphate synthetase I/p	97.31
PRK12269	863	bifunctional cytidylate kinase/ribosomal protein S	97.3
PTZ00162	176	DNA-directed RNA polymerase II subunit 7; Provisio	97.3
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	97.29
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	97.27
COG1093	269	SUI2 Translation initiation factor 2, alpha subuni	97.26
cd04453	88	S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik	97.21
cd04462	88	S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly	97.2
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	97.2
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	97.16
cd04455	67	S1_NusA S1_NusA: N-utilizing substance A protein (	97.09
TIGR03591	684	polynuc_phos polyribonucleotide nucleotidyltransfe	97.08
cd04454	82	S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-	97.03
PRK06676	390	rpsA 30S ribosomal protein S1; Reviewed	96.97
TIGR00717	516	rpsA ribosomal protein S1. This model provides tru	96.95
COG2183	780	Tex Transcriptional accessory protein [Transcripti	96.82
PRK07400	318	30S ribosomal protein S1; Reviewed	96.8
PRK06299	565	rpsA 30S ribosomal protein S1; Reviewed	96.78
PRK09202	470	nusA transcription elongation factor NusA; Validat	96.27
PRK00087	647	4-hydroxy-3-methylbut-2-enyl diphosphate reductase	96.13
COG1185	692	Pnp Polyribonucleotide nucleotidyltransferase (pol	96.02
PRK12327	362	nusA transcription elongation factor NusA; Provisi	95.71
PRK09521	189	exosome complex RNA-binding protein Csl4; Provisio	95.47
PRK04163	235	exosome complex RNA-binding protein Rrp4; Provisio	95.21
TIGR01953	341	NusA transcription termination factor NusA. This m	95.12
PHA02858	86	EIF2a-like PKR inhibitor; Provisional	94.8
cd05699	72	S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t	94.54
PF08206	58	OB_RNB: Ribonuclease B OB domain; InterPro: IPR013	93.24
KOG3298	170	consensus DNA-directed RNA polymerase subunit E' [	93.16
KOG1067	760	consensus Predicted RNA-binding polyribonucleotide	91.71
TIGR00008	68	infA translation initiation factor IF-1. This fami	91.46
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	91.26
COG2996	287	Predicted RNA-bindining protein (contains S1 and H	91.03
PRK12442	87	translation initiation factor IF-1; Reviewed	90.21
PRK12328	374	nusA transcription elongation factor NusA; Provisi	89.76
PRK12329	449	nusA transcription elongation factor NusA; Provisi	89.47
cd05791	92	S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain.	88.23
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	87.21
PF08292	122	RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I	84.79
TIGR02063	709	RNase_R ribonuclease R. This family consists of an	84.36
COG0361	75	InfA Translation initiation factor 1 (IF-1) [Trans	82.27
COG1107	715	Archaea-specific RecJ-like exonuclease, contains D	82.16
TIGR00757	414	RNaseEG ribonuclease, Rne/Rng family. The C-termin	80.43

>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases

Probab=100.00  E-value=8.1e-121  Score=1022.93  Aligned_cols=548  Identities=26%  Similarity=0.415  Sum_probs=503.0

Q ss_pred             ccEEEEEeCCCCCCc-eEecCCcc--CcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCC
Q 008167           10 VAHALFVPKDRRIPK-IRIQTRQL--GNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPF   86 (575)
Q Consensus        10 ~~~~~~~P~d~r~p~-i~i~~~~~--~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f   86 (575)
                      ++..+++|.|+|++. |.|++...  ....|++|+|+|++||..+.+|.|+|+++||..+++++++++++.+|||+. .|
T Consensus        93 ~~~~~v~p~~~~~~~~i~i~~~~~~~~~~~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~-~f  171 (654)
T TIGR00358        93 NDFGFVVPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPF-EF  171 (654)
T ss_pred             CCeEEEEECCCCCCCcEEEcCCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCC-CC
Confidence            346789999999984 88877632  345799999999999999999999999999999999999999999999998 69


Q ss_pred             cHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHH
Q 008167           87 STQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDE  166 (575)
Q Consensus        87 ~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~e  166 (575)
                      |++++++++..++.+++++..  +|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+|
T Consensus       172 ~~~v~~~a~~~~~~~~~~~~~--~R~Dlr~~~~~TID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~e  249 (654)
T TIGR00358       172 PDGVEQQAAKLQFDVDEQAKK--YREDLTDLAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKE  249 (654)
T ss_pred             CHHHHHHHHhccccCChhHhh--CccccccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHH
Confidence            999999999888888777776  899999999999999999999999999999889999999999999999999999999


Q ss_pred             HHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCC
Q 008167          167 ASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL  246 (575)
Q Consensus       167 A~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~  246 (575)
                      |++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|.+++|++|+|+|+++|||++|+++|+++..
T Consensus       250 A~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~  329 (654)
T TIGR00358       250 AKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDE  329 (654)
T ss_pred             HHHhCcCccCCCCeecCCCHHHhcCccccCCCCcceEEEEEEEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999987532


Q ss_pred             ----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHH
Q 008167          247 ----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQI  322 (575)
Q Consensus       247 ----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l  322 (575)
                          ..++.++|..|+++|++|+++|.++|+++|+.||.+|.+|++ |.+..+...+++.||.|||||||+||++||+|+
T Consensus       330 ~~~~~~~~~~~L~~l~~la~~lr~~R~~~Gai~~~~~e~~~~~d~~-g~~~~i~~~~~~~a~~lIeE~MilAN~~vA~~~  408 (654)
T TIGR00358       330 LQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEE-GRVIDIVAEVRRIAEKIIEEAMIVANICAARFL  408 (654)
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceeEEECCC-CCeeEEEeccCcHHHHHHHHHHHHHHHHHHHHH
Confidence                235678999999999999999999999999999999999875 678888888899999999999999999999999


Q ss_pred             HHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC-----CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceec
Q 008167          323 LRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS-----SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYF  397 (575)
Q Consensus       323 ~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~-----~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~  397 (575)
                      .++ +.|++||+|++|+++++++|.++++.+|+.++..     ++.+++..|.++.+. + ...+++.+++|+|++|+| 
T Consensus       409 ~~~-~~p~iyR~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~-~-~~~~l~~~llr~m~~A~y-  484 (654)
T TIGR00358       409 HNH-KVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDR-P-EYEILVTRLLRSLSQAEY-  484 (654)
T ss_pred             HHc-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCcCCCChHHHHHHHHHhhCC-C-HHHHHHHHHHHhhccccc-
Confidence            987 8899999999999999999999999999986431     467788888877652 2 344788899999999999 


Q ss_pred             ccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCC-CCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 008167          398 CSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKL-PSVFQDRPQLTSIADNLNYRHRNAQMASRGS  476 (575)
Q Consensus       398 ~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~-~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~  476 (575)
                           +.+|.+|||||++.|||||||||||+||+|||||+++|.+++. +....+.++|..+|.+||.+++.|++|||++
T Consensus       485 -----~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~  559 (654)
T TIGR00358       485 -----SPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDV  559 (654)
T ss_pred             -----CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 5689999999999999999999999999999999999987642 1112355789999999999999999999999


Q ss_pred             HHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEE
Q 008167          477 VELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVN  555 (575)
Q Consensus       477 ~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~  555 (575)
                      .++|.|+||+++. ++|+|+|++|+++|++|.|+++|+||+||++++++++   |.||+.++++.|+++++.|++||+|+
T Consensus       560 ~~~~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~---y~~d~~~~~l~g~~~~~~~~lGD~V~  636 (654)
T TIGR00358       560 ADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDY---YVFDQEKMALIGKGTGKVYRIGDRVT  636 (654)
T ss_pred             HHHHHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcc---eEEeccccEEEeccCCcEECCCCEEE
Confidence            9999999999987 7899999999999999999999999999999999886   99999999999998899999999999


Q ss_pred             EEEEEecCCCCCCceEEEeC
Q 008167          556 IHMEVVEPQPNRPKLQLTLI  575 (575)
Q Consensus       556 V~V~~vd~~~~~~~i~l~l~  575 (575)
                      |+|.++|.+  +++|.|+++
T Consensus       637 Vki~~vd~~--~~~I~f~l~  654 (654)
T TIGR00358       637 VKLTEVNME--TRSIIFELV  654 (654)
T ss_pred             EEEEEEecc--cCeEEEEEC
Confidence            999999976  899999974

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.

>PRK11642 exoribonuclease R; Provisional

Probab=100.00  E-value=8.7e-120  Score=1025.06  Aligned_cols=547  Identities=27%  Similarity=0.430  Sum_probs=501.5

Q ss_pred             cEEEEEeCCCCCC-ceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCCcH
Q 008167           11 AHALFVPKDRRIP-KIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFST   88 (575)
Q Consensus        11 ~~~~~~P~d~r~p-~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f~~   88 (575)
                      +..+++|.|.|++ .|.|+..... ...|++|+|+|++||..+.+|.|+|+++||..+++++++++++.+|+|+. .||+
T Consensus       161 ~~~~v~P~d~r~~~~i~i~~~~~~~~~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~-~Fp~  239 (813)
T PRK11642        161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPY-IWPQ  239 (813)
T ss_pred             CeEEEEECCCCCCCcEEeccccccCCCCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCC-CCCH
Confidence            4578999999998 5999876543 34689999999999999999999999999999999999999999999998 5999


Q ss_pred             HHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHH
Q 008167           89 QVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEAS  168 (575)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~  168 (575)
                      +|++++..+++.+++++.+  +|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+||+
T Consensus       240 ~v~~ea~~~~~~~~~~~~~--~R~DLr~l~~vTID~~~akD~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~  317 (813)
T PRK11642        240 AVEQQVAGLKEEVPEEAKA--GRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREAR  317 (813)
T ss_pred             HHHHHHHhccccCChhHhc--cccccccCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHH
Confidence            9999999888888777766  89999999999999999999999999999988899999999999999999999999999


Q ss_pred             hCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCC--
Q 008167          169 KRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL--  246 (575)
Q Consensus       169 ~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~--  246 (575)
                      +||||+|||++++||||+.||+++|||+||++|+||||.|+||.+|+|.+++|++|+|+|+++|||++|+++|+++..  
T Consensus       318 ~RgtSvYlpd~viPMLP~~Lsn~lcSL~p~~dRla~s~~~~id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~  397 (813)
T PRK11642        318 NRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLR  397 (813)
T ss_pred             HhCCeEeCCCceeeCCCHHHhcCccccCCCCceeEEEEEEEECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999987532  


Q ss_pred             --CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHH
Q 008167          247 --MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILR  324 (575)
Q Consensus       247 --~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~  324 (575)
                        ..++.++|..|+++|+.|+++|.++|+|+|+.||.+|.+|++ |.+..+...++.+||.|||||||+||++||+|+.+
T Consensus       398 ~~~~~~~~~L~~l~~la~~Lr~~R~~~Gai~~d~~E~~i~ld~~-g~~~~i~~~~~~~a~~lIEE~MllAN~~vA~~l~~  476 (813)
T PRK11642        398 EQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAE-RRIERIEQTQRNDAHKLIEECMILANISAARFVEK  476 (813)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceEEEECCC-CCEeeEEecccccHHHHHHHHHHHHHHHHHHHHHH
Confidence              235678899999999999999999999999999999999976 67888888899999999999999999999999998


Q ss_pred             hCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC---CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCC
Q 008167          325 QFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS---SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGD  401 (575)
Q Consensus       325 ~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~  401 (575)
                      + +.|++||+|+.|+++++++|.+++..+|+.++..   +++.+++.++.+.+ .| ...+++.+++|+|++|.|     
T Consensus       477 ~-~~p~lyR~H~~P~~ekl~~l~~~l~~lG~~l~~~~~~~~~~~~~ll~~~~~-~~-~~~~l~~~llRsm~~A~Y-----  548 (813)
T PRK11642        477 A-KEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVAD-RP-DAEMLQTMLLRSMKQAIY-----  548 (813)
T ss_pred             C-CCCEEEEeCCCCCHHHHHHHHHHHHHcCCcccCCCCCCHHHHHHHHHHHhC-Cc-HHHHHHHHHHHhcccccc-----
Confidence            6 8999999999999999999999999999988542   46778888887755 33 235788999999999999     


Q ss_pred             CCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCC-------C-CCCChhHHHHHHHHHHHHHHHHHHHH
Q 008167          402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLP-------S-VFQDRPQLTSIADNLNYRHRNAQMAS  473 (575)
Q Consensus       402 ~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~-------~-~~~~~~~l~~~~~~~n~~~~~a~~a~  473 (575)
                       ++++.+|||||++.|||||||||||+||+|||+|+++|.++...       . .....+.|..+|++||.++++|.+|+
T Consensus       549 -~~~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~s~~er~A~~ae  627 (813)
T PRK11642        549 -DPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEAT  627 (813)
T ss_pred             -CCCCCCccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCcccccccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence             67899999999999999999999999999999999999764311       0 01123568999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCc
Q 008167          474 RGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQ  552 (575)
Q Consensus       474 r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD  552 (575)
                      |++.+++.|+||++++ ++|+|+|++|.++|+||.|+++++||+||+++++++|   |.|++.+++++|+++++.|++||
T Consensus       628 R~~~~~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~---y~~d~~~~~L~g~~~~~~~~lGD  704 (813)
T PRK11642        628 RDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDY---YRFDQVGQRLIGESSGQTYRLGD  704 (813)
T ss_pred             HHHHHHHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcc---eEecchheEEecccCCcEECCCC
Confidence            9999999999999877 7899999999999999999998899999999999888   99999999999999999999999


Q ss_pred             EEEEEEEEecCCCCCCceEEEeC
Q 008167          553 TVNIHMEVVEPQPNRPKLQLTLI  575 (575)
Q Consensus       553 ~V~V~V~~vd~~~~~~~i~l~l~  575 (575)
                      +|+|+|..+|..  +++|.|+++
T Consensus       705 ~V~VkV~~vD~~--~rkI~f~l~  725 (813)
T PRK11642        705 RVEVRVEAVNMD--ERKIDFSLI  725 (813)
T ss_pred             EEEEEEEEeecC--CCeEEEEEe
Confidence            999999999976  899999974

>TIGR02063 RNase_R ribonuclease R

Probab=100.00  E-value=1.7e-118  Score=1016.36  Aligned_cols=547  Identities=31%  Similarity=0.480  Sum_probs=503.4

Q ss_pred             cEEEEEeCCCCCC-ceEecCCccCc-CCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCCcH
Q 008167           11 AHALFVPKDRRIP-KIRIQTRQLGN-LLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFST   88 (575)
Q Consensus        11 ~~~~~~P~d~r~p-~i~i~~~~~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f~~   88 (575)
                      +..+++|.|+|++ .|.|++....+ ..|++|+|+|++||..+.+|.|+|+++||..+++++++++++.+|||+. .||+
T Consensus       147 ~~~~v~p~d~~~~~~I~i~~~~~~~~~~g~~v~v~i~~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~-~f~~  225 (709)
T TIGR02063       147 GIGFVIPDDKRIYLDIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY-EFPE  225 (709)
T ss_pred             cEEEEEECCCCCCCCEEECCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCcCC-CCCH
Confidence            4688999999998 59998775433 4689999999999999999999999999999999999999999999998 6999


Q ss_pred             HHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHH
Q 008167           89 QVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEAS  168 (575)
Q Consensus        89 ~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~  168 (575)
                      ++++++...++.+++++.+  +|+|||++++|||||++|+|+||||||++.++|+|+|||||||||+||++||+||+||+
T Consensus       226 ~v~~~a~~~~~~~~~~~~~--~R~Dl~~~~~~tID~~~a~D~DDAisie~~~~g~~~l~VhIADVs~~V~~~s~lD~eA~  303 (709)
T TIGR02063       226 EVLDEAAKIPEEVPEEEIK--GRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEAL  303 (709)
T ss_pred             HHHHHHHhCCCCCChhHhh--cccccccCcEEEECCCCCcccccEEEEEEcCCCCEEEEEEEechhhEeCCCChHHHHHH
Confidence            9999999888888766666  89999999999999999999999999999988899999999999999999999999999


Q ss_pred             hCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCC--
Q 008167          169 KRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL--  246 (575)
Q Consensus       169 ~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~--  246 (575)
                      +||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++++|++|+|+|+++|||++|+++|+++..  
T Consensus       304 ~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~~~id~~G~i~~~~~~~svI~s~~~ltY~~v~~~l~~~~~~~  383 (709)
T TIGR02063       304 KRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALD  383 (709)
T ss_pred             HhCeeEeCCCCcccCCChHHccCccccCCCCceEEEEEEEEECCCCCEEEeEEEEEEEEeCeEEcHHHHHHHHcCCcccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999987542  


Q ss_pred             --CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHH
Q 008167          247 --MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILR  324 (575)
Q Consensus       247 --~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~  324 (575)
                        ..++.++|..|+++|+.|+++|.++|+++|+.|+.+|.+|++ |.+..+...+++.||.|||||||+||++||+++.+
T Consensus       384 ~~~~~~~~~L~~l~~la~~l~~~R~~~G~i~~~~~e~~~~~d~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~  462 (709)
T TIGR02063       384 KKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDEN-GKPIDIVPRERGDAHKLIEEFMIAANETVAEHLEK  462 (709)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHhCCCcccCCccceeEECCC-CCeEEEEeccchHHHHHHHHHHHHHHHHHHHHHHh
Confidence              235778999999999999999999999999999999999976 77889988899999999999999999999999987


Q ss_pred             hCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCC-----CCHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceeccc
Q 008167          325 QFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDV-----SSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCS  399 (575)
Q Consensus       325 ~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~-----~~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~  399 (575)
                      + +.|++||+|++|+++++++|.++++.+|++++.     .++++++++|+++.+ .+ ...+++.+++|+|++|.|   
T Consensus       463 ~-~~p~iyR~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~-~~-~~~~l~~~llr~m~~A~y---  536 (709)
T TIGR02063       463 A-KLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVKG-RP-EEELINTVLLRSMQQAKY---  536 (709)
T ss_pred             C-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCCCCCCHHHHHHHHHHhhC-Cc-HHHHHHHHHHHHhcCccc---
Confidence            5 899999999999999999999999999998753     367888999887765 23 335788999999999999   


Q ss_pred             CCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCC-C-CC--CCChhHHHHHHHHHHHHHHHHHHHHHH
Q 008167          400 GDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKL-P-SV--FQDRPQLTSIADNLNYRHRNAQMASRG  475 (575)
Q Consensus       400 ~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~-~-~~--~~~~~~l~~~~~~~n~~~~~a~~a~r~  475 (575)
                         +..|.+|||||++.|||||||||||+||+|||||+++|.+++. + ..  ....+.|+.+|.+||.++++|++|||+
T Consensus       537 ---~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~  613 (709)
T TIGR02063       537 ---SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERD  613 (709)
T ss_pred             ---CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence               6688999999999999999999999999999999999987632 1 11  223567999999999999999999999


Q ss_pred             HHHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEE
Q 008167          476 SVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTV  554 (575)
Q Consensus       476 ~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V  554 (575)
                      +.++|+|+||+.+. ++++|+|++|.++|+||.|+++|++|+||++++++++   |.|++..+.+.|++.++.|++||+|
T Consensus       614 ~~~~~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~---~~~d~~~~~l~g~~~~~~~~lGd~V  690 (709)
T TIGR02063       614 VNDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDY---YVFDEKGLALVGERTGKVFRLGDRV  690 (709)
T ss_pred             HHHHHHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCc---EEEcccceEEEeccCCcEECCCCEE
Confidence            99999999999887 7899999999999999999998999999999999887   8999999999999889999999999


Q ss_pred             EEEEEEecCCCCCCceEEEeC
Q 008167          555 NIHMEVVEPQPNRPKLQLTLI  575 (575)
Q Consensus       555 ~V~V~~vd~~~~~~~i~l~l~  575 (575)
                      +|+|.+||..  +++|.|+|.
T Consensus       691 ~Vkv~~vd~~--~~~I~~~l~  709 (709)
T TIGR02063       691 KVRVVKADLD--TGKIDFELV  709 (709)
T ss_pred             EEEEEEEecc--cCeEEEEEC
Confidence            9999999975  899999974

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.

>COG0557 VacB Exoribonuclease R [Transcription]

Probab=100.00  E-value=4e-114  Score=977.25  Aligned_cols=546  Identities=36%  Similarity=0.593  Sum_probs=507.1

Q ss_pred             EEEEEeCCCCCC-ceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCCcHH
Q 008167           12 HALFVPKDRRIP-KIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPFSTQ   89 (575)
Q Consensus        12 ~~~~~P~d~r~p-~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f~~~   89 (575)
                      +++++|.|+|++ .|.|++++.+ ...|++++|+|+.||.++.+|.|+++++||..+++..++++++++|++++. ||++
T Consensus       150 ~~~~~p~d~r~~~~i~i~~~~~~~~~~~~~v~~~i~~~~~~~~~~~g~v~~~lG~~~~~~~~~~~il~~~~i~~~-f~~~  228 (706)
T COG0557         150 IGRVLPDDKRLPFLIAIPPEQAPGAEEGHLVVVEITRWPDTSRPPFGEVVEVLGDLGDPGADIEAILRDHGIPSE-FPEK  228 (706)
T ss_pred             eEEEEecCCCCccceeeccccccccccCCEEEEEecccCCcCCCCceeEEEeecCCCCcchhHHHHHHHcCCCCC-CCHH
Confidence            799999999999 6999987765 567999999999999999999999999999999999999999999999995 9999


Q ss_pred             HHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHh
Q 008167           90 VLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK  169 (575)
Q Consensus        90 v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~  169 (575)
                      +++++...+..+.+++..  +|.|||++++|||||++|+|+|||||++++.+|+|+|||||||||+||+|||+||+||++
T Consensus       229 v~~~a~~~~~~~~~~~~~--~R~Dlr~l~~~TID~~~akD~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~  306 (706)
T COG0557         229 VLDEAAALPDEVPEEDLK--GRVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARK  306 (706)
T ss_pred             HHHHHHhccCcCChhhhc--CccccccCCEEEECCCCCccccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHH
Confidence            999999888877677777  999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCC--CCC
Q 008167          170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDS--RLM  247 (575)
Q Consensus       170 R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~--~~~  247 (575)
                      ||||||||++++||||+.||+++|||+|+++|+|+||.|++|++|+|.+++|++|+|+|+++|||++|+++|++.  ...
T Consensus       307 RgtSVYlp~~vipMLPe~Ls~~lcSL~p~~dRla~s~~m~ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~  386 (706)
T COG0557         307 RGTSVYLPDRVIPMLPEALSNGLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKY  386 (706)
T ss_pred             cCCeEEcCCcccCCCchhhcCCccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcchhc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999986  344


Q ss_pred             CchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHHhCC
Q 008167          248 DPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFP  327 (575)
Q Consensus       248 ~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~~~~  327 (575)
                      .++.+.|..|.++++.++++|.++|+++|+.+|.++.+|++ |.|..|...++..+|.||||||++||++||+++.++ .
T Consensus       387 ~~l~~~l~~~~~l~~~l~~~R~~rg~i~~~~~E~ki~~d~~-~~~~~i~~~~r~~a~~lIee~Ml~AN~~vA~~l~~~-~  464 (706)
T COG0557         387 APLLDSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLDEE-GRPVEIEIRERLDAEKLIEEFMLLANETVAEHLEKH-K  464 (706)
T ss_pred             ccchHHHHHHHHHHHHHHHHHHhCCCcccCCcceeEEECCC-CCeeeEEEecccHHHHHHHHHHHHHHHHHHHHHHHc-C
Confidence            56778999999999999999999999999999999999976 678999999999999999999999999999999998 5


Q ss_pred             CceeeeeCCCCChhhHHHHHHHHHHcCCccCCCC----HHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCC
Q 008167          328 LCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS----SKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLT  403 (575)
Q Consensus       328 ~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~----~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~  403 (575)
                      .|.+||+|+.|+.++++.|.+++..+|+.+....    +..++..+++..+ .| ...+++.+++|+|++|.|      +
T Consensus       465 ~~~~~R~h~~P~~ek~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~-~~-~~~v~~~~~lRsm~~a~Y------s  536 (706)
T COG0557         465 IPLLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKG-RP-LEAVLQTLLLRSMKQAEY------S  536 (706)
T ss_pred             CCcceeCCCCCCHHHHHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccC-Ch-HHHHHHHHHHHhhhcCee------c
Confidence            6789999999999999999999999999887442    5567777766542 23 456788899999999999      6


Q ss_pred             CCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167          404 PPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLI  483 (575)
Q Consensus       404 ~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~  483 (575)
                      +.+.+|||||++.|||||||||||+||+|||||+++|.++..+......++|..+|.+||.++|+|..|+|++.++|+|.
T Consensus       537 ~~~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~  616 (706)
T COG0557         537 PDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAE  616 (706)
T ss_pred             CCCCCceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHH
Confidence            77999999999999999999999999999999999999876654332347899999999999999999999999999999


Q ss_pred             HHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167          484 YFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE  562 (575)
Q Consensus       484 ~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd  562 (575)
                      ||++++ ++|+|+|++|.++|++|.|+++|++|+||++.+++++   |.|++..+.+.|++.+..|++||.|+|+|.+++
T Consensus       617 ~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~---y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~  693 (706)
T COG0557         617 YMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDY---YHFDERGQALVGEKSGKVYRLGDEVKVKVTSVD  693 (706)
T ss_pred             HHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCce---eeeccccceeeccccccccccCCEEEEEEEEEc
Confidence            999998 5999999999999999999999999999999999987   999999999999999999999999999999999


Q ss_pred             CCCCCCceEEEeC
Q 008167          563 PQPNRPKLQLTLI  575 (575)
Q Consensus       563 ~~~~~~~i~l~l~  575 (575)
                      ..  .++|.|+++
T Consensus       694 ~~--~~~i~~~~v  704 (706)
T COG0557         694 LD--ERKIDFELV  704 (706)
T ss_pred             cc--ccceEEEec
Confidence            75  899999875

>PRK05054 exoribonuclease II; Provisional

Probab=100.00  E-value=2.6e-113  Score=957.38  Aligned_cols=532  Identities=21%  Similarity=0.287  Sum_probs=466.9

Q ss_pred             cEEEEEeCCCCCC-ceEecCC-c-c-CcCCCCEEEEEEeecCCC-CCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCC
Q 008167           11 AHALFVPKDRRIP-KIRIQTR-Q-L-GNLLDKRIIVAVDSWDCQ-SRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARP   85 (575)
Q Consensus        11 ~~~~~~P~d~r~p-~i~i~~~-~-~-~~~~~~~~~v~i~~w~~~-~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~   85 (575)
                      +..+++|.|.+++ .|.|+.. . . ....|++|+|+|++||.. ...|.|+|+++||..+++++++++++++|+|+. .
T Consensus        95 ~~~~~~p~d~~~~~~i~i~~~~~~~~~~~~gd~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~-~  173 (644)
T PRK05054         95 DRLSIVPDHPLLKDAIPCRAAKGLNHEFKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLER-E  173 (644)
T ss_pred             ceEEEEECCCCCCccEEeccccccccCCCCCCEEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCC-C
Confidence            4678999999998 5888532 2 2 334689999999999986 456999999999999999999999999999998 5


Q ss_pred             CcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHH
Q 008167           86 FSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDD  165 (575)
Q Consensus        86 f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~  165 (575)
                      ||+++++.      .+.+++ .  +|+|||++++|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+
T Consensus       174 f~~~~~~~------~~~~~~-~--~R~Dlr~~~~~TID~~~akD~DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~  244 (644)
T PRK05054        174 APAGGVAW------EMLDEG-L--EREDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDK  244 (644)
T ss_pred             CCchhhhc------cCChhc-c--CcccccCCcEEEECCCCCCcccceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHH
Confidence            99987542      222222 2  79999999999999999999999999999988899999999999999999999999


Q ss_pred             HHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEE-EEEEEEEEeecceeCHHHHHHHhcCC
Q 008167          166 EASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS-TRYTKSVIKSCAALSYVEAQARMDDS  244 (575)
Q Consensus       166 eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~-~~~~~s~I~s~~~ltY~~v~~~l~~~  244 (575)
                      ||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++ ++|++|+|+|+++|||++|+++|+++
T Consensus       245 eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~~~R~als~~~~id~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~  324 (644)
T PRK05054        245 AARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENG  324 (644)
T ss_pred             HHHHhCceEeCCCCcccCCChHHhcCccccCCCCCceEEEEEEEEeCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCC
Confidence            99999999999999999999999999999999999999999999999999998 89999999999999999999999875


Q ss_pred             CC----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHH
Q 008167          245 RL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAE  320 (575)
Q Consensus       245 ~~----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~  320 (575)
                      ..    ..++.+.|..|.++++.|+++|.++|+++|+.||+++.+|++ |.+..+...++.+||.|||||||+||++||+
T Consensus       325 ~~~~~~~~~i~~~l~~L~~l~~~l~~~R~~~G~i~~d~~e~~i~ld~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~  403 (644)
T PRK05054        325 GDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEK-GEVLDIVAEPRRIANRIVEESMIAANICAAR  403 (644)
T ss_pred             CccccchhHHHHHHHHHHHHHHHHHHHHHhCCCccccCCceEEEECCC-CCEEEEEEecCcHHHHHHHHHHHHHHHHHHH
Confidence            32    245778899999999999999999999999999999999976 6788999999999999999999999999999


Q ss_pred             HHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCCC---HHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceec
Q 008167          321 QILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS---SKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYF  397 (575)
Q Consensus       321 ~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~---~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~  397 (575)
                      ++.++ +.|++||+|+.|++++++++.+++..+|+.++..+   ...+++.++...+ .+. . .+..+++|+|++|.| 
T Consensus       404 ~l~~~-~~p~iyRvH~~P~~~~l~~l~~~~~~~g~~~~~~~~~~l~~~~~~~~~l~~-~~~-~-~l~~~llr~~~~a~y-  478 (644)
T PRK05054        404 VLRDK-LGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRRELDA-QPT-G-YLDSRIRRFQSFAEI-  478 (644)
T ss_pred             HHHHc-CCCEEEECCCCCCHHHHHHHHHHHHHCCCCcCCCcccChHHHHHHHHHHhc-chH-H-HHHHHHHHHHhceec-
Confidence            99987 78999999999999999999999999999886543   2334444443322 221 2 233446899999999 


Q ss_pred             ccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167          398 CSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSV  477 (575)
Q Consensus       398 ~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~  477 (575)
                           ++.|.+|||||++.|||||||||||+||+|||||+++|.+++.+      ..++.+|.+||.++++|++|+|++.
T Consensus       479 -----s~~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L~a~l~~~~~~------~~~~~~~~~~s~~er~a~~aer~~~  547 (644)
T PRK05054        479 -----STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAE------RPQDEITVQLAERRRLNRMAERDVG  547 (644)
T ss_pred             -----CCCCcCccccccccccccCChhhhhHHHHHHHHHHHHHcCCCCC------ccHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 67899999999999999999999999999999999999876532      2378899999999999999999999


Q ss_pred             HHHHHHHHhcCC---ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceec--CCcEEEEeeCCCeEEeeCc
Q 008167          478 ELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVD--EQQQKIVKMDGNLSYSVLQ  552 (575)
Q Consensus       478 ~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d--~~~~~l~g~~~~~~~~lGD  552 (575)
                      ++|.+.||++++   ++|+|+|++|+++|+||.|+++|++|+||++.+.++| ..|.|+  +..+.+   +++++|++||
T Consensus       548 ~~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~-~~y~~~~~~~~~~~---~~~~~~~lGd  623 (644)
T PRK05054        548 DWLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVR-DELVCNQENGTVQI---KGETVYKLGD  623 (644)
T ss_pred             HHHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCc-cceEEccccceEEE---eCCEEEcCCC
Confidence            999999999986   3899999999999999999999999999999998875 124444  444444   3458999999


Q ss_pred             EEEEEEEEecCCCCCCceEEEeC
Q 008167          553 TVNIHMEVVEPQPNRPKLQLTLI  575 (575)
Q Consensus       553 ~V~V~V~~vd~~~~~~~i~l~l~  575 (575)
                      +|+|+|.+||..  +++|.|+++
T Consensus       624 ~V~V~v~~vd~~--~~~i~~~~~  644 (644)
T PRK05054        624 VIDVTLAEVRME--TRSIIARPV  644 (644)
T ss_pred             EEEEEEEEEccc--cCeEEEEEC
Confidence            999999999976  999999875

>TIGR02062 RNase_B exoribonuclease II

Probab=100.00  E-value=1.1e-111  Score=942.35  Aligned_cols=529  Identities=21%  Similarity=0.275  Sum_probs=465.0

Q ss_pred             cEEEEEeCCCCCCc-eEecCC-cc--CcCCCCEEEEEEeecCCCC-CCcceEEEEeecCCCChhhHHHHHHhhCCCCCCC
Q 008167           11 AHALFVPKDRRIPK-IRIQTR-QL--GNLLDKRIIVAVDSWDCQS-RYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARP   85 (575)
Q Consensus        11 ~~~~~~P~d~r~p~-i~i~~~-~~--~~~~~~~~~v~i~~w~~~~-~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~   85 (575)
                      +..+++|.|.+++. |.+... ..  ....|+.|+|+|++||... ..|.|+|+++||..+++++++++++.+|+|+. .
T Consensus        92 ~~~~v~p~d~~~~~~i~~~~~~~~~~~~~~gd~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~-~  170 (639)
T TIGR02062        92 DKLAIVPDHPLLKDAIPCRAAKGLNHEFQEGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLER-E  170 (639)
T ss_pred             CeEEEEECCCCCCccEEecCccccccCCCCCCEEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCC-C
Confidence            46789999988875 555322 21  2236889999999999865 55899999999999999999999999999998 5


Q ss_pred             CcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHH
Q 008167           86 FSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDD  165 (575)
Q Consensus        86 f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~  165 (575)
                      ||+++++++..        +..  +|+|||++++|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+
T Consensus       171 f~~~v~~ea~~--------~~~--~R~DLr~~~~~TID~~~akD~DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~  240 (639)
T TIGR02062       171 EPDGVADEMLL--------DGL--VREDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDK  240 (639)
T ss_pred             CCHHHHHhhhh--------ccc--cCcccccCCEEEECCCCCCcccceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHH
Confidence            99999988731        113  79999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEE-EEEEEEEEeecceeCHHHHHHHhcCC
Q 008167          166 EASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS-TRYTKSVIKSCAALSYVEAQARMDDS  244 (575)
Q Consensus       166 eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~-~~~~~s~I~s~~~ltY~~v~~~l~~~  244 (575)
                      ||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++ ++|++|+|+|+++|||++|+++|+++
T Consensus       241 eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e~R~als~~~~ld~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~  320 (639)
T TIGR02062       241 AAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENT  320 (639)
T ss_pred             HHHHhCCcEeCCCceecCCCHHHhcCccccCCCCCeeEEEEEEEEcCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCC
Confidence            99999999999999999999999999999999999999999999999999999 79999999999999999999999875


Q ss_pred             CC----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHH
Q 008167          245 RL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAE  320 (575)
Q Consensus       245 ~~----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~  320 (575)
                      ..    ..++.++|..|.++|+.|+++|.++|++.|+.||+++.+|++ |.+..+...++.+||.|||||||+||++||+
T Consensus       321 ~~~~~~~~~i~~~L~~L~~la~~l~~~R~~~G~i~ld~pE~~~~ld~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~vA~  399 (639)
T TIGR02062       321 SDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEK-GEVLDIVAEPRRIANRIVEEAMIIANICAAR  399 (639)
T ss_pred             cccccchHHHHHHHHHHHHHHHHHHHHHHhCCcccccCCceEEEECCC-CCEEEEEEecCCHHHHHHHHHHHHHHHHHHH
Confidence            42    234667899999999999999999999999999999999976 6788888889999999999999999999999


Q ss_pred             HHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC---CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceec
Q 008167          321 QILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS---SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYF  397 (575)
Q Consensus       321 ~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~  397 (575)
                      |+.++ ..|++||+|+.|+++++++|.++++.+|+.++..   +...+...++.+.+ .+  ...+..+++|+|++|.| 
T Consensus       400 ~l~~~-~~p~iyR~H~~P~~~~l~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~l~~~~~r~~~~a~y-  474 (639)
T TIGR02062       400 FLRDK-LGFGIYNTHAGFDPANAENVVALLKTNGLHVDAEELATLDGFCKLRRELDA-QE--TGYLDSRIRRYQSFAEI-  474 (639)
T ss_pred             HHHHh-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCCCcccccCHHHHHHHHHHhhc-ch--HHHHHHHHHHHhhhccc-
Confidence            99987 5689999999999999999999999999987543   23444444443332 22  13466778899999999 


Q ss_pred             ccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167          398 CSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSV  477 (575)
Q Consensus       398 ~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~  477 (575)
                           ++++.+|||||++.|||||||||||+||+|||||+++|.+++.+.      .++.+|.+||.+++.|++|+|++.
T Consensus       475 -----s~~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~~~l~~~~~~~------~~~~~~~~~s~~er~a~~aeR~~~  543 (639)
T TIGR02062       475 -----STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR------PQEDITVQLAERRRLNRIAERDVA  543 (639)
T ss_pred             -----CCCCcCcchhccccccccCChhhhhHHHHHHHHHHHHHcCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 678999999999999999999999999999999999998764321      367889999999999999999999


Q ss_pred             HHHHHHHHhcCC---ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCc
Q 008167          478 ELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQ  552 (575)
Q Consensus       478 ~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD  552 (575)
                      ++|++.||++++   ++|+|+|+++.++|++|.|++.|++|+||++.+.+++ ..|.|++  ..+.++|+   ++|++||
T Consensus       544 ~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~-~~~~~~~~~~~~~l~g~---~~~~lgd  619 (639)
T TIGR02062       544 DWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANR-EELVCNQENGTVQIKGE---TVYKIGD  619 (639)
T ss_pred             HHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCC-cceEEcccccEEEEecc---EEEecCC
Confidence            999999999986   3799999999999999999999999999999998731 1255655  44677654   5999999


Q ss_pred             EEEEEEEEecCCCCCCceEEE
Q 008167          553 TVNIHMEVVEPQPNRPKLQLT  573 (575)
Q Consensus       553 ~V~V~V~~vd~~~~~~~i~l~  573 (575)
                      +|+|+|.+||.+  +++|.|+
T Consensus       620 ~v~V~v~~vd~~--~~~i~~~  638 (639)
T TIGR02062       620 VIDVVLTEVRME--TRSIIAR  638 (639)
T ss_pred             EEEEEEEEeccc--cCcEeee
Confidence            999999999976  8999886

This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.

>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=7.1e-105  Score=908.82  Aligned_cols=555  Identities=51%  Similarity=0.858  Sum_probs=508.5

Q ss_pred             CCCCCccEEEEEeCCCCCCceEecCC-ccCcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCC
Q 008167            5 AGSGSVAHALFVPKDRRIPKIRIQTR-QLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDA   83 (575)
Q Consensus         5 ~~~~~~~~~~~~P~d~r~p~i~i~~~-~~~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~   83 (575)
                      ..+....++||+|.|+|+|+|.|+++ +..++.++++++.|++||.++.||.|++++.||..++.++++++||.+++++.
T Consensus       366 ~~~~~~~~~~~~p~DkRvP~i~i~t~~~~~~~~~~~~~~~I~~W~~ts~~p~g~~v~~lG~i~~~~~e~~aLL~en~v~~  445 (941)
T KOG2102|consen  366 LKGSSALIVLFIPSDKRVPLIRILTDDQAQDLIDKRIVAAIDRWPRTSLYPFGHLVRELGTIGDTETETEALLLENGVPH  445 (941)
T ss_pred             ccccccceeeeccccCCCCeeeccccccccchhceeEEEEecccccCCcccCceehhhccCcCCccchhhhhhhcCCCcc
Confidence            34678899999999999999999999 88899999999999999999999999999999999999999999999999999


Q ss_pred             CCCcHHHHhcCCC-CCCCCCccccCCCC-CccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCC
Q 008167           84 RPFSTQVLACLPP-LPWSVSSEDLANPI-RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGT  161 (575)
Q Consensus        84 ~~f~~~v~~~~~~-~~~~~~~~~~~~~~-R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s  161 (575)
                      .+|+++++.+++. .+|.++.++..  . |.|||++.+|+|||++|.|||||+|+..++||+|+|||||||||+||+|||
T Consensus       446 ~~f~~~~~~~lp~~~~~~~~~~~~~--~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evGVHIADVt~fV~pgs  523 (941)
T KOG2102|consen  446 KPFSQALLDCLPRSHPWPITEEELQ--KLRKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVGVHIADVTHFVKPGS  523 (941)
T ss_pred             cccCHHHHhcCCccCCCCcChHHhh--hhhhhhhhceEEeecCCCccchhhhhheeecCCCcEEEEEEeccchhhcCCCC
Confidence            9999999999999 99999888887  6 999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHh
Q 008167          162 PLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARM  241 (575)
Q Consensus       162 ~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l  241 (575)
                      +||+||++||||||||++++||||+.||+++|||+||++|+||||.|+++.+|.|++.||++|+|+|+++|+|+++|++|
T Consensus       524 ~lD~eA~~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~~f~ksvI~s~~~lsye~Aq~~i  603 (941)
T KOG2102|consen  524 ALDREAARRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILKTWFGKSVIRSKAALSYEEAQDIL  603 (941)
T ss_pred             ccCHHHHhhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceeeceecchhcccchhhhHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHH
Q 008167          242 DDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQ  321 (575)
Q Consensus       242 ~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~  321 (575)
                      +++...+++...|+.|.++|+.||++|+++|++.+..+|+.+.+|+++.+|.+++.++..+++.||||||++||..||++
T Consensus       604 d~~~~~~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~~~~p~~~e~~~~~~~n~lveEfmllaN~~vA~~  683 (941)
T KOG2102|consen  604 DTPNSSDPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEEKPNPQDVEVKELTETNFLVEEFMLLANISVAEK  683 (941)
T ss_pred             cCCcccchhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccCCCCccccceeeeehhhhHHHHHHHHHhHHHHHH
Confidence            99887789999999999999999999999999999999999999999888999999899999999999999999999999


Q ss_pred             HHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCCCHHHHHHHHHHHhC-CChhHHHHHHHHHHhhccCceecccC
Q 008167          322 ILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSG  400 (575)
Q Consensus       322 l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~l~~~l~~~~~-~~~~~~~~l~~~~~r~m~~a~Y~~~~  400 (575)
                      +.+.|+.++++|+|+.|....++.+.+.+.++|.+++..+++.|.++++++.+ ..|++..+++.+.+|+|.+|+|||+|
T Consensus       684 I~~~f~~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~~p~~~~~l~~l~~r~m~~A~yf~sg  763 (941)
T KOG2102|consen  684 ILASFPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDDKPYLNTLLRILATRSMTRAVYFCSG  763 (941)
T ss_pred             HHHhCCchhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCchHHHHHHHHHHHhhhhhceeEEeec
Confidence            99999999999999999999999999999999999999999999999999988 44688888999999999999999999


Q ss_pred             CCCCCCCCccccCCCCccccccccccchhHHHHHHHHH-HhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008167          401 DLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSA-SLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVEL  479 (575)
Q Consensus       401 ~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~-~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~  479 (575)
                      ....+.++|||||++.|||||||||||+|++|||||++ ++...+   ...+...+..+|.+||.+.+.++.|++++.++
T Consensus       764 ~~~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~~---~~~~~~~l~~i~~~~N~r~~~a~~a~~~S~~l  840 (941)
T KOG2102|consen  764 SSDTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERSP---TAPDRPNLSSLAANCNERKKAAKKAQEASTEL  840 (941)
T ss_pred             ccCcchhhchhhcccchhhccCcccccchHHHHHHHHHHhhccCc---cccccccHHHHHhhhhhhHHHHHHHHHhhHHH
Confidence            87888899999999999999999999999999999995 333322   22334589999999999999999999999999


Q ss_pred             HHHHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEE
Q 008167          480 HTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME  559 (575)
Q Consensus       480 ~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~  559 (575)
                      |.+.|++++....+|+|..|.++|+.|++|+||++|.|+++.+....  .+..++        .....+.+.|.|.+.+.
T Consensus       841 ~~~~~~k~~~~~~~a~v~~V~~~~~~v~ipe~G~e~~v~l~~~~~~~--~~~~~~--------~~~~~~~~~~~v~~~~~  910 (941)
T KOG2102|consen  841 YLCEYLKDKQVLEEAVVLFVRPNGIDVVIPEYGLEGRVYLDLLKPSQ--TFFLDD--------EVSLRFEESDPVVVRIK  910 (941)
T ss_pred             HHHHHHHhcccccceEEEEEecCceEEEEcccCceEEEEecccCCcc--ceeecc--------cccccccccCCceeeec
Confidence            99999999977889999999999999999999999999998333221  112111        11122677777777766


Q ss_pred             EecCCCCCCceEEEe
Q 008167          560 VVEPQPNRPKLQLTL  574 (575)
Q Consensus       560 ~vd~~~~~~~i~l~l  574 (575)
                      .........+|.+.+
T Consensus       911 ~~~~~~~~~~l~~~~  925 (941)
T KOG2102|consen  911 LDKLVPQPDRLRIEL  925 (941)
T ss_pred             ccccccCcceEEEEe
Confidence            555445566666654

>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam

Probab=100.00  E-value=3.5e-79  Score=637.86  Aligned_cols=317  Identities=45%  Similarity=0.727  Sum_probs=257.5

Q ss_pred             CccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHhCCCceEcCCccccCCChhhhc
Q 008167          111 RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTE  190 (575)
Q Consensus       111 R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~  190 (575)
                      |+|||++++|||||++|+|+||||||++.++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++
T Consensus         1 R~Dl~~~~~~tID~~~~~d~DDAisie~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~   80 (325)
T PF00773_consen    1 RKDLRDLPVFTIDPPGAKDIDDAISIEKLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSE   80 (325)
T ss_dssp             SEECTTSEEEEEESTTSS---EEEEEEEETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHC
T ss_pred             CccCCCCCEEEEcCCCCCCCCCeEEEEECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhc
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCCCCc---hHHHHHHHHHHHHHHHHH
Q 008167          191 DICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDP---LTTDLRNMNSLAKKMRQR  267 (575)
Q Consensus       191 ~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~---~~~~L~~L~~la~~lr~~  267 (575)
                      ++|||.||++|+|||+.+++|++|+|.+++|++|+|+|.++|||++|+++|++......   ..++|..|+++|+.|+++
T Consensus        81 ~~~SL~~~~~r~a~S~~~~l~~~G~i~~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~~~~~~~~L~~l~~la~~l~~~  160 (325)
T PF00773_consen   81 DLCSLNPGKDRLAFSVIFTLDEDGEILDYEIYPSIIRSVARLTYEEVDEILEGKSQEEPESPIEEDLKLLYELAKALRKK  160 (325)
T ss_dssp             TTSSTTBTSEEEEEEEEEEE-TTS-EEEEEEEEEEEEBSEEEEHHHHHHHHHTTTS--HCSHCHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCCceEEEEEEEEeeCCeEeeeEEEEEEEecccccCHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999998654433   378999999999999999


Q ss_pred             HHhcCCccc-cCcceEEEecCCCCCeeeEEEee---cchHHHHHHHHHHHHHHHHHHHHHHhCCCceeeeeCCCCChhhH
Q 008167          268 RIERGALTL-ASAEVKFQIDTETHDPLDIGMYQ---IREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEML  343 (575)
Q Consensus       268 R~~~Gal~~-~~~e~~~~~d~~~~~~~~v~~~~---~~~s~~lVeE~MilAN~~vA~~l~~~~~~~~~~R~h~~P~~~~~  343 (575)
                      |.++|++.+ +.|+..+.++++ +.+..+....   ...|+.||+||||+||++||+|+.++ +.|++||+|+.|+..++
T Consensus       161 R~~~Ga~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~~-~ip~iyR~~~~p~~~~~  238 (325)
T PF00773_consen  161 RLSRGAIELFNSPELKFSLDED-GPPKEINRESSDESSPAHSLVEELMILANRAVAQFLSEN-GIPAIYRVQPEPDPERL  238 (325)
T ss_dssp             HHHTTS-----SHCEEEEEETT-TTEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHHC-TTTSEEEEB-SSSCCCH
T ss_pred             hhhccCccccCCCceEEEEecC-CCcceEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHHc-CCCceeeeCCCCCHHHH
Confidence            999999999 889999999875 5566666555   88999999999999999999999975 99999999999999998


Q ss_pred             HHHHHHHHHcCCccCCCCHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCCCccccCCCCccccccc
Q 008167          344 EPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSP  423 (575)
Q Consensus       344 ~~l~~~~~~~g~~~~~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSP  423 (575)
                      +++.+.+   +++++.....++++.+.. .  ++.....++.++.++|.+|+|      +..|.+|||||++.|||||||
T Consensus       239 ~~~~~~~---~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~l~~~l~~a~y------~~~p~~H~~L~l~~Yt~~TSP  306 (325)
T PF00773_consen  239 EELLKLL---KLDLDETKSLTLQNLLQA-E--NPPNSLALRYLLLKTLPPAEY------STEPSGHFGLGLPAYTHFTSP  306 (325)
T ss_dssp             HHHHHHH---T---STCHHHCHHCHHCC-C--CTTSSHHHHHHHHCCC--EEE------ESSGC-BTTTTBSS-B--S-T
T ss_pred             HHHHHHh---cCCCCCcchhhHHHHHHh-c--CChHHHHHHHHHHHhhccccc------ccCCCcceeeeccccccccCh
Confidence            8888777   444443333345555554 2  222334567788999999999      678889999999999999999


Q ss_pred             cccchhHHHHHHHHHHhC
Q 008167          424 IRRYADVVVHRLLSASLG  441 (575)
Q Consensus       424 IRRY~DlvvHr~L~~~l~  441 (575)
                      ||||+||+|||||+++|.
T Consensus       307 lRRY~Dl~~hrql~~~L~  324 (325)
T PF00773_consen  307 LRRYADLVVHRQLKAALR  324 (325)
T ss_dssp             TTBHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHHHHHHHhh
Confidence            999999999999999985

; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.

>COG4776 Rnb Exoribonuclease II [Transcription]

Probab=100.00  E-value=1.1e-75  Score=592.54  Aligned_cols=526  Identities=22%  Similarity=0.315  Sum_probs=422.0

Q ss_pred             CccEEEEEeCCCCCCceEecCCccC----c-CCCCEEEEEEeecCCCCC-CcceEEEEeecCCCChhhHHHHHHhhCCCC
Q 008167            9 SVAHALFVPKDRRIPKIRIQTRQLG----N-LLDKRIIVAVDSWDCQSR-YPFGHYVRVIGEIGDRDTESEMVLIDNDID   82 (575)
Q Consensus         9 ~~~~~~~~P~d~r~p~i~i~~~~~~----~-~~~~~~~v~i~~w~~~~~-~p~g~i~~~lG~~~~~~~~~~~il~~~~i~   82 (575)
                      +.+...++|+.+-+-.. |+-.+..    . ..|+.+|+++.+-|-... .-.+.|.+.|...+|.-+-.=..|++|+++
T Consensus        93 kd~rL~i~pDhP~lk~~-i~~~~~k~l~~~fQeGDW~VA~lk~HpLkgDr~F~a~lt~~It~~dD~l~PWWVTLArh~l~  171 (645)
T COG4776          93 KDDRLQIVPDHPLLKDA-IPCRAAKGLNEEFQEGDWAVAELKRHPLKGDRSFYAELTQKITFADDHLAPWWVTLARHNLE  171 (645)
T ss_pred             cCCceEEcCCChhhhhh-cccccccchhhhhhcCceehhhhhcCCCCCchhHHHHHHHHhhccCCcccceeeehhhccCC
Confidence            34445566665444321 3322221    2 268899999998887653 335566666666666555555567778877


Q ss_pred             CCCCcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCH
Q 008167           83 ARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTP  162 (575)
Q Consensus        83 ~~~f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~  162 (575)
                      ..+ |.      ...++.+..+.+   .|+||+.++++|||+++++|+|||++++++++|.|.|-|+||||++||.+||.
T Consensus       172 r~~-p~------g~~d~~m~d~~l---~RedLTaL~FvTID~~sT~DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~s~  241 (645)
T COG4776         172 REA-PA------GIVDTEMLDEGL---VREDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSK  241 (645)
T ss_pred             ccC-CC------cccchhhhhhhh---hhccccccceEEecCccccccchhhhccccCCCcEEEEEEecCCccccCCcch
Confidence            531 11      112333322222   69999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEE-EEEEEEEEEeecceeCHHHHHHHh
Q 008167          163 LDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKSCAALSYVEAQARM  241 (575)
Q Consensus       163 LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~-~~~~~~s~I~s~~~ltY~~v~~~l  241 (575)
                      ||++|+.|+.|.|||+..|||||++||+++|||.||+.|+++.|.++++++|+|. +.+|..+.|+|+++|.|++|..+|
T Consensus       242 ld~~A~~R~FTnYLPGfNIPMLPreLsd~lCSL~~ne~RPaL~C~it~~~~G~I~~~i~F~aA~i~SkakL~YdhVSDwl  321 (645)
T COG4776         242 LDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPALACRITIDKDGNITDKIRFFAATIESKAKLVYDHVSDWL  321 (645)
T ss_pred             hhHHHHHHHHhhcCCCCCCCCCChhhhhhhhhccccccCceEEEEEEEecCCccccchhhHHHhhhhhhhhhhhhHHHHH
Confidence            9999999999999999999999999999999999999999999999999999997 589999999999999999999999


Q ss_pred             cCCC----CCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHH
Q 008167          242 DDSR----LMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVS  317 (575)
Q Consensus       242 ~~~~----~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~  317 (575)
                      ++..    .+.++.+++..|+.++++.-++|..+.-+.-++|+++|.+.++ |.+.+|....++.|++||||+||+||.+
T Consensus       322 E~~~~WqPe~~~iAqqi~~L~~~~~aR~~WRk~hal~FkdrpdYrF~l~e~-g~V~~I~ae~RRiAnriVEE~MI~ANIc  400 (645)
T COG4776         322 ENTGDWQPESEAIAQQIRLLHQFCQARIEWRKTHALVFKDRPDYRFILGEK-GEVLDIVAEPRRIANRIVEESMIAANIC  400 (645)
T ss_pred             hcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhhceeeccCCCceEEEecCC-CceEeeehhHHHHHHHHHHHHHHHHHHH
Confidence            9653    3567889999999999999999999877777899999999865 7888888888999999999999999999


Q ss_pred             HHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCCCHHHHHH------HHHHHhCCChhHHHHHHHHHHhhc
Q 008167          318 VAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALAD------SLDRAVGDDPYFNKLIRILATRCM  391 (575)
Q Consensus       318 vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~l~~------~l~~~~~~~~~~~~~l~~~~~r~m  391 (575)
                      +|.+|.++++ .++|.+|...++..++....++...|...+..+-.+|..      .|+..  ...+...-+    .|  
T Consensus       401 Aa~~L~~~~g-fGI~N~HsGFd~~~~e~a~~~l~~~~~~~~~e~l~Tl~Gfc~lRr~l~~~--~t~yld~Ri----Rr--  471 (645)
T COG4776         401 AARVLREKLG-FGIYNVHSGFDPANAEAAAALLKTNGLNVDAEELLTLEGFCKLRRELDAQ--PTGYLDSRI----RR--  471 (645)
T ss_pred             HHHHHHHhcC-cceeeccccCCHHHHHHHHHHHHhcCcCCCHHHHhhhHHHHHHHHHhhcc--ccchHHHHH----HH--
Confidence            9999999865 689999999999999999999999998776543333322      23222  223333222    22  


Q ss_pred             cCceecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 008167          392 TQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQM  471 (575)
Q Consensus       392 ~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~  471 (575)
                          |.+.++++..|.+|||||++.|+.||||||+|+|+++||+|++++.+++....      =+.+..++.++.|.-+.
T Consensus       472 ----fqsfae~~t~p~PHFglGl~~YATWTSPIRKY~DMiNHRLlKavi~~~~~~kP------qedi~v~lae~Rr~nrm  541 (645)
T COG4776         472 ----FQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAEKP------QEDITVQLAERRRLNRM  541 (645)
T ss_pred             ----HHhHHhhccCcCccccccchheeeccchhhhhhhHHHHHHHHHHHcCCCcCCC------chHHHHHHHHHHHhhhh
Confidence                33445668899999999999999999999999999999999999998753221      13455678889999999


Q ss_pred             HHHHHHHHHHHHHHhcCC---ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCe
Q 008167          472 ASRGSVELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNL  546 (575)
Q Consensus       472 a~r~~~~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~  546 (575)
                      |||+.-+|..|+||+.+.   ..|.|.|.+|...|+.|+|-+.|.-.+|+-.-+.+.. .+..++.  .++.+   ++..
T Consensus       542 aERdv~DWLY~r~L~~k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~r-eei~~n~e~gtv~I---~ge~  617 (645)
T COG4776         542 AERDVADWLYARFLADKAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANR-EELVCNQENGTVQI---KGET  617 (645)
T ss_pred             hhhhhHHHHHHHHhccccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccch-hheEecCCCceEEE---ccEE
Confidence            999999999999998876   5799999999999999999999999999987766542 2344444  33444   3568


Q ss_pred             EEeeCcEEEEEEEEecCCCCCCceE
Q 008167          547 SYSVLQTVNIHMEVVEPQPNRPKLQ  571 (575)
Q Consensus       547 ~~~lGD~V~V~V~~vd~~~~~~~i~  571 (575)
                      +|++||.|+|++..|..+  .|.|-
T Consensus       618 ~Yk~~D~i~V~l~eVr~e--tRsii  640 (645)
T COG4776         618 VYKVGDVIDVTLAEVRME--TRSII  640 (645)
T ss_pred             EEeeccEEEEEeHHHHHh--hhhhh
Confidence            899999999999999865  56654

>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain

Probab=99.22  E-value=1e-10  Score=96.89  Aligned_cols=81  Identities=20%  Similarity=0.331  Sum_probs=73.7

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|+++.++|++|.++.+|++|++|++++++++   |.+|+..+.+.+++.++.|++||.|+|+|.++|.+  +++
T Consensus         3 ~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~---~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~--~~~   77 (83)
T cd04471           3 EEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDY---YEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD--RRK   77 (83)
T ss_pred             CEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCc---EEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc--cCE
Confidence            5789999999999999999999999999999998665   89999998888877789999999999999999974  899


Q ss_pred             eEEEeC
Q 008167          570 LQLTLI  575 (575)
Q Consensus       570 i~l~l~  575 (575)
                      |.|+|.
T Consensus        78 i~~~l~   83 (83)
T cd04471          78 IDFELV   83 (83)
T ss_pred             EEEEEC
Confidence            999874

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.

>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain

Probab=98.73  E-value=5.7e-08  Score=83.51  Aligned_cols=80  Identities=15%  Similarity=0.202  Sum_probs=69.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC---
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN---  566 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~---  566 (575)
                      +.+.|.|+++.++|++|.+.  +++|+++++++.+++   +.+++..+++.+.+.+..|++||.|+|+|.++|.+..   
T Consensus         1 ~vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~~---~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~   75 (99)
T cd04460           1 EVVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDDY---ISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPR   75 (99)
T ss_pred             CEEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCCc---eEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCC
Confidence            36899999999999999996  599999999998775   7888888999988888999999999999999997532   


Q ss_pred             CCceEEEe
Q 008167          567 RPKLQLTL  574 (575)
Q Consensus       567 ~~~i~l~l  574 (575)
                      ..+|.||+
T Consensus        76 ~~~i~ls~   83 (99)
T cd04460          76 ESKIGLTM   83 (99)
T ss_pred             CceEEEEE
Confidence            25788875

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.

>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain

Probab=98.72  E-value=7.8e-08  Score=77.78  Aligned_cols=69  Identities=20%  Similarity=0.176  Sum_probs=58.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|+++.++|+||.+++++.+|++|++++.++.     ++         +.+..|++||+|+|+|.+++.+  + +
T Consensus         5 ~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~-----~~---------~~~~~~~~Gd~v~vkv~~vd~~--~-k   67 (73)
T cd05686           5 QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCR-----VD---------DPSEVVDVGEKVWVKVIGREMK--D-K   67 (73)
T ss_pred             CEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCc-----cc---------CHhhEECCCCEEEEEEEEECCC--C-c
Confidence            6789999999999999999876689999999887542     11         3467799999999999999975  4 9


Q ss_pred             eEEEeC
Q 008167          570 LQLTLI  575 (575)
Q Consensus       570 i~l~l~  575 (575)
                      |.||+.
T Consensus        68 i~ls~~   73 (73)
T cd05686          68 MKLSLS   73 (73)
T ss_pred             EEEEeC
Confidence            999873

pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.

>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.63  E-value=9.4e-08  Score=76.31  Aligned_cols=68  Identities=25%  Similarity=0.274  Sum_probs=58.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +.++|.|++|.++|++|.+++ |++|+||.+++.+++   +           .+....|++||.|+|+|.++|.+  +++
T Consensus         2 ~~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~l~~~~---~-----------~~~~~~~~~Gd~i~~~V~~id~~--~~~   64 (69)
T cd05697           2 QVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLADVR---L-----------KHPEKKFKPGLKVKCRVLSVEPE--RKR   64 (69)
T ss_pred             CEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCCCcc---c-----------cCHHHcCCCCCEEEEEEEEEECC--CCE
Confidence            468999999999999999986 899999999987653   1           12356799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|+|
T Consensus        65 i~ls~   69 (69)
T cd05697          65 LVLTL   69 (69)
T ss_pred             EEEEC
Confidence            99986

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 H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.53  E-value=5.1e-07  Score=72.81  Aligned_cols=68  Identities=16%  Similarity=0.188  Sum_probs=58.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.|+. +++|++|.+++.+++    ..          +....|++||.|+++|.++|..  +++
T Consensus         5 ~iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~l~~~~----~~----------~~~~~~~~Gd~v~~~V~~~d~~--~~~   67 (73)
T cd05706           5 DILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDDY----SE----------ALPYKFKKNDIVRACVLSVDVP--NKK   67 (73)
T ss_pred             CEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCcc----cc----------ccccccCCCCEEEEEEEEEeCC--CCE
Confidence            678999999999999999987 899999999998653    11          2246799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        68 i~ls~   72 (73)
T cd05706          68 IALSL   72 (73)
T ss_pred             EEEEE
Confidence            99986

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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain

Probab=98.51  E-value=2.8e-07  Score=73.34  Aligned_cols=68  Identities=21%  Similarity=0.199  Sum_probs=55.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.++. +++|++|.++++..     ..        ..+....|++||+|+|+|.++|.+  +++
T Consensus         2 ~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~~~-----~~--------~~~~~~~~~~G~~v~v~v~~id~~--~~~   65 (69)
T cd05690           2 TVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISWT-----QR--------VRHPSEIYKKGQEVEAVVLNIDVE--RER   65 (69)
T ss_pred             CEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCCCc-----cc--------cCChhhEECCCCEEEEEEEEEECC--cCE
Confidence            468999999999999999986 89999999988621     10        123457899999999999999975  888


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.|+
T Consensus        66 i~l~   69 (69)
T cd05690          66 ISLG   69 (69)
T ss_pred             EeCC
Confidence            8774

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 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain

Probab=98.47  E-value=6.1e-07  Score=72.15  Aligned_cols=68  Identities=16%  Similarity=0.251  Sum_probs=55.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.+++ |++|++|.++++.+     ...        .+....|++||+|+|+|.++|.+  +++
T Consensus         5 ~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l~~~-----~~~--------~~~~~~~~~Gd~v~v~v~~id~~--~~~   68 (72)
T cd05689           5 TRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEMDWT-----NKN--------IHPSKVVSLGDEVEVMVLDIDEE--RRR   68 (72)
T ss_pred             CEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEeccCc-----ccc--------cCcccEeCCCCEEEEEEEEeeCC--cCE
Confidence            579999999999999999987 89999999988521     010        13457899999999999999975  788


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.|+
T Consensus        69 i~~~   72 (72)
T cd05689          69 ISLG   72 (72)
T ss_pred             EeCC
Confidence            8763

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 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.46  E-value=5.8e-07  Score=72.30  Aligned_cols=68  Identities=16%  Similarity=0.182  Sum_probs=56.3

Q ss_pred             ceeE-EEEEEE-ecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC
Q 008167          490 TDTE-ARIVKI-RSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR  567 (575)
Q Consensus       490 ~~~~-g~V~~v-~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~  567 (575)
                      +.++ |.|+.+ .++|++|.|++ |++|++|.++++++.    .          ......|++||.|+++|.++|..  +
T Consensus         2 ~v~~~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~----~----------~~~~~~~~vG~~v~~kV~~id~~--~   64 (71)
T cd05696           2 AVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDK----V----------PSDTGPFKAGTTHKARIIGYSPM--D   64 (71)
T ss_pred             cEeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcch----h----------cCcccccCCCCEEEEEEEEEeCC--C
Confidence            3567 999998 69999999987 899999999987542    1          12346799999999999999976  8


Q ss_pred             CceEEEe
Q 008167          568 PKLQLTL  574 (575)
Q Consensus       568 ~~i~l~l  574 (575)
                      ++|.||+
T Consensus        65 ~~i~lS~   71 (71)
T cd05696          65 GLLQLSL   71 (71)
T ss_pred             CEEEEeC
Confidence            9999986

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 H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.46  E-value=5.1e-07  Score=73.01  Aligned_cols=70  Identities=10%  Similarity=0.116  Sum_probs=57.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ....|.|..+.++|++|.|.+ +++|+|++++++++.    ...        ++....|++||.|+++|.++|.+  +++
T Consensus         2 ~~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~ls~~~----~~~--------~~~~~~~~vG~~v~~kV~~id~~--~~~   66 (73)
T cd05703           2 QEVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDDV----SVL--------EHPEKKFPIGQALKAKVVGVDKE--HKL   66 (73)
T ss_pred             CEEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCcc----ccc--------cCHHHhCCCCCEEEEEEEEEeCC--CCE
Confidence            357899999999999999976 899999999987431    000        13457799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        67 i~Ls~   71 (73)
T cd05703          67 LRLSA   71 (73)
T ss_pred             EEEEe
Confidence            99986

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 H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.45  E-value=4.6e-07  Score=72.07  Aligned_cols=67  Identities=18%  Similarity=0.287  Sum_probs=56.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+++ +++|++|.+++++++    .          .+....|++||.|+|+|.++|.+  +++
T Consensus         2 ~~v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~l~~~~----~----------~~~~~~~~~Gd~v~~~v~~~d~~--~~~   64 (68)
T cd05707           2 DVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDSY----L----------KDWKKRFKVGQLVKGKIVSIDPD--NGR   64 (68)
T ss_pred             CEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCCchh----h----------cCHhhccCCCCEEEEEEEEEeCC--CCE
Confidence            368999999999999999986 799999999998653    1          13467799999999999999975  788


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.||
T Consensus        65 i~ls   68 (68)
T cd05707          65 IEMT   68 (68)
T ss_pred             EecC
Confidence            8775

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 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.44  E-value=1.1e-06  Score=71.40  Aligned_cols=69  Identities=10%  Similarity=0.229  Sum_probs=59.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.+.+++|++|.+++.+++    ..          +....|++||.|+|+|.+++.+  +++
T Consensus         4 ~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~----~~----------~~~~~~~~Gd~v~v~i~~vd~~--~~~   67 (77)
T cd05708           4 QKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR----VA----------DASKLFRVGDKVRAKVLKIDAE--KKR   67 (77)
T ss_pred             CEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCc----cC----------CHhHeecCCCEEEEEEEEEeCC--CCE
Confidence            5789999999999999999877899999999987642    11          2457899999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|++
T Consensus        68 i~ls~   72 (77)
T cd05708          68 ISLGL   72 (77)
T ss_pred             EEEEE
Confidence            99886

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.

>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.42  E-value=8e-07  Score=71.01  Aligned_cols=68  Identities=24%  Similarity=0.315  Sum_probs=57.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|++|.++. +++|++|.+++..++    ..          +....|++||.|+|+|.++|.+  +++
T Consensus         2 ~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l~~~~----~~----------~~~~~~~~G~~i~v~v~~~d~~--~~~   64 (70)
T cd05698           2 LKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAF----IK----------DPEEHFRVGQVVKVKVLSCDPE--QQR   64 (70)
T ss_pred             CEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcChhh----cC----------CHHHcccCCCEEEEEEEEEcCC--CCE
Confidence            368999999999999999986 799999999997652    22          2246799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus        65 i~ls~   69 (70)
T cd05698          65 LLLSC   69 (70)
T ss_pred             EEEEe
Confidence            99986

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 H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.42  E-value=7.8e-07  Score=72.14  Aligned_cols=70  Identities=11%  Similarity=0.049  Sum_probs=56.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ....|.|.++.++|+||.+.. |++|+||++++++++   +. +.       .+..+.|++||.|+++|.++|.+  +++
T Consensus         5 ~~V~g~V~~i~~~G~fV~l~~-~v~G~v~~~~ls~~~---~~-~~-------~~~~~~~~~G~~v~~kVl~id~~--~~~   70 (74)
T cd05705           5 QLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKYF---VS-DP-------SLYNKYLPEGKLLTAKVLSVNSE--KNL   70 (74)
T ss_pred             CEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCcc---cc-Ch-------hhHhcccCCCCEEEEEEEEEECC--CCE
Confidence            578999999999999999975 999999999998653   11 10       01247899999999999999976  788


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.||
T Consensus        71 i~LS   74 (74)
T cd05705          71 VELS   74 (74)
T ss_pred             EecC
Confidence            8875

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 H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form

Probab=98.42  E-value=5.4e-07  Score=86.03  Aligned_cols=88  Identities=15%  Similarity=0.233  Sum_probs=72.9

Q ss_pred             HHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167          482 LIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV  560 (575)
Q Consensus       482 ~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~  560 (575)
                      +.+++... +.++|+|++++++|++|.+.  .++|.++.+++.+++   +.||+....+.+++.+..|++||+|+|+|.+
T Consensus        74 ~i~f~p~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~~---~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~  148 (179)
T TIGR00448        74 ALVFKPELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDDY---CYYDPKESALIGKETKKVLDEGDKVRARIVA  148 (179)
T ss_pred             EEEEeccCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCCc---eEEccccceEEEccCCeEEcCCCEEEEEEEE
Confidence            34455554 78999999999999999994  489999999988775   7788888888888888999999999999999


Q ss_pred             ecCC---CCCCceEEEe
Q 008167          561 VEPQ---PNRPKLQLTL  574 (575)
Q Consensus       561 vd~~---~~~~~i~l~l  574 (575)
                      ++..   +...+|.+++
T Consensus       149 v~~~~~~~~~~~I~lt~  165 (179)
T TIGR00448       149 LSLKDRRPEGSKIGLTM  165 (179)
T ss_pred             EEccCCCCCcceEEEEe
Confidence            9852   2356788775

This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.

>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains

Probab=98.40  E-value=8.2e-07  Score=73.63  Aligned_cols=68  Identities=16%  Similarity=0.201  Sum_probs=59.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|++|.+.. |++|++|.++++.++    .          .+....|++||.|+|+|.++|.+  +++
T Consensus        16 ~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el~~~~----~----------~~~~~~~~~Gd~v~vkV~~id~~--~~~   78 (83)
T cd04461          16 MVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEF----V----------TDPSFGFKKGQSVTAKVTSVDEE--KQR   78 (83)
T ss_pred             CEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHCCccc----c----------cCHHHhcCCCCEEEEEEEEEcCC--CCE
Confidence            789999999999999999976 899999999987652    1          13467899999999999999975  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|||
T Consensus        79 i~lsl   83 (83)
T cd04461          79 FLLSL   83 (83)
T ss_pred             EEEeC
Confidence            99986

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.

>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]

Probab=98.39  E-value=2.8e-07  Score=79.93  Aligned_cols=67  Identities=19%  Similarity=0.204  Sum_probs=58.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ...+|.|++|+++|+||.|+. |-.|+||+|++.+.|    .-          +-+..+++||.|.|+|.++|.   +.+
T Consensus         7 ~~l~GkItgI~~yGAFV~l~~-g~tGLVHISEIa~~f----Vk----------dI~d~L~vG~eV~vKVl~ide---~GK   68 (129)
T COG1098           7 SKLKGKITGITPYGAFVELEG-GKTGLVHISEIADGF----VK----------DIHDHLKVGQEVKVKVLDIDE---NGK   68 (129)
T ss_pred             ceEEEEEEeeEecceEEEecC-CCcceEEehHhhhhh----HH----------hHHHHhcCCCEEEEEEEeecc---CCC
Confidence            578999999999999999986 899999999998763    32          346779999999999999996   688


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |+|||
T Consensus        69 isLSI   73 (129)
T COG1098          69 ISLSI   73 (129)
T ss_pred             cceeh
Confidence            99886

>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.38  E-value=1.3e-06  Score=70.65  Aligned_cols=68  Identities=22%  Similarity=0.334  Sum_probs=59.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +.++|.|.++.++|++|.+. .|++|+||.+++..++    .          ......|++||+|+|+|.++|.+  +++
T Consensus         6 ~iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~~~----~----------~~~~~~~~~G~~v~v~v~~vd~~--~~~   68 (74)
T PF00575_consen    6 DIVEGKVTSVEDFGVFVDLG-NGIEGFIPISELSDDR----I----------DDPSEVYKIGQTVRVKVIKVDKE--KGR   68 (74)
T ss_dssp             SEEEEEEEEEETTEEEEEES-TSSEEEEEGGGSSSSE----E----------SSSHGTCETTCEEEEEEEEEETT--TTE
T ss_pred             CEEEEEEEEEECCEEEEEEC-CcEEEEEEeehhcCcc----c----------cccccccCCCCEEEEEEEEEECC--CCe
Confidence            68999999999999999998 6999999999998541    1          24567899999999999999976  889


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        69 i~lS~   73 (74)
T PF00575_consen   69 IRLSL   73 (74)
T ss_dssp             EEEES
T ss_pred             EEEEE
Confidence            99985

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....

>PRK07252 hypothetical protein; Provisional

Probab=98.38  E-value=1.5e-06  Score=77.20  Aligned_cols=68  Identities=16%  Similarity=0.130  Sum_probs=58.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|++|.++|++|.++. +++|++|++++.+++   +.           .....|++||.|+|+|.++|.+  +++
T Consensus         5 ~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~~---~~-----------~~~~~~~vGD~V~VkI~~iD~~--~~r   67 (120)
T PRK07252          5 DKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTGF---ID-----------NIHQLLKVGEEVLVQVVDFDEY--TGK   67 (120)
T ss_pred             CEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCcc---cc-----------ChhhccCCCCEEEEEEEEEeCC--CCE
Confidence            678999999999999999976 799999999997653   21           2346799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus        68 i~lSl   72 (120)
T PRK07252         68 ASLSL   72 (120)
T ss_pred             EEEEE
Confidence            99886

>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide

Probab=98.37  E-value=2.1e-06  Score=70.49  Aligned_cols=68  Identities=18%  Similarity=0.207  Sum_probs=56.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC--ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF--GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR  567 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~--gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~  567 (575)
                      ..++|.|+++.++|+||.+.+.  +++|++|.++++.++   +         . .+....|++||.|+|+|.++|    +
T Consensus         2 ~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~---~---------~-~~~~~~~~~Gd~v~v~v~~vd----~   64 (79)
T cd05684           2 KIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEG---R---------V-ANPSDVVKRGQKVKVKVISIQ----N   64 (79)
T ss_pred             CEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCC---C---------c-CChhheeCCCCEEEEEEEEEe----C
Confidence            4689999999999999999864  799999999987553   2         1 134578999999999999998    5


Q ss_pred             CceEEEe
Q 008167          568 PKLQLTL  574 (575)
Q Consensus       568 ~~i~l~l  574 (575)
                      +++.|++
T Consensus        65 ~~i~~s~   71 (79)
T cd05684          65 GKISLSM   71 (79)
T ss_pred             CEEEEEE
Confidence            7888876

The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

>PRK08582 hypothetical protein; Provisional

Probab=98.37  E-value=1.9e-06  Score=78.55  Aligned_cols=67  Identities=22%  Similarity=0.269  Sum_probs=57.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|+|++|.++|+||.|++ +++|+||++++.+++    ..          +....|++||.|+|+|.+++.   .++
T Consensus         7 ~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels~~~----v~----------~~~~~l~vGD~VkvkV~~id~---~gk   68 (139)
T PRK08582          7 SKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNY----VK----------DINDHLKVGDEVEVKVLNVED---DGK   68 (139)
T ss_pred             CEEEEEEEEEECCeEEEEECC-CCEEEEEeeccCccc----cc----------ccccccCCCCEEEEEEEEECC---CCc
Confidence            689999999999999999986 899999999997653    22          234679999999999999985   478


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus        69 I~LSl   73 (139)
T PRK08582         69 IGLSI   73 (139)
T ss_pred             EEEEE
Confidence            99986

>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain

Probab=98.34  E-value=2.6e-06  Score=69.09  Aligned_cols=69  Identities=14%  Similarity=0.131  Sum_probs=58.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|.|+++.++|++|.+.++ |++|++|.+++++++   +.           +....|++||.|+|+|.+++..  ++
T Consensus         5 ~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~---~~-----------~~~~~~~~Gd~v~vkv~~~d~~--~~   68 (76)
T cd04452           5 ELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRR---IR-----------SIRKLVKVGRKEVVKVIRVDKE--KG   68 (76)
T ss_pred             CEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcc---cC-----------CHHHeeCCCCEEEEEEEEEECC--CC
Confidence            5789999999999999999765 699999999987653   11           2357799999999999999975  78


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      ++.|++
T Consensus        69 ~i~ls~   74 (76)
T cd04452          69 YIDLSK   74 (76)
T ss_pred             EEEEEE
Confidence            899886

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c

>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]

Probab=98.28  E-value=3.5e-06  Score=78.79  Aligned_cols=80  Identities=19%  Similarity=0.205  Sum_probs=69.9

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC--
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR--  567 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~--  567 (575)
                      +..+|.|+.+.++|+||.+.  .++|+||.+++.+|+   +.+|+..-.++|+.+++.++.||.|+++|.+++....+  
T Consensus        83 EVV~GeVv~~~~~G~fV~ig--p~dglvh~sqi~dd~---~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~  157 (183)
T COG1095          83 EVVEGEVVEVVEFGAFVRIG--PLDGLVHVSQIMDDY---IDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPR  157 (183)
T ss_pred             cEEEEEEEEEeecceEEEec--cccccccHhhccCcc---cccCcccceeeecccceEEecCCEEEEEEEEEecccCccc
Confidence            67899999999999999997  589999999999986   89999999999999999999999999999999875322  


Q ss_pred             -CceEEEe
Q 008167          568 -PKLQLTL  574 (575)
Q Consensus       568 -~~i~l~l  574 (575)
                       -+|.+++
T Consensus       158 ~~~I~lTm  165 (183)
T COG1095         158 ESKIGLTM  165 (183)
T ss_pred             cceEEEEe
Confidence             4555543

>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.28  E-value=2.8e-06  Score=67.28  Aligned_cols=64  Identities=23%  Similarity=0.274  Sum_probs=54.1

Q ss_pred             eeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCce
Q 008167          491 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL  570 (575)
Q Consensus       491 ~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i  570 (575)
                      ..+|.|+.+.++|++|.|.+ +++|+++.+++..+.    .           . ...|++||+|+++|..+|++  +++|
T Consensus         3 ~V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~----~-----------~-~~~~~~G~~i~~kVi~id~~--~~~i   63 (66)
T cd05695           3 LVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEK----S-----------S-KSTYKEGQKVRARILYVDPS--TKVV   63 (66)
T ss_pred             EEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCcc----C-----------c-ccCcCCCCEEEEEEEEEeCC--CCEE
Confidence            57899999999999999987 899999999886442    0           1 46699999999999999976  7888


Q ss_pred             EEE
Q 008167          571 QLT  573 (575)
Q Consensus       571 ~l~  573 (575)
                      .||
T Consensus        64 ~LS   66 (66)
T cd05695          64 GLS   66 (66)
T ss_pred             ecC
Confidence            775

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 H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa

Probab=98.27  E-value=1.8e-06  Score=68.06  Aligned_cols=67  Identities=13%  Similarity=0.147  Sum_probs=55.7

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.. +.+|++|.+++.+++   +.           +....|++||.|+|+|.++|.+  +++
T Consensus         2 ~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~~---~~-----------~~~~~~~~Gd~v~v~i~~vd~~--~~~   64 (68)
T cd05685           2 MVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADRF---VS-----------HPSDVVSVGDIVEVKVISIDEE--RGR   64 (68)
T ss_pred             CEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCcc---cc-----------CHHHhcCCCCEEEEEEEEEECC--CCE
Confidence            468999999999999999975 799999999887653   11           2346799999999999999975  788


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      +.||
T Consensus        65 i~ls   68 (68)
T cd05685          65 ISLS   68 (68)
T ss_pred             EecC
Confidence            8775

The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.

>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional

Probab=98.26  E-value=1.7e-06  Score=88.64  Aligned_cols=77  Identities=16%  Similarity=0.219  Sum_probs=63.8

Q ss_pred             HHHHhc-CC---ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167          482 LIYFRK-RP---TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI  556 (575)
Q Consensus       482 ~~~l~~-~~---~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V  556 (575)
                      |+|..+ .+   ..+.|.|+.|.++|+||.|.+| |++|+||+++++..+    .          ++....+++||+|.|
T Consensus         7 cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~r----i----------~~i~d~vkvGd~v~v   72 (319)
T PTZ00248          7 CRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRR----I----------RSINKLIRVGRHEVV   72 (319)
T ss_pred             ccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccc----c----------CCHHHhcCCCCEEEE
Confidence            555544 34   5789999999999999999888 999999999987542    1          234678999999999


Q ss_pred             EEEEecCCCCCCceEEEe
Q 008167          557 HMEVVEPQPNRPKLQLTL  574 (575)
Q Consensus       557 ~V~~vd~~~~~~~i~l~l  574 (575)
                      +|..||.+  +++|.||+
T Consensus        73 kVl~VD~e--kg~IdLS~   88 (319)
T PTZ00248         73 VVLRVDKE--KGYIDLSK   88 (319)
T ss_pred             EEEEEeCC--CCEEEEEe
Confidence            99999976  89999986

>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=98.17  E-value=4.5e-06  Score=67.30  Aligned_cols=66  Identities=20%  Similarity=0.146  Sum_probs=55.1

Q ss_pred             ceeEEEEEEEec-CeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRS-NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~-~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|.|.++.+ +|++|.++. |.+|++|++++.+++    .          ......|++||.|+|+|.+++    +.
T Consensus         5 ~iv~G~V~~i~~~~g~~v~l~~-~~~Glvhis~~s~~~----~----------~~~~~~~~~Gd~v~~kV~~~~----~~   65 (72)
T cd05704           5 AVTLGMVTKVIPHSGLTVQLPF-GKTGLVSIFHLSDSY----T----------ENPLEGFKPGKIVRCCILSKK----DG   65 (72)
T ss_pred             CEEEEEEEEeeCCcEEEEECCC-CCEEEEEHHHhcCcc----c----------CCHHHhCCCCCEEEEEEEEec----CC
Confidence            678999999986 899999986 999999999988653    1          122367899999999999987    48


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|+||+
T Consensus        66 ~i~LSl   71 (72)
T cd05704          66 KYQLSL   71 (72)
T ss_pred             EEEEEe
Confidence            899987

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 H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain

Probab=98.16  E-value=7.9e-06  Score=65.60  Aligned_cols=68  Identities=16%  Similarity=0.286  Sum_probs=57.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.+ +++|++|.+++.+++    .          .+....|++||.|+++|.++|..  +++
T Consensus         2 ~~v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~~~~~~----~----------~~~~~~~~~Gd~v~~~v~~~d~~--~~~   64 (73)
T cd05691           2 SIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDR----V----------EDATERFKVGDEVEAKITNVDRK--NRK   64 (73)
T ss_pred             CEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCcc----c----------cCHHHccCCCCEEEEEEEEEeCC--CCE
Confidence            367899999999999999976 799999999988653    1          13456799999999999999975  788


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|++
T Consensus        65 i~ls~   69 (73)
T cd05691          65 ISLSI   69 (73)
T ss_pred             EEEEE
Confidence            88876

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 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>PHA02945 interferon resistance protein; Provisional

Probab=98.15  E-value=1.4e-05  Score=65.49  Aligned_cols=66  Identities=8%  Similarity=0.066  Sum_probs=55.7

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCC--CCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPR--GQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN  566 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l--~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~  566 (575)
                      +..-|+|.. .++|++|.|++| |+||+||++..  .+.|    .           +....+ .|++|.++|..+|..  
T Consensus        13 elvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~w----v-----------K~rd~l-~GqkvV~KVirVd~~--   73 (88)
T PHA02945         13 DVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRY----F-----------KYRDKL-VGKTVKVKVIRVDYT--   73 (88)
T ss_pred             cEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccce----E-----------eeeeEe-cCCEEEEEEEEECCC--
Confidence            567899999 999999999999 99999999955  5543    2           224566 999999999999976  


Q ss_pred             CCceEEEe
Q 008167          567 RPKLQLTL  574 (575)
Q Consensus       567 ~~~i~l~l  574 (575)
                      +..|++||
T Consensus        74 kg~IDlSl   81 (88)
T PHA02945         74 KGYIDVNY   81 (88)
T ss_pred             CCEEEeEe
Confidence            89999987

>PRK05807 hypothetical protein; Provisional

Probab=98.09  E-value=1.7e-05  Score=72.05  Aligned_cols=66  Identities=20%  Similarity=0.225  Sum_probs=55.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|+++.++|++|.| + +.+|+||++++.+++    ..          +....|++||.|+|+|.+++.   .++
T Consensus         7 ~vv~G~Vt~i~~~GafV~L-~-~~~Glvhiseis~~~----v~----------~~~~~~kvGd~V~VkV~~id~---~gk   67 (136)
T PRK05807          7 SILEGTVVNITNFGAFVEV-E-GKTGLVHISEVADTY----VK----------DIREHLKEQDKVKVKVISIDD---NGK   67 (136)
T ss_pred             CEEEEEEEEEECCeEEEEE-C-CEEEEEEhhhccccc----cc----------CccccCCCCCEEEEEEEEECC---CCc
Confidence            6899999999999999999 4 789999999998653    22          224569999999999999985   588


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus        68 I~LSl   72 (136)
T PRK05807         68 ISLSI   72 (136)
T ss_pred             EEEEE
Confidence            99886

>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain

Probab=98.08  E-value=1.4e-05  Score=63.05  Aligned_cols=67  Identities=21%  Similarity=0.241  Sum_probs=55.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.++. +.+|++|.+++..++    .          ......|++||.|+|+|.+++.   +++
T Consensus         2 ~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~~~~----~----------~~~~~~~~~Gd~v~v~v~~~d~---~~~   63 (68)
T cd04472           2 KIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDER----V----------EKVEDVLKVGDEVKVKVIEVDD---RGR   63 (68)
T ss_pred             CEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCcc----c----------cCHHHccCCCCEEEEEEEEECC---CCc
Confidence            468999999999999999985 799999999887542    1          1234689999999999999985   578


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||.
T Consensus        64 i~ls~   68 (68)
T cd04472          64 ISLSR   68 (68)
T ss_pred             EEeeC
Confidence            88773

PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain

Probab=98.07  E-value=1.5e-05  Score=62.79  Aligned_cols=67  Identities=18%  Similarity=0.275  Sum_probs=55.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.+ +.+|++|.+++.+++    ..          .....|++||.|+|+|.+++.   +++
T Consensus         2 ~~~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~l~~~~----~~----------~~~~~~~~Gd~v~v~v~~~~~---~~~   63 (69)
T cd05692           2 SVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKR----VK----------DVKDVLKEGDKVKVKVLSIDA---RGR   63 (69)
T ss_pred             CEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCcc----cC----------CHHHccCCCCEEEEEEEEECC---CCc
Confidence            468999999999999999976 799999999887652    11          234679999999999999985   578


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|++
T Consensus        64 i~ls~   68 (69)
T cd05692          64 ISLSI   68 (69)
T ss_pred             EEEEE
Confidence            88876

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 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain

Probab=98.06  E-value=1.6e-05  Score=62.77  Aligned_cols=66  Identities=15%  Similarity=0.202  Sum_probs=54.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.  +++|++|.+++...+    .          ...+..|++||.|+|+|.+++.+  +++
T Consensus         3 ~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~~~~----~----------~~~~~~~~~Gd~v~v~i~~vd~~--~~~   64 (68)
T cd05688           3 DVVEGTVKSITDFGAFVDLG--GVDGLLHISDMSWGR----V----------KHPSEVVNVGDEVEVKVLKIDKE--RKR   64 (68)
T ss_pred             CEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCCCcc----c----------cCHhHEECCCCEEEEEEEEEECC--CCE
Confidence            46899999999999999995  699999999886321    1          13457799999999999999975  788


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      +.||
T Consensus        65 i~ls   68 (68)
T cd05688          65 ISLG   68 (68)
T ss_pred             EecC
Confidence            8775

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.

>PRK08059 general stress protein 13; Validated

Probab=98.05  E-value=1.5e-05  Score=71.34  Aligned_cols=68  Identities=18%  Similarity=0.199  Sum_probs=57.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.. +++|++|+++++.++    ..          +....|++||.|+|+|.+++.+  +++
T Consensus         9 ~iv~G~V~~i~~~G~fV~i~~-~~~Gli~~sel~~~~----~~----------~~~~~~~vGD~I~vkI~~id~~--~~~   71 (123)
T PRK08059          9 SVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGF----VK----------DIHDFLSVGDEVKVKVLSVDEE--KGK   71 (123)
T ss_pred             CEEEEEEEEEecceEEEEECC-CCEEEEEHHHCCccc----cc----------CHHHcCCCCCEEEEEEEEEECC--CCe
Confidence            689999999999999999975 899999999987542    11          2346799999999999999865  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|++
T Consensus        72 i~lsl   76 (123)
T PRK08059         72 ISLSI   76 (123)
T ss_pred             EEEEE
Confidence            99886

>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease

Probab=98.03  E-value=2.7e-05  Score=63.57  Aligned_cols=60  Identities=13%  Similarity=0.202  Sum_probs=52.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|.+++++|++|.+.+ +.+|++|.+++.                      ..|++||+|+|+|.++ .+  +++
T Consensus        18 ~~~~g~V~~i~~~G~fV~l~~-~~~Glv~~se~~----------------------~~~~iGd~v~v~I~~i-~e--~~~   71 (77)
T cd04473          18 KLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLL----------------------RDYEVGDEVIVQVTDI-PE--NGN   71 (77)
T ss_pred             CEEEEEEEeEecceEEEEECC-CcEEEEEchhcc----------------------CcCCCCCEEEEEEEEE-CC--CCc
Confidence            689999999999999999986 799999987542                      3499999999999998 44  899


Q ss_pred             eEEEeC
Q 008167          570 LQLTLI  575 (575)
Q Consensus       570 i~l~l~  575 (575)
                      |.|+++
T Consensus        72 i~l~~~   77 (77)
T cd04473          72 IDLIPV   77 (77)
T ss_pred             EEEEEC
Confidence            999874

The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.

>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional

Probab=97.99  E-value=5.2e-05  Score=72.95  Aligned_cols=80  Identities=16%  Similarity=0.217  Sum_probs=68.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC--
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR--  567 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~--  567 (575)
                      +.++|.|+++.++|++|.+.  .++|+++.+.+..++   +.||+....+.+++....|++||.|+|+|.+++.+..+  
T Consensus        83 EVv~g~V~~v~~~Gi~V~lg--~~~g~v~~~~l~~~~---~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~  157 (187)
T PRK08563         83 EVVEGEVVEVVEFGAFVRIG--PVDGLLHISQIMDDY---ISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR  157 (187)
T ss_pred             CEEEEEEEEEEccEEEEEEe--CceEEEEcHHcCCCc---eEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence            78999999999999999996  489999999998765   67888888888888889999999999999999875322  


Q ss_pred             -CceEEEe
Q 008167          568 -PKLQLTL  574 (575)
Q Consensus       568 -~~i~l~l  574 (575)
                       .+|.+|+
T Consensus       158 ~~~I~ls~  165 (187)
T PRK08563        158 GSKIGLTM  165 (187)
T ss_pred             CCEEEEEe
Confidence             3777765

>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional

Probab=97.96  E-value=2.8e-05  Score=89.42  Aligned_cols=78  Identities=14%  Similarity=0.155  Sum_probs=61.2

Q ss_pred             HHHHHHHhcCC-ceeE-EEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167          479 LHTLIYFRKRP-TDTE-ARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI  556 (575)
Q Consensus       479 ~~~~~~l~~~~-~~~~-g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V  556 (575)
                      +....|+.... ..|+ |.|++|.++|+||.|.. |++|+||++++.+++   +.           +....|++||.|+|
T Consensus       743 ~I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~r---v~-----------~~~dv~kvGD~V~V  807 (891)
T PLN00207        743 IISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSNW---LA-----------KPEDAFKVGDRIDV  807 (891)
T ss_pred             HHHHHhcCcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCcc---cc-----------CHHHhcCCCCEEEE
Confidence            33344444444 6785 69999999999999975 899999999998653   22           22467999999999


Q ss_pred             EEEEecCCCCCCceEEEe
Q 008167          557 HMEVVEPQPNRPKLQLTL  574 (575)
Q Consensus       557 ~V~~vd~~~~~~~i~l~l  574 (575)
                      +|.++|.   ++||.|++
T Consensus       808 kVi~ID~---~grI~LSl  822 (891)
T PLN00207        808 KLIEVND---KGQLRLSR  822 (891)
T ss_pred             EEEEECC---CCcEEEEE
Confidence            9999995   57999986

>smart00316 S1 Ribosomal protein S1-like RNA-binding domain

Probab=97.94  E-value=4e-05  Score=60.48  Aligned_cols=68  Identities=21%  Similarity=0.288  Sum_probs=57.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|++|.+.. +++|+++.+++.+.+              ..+....|++||.|+|+|..++.+  +++
T Consensus         4 ~~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~~~~~~--------------~~~~~~~~~~G~~v~~~V~~~~~~--~~~   66 (72)
T smart00316        4 DVVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDKR--------------VKDPEEVLKVGDEVKVKVLSVDEE--KGR   66 (72)
T ss_pred             CEEEEEEEEEEccEEEEEeCC-CCEEEEEHHHCCccc--------------cCCHHHeecCCCEEEEEEEEEeCC--CCE
Confidence            578999999999999999975 899999999887542              123456799999999999999965  699


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|++
T Consensus        67 i~ls~   71 (72)
T smart00316       67 IILSL   71 (72)
T ss_pred             EEEEe
Confidence            99886

>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.93  E-value=5.3e-05  Score=61.41  Aligned_cols=63  Identities=16%  Similarity=0.124  Sum_probs=54.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.+|.++|++|.+..-|++|+++.++++.+                    ..+++||.|.++|.+++.+  +++
T Consensus         6 ~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~--------------------~~~~~Gq~v~~~V~~vd~~--~~~   63 (74)
T cd05694           6 MVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF--------------------SKLKVGQLLLCVVEKVKDD--GRV   63 (74)
T ss_pred             CEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc--------------------cccCCCCEEEEEEEEEECC--CCE
Confidence            568999999999999999953489999999877521                    5689999999999999975  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus        64 v~ls~   68 (74)
T cd05694          64 VSLSA   68 (74)
T ss_pred             EEEEE
Confidence            99986

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 H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK03987 translation initiation factor IF-2 subunit alpha; Validated

Probab=97.92  E-value=2.6e-05  Score=78.56  Aligned_cols=69  Identities=16%  Similarity=0.173  Sum_probs=59.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|.|.+|.++|++|.|.++ |++|+||++++..++   +.           .....|++||.|.|+|.++|.+  ++
T Consensus        10 diV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~---i~-----------~i~~~~kvGd~V~vkVi~VD~~--k~   73 (262)
T PRK03987         10 ELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGW---VK-----------NIRDHVKEGQKVVCKVIRVDPR--KG   73 (262)
T ss_pred             CEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCccc---cc-----------CHHHhCCCCCEEEEEEEEEecc--cC
Confidence            6789999999999999999988 899999999987653   11           1246799999999999999976  78


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|.||+
T Consensus        74 ~I~LSl   79 (262)
T PRK03987         74 HIDLSL   79 (262)
T ss_pred             eEEEEE
Confidence            999986

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=97.92  E-value=3.7e-05  Score=83.89  Aligned_cols=67  Identities=18%  Similarity=0.235  Sum_probs=58.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +..+|+|.+++++|+||.|.  |++|+||+++++...    .          ..+...+++||+|+|+|.++|.+  +.|
T Consensus       194 ~vV~G~V~~It~~GafVdig--GvdGLlHiseiS~~r----v----------~~P~~vvkvGd~VkvkVi~~D~e--~~R  255 (541)
T COG0539         194 EVVEGVVKNITDYGAFVDIG--GVDGLLHISEISWKR----V----------DHPSEVVKVGDEVKVKVISLDEE--RGR  255 (541)
T ss_pred             ceEEEEEEEeecCcEEEEec--CeeeEEehhhccccc----c----------CCHHHhcccCCEEEEEEEEEccC--CCe
Confidence            78999999999999999996  799999999997442    1          14568899999999999999976  999


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|||
T Consensus       256 VsLSl  260 (541)
T COG0539         256 VSLSL  260 (541)
T ss_pred             EEEEe
Confidence            99987

>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]

Probab=97.86  E-value=2.9e-05  Score=84.66  Aligned_cols=68  Identities=21%  Similarity=0.314  Sum_probs=59.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ....|+|+.+.++|+||.+.+ |+||++|+|+++..      ..        ..+...+++||.|+|+|..+|++  +||
T Consensus       279 ~~v~G~Vt~i~~~GafVei~~-GvEGlvhvSEisw~------~~--------~~P~evv~~Gq~V~V~Vl~id~e--~rR  341 (541)
T COG0539         279 DKVEGKVTNLTDYGAFVEIEE-GVEGLVHVSEISWT------KK--------NVPSEVVKVGQEVEVKVLDIDPE--RRR  341 (541)
T ss_pred             CEEEEEEEEeecCcEEEEecC-Cccceeechhhccc------cc--------CCHHHhcccCCEEEEEEEeeCch--hce
Confidence            689999999999999999976 99999999988733      21        12567899999999999999986  999


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |+|+|
T Consensus       342 IsL~i  346 (541)
T COG0539         342 ISLGL  346 (541)
T ss_pred             EEeee
Confidence            99987

>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain

Probab=97.86  E-value=6e-05  Score=60.12  Aligned_cols=68  Identities=15%  Similarity=0.154  Sum_probs=55.9

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|++|.|.. +.+|++|.+++...+    .          .+....|++||.|+++|.+++.+  ..+
T Consensus         2 ~iv~g~V~~i~~~~~~v~l~~-~~~g~l~~~e~~~~~----~----------~~~~~~~~~Gd~i~~~i~~~~~~--~~~   64 (70)
T cd05687           2 DIVKGTVVSVDDDEVLVDIGY-KSEGIIPISEFSDDP----I----------ENGEDEVKVGDEVEVYVLRVEDE--EGN   64 (70)
T ss_pred             CEEEEEEEEEeCCEEEEEeCC-CceEEEEHHHhCccc----c----------CCHhHcCCCCCEEEEEEEEEECC--CCe
Confidence            357899999999999999964 899999999886542    1          12356799999999999999964  688


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        65 i~lS~   69 (70)
T cd05687          65 VVLSK   69 (70)
T ss_pred             EEEEe
Confidence            99886

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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain

Probab=97.84  E-value=5.3e-05  Score=58.55  Aligned_cols=65  Identities=23%  Similarity=0.376  Sum_probs=53.1

Q ss_pred             eEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCceE
Q 008167          492 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQ  571 (575)
Q Consensus       492 ~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i~  571 (575)
                      +.|.|.++.++|++|.+.. +.+|+++.+++.+++   +           .+....|++||.|+|+|.++|..  ++++.
T Consensus         1 v~g~V~~v~~~g~~v~l~~-~~~g~~~~~~~~~~~---~-----------~~~~~~~~~G~~v~~~v~~~d~~--~~~i~   63 (65)
T cd00164           1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKF---V-----------KDPSEVFKVGDEVEVKVLEVDPE--KGRIS   63 (65)
T ss_pred             CEEEEEEEEeeeEEEEecC-CCEEEEEHHHCCCcc---c-----------cCHhhEeCCCCEEEEEEEEEcCC--cCEEe
Confidence            3799999999999999975 799999999887542   1           13457799999999999999964  67776


Q ss_pred             EE
Q 008167          572 LT  573 (575)
Q Consensus       572 l~  573 (575)
                      ||
T Consensus        64 ls   65 (65)
T cd00164          64 LS   65 (65)
T ss_pred             cC
Confidence            64

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.

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.80  E-value=7e-05  Score=81.91  Aligned_cols=68  Identities=21%  Similarity=0.243  Sum_probs=58.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.|++ |++|++|++++..+.   +.           .....|++||+|+|+|..+|.+  ++|
T Consensus       295 ~vv~G~V~~I~~fGvFVeL~~-gieGLvh~SeLs~~~---v~-----------~~~~~~kvGd~V~VkIi~ID~e--~rr  357 (486)
T PRK07899        295 QIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAERH---VE-----------VPEQVVQVGDEVFVKVIDIDLE--RRR  357 (486)
T ss_pred             CEEEEEEEEEeccEEEEEeCC-CcEEEEEHHHcCccc---cc-----------CccceeCCCCEEEEEEEEEECC--CCE
Confidence            789999999999999999986 899999999987542   11           2346799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       358 I~LSl  362 (486)
T PRK07899        358 ISLSL  362 (486)
T ss_pred             EEEEE
Confidence            99987

>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain

Probab=97.68  E-value=0.00018  Score=56.85  Aligned_cols=65  Identities=14%  Similarity=0.185  Sum_probs=51.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|..+.++|++|.+ + |++|++|.+++...+    ..          +...  .+||.++|+|..+|.+  +++
T Consensus         2 ~iv~g~V~~v~~~G~~v~l-~-g~~gfip~s~~~~~~----~~----------~~~~--~vG~~i~~~i~~vd~~--~~~   61 (67)
T cd04465           2 EIVEGKVTEKVKGGLIVDI-E-GVRAFLPASQVDLRP----VE----------DLDE--YVGKELKFKIIEIDRE--RNN   61 (67)
T ss_pred             CEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcc----cC----------ChHH--hCCCEEEEEEEEEeCC--CCE
Confidence            3679999999999999999 4 899999999886432    10          1111  3899999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||.
T Consensus        62 i~lS~   66 (67)
T cd04465          62 IVLSR   66 (67)
T ss_pred             EEEEc
Confidence            99885

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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.65  E-value=6.7e-05  Score=64.52  Aligned_cols=84  Identities=17%  Similarity=0.205  Sum_probs=59.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcce-----ecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWY-----VDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~-----~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      ..+.|.|..+.++|++|.||. |++|+++++++.+++..+..     ...........+....|++||.|+++|.+++..
T Consensus         5 ~vV~G~V~~v~~~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~   83 (100)
T cd05693           5 MLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKS   83 (100)
T ss_pred             CEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCC
Confidence            578999999999999999996 99999999998754200000     000001111123357799999999999999963


Q ss_pred             C-CCCceEEEe
Q 008167          565 P-NRPKLQLTL  574 (575)
Q Consensus       565 ~-~~~~i~l~l  574 (575)
                      . .+++|.|||
T Consensus        84 ~~~~~~i~LSl   94 (100)
T cd05693          84 KSGKKRIELSL   94 (100)
T ss_pred             cCCCcEEEEEe
Confidence            1 268999987

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 H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=97.59  E-value=0.0002  Score=57.15  Aligned_cols=62  Identities=6%  Similarity=0.033  Sum_probs=50.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      ....|.|+.+.++|++|.++. |++|++|.+++.++|    ..        .......|++||.|+++|.+++.+
T Consensus         2 ~iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~~----~~--------~~~~~~~~~~Gd~i~~kVl~~d~~   63 (70)
T cd05702           2 DLVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDEW----PD--------GKNPLSKFKIGQKIKARVIGGHDA   63 (70)
T ss_pred             CEEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhcccc----cc--------ccChhHhCCCCCEEEEEEEEEeCc
Confidence            357899999999999999986 999999999887542    10        112346799999999999999875

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 H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=97.58  E-value=0.0002  Score=83.40  Aligned_cols=71  Identities=20%  Similarity=0.245  Sum_probs=59.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|+++.++|+||.|++ |++|+||++++++++    ..+      .+ ..++.|++||.|+|+|.++|.+  +++
T Consensus       754 ~iV~GkV~~v~~~GvFVeL~~-gVeGlI~~s~lsdd~----~~~------~~-~~~~~f~vGD~V~v~Vl~iD~~--~rk  819 (863)
T PRK12269        754 STVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVENR----DGD------PG-EALRKYAVGDRVKAVIVDMNVK--DRK  819 (863)
T ss_pred             CEEEEEEEEEecCeEEEEcCC-CeEEEEEHHHcCCcc----ccc------ch-hhccccCCCCEEEEEEEEEEcC--CCE
Confidence            789999999999999999987 899999999998652    211      01 1246799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       820 I~LSl  824 (863)
T PRK12269        820 VAFSV  824 (863)
T ss_pred             EEEEE
Confidence            99987

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=97.58  E-value=0.00021  Score=74.33  Aligned_cols=67  Identities=10%  Similarity=0.224  Sum_probs=57.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.+.  |++|+||.++++.++    .          .+....|++||.|+|+|.++|.+  +++
T Consensus       198 ~vv~G~V~~I~~~G~fV~i~--gv~Gllhisels~~~----~----------~~~~~~~~vGd~VkvkVl~iD~e--~~r  259 (318)
T PRK07400        198 EVVVGTVRGIKPYGAFIDIG--GVSGLLHISEISHEH----I----------ETPHSVFNVNDEMKVMIIDLDAE--RGR  259 (318)
T ss_pred             CEEEEEEEEEECCeEEEEEC--CEEEEEEHHHccccc----c----------cChhhccCCCCEEEEEEEEEeCC--CCE
Confidence            78999999999999999994  899999999987542    1          13457799999999999999975  799


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       260 I~LS~  264 (318)
T PRK07400        260 ISLST  264 (318)
T ss_pred             EEEEE
Confidence            99886

>PRK07899 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.55  E-value=0.0004  Score=76.06  Aligned_cols=67  Identities=21%  Similarity=0.202  Sum_probs=56.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|+++.++|+||.|.  |++|+||.++++..+    .          .+....|++||.|+|+|..+|.+  +++
T Consensus       210 ~iv~G~V~~i~~~G~FVdlg--gv~Glv~~Sels~~~----v----------~~~~~~~kvGd~V~vkVl~iD~e--~~r  271 (486)
T PRK07899        210 QVRKGVVSSIVNFGAFVDLG--GVDGLVHVSELSWKH----I----------DHPSEVVEVGQEVTVEVLDVDMD--RER  271 (486)
T ss_pred             CEEEEEEEEEECCeEEEEEC--CEEEEEEHHHCCCcc----c----------CCHHHhcCCCCEEEEEEEEEECC--CCE
Confidence            78999999999999999995  899999999987431    1          12346799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       272 I~LSl  276 (486)
T PRK07899        272 VSLSL  276 (486)
T ss_pred             EEEEE
Confidence            99886

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.52  E-value=0.00019  Score=79.29  Aligned_cols=68  Identities=16%  Similarity=0.196  Sum_probs=58.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|+++.++|+||.+.+ |++|+||.+++..+.    .          .+....+++||+|+|+|..+|.+  ++|
T Consensus       381 ~~v~G~V~~i~~~G~FV~l~~-gv~Gli~~se~s~~~----~----------~~~~~~~~~Gd~v~~~V~~id~e--~~r  443 (491)
T PRK13806        381 TTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISRAG----K----------PATYEKLKPGDSVTLVVEEIDTA--KRK  443 (491)
T ss_pred             CEEEEEEEEEecCceEEEcCC-CcEEEEEHHHcCccc----c----------cchhhcCCCCCEEEEEEEEEeCC--CCE
Confidence            689999999999999999976 999999999887542    1          13457799999999999999976  889


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       444 i~Ls~  448 (491)
T PRK13806        444 ISLAP  448 (491)
T ss_pred             EEEEe
Confidence            99986

>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional

Probab=97.48  E-value=0.00071  Score=77.64  Aligned_cols=67  Identities=15%  Similarity=0.177  Sum_probs=56.9

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|++|.++|+||.|.. |.+|+||++++.+++    .          .+....|++||.|+|+|.++|.+   ++
T Consensus       623 ~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~----v----------~~~~~v~kvGD~V~VkV~~iD~~---gr  684 (693)
T PRK11824        623 EIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADER----V----------EKVEDVLKEGDEVKVKVLEIDKR---GR  684 (693)
T ss_pred             eEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCcc----c----------cCccceeCCCCEEEEEEEEECCC---Cc
Confidence            789999999999999999975 899999999987542    1          13457899999999999999953   78


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       685 I~LS~  689 (693)
T PRK11824        685 IRLSR  689 (693)
T ss_pred             EEEEE
Confidence            88875

>PRK13806 rpsA 30S ribosomal protein S1; Provisional

Probab=97.38  E-value=0.00037  Score=76.98  Aligned_cols=69  Identities=17%  Similarity=0.273  Sum_probs=57.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.+.. |++|+||+++++..     ..        ..+....|++||.|+|+|..+|.+  +++
T Consensus       294 ~~v~G~V~~v~~~G~fV~l~~-gv~Glvh~sels~~-----~~--------~~~~~~~~~~Gd~v~vkVl~iD~e--~~r  357 (491)
T PRK13806        294 DKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMSWT-----RR--------VNKPEDVVAPGDAVAVKIKDIDPA--KRR  357 (491)
T ss_pred             CEEEEEEEEEeCceEEEEeCC-CcEEEEEHHHcCcc-----cc--------cCCHHHcCCCCCEEEEEEEEEEcc--CCE
Confidence            789999999999999999965 89999999988621     10        013456799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       358 i~Ls~  362 (491)
T PRK13806        358 ISLSL  362 (491)
T ss_pred             EEEEE
Confidence            99986

>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain

Probab=97.37  E-value=0.00052  Score=57.10  Aligned_cols=71  Identities=8%  Similarity=0.031  Sum_probs=55.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+.. +.+|++|.+++..+.   +...       ..+....+++||.|+++|.+++.+   ++
T Consensus         8 diV~g~V~~i~~~g~~v~i~~-~~~G~l~~se~~~~~---~~~~-------~~~~~~~l~vGd~i~~~V~~~~~~---~~   73 (86)
T cd05789           8 DVVIGRVTEVGFKRWKVDINS-PYDAVLPLSEVNLPR---TDED-------ELNMRSYLDEGDLIVAEVQSVDSD---GS   73 (86)
T ss_pred             CEEEEEEEEECCCEEEEECCC-CeEEEEEHHHccCCC---Cccc-------hHHHHhhCCCCCEEEEEEEEECCC---CC
Confidence            678999999999999999975 899999999886321   1000       012345699999999999999753   78


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus        74 i~LS~   78 (86)
T cd05789          74 VSLHT   78 (86)
T ss_pred             EEEEe
Confidence            88885

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase

Probab=97.31  E-value=0.00047  Score=77.91  Aligned_cols=69  Identities=20%  Similarity=0.179  Sum_probs=55.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCC-CCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQK-GSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d-~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..++|.|++|.++|+||.|.. |++|+||++++.+- |   +...        .+....+++||+|+|+|.++|.   ++
T Consensus       649 ~i~~GkV~~I~dfGaFVel~~-G~eGLvHISeisdls~---~~rv--------~~~~dv~kvGd~V~VKVl~ID~---~g  713 (719)
T TIGR02696       649 ERFLGTVVKTTAFGAFVSLLP-GKDGLLHISQIRKLAG---GKRV--------ENVEDVLSVGQKIQVEIADIDD---RG  713 (719)
T ss_pred             CEEEEEEEEEECceEEEEecC-CceEEEEhhhcccccc---ccCc--------CCHHHcCCCCCEEEEEEEEECC---CC
Confidence            789999999999999999974 89999999988531 1   1110        1345779999999999999994   67


Q ss_pred             ceEEE
Q 008167          569 KLQLT  573 (575)
Q Consensus       569 ~i~l~  573 (575)
                      ||.|+
T Consensus       714 KI~L~  718 (719)
T TIGR02696       714 KLSLV  718 (719)
T ss_pred             Ceeec
Confidence            88875

Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.

>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Probab=97.30  E-value=0.00051  Score=80.01  Aligned_cols=69  Identities=17%  Similarity=0.258  Sum_probs=57.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|.++.++|+||.+.+ |++|+||.++++.      ....       ......|++||.|+|+|..+|.+  +++
T Consensus       667 ~~v~G~V~~i~~~G~fV~l~~-gV~GlIh~sels~------~~~~-------~~~~~~~kvGq~VkvkVl~ID~e--~rr  730 (863)
T PRK12269        667 ARFTRRIVKVTNAGAFIEMEE-GIDGFLHVDDLSW------VKRT-------RPADHELEVGKEIECMVIECDPQ--ARR  730 (863)
T ss_pred             CEEEEEEEEEecceEEEEeCC-CcEEEEEhHHhhc------cccc-------cchhhccCCCCEEEEEEEEEecc--CCE
Confidence            789999999999999999976 9999999988752      2111       12235699999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       731 I~LS~  735 (863)
T PRK12269        731 IRLGV  735 (863)
T ss_pred             EEEEe
Confidence            99986

>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional

Probab=97.30  E-value=0.0016  Score=61.88  Aligned_cols=70  Identities=13%  Similarity=0.153  Sum_probs=58.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCcEEEEEEEEecCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQTVNIHMEVVEPQP  565 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~  565 (575)
                      +..+|.|+++.++|++|.+.  -++++||.+.++++    +.||+  ....|.++++...++.||.|+++|.++..+.
T Consensus        83 EVv~g~V~~v~~~G~~v~~G--p~~ifI~~~~l~~~----~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~  154 (176)
T PTZ00162         83 EVLDAIVTDVNKLGFFAQAG--PLKAFVSRSAIPPD----FVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA  154 (176)
T ss_pred             CEEEEEEEEEecceEEEEee--CeEEEEcHHHCCCc----cEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence            78999999999999999996  35699999999876    45655  4446666667899999999999999998753

>TIGR00717 rpsA ribosomal protein S1

Probab=97.29  E-value=0.00063  Score=75.81  Aligned_cols=68  Identities=18%  Similarity=0.273  Sum_probs=59.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|.|++++++|+||.+++ |++|++|.+++++++    .          .+....|++||.|+|+|..+|.+  +++
T Consensus       448 ~~v~g~V~~v~~~G~fV~l~~-~~~Glv~~s~l~~~~----~----------~~~~~~~~~Gd~v~~~V~~id~~--~~~  510 (516)
T TIGR00717       448 SVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSENR----D----------EDKTDEIKVGDEVEAKVVDIDKK--NRK  510 (516)
T ss_pred             eEEEEEEEEEecceEEEEcCC-CeEEEEEHHHcCccc----c----------ccccccCCCCCEEEEEEEEEeCC--CCE
Confidence            689999999999999999987 899999999998652    1          13467899999999999999975  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       511 i~ls~  515 (516)
T TIGR00717       511 VSLSV  515 (516)
T ss_pred             EEEEE
Confidence            99987

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.

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.27  E-value=0.00053  Score=77.30  Aligned_cols=69  Identities=19%  Similarity=0.200  Sum_probs=58.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|++|.|++ |++|++|++++..++    .         +.+....|++||.|+|+|..+|.+  +++
T Consensus       375 ~~v~g~V~~v~~~G~fV~l~~-~v~g~i~~s~l~~~~----~---------~~~~~~~~~~Gd~v~v~Il~vd~~--~~~  438 (565)
T PRK06299        375 DVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISWDK----K---------GEEAVELYKKGDEVEAVVLKVDVE--KER  438 (565)
T ss_pred             CEEEEEEEEEecceEEEECCC-CCEEEEEHHHcCccc----c---------ccChHhhCCCCCEEEEEEEEEeCC--CCE
Confidence            789999999999999999976 899999999987431    1         123457899999999999999975  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       439 i~ls~  443 (565)
T PRK06299        439 ISLGI  443 (565)
T ss_pred             EEEEE
Confidence            99986

>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]

Probab=97.26  E-value=0.00025  Score=69.72  Aligned_cols=69  Identities=16%  Similarity=0.125  Sum_probs=59.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCc-eEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFG-IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~g-leg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      +.+-|.|..|.++|++|.|.+|+ +||+||+|.+...|    .          ++-...++.|++|-++|.+||+.  +.
T Consensus        13 EiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~w----V----------knIrd~vkegqkvV~kVlrVd~~--rg   76 (269)
T COG1093          13 EIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGW----V----------KNIRDYVKEGQKVVAKVLRVDPK--RG   76 (269)
T ss_pred             cEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHH----H----------HHHHHHhhcCCeEEEEEEEEcCC--CC
Confidence            46789999999999999999998 99999999988764    2          12356789999999999999986  89


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      .|+|||
T Consensus        77 ~IDLSl   82 (269)
T COG1093          77 HIDLSL   82 (269)
T ss_pred             eEeeeh
Confidence            999997

>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain

Probab=97.21  E-value=0.0014  Score=54.90  Aligned_cols=63  Identities=13%  Similarity=-0.054  Sum_probs=49.1

Q ss_pred             ceeEEEEEEEecC--eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          490 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       490 ~~~~g~V~~v~~~--g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      ..+.|.|+.+.++  |+||.|.+ |.+|++|+++++...   |  +.    .  .+....+++||.|.|+|......
T Consensus         9 ~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~~---~--~~----v--~~~~~~~~~Gd~v~VqV~~~~~~   73 (88)
T cd04453           9 NIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPAY---F--KK----H--KKIAKLLKEGQEILVQVVKEPIG   73 (88)
T ss_pred             CEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCchh---c--cc----c--CCHHHcCCCCCEEEEEEEEecCC
Confidence            6899999999996  99999987 899999999885321   1  10    0  12346799999999999987654

RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th

>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain

Probab=97.20  E-value=0.0029  Score=53.02  Aligned_cols=68  Identities=9%  Similarity=0.034  Sum_probs=55.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      ++.+|+|+++.+.|++|.+.  .++++++-..++++    +.|+.  ..-.+.+ +....++.|+.|+++|.++..+
T Consensus         3 EVi~g~V~~v~~~G~~v~~G--pl~~f~~~~~ip~~----~~~~~~~~~~~~~~-~~~~~i~~g~~VR~rV~~v~~~   72 (88)
T cd04462           3 EVVDAIVTSVNKTGFFAEVG--PLSIFISRHLIPSD----MEFDPNASPPCFTS-NEDIVIKKDTEVRLKIIGTRVD   72 (88)
T ss_pred             cEEEEEEEEEeccEEEEEEc--CceEEEEeeecCcc----ceECCcCCCCeEeC-CCcEEECCCCEEEEEEEEEEEc
Confidence            67899999999999999996  57899999999876    46654  2225553 3578999999999999999875

RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=97.20  E-value=0.00098  Score=71.60  Aligned_cols=68  Identities=19%  Similarity=0.239  Sum_probs=57.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.+++ |++|++|.+.+....    .          .+....|++||+|+|+|..+|.+  +++
T Consensus       279 ~~v~g~V~~i~~~G~fV~l~~-gi~Glv~~se~~~~~----~----------~~~~~~~~~Gd~v~v~V~~id~e--~~~  341 (390)
T PRK06676        279 DVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQISHKH----I----------ATPSEVLEEGQEVKVKVLEVNEE--EKR  341 (390)
T ss_pred             cEEEEEEEEEeCceEEEEECC-CCeEEEEhHHcCccc----c----------CChhhccCCCCEEEEEEEEEECC--CCE
Confidence            689999999999999999975 899999999886431    0          12346799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       342 i~ls~  346 (390)
T PRK06676        342 ISLSI  346 (390)
T ss_pred             EEEEE
Confidence            99986

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=97.16  E-value=0.00098  Score=76.19  Aligned_cols=68  Identities=19%  Similarity=0.266  Sum_probs=58.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|+||.+.+ |++|++|.+++.++.    .          .+....|++||.|+|+|.++|.+  +++
T Consensus       564 ~~v~g~V~~i~~~G~fV~l~~-~i~Gli~~sel~~~~----~----------~~~~~~~kvGd~V~vkV~~id~e--~~r  626 (647)
T PRK00087        564 SIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISWKR----I----------DKPEDVLSEGEEVKAKILEVDPE--EKR  626 (647)
T ss_pred             eEEEEEEEEEECCeEEEEECC-CCEEEEEhhhcCccc----c----------CCHhhcCCCCCEEEEEEEEEeCC--CCE
Confidence            689999999999999999975 899999999887542    1          23456799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       627 I~lsl  631 (647)
T PRK00087        627 IRLSI  631 (647)
T ss_pred             EEEEE
Confidence            99986

>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain

Probab=97.09  E-value=0.0024  Score=50.53  Aligned_cols=62  Identities=13%  Similarity=0.109  Sum_probs=49.9

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ...+|.|.++.++|++|.+.  +.+|+++.+++..                    +..|++||+|+|.|.+++.+....+
T Consensus         5 ~iV~G~V~~~~~~~~~vdig--~~eg~lp~~e~~~--------------------~~~~~~Gd~v~v~v~~v~~~~~~~~   62 (67)
T cd04455           5 EIVTGIVKRVDRGNVIVDLG--KVEAILPKKEQIP--------------------GESYRPGDRIKAYVLEVRKTSKGPQ   62 (67)
T ss_pred             CEEEEEEEEEcCCCEEEEcC--CeEEEeeHHHCCC--------------------CCcCCCCCEEEEEEEEEecCCCCCE
Confidence            57899999999999999995  4899999876531                    2358999999999999987544456


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.+|
T Consensus        63 i~lS   66 (67)
T cd04455          63 IILS   66 (67)
T ss_pred             EEEe
Confidence            7665

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.

>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase

Probab=97.08  E-value=0.0019  Score=73.96  Aligned_cols=65  Identities=15%  Similarity=0.179  Sum_probs=54.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|++|.++|+||.+.. |.+|++|++++.+.+   +           .+....|++||+|+|+|.++|.   +.+
T Consensus       620 ~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~~---v-----------~~~~~~~kvGD~V~VkVi~id~---~gk  681 (684)
T TIGR03591       620 KIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANER---V-----------EKVEDVLKEGDEVKVKVLEIDK---QGR  681 (684)
T ss_pred             cEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCCc---c-----------cChhhccCCCCEEEEEEEEECC---CCC
Confidence            789999999999999999975 899999999997542   1           1346789999999999999995   456


Q ss_pred             eEE
Q 008167          570 LQL  572 (575)
Q Consensus       570 i~l  572 (575)
                      |.|
T Consensus       682 i~L  684 (684)
T TIGR03591       682 IKL  684 (684)
T ss_pred             ccC
Confidence            543

Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).

>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain

Probab=97.03  E-value=0.0021  Score=52.91  Aligned_cols=67  Identities=9%  Similarity=-0.078  Sum_probs=55.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ....|.|+++.+++++|.+.. +.+|.++.+++..++    .          .+....+++||.|+++|.+++..   ++
T Consensus         8 diV~G~V~~v~~~~~~V~i~~-~~~g~l~~~~~~~~~----~----------~~~~~~~~~GD~i~~~V~~~~~~---~~   69 (82)
T cd04454           8 DIVIGIVTEVNSRFWKVDILS-RGTARLEDSSATEKD----K----------KEIRKSLQPGDLILAKVISLGDD---MN   69 (82)
T ss_pred             CEEEEEEEEEcCCEEEEEeCC-CceEEeechhccCcc----h----------HHHHhcCCCCCEEEEEEEEeCCC---CC
Confidence            678999999999999999964 899999999886542    1          12346699999999999999852   78


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus        70 i~LS~   74 (82)
T cd04454          70 VLLTT   74 (82)
T ss_pred             EEEEE
Confidence            88886

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>PRK06676 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.97  E-value=0.0032  Score=67.60  Aligned_cols=67  Identities=18%  Similarity=0.262  Sum_probs=56.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|++|.+.  |++|+||.++++..+    .          .+....|++||.|+|+|..+|.+  +++
T Consensus       194 ~~v~g~V~~v~~~G~fV~l~--~v~g~v~~sels~~~----~----------~~~~~~~~vGd~i~~~Vl~vd~~--~~~  255 (390)
T PRK06676        194 DVVEGTVARLTDFGAFVDIG--GVDGLVHISELSHER----V----------EKPSEVVSVGQEVEVKVLSIDWE--TER  255 (390)
T ss_pred             CEEEEEEEEEecceEEEEeC--CeEEEEEHHHcCccc----c----------CCHHHhcCCCCEEEEEEEEEeCC--CCE
Confidence            78999999999999999995  799999999887432    1          12346699999999999999975  788


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       256 i~lS~  260 (390)
T PRK06676        256 ISLSL  260 (390)
T ss_pred             EEEEE
Confidence            88875

>TIGR00717 rpsA ribosomal protein S1

Probab=96.95  E-value=0.0017  Score=72.39  Aligned_cols=69  Identities=17%  Similarity=0.236  Sum_probs=57.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.++. |++|+||+++++.++    ..         ......|++||.|+|+|..+|.+  +++
T Consensus       361 ~~v~g~V~~v~~~G~fV~l~~-~v~glv~~s~ls~~~----~~---------~~~~~~~~~G~~V~~~Vl~vd~~--~~~  424 (516)
T TIGR00717       361 DRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWDK----DG---------READHLYKKGDEIEAVVLAVDKE--KKR  424 (516)
T ss_pred             CEEEEEEEEEecceEEEECCC-CCEEEEEHHHCcCcc----cC---------CCHhHccCCCCEEEEEEEEEeCc--CCE
Confidence            789999999999999999985 999999999987431    11         12347799999999999999975  788


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       425 i~ls~  429 (516)
T TIGR00717       425 ISLGV  429 (516)
T ss_pred             EEEee
Confidence            98876

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.

>COG2183 Tex Transcriptional accessory protein [Transcription]

Probab=96.82  E-value=0.0015  Score=73.55  Aligned_cols=68  Identities=19%  Similarity=0.230  Sum_probs=59.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ...+|+|.+|..||.||.|. ...+|+||++.+.+.    |..+          +...+++||.|+|+|..+|..  +++
T Consensus       660 m~leg~Vrnv~~fgafVdIg-v~qDglvHis~ls~~----fv~~----------P~~vv~vGdiV~v~V~~vD~~--r~r  722 (780)
T COG2183         660 MILEGTVRNVVDFGAFVDIG-VHQDGLVHISQLSDK----FVKD----------PNEVVKVGDIVKVKVIEVDTA--RKR  722 (780)
T ss_pred             CEEEEEEEEeeeccceEEec-cccceeeeHHHhhhh----hcCC----------hHHhcccCCEEEEEEEEEecc--cCe
Confidence            57899999999999999996 488999999999876    4433          467899999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus       723 I~Lsm  727 (780)
T COG2183         723 IALSM  727 (780)
T ss_pred             eeeEe
Confidence            99986

>PRK07400 30S ribosomal protein S1; Reviewed

Probab=96.80  E-value=0.0066  Score=63.29  Aligned_cols=64  Identities=14%  Similarity=0.186  Sum_probs=52.8

Q ss_pred             CceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          489 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       489 ~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ...++|.|+++.++|++|.+.  |++|+||.+.++..      +           ... ..+|+.|+++|..+|.+  ++
T Consensus       119 ~~~V~g~V~~~~~~G~~V~l~--Gv~gfip~s~ls~~------~-----------~~~-~~vG~~i~~kVl~id~~--~~  176 (318)
T PRK07400        119 DATVRSEVFATNRGGALVRIE--GLRGFIPGSHISTR------K-----------PKE-ELVGEELPLKFLEVDEE--RN  176 (318)
T ss_pred             CCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCcc------C-----------Ccc-ccCCCEEEEEEEEEEcc--cC
Confidence            478999999999999999994  99999999988631      1           112 34999999999999976  78


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|.||+
T Consensus       177 ~i~lS~  182 (318)
T PRK07400        177 RLVLSH  182 (318)
T ss_pred             EEEEEh
Confidence            998875

>PRK06299 rpsA 30S ribosomal protein S1; Reviewed

Probab=96.78  E-value=0.0025  Score=71.94  Aligned_cols=69  Identities=20%  Similarity=0.299  Sum_probs=56.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.++. |++|+||+++++.+.      .       ..+....|++||.|+|+|..+|.+  +++
T Consensus       288 ~~v~g~V~~i~~~G~fV~l~~-~v~Glv~~sel~~~~------~-------~~~~~~~~~~G~~v~v~V~~id~~--~~~  351 (565)
T PRK06299        288 SKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWTK------K-------NKHPSKVVSVGQEVEVMVLEIDEE--KRR  351 (565)
T ss_pred             CEEEEEEEEEeCCeEEEEeCC-CCEEEEEHHHcCccc------c-------ccCHHHhcCCCCEEEEEEEEEcCC--CCE
Confidence            789999999999999999975 899999999886321      0       012345689999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       352 i~ls~  356 (565)
T PRK06299        352 ISLGL  356 (565)
T ss_pred             EEEeh
Confidence            99875

>PRK09202 nusA transcription elongation factor NusA; Validated

Probab=96.27  E-value=0.038  Score=60.46  Aligned_cols=63  Identities=11%  Similarity=0.062  Sum_probs=52.5

Q ss_pred             CceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          489 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       489 ~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      .....|+|.++.++|++|.|.  |++|++|.++..                    .+..|++||+|+|.|..|+.+....
T Consensus       135 GeIV~G~V~ri~~~giiVDLg--gvea~LP~sE~i--------------------p~E~~~~GdrIka~I~~Vd~~~kg~  192 (470)
T PRK09202        135 GEIITGVVKRVERGNIIVDLG--RAEAILPRKEQI--------------------PRENFRPGDRVRAYVYEVRKEARGP  192 (470)
T ss_pred             CCEEEEEEEEEecCCEEEEEC--CeEEEecHHHcC--------------------CCccCCCCCEEEEEEEEEecCCCCC
Confidence            478999999999999999994  899999977542                    3466999999999999999764445


Q ss_pred             ceEEE
Q 008167          569 KLQLT  573 (575)
Q Consensus       569 ~i~l~  573 (575)
                      +|.||
T Consensus       193 qIilS  197 (470)
T PRK09202        193 QIILS  197 (470)
T ss_pred             eEEEE
Confidence            88776

>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed

Probab=96.13  E-value=0.021  Score=65.49  Aligned_cols=68  Identities=15%  Similarity=0.195  Sum_probs=56.4

Q ss_pred             CceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          489 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       489 ~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ...+.|.|.++.++|++|.+ . |++|++|.+++...+    .          .+....|++||.|+|+|.++|.+  ++
T Consensus       478 G~iV~g~V~~v~~~G~fV~l-~-gv~Gll~~sels~~~----~----------~~~~~~~~vGd~V~vkV~~id~~--~~  539 (647)
T PRK00087        478 GDVVEGEVKRLTDFGAFVDI-G-GVDGLLHVSEISWGR----V----------EKPSDVLKVGDEIKVYILDIDKE--NK  539 (647)
T ss_pred             CCEEEEEEEEEeCCcEEEEE-C-CEEEEEEHHHcCccc----c----------CCHHHhcCCCCEEEEEEEEEECC--CC
Confidence            37899999999999999999 3 899999999886431    1          12456799999999999999975  78


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|.||+
T Consensus       540 ~I~lS~  545 (647)
T PRK00087        540 KLSLSL  545 (647)
T ss_pred             EEEEEe
Confidence            888875

>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]

Probab=96.02  E-value=0.013  Score=65.12  Aligned_cols=67  Identities=15%  Similarity=0.212  Sum_probs=55.9

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +.+.|.|+.+.+||+||.+.. |-+|++|++.+....            +  ++....+++||.|.|+|..+|.   +-|
T Consensus       621 ~iy~G~V~ri~~fGaFv~l~~-gkdgl~hiS~~~~~r------------v--~kv~dvlk~Gd~v~Vkv~~iD~---~Gr  682 (692)
T COG1185         621 EVYEGTVVRIVDFGAFVELLP-GKDGLVHISQLAKER------------V--EKVEDVLKEGDEVKVKVIEIDK---QGR  682 (692)
T ss_pred             cEEEEEEEEEeecceEEEecC-CcceeEEehhhhhhh------------h--hcccceeecCceEEEEEeeecc---cCC
Confidence            689999999999999999986 889999999987541            1  2345889999999999999996   466


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|++
T Consensus       683 i~ls~  687 (692)
T COG1185         683 IRLSI  687 (692)
T ss_pred             cccee
Confidence            76664

>PRK12327 nusA transcription elongation factor NusA; Provisional

Probab=95.71  E-value=0.093  Score=55.48  Aligned_cols=70  Identities=10%  Similarity=0.053  Sum_probs=54.5

Q ss_pred             HHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167          482 LIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV  561 (575)
Q Consensus       482 ~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v  561 (575)
                      ..|..+..+...|+|..+.++|++|.+.  |++|+++.++..                    .+..|+.||+|+|.|..|
T Consensus       128 ~ef~~k~GeiV~G~V~~~~~~~~~Vdlg--~vEa~LP~~E~i--------------------p~e~~~~Gd~Ika~V~~V  185 (362)
T PRK12327        128 NEFSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPAEQI--------------------PGETYKHGDRIKVYVVKV  185 (362)
T ss_pred             HHHHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHHHcC--------------------CCCCCCCCCEEEEEEEEE
Confidence            3344444478899999999999999985  699999965432                    245699999999999999


Q ss_pred             cCCCCCCceEEE
Q 008167          562 EPQPNRPKLQLT  573 (575)
Q Consensus       562 d~~~~~~~i~l~  573 (575)
                      +.+....+|.+|
T Consensus       186 ~~~~kgp~IivS  197 (362)
T PRK12327        186 EKTTKGPQIFVS  197 (362)
T ss_pred             ecCCCCCeEEEE
Confidence            977556677776

>PRK09521 exosome complex RNA-binding protein Csl4; Provisional

Probab=95.47  E-value=0.032  Score=53.76  Aligned_cols=66  Identities=11%  Similarity=0.043  Sum_probs=52.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcC---------CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167          490 TDTEARIVKIRSNGFIVFVPK---------FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV  560 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~---------~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~  560 (575)
                      ..+.|.|+++.++|++|.|..         .+++|++|.+++...+    .          .+....|++||.|+++|.+
T Consensus        66 diV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~----~----------~~~~~~~~~GD~V~akV~~  131 (189)
T PRK09521         66 DIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGY----V----------ESLTDAFKIGDIVRAKVIS  131 (189)
T ss_pred             CEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhh----h----------hhHHhccCCCCEEEEEEEe
Confidence            688999999999999999953         3689999999876432    1          1234679999999999998


Q ss_pred             ecCCCCCCceEEEe
Q 008167          561 VEPQPNRPKLQLTL  574 (575)
Q Consensus       561 vd~~~~~~~i~l~l  574 (575)
                      ++     +++.||+
T Consensus       132 i~-----~~i~LS~  140 (189)
T PRK09521        132 YT-----DPLQLST  140 (189)
T ss_pred             cC-----CcEEEEE
Confidence            87     4677664

>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional

Probab=95.21  E-value=0.058  Score=53.78  Aligned_cols=71  Identities=11%  Similarity=0.061  Sum_probs=55.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.+++++|.|.. +.+|++|++++...+   ...|+       .+....|++||.|.++|.+++.+   ++
T Consensus        65 DiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~i~~~~---~~~d~-------~~~~~~~~~GDlV~akV~~i~~~---~~  130 (235)
T PRK04163         65 DLVIGKVTDVTFSGWEVDINS-PYKAYLPVSEVLGRP---VNVEG-------TDLRKYLDIGDYIIAKVKDVDRT---RD  130 (235)
T ss_pred             CEEEEEEEEEeCceEEEEeCC-CceeEEEHHHcCCCc---cccch-------hhhHhhCCCCCEEEEEEEEECCC---Cc
Confidence            688999999999999999975 689999999886542   11222       23456799999999999999864   45


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus       131 ~~LS~  135 (235)
T PRK04163        131 VVLTL  135 (235)
T ss_pred             EEEEE
Confidence            77764

>TIGR01953 NusA transcription termination factor NusA

Probab=95.12  E-value=0.2  Score=52.56  Aligned_cols=70  Identities=11%  Similarity=0.120  Sum_probs=53.8

Q ss_pred             HHHHhcCCceeEEEEEEEecCe-EEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167          482 LIYFRKRPTDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV  560 (575)
Q Consensus       482 ~~~l~~~~~~~~g~V~~v~~~g-~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~  560 (575)
                      ..|-....+...|+|.++.+.| ++|.+.  |++|+++.++..                    .+..|++||+|+|.|..
T Consensus       125 ~ey~~k~GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP~~E~i--------------------p~E~~~~Gd~ik~~V~~  182 (341)
T TIGR01953       125 DEFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILPKKEQI--------------------PGEKFRIGDRIKAYVYE  182 (341)
T ss_pred             HHHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEecHHHcC--------------------CCcCCCCCCEEEEEEEE
Confidence            3444334478899999999988 588884  899999977543                    12449999999999999


Q ss_pred             ecCCCCCCceEEE
Q 008167          561 VEPQPNRPKLQLT  573 (575)
Q Consensus       561 vd~~~~~~~i~l~  573 (575)
                      |+......+|.||
T Consensus       183 V~~~~kg~qIivS  195 (341)
T TIGR01953       183 VRKTAKGPQIILS  195 (341)
T ss_pred             EEcCCCCCeEEEE
Confidence            9976556677776

This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.

>PHA02858 EIF2a-like PKR inhibitor; Provisional

Probab=94.80  E-value=0.042  Score=44.86  Aligned_cols=64  Identities=16%  Similarity=0.209  Sum_probs=50.1

Q ss_pred             EEEEEecCeEEEEEcCCceEEEEE-ccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCceEEE
Q 008167          495 RIVKIRSNGFIVFVPKFGIEGPVY-LTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT  573 (575)
Q Consensus       495 ~V~~v~~~g~~V~l~~~gleg~v~-~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i~l~  573 (575)
                      -|..+.+.|+.|.|.+||+||.|- .+++.-+.          .    +.-++.+ +|-.+.|+|..+|.+  +.=|+||
T Consensus        22 ~Vv~i~d~~~YV~LleY~iegmIl~~selsr~r----------i----rsi~kll-VGk~e~v~ViRVDk~--KGYIDLs   84 (86)
T PHA02858         22 GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADR----------A----EKLKKKL-VGKTINVQVIRTDKL--KGYIDVR   84 (86)
T ss_pred             EEEEEeccEEEEEEecCccceEEecHHHHhHHH----------H----Hhhhhhh-cCCeeEEEEEEECCC--CCEEEeE
Confidence            677889999999999999999987 66554331          1    1224567 999999999999976  8888888


Q ss_pred             eC
Q 008167          574 LI  575 (575)
Q Consensus       574 l~  575 (575)
                      .+
T Consensus        85 ~~   86 (86)
T PHA02858         85 HV   86 (86)
T ss_pred             cC
Confidence            64

>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits

Probab=94.54  E-value=0.093  Score=41.97  Aligned_cols=67  Identities=16%  Similarity=-0.011  Sum_probs=52.9

Q ss_pred             eeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEE-EEEEEEecCCCCCCc
Q 008167          491 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTV-NIHMEVVEPQPNRPK  569 (575)
Q Consensus       491 ~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V-~V~V~~vd~~~~~~~  569 (575)
                      ..+|.|..-+++++.|.+.+.|+.|+++...++|.    +.-.        +..-+.+++||++ ++.|.  +.  .+|.
T Consensus         3 lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~----~~k~--------~~~~~klrvG~~L~~~lvL--~~--~~r~   66 (72)
T cd05699           3 LVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDH----VSNC--------PLLWHCLQEGDTIPNLMCL--SN--YKGR   66 (72)
T ss_pred             eEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCc----hhhC--------HHHHhhhhcCCCccceEEE--ec--cccE
Confidence            57899999999999999999999999999988873    2211        1124779999999 88888  43  3777


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.++
T Consensus        67 i~lt   70 (72)
T cd05699          67 IILT   70 (72)
T ss_pred             EEEe
Confidence            7776

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 H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies

Probab=93.24  E-value=0.093  Score=40.24  Aligned_cols=52  Identities=21%  Similarity=0.379  Sum_probs=38.1

Q ss_pred             CCccEEEEEeCCCCCCceEecCCccCc-CCCCEEEEEEeecCCCCCCcceEEEEe
Q 008167            8 GSVAHALFVPKDRRIPKIRIQTRQLGN-LLDKRIIVAVDSWDCQSRYPFGHYVRV   61 (575)
Q Consensus         8 ~~~~~~~~~P~d~r~p~i~i~~~~~~~-~~~~~~~v~i~~w~~~~~~p~g~i~~~   61 (575)
                      ..+.+.+++|.| .-..|.|+.+.... ..|++|+|++.. +.....|.|+|+++
T Consensus         6 ~~~GfGFv~~~~-~~~DifIp~~~l~~A~~gD~V~v~i~~-~~~~~~~eg~vv~V   58 (58)
T PF08206_consen    6 HPKGFGFVIPDD-GGEDIFIPPRNLNGAMDGDKVLVRITP-PSRGKRPEGEVVEV   58 (58)
T ss_dssp             -SSS-EEEEECT--TEEEEE-HHHHTTS-TT-EEEEEEEE-SSSEEEEEEEEEE-
T ss_pred             EcCCCEEEEECC-CCCCEEECHHHHCCCCCCCEEEEEEec-CCCCCCCCEEEEeC
Confidence            356789999999 33469999887654 578999999999 88888999999975

; PDB: 2ID0_D 2IX1_A 2IX0_A.

>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]

Probab=93.16  E-value=0.47  Score=43.65  Aligned_cols=70  Identities=9%  Similarity=-0.002  Sum_probs=48.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      +..+|+|+.|.+.|+|+....  ++.++.--..+.|+  +|+..+..-.+.+++.. +++.|++|+++|.....+
T Consensus        83 EVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd~--~f~p~~n~P~f~~~d~s-~I~~~~~VR~kiigtr~~  152 (170)
T KOG3298|consen   83 EVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPDY--EFDPGENPPNFQTEDES-VIQKGVEVRLKIIGTRVD  152 (170)
T ss_pred             cEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCCc--ccCCCCCCCcccccccc-eeeeCcEEEEEEEEEEEe
Confidence            788999999999999999974  55555433445443  24433332334333333 899999999999988764

>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]

Probab=91.71  E-value=0.41  Score=52.16  Aligned_cols=60  Identities=18%  Similarity=0.134  Sum_probs=51.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      ..+.|.|+.+++.|++|.++. +.+|++|.++++..|    .          .+....+.+||.|.|+....|+.
T Consensus       670 ~vy~~tIt~~rd~G~~V~l~p-~~~~Llh~sqL~~e~----i----------akpsd~levGq~I~vk~ie~d~~  729 (760)
T KOG1067|consen  670 GVYTATITEIRDTGVMVELYP-MQQGLLHNSQLDQEK----I----------AKPSDLLEVGQEIQVKYIERDPR  729 (760)
T ss_pred             eEEEEEEeeecccceEEEecC-Cchhhccchhccccc----c----------cChHHHHhhcceeEEEEEeecCc
Confidence            457999999999999999987 999999999998664    1          13445699999999999999985

>TIGR00008 infA translation initiation factor IF-1

Probab=91.46  E-value=1.2  Score=35.25  Aligned_cols=62  Identities=11%  Similarity=0.123  Sum_probs=45.9

Q ss_pred             ceeEEEEEEEecCeE-EEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~-~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      -+++|+|+..-+++. .|.+++ |.+-..|++...-                  ...-.+..||.|.|.+..-|++  +.
T Consensus         5 ie~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKmr------------------~~rI~I~~GD~V~Ve~spyd~t--kg   63 (68)
T TIGR00008         5 IEMEGKVTESLPNAMFRVELEN-GHEVLAHISGKIR------------------MHYIRILPGDKVKVELSPYDLT--RG   63 (68)
T ss_pred             EEEEEEEEEECCCCEEEEEECC-CCEEEEEecCcch------------------hccEEECCCCEEEEEECcccCC--cE
Confidence            367999999988775 578875 8888888764321                  2345689999999999887754  77


Q ss_pred             ceEE
Q 008167          569 KLQL  572 (575)
Q Consensus       569 ~i~l  572 (575)
                      +|.+
T Consensus        64 rIi~   67 (68)
T TIGR00008        64 RITY   67 (68)
T ss_pred             eEEe
Confidence            7654

This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=91.26  E-value=0.18  Score=60.09  Aligned_cols=68  Identities=21%  Similarity=0.286  Sum_probs=58.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|..+.++|.+|.++. |++|+.+.+...+++    .-          +....|.+||+|+++|..+|.+  +++
T Consensus       601 ~~~~G~l~~~~~~g~~V~F~g-~lsGf~p~s~~sd~~----v~----------~~~ehf~vGqTv~~~i~nvd~e--k~r  663 (1710)
T KOG1070|consen  601 KITKGTLCAIKENGAFVTFTG-GLSGFAPVSEMSDDF----VL----------SDSEHFPVGQTVRAKIVNVDDE--KRR  663 (1710)
T ss_pred             ceEEEEEeeeccCCeEEEecC-ccccccchhhhhhhh----hc----------ChhhhcccccEEEEEEEecCch--hce
Confidence            578999999999999999997 999999999988874    32          3456799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.+++
T Consensus       664 m~l~~  668 (1710)
T KOG1070|consen  664 MPLGL  668 (1710)
T ss_pred             eehhh
Confidence            88764

>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]

Probab=91.03  E-value=0.58  Score=46.79  Aligned_cols=59  Identities=19%  Similarity=0.218  Sum_probs=50.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +..+|+|-.+...|.||.+ +.+.-|+||-++.-                      ...++|++++++|..+..   .++
T Consensus       157 q~v~~tVYr~~~~G~fv~~-e~~~~GfIh~sEr~----------------------~~prlG~~l~~rVi~~re---Dg~  210 (287)
T COG2996         157 QEVDATVYRLLESGTFVIT-ENGYLGFIHKSERF----------------------AEPRLGERLTARVIGVRE---DGK  210 (287)
T ss_pred             CeeeeEEEEEeccceEEEE-cCCeEEEEcchhhc----------------------ccccCCceEEEEEEEEcc---CCe
Confidence            6889999999999999999 55999999965432                      347999999999999996   589


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       211 lnLSl  215 (287)
T COG2996         211 LNLSL  215 (287)
T ss_pred             eeccc
Confidence            99886

>PRK12442 translation initiation factor IF-1; Reviewed

Probab=90.21  E-value=2  Score=35.56  Aligned_cols=63  Identities=10%  Similarity=0.165  Sum_probs=47.5

Q ss_pred             ceeEEEEEEEecCeEE-EEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFI-VFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~-V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      -+++|+|+.+.+++.| |.|. .|.+-..|++..-                  +...-.+.+||+|.|.+.--|++  +.
T Consensus         7 ie~~G~V~e~Lp~~~frV~Le-nG~~vla~isGKm------------------R~~rIrIl~GD~V~VE~spYDlt--kG   65 (87)
T PRK12442          7 IELDGIVDEVLPDSRFRVTLE-NGVEVGAYASGRM------------------RKHRIRILAGDRVTLELSPYDLT--KG   65 (87)
T ss_pred             EEEEEEEEEECCCCEEEEEeC-CCCEEEEEeccce------------------eeeeEEecCCCEEEEEECcccCC--ce
Confidence            4689999999887754 7775 4888888876432                  12245689999999999988865  88


Q ss_pred             ceEEE
Q 008167          569 KLQLT  573 (575)
Q Consensus       569 ~i~l~  573 (575)
                      +|.+.
T Consensus        66 RIiyR   70 (87)
T PRK12442         66 RINFR   70 (87)
T ss_pred             eEEEE
Confidence            88765

>PRK12328 nusA transcription elongation factor NusA; Provisional

Probab=89.76  E-value=3.4  Score=43.76  Aligned_cols=70  Identities=14%  Similarity=0.138  Sum_probs=52.3

Q ss_pred             HHHHhcCCceeEEEEEEEecC-eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEE
Q 008167          482 LIYFRKRPTDTEARIVKIRSN-GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV  560 (575)
Q Consensus       482 ~~~l~~~~~~~~g~V~~v~~~-g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~  560 (575)
                      -.|.....+...|+|..+... +++|.|.  +.+|.++-++.                    -.+..|+.||+|+|.|..
T Consensus       132 ~ey~~~~Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP~~eq--------------------ip~E~~~~Gdrik~~i~~  189 (374)
T PRK12328        132 EKYKKKVGKIVFGTVVRVDNEENTFIEID--EIRAVLPMKNR--------------------IKGEKFKVGDVVKAVLKR  189 (374)
T ss_pred             HHHHHhcCcEEEEEEEEEecCCCEEEEcC--CeEEEeCHHHc--------------------CCCCcCCCCCEEEEEEEE
Confidence            344444458899999999864 5788885  68998876532                    135679999999999999


Q ss_pred             ecCCCC-CCceEEE
Q 008167          561 VEPQPN-RPKLQLT  573 (575)
Q Consensus       561 vd~~~~-~~~i~l~  573 (575)
                      |+.... ..+|.||
T Consensus       190 V~~~~k~gp~IilS  203 (374)
T PRK12328        190 VKIDKNNGILIELS  203 (374)
T ss_pred             EecCCCCCCEEEEE
Confidence            998654 4677776

>PRK12329 nusA transcription elongation factor NusA; Provisional

Probab=89.47  E-value=3.7  Score=44.34  Aligned_cols=71  Identities=21%  Similarity=0.316  Sum_probs=51.7

Q ss_pred             HHHhcCCceeEEEEEEEecCeEEEEEc-CCc---eEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEE
Q 008167          483 IYFRKRPTDTEARIVKIRSNGFIVFVP-KFG---IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHM  558 (575)
Q Consensus       483 ~~l~~~~~~~~g~V~~v~~~g~~V~l~-~~g---leg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V  558 (575)
                      .|-....+...|+|..+...++.|.+. .+|   ++|.++.++.                    -.+..|+.||+|+|.|
T Consensus       147 ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eq--------------------ip~E~y~~Gdrika~i  206 (449)
T PRK12329        147 EFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQ--------------------LPNDNYRANATFKVFL  206 (449)
T ss_pred             HHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHc--------------------CCCCcCCCCCEEEEEE
Confidence            343334478999999998888888873 233   7888876532                    1356799999999999


Q ss_pred             EEecCCC-CCCceEEE
Q 008167          559 EVVEPQP-NRPKLQLT  573 (575)
Q Consensus       559 ~~vd~~~-~~~~i~l~  573 (575)
                      ..|+... ...+|.||
T Consensus       207 ~~V~~~~~kGpqIilS  222 (449)
T PRK12329        207 KEVSEGPRRGPQLFVS  222 (449)
T ss_pred             EEeecCCCCCCEEEEE
Confidence            9998752 44667665

>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain

Probab=88.23  E-value=1.2  Score=37.47  Aligned_cols=69  Identities=12%  Similarity=0.042  Sum_probs=50.4

Q ss_pred             ceeEEEEEEEecCeEEEEE--------cCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167          490 TDTEARIVKIRSNGFIVFV--------PKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV  561 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l--------~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v  561 (575)
                      ..+-|.|++++...+.|.|        +. ...|.+|.++....+     .++.       +....|++||-|+.+|.+.
T Consensus         8 DiVig~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~~dv~~~~-----~d~~-------~~~~~f~~GDiV~AkVis~   74 (92)
T cd05791           8 SIVIARVTRINPRFAKVDILCVGGRPLKE-SFRGVIRKEDIRATE-----KDKV-------EMYKCFRPGDIVRAKVISL   74 (92)
T ss_pred             CEEEEEEEEEcCCEEEEEEEEecCeecCC-CcccEEEHHHccccc-----cchH-------HHHhhcCCCCEEEEEEEEc
Confidence            5788999999999999988        54 568889988765431     1111       1346799999999999998


Q ss_pred             cCCCCCCceEEEe
Q 008167          562 EPQPNRPKLQLTL  574 (575)
Q Consensus       562 d~~~~~~~i~l~l  574 (575)
                      ..   .+.+.||+
T Consensus        75 ~~---~~~~~Lst   84 (92)
T cd05791          75 GD---ASSYYLST   84 (92)
T ss_pred             CC---CCCcEEEe
Confidence            74   25566654

S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=87.21  E-value=1.8  Score=52.28  Aligned_cols=68  Identities=13%  Similarity=0.121  Sum_probs=57.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ....|.|..+.+.|+|+.+- .+++++++++++.+.+    .-          ...+.|..|+.|.++|.+++..  .++
T Consensus      1164 ~iv~G~V~nv~~~glfi~ls-~~v~a~v~is~~~ds~----~k----------~w~k~~~~gklv~~rv~~ve~~--s~r 1226 (1710)
T KOG1070|consen 1164 DIVRGFVKNVETKGLFIALS-RKVEAFVPISGLSDSF----EK----------EWEKHLPVGKLVTGRVLSVEED--SKR 1226 (1710)
T ss_pred             ceeEEEEEEecCCcEEEEEc-cceEEEEEccccccch----hh----------hhhccCCccceeeeEEEEeecc--Cce
Confidence            57899999999999999996 5999999999887753    11          2246799999999999999975  778


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.++|
T Consensus      1227 iel~L 1231 (1710)
T KOG1070|consen 1227 IELSL 1231 (1710)
T ss_pred             EEEEE
Confidence            88876

>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit

Probab=84.79  E-value=9.9  Score=33.85  Aligned_cols=69  Identities=14%  Similarity=0.050  Sum_probs=50.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEe---eCCCeEEeeCcEEEEEEEEecC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK---MDGNLSYSVLQTVNIHMEVVEP  563 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g---~~~~~~~~lGD~V~V~V~~vd~  563 (575)
                      ++..|.|.+....|+.|.| .|--+-+|+-..|...    -.||+.+..++.   ......+..|+.|+.+|.++..
T Consensus         5 Evl~g~I~~~~~~Gi~vsl-gFFddI~IP~~~L~~p----s~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f   76 (122)
T PF08292_consen    5 EVLTGKIKSSTAEGIRVSL-GFFDDIFIPPSLLPEP----SRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF   76 (122)
T ss_dssp             -EEEEEEEEEETTEEEEEE-CCEEEEEEECCCC-TT----EEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred             CEEEEEEEecCCCcEEEEe-cccccEEECHHHCCCC----CccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence            5789999999999999999 4667888998888865    345555555543   3345667999999999998875

Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.

>TIGR02063 RNase_R ribonuclease R

Probab=84.36  E-value=2  Score=49.88  Aligned_cols=60  Identities=15%  Similarity=0.238  Sum_probs=46.9

Q ss_pred             CccEEEEEeCCCCCCceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeecCCCCh
Q 008167            9 SVAHALFVPKDRRIPKIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDR   68 (575)
Q Consensus         9 ~~~~~~~~P~d~r~p~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~   68 (575)
                      .+++++++|.|..-..|.|+..+.. ...|++|+|+|..|+.....|.|+|+++||...+.
T Consensus        77 ~~g~gFv~~~~~~~~di~I~~~~~~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~  137 (709)
T TIGR02063        77 RDGFGFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVRITGKPDGGDRFEARVIKILERANDQ  137 (709)
T ss_pred             CCccEEEEECCCCCCcEEEChHHhCcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCCCE
Confidence            4567888998722236999877664 45799999999999876667899999999998773

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.

>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]

Probab=82.27  E-value=10  Score=30.65  Aligned_cols=63  Identities=13%  Similarity=0.219  Sum_probs=46.1

Q ss_pred             ceeEEEEEEEecCe-EEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g-~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|+|..+-+++ |.|.+.+ |.+-.-|++...-                  ...-.+..||.|.|.+...+.+  +-
T Consensus         7 ~e~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKmr------------------~~~i~I~~GD~V~Ve~~~~d~~--kg   65 (75)
T COG0361           7 IEMEGTVIEMLPNGRFRVELEN-GHERLAHISGKMR------------------KNRIRILPGDVVLVELSPYDLT--KG   65 (75)
T ss_pred             cEEEEEEEEecCCCEEEEEecC-CcEEEEEccCcch------------------heeEEeCCCCEEEEEecccccc--cc
Confidence            46789999988776 5588765 8888888765431                  2245689999999999887754  66


Q ss_pred             ceEEE
Q 008167          569 KLQLT  573 (575)
Q Consensus       569 ~i~l~  573 (575)
                      +|...
T Consensus        66 ~I~~R   70 (75)
T COG0361          66 RIVYR   70 (75)
T ss_pred             cEEEE
Confidence            66543

>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]

Probab=82.16  E-value=1  Score=49.55  Aligned_cols=62  Identities=13%  Similarity=0.255  Sum_probs=52.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|.+|.++|+||.|.+ .+.|++|-+++.++                    ..+.+||.+-|++..+.++  ++.
T Consensus       124 ~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~--------------------~~~~vgdeiiV~v~~vr~~--~ge  180 (715)
T COG1107         124 KYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD--------------------PDYAVGDEIIVQVSDVRPE--KGE  180 (715)
T ss_pred             eeeeccccchhhhcceeecCh-hhhccccccccCCC--------------------CCCCCCCeEEEEeeccCCC--CCc
Confidence            568999999999999999987 78898887766542                    4589999999999999875  788


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |+|..
T Consensus       181 idf~~  185 (715)
T COG1107         181 IDFEP  185 (715)
T ss_pred             cceee
Confidence            88864

>TIGR00757 RNaseEG ribonuclease, Rne/Rng family

Probab=80.43  E-value=4.4  Score=43.90  Aligned_cols=69  Identities=10%  Similarity=0.001  Sum_probs=46.8

Q ss_pred             ceeEEEEEEEecC--eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167          490 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV  561 (575)
Q Consensus       490 ~~~~g~V~~v~~~--g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v  561 (575)
                      ..+.|.|.++.++  |+||.+.. |-.|++|++++....  .+.+......-...+....++.||.|.|+|..-
T Consensus        27 nIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~--~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke   97 (414)
T TIGR00757        27 NIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNY--ECLAPAEAKREAGPSISELLRPGQSVLVQVVKE   97 (414)
T ss_pred             CEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchh--hccccccccccccCCHHHhCcCCCEEEEEEeeC
Confidence            6799999999997  99999975 889999999886432  011111000000011234689999999999873

The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	575
2wp8_J	977	Yeast Rrp44 Nuclease Length = 977		1e-141
4ifd_J	1003	Crystal Structure Of An 11-subunit Eukaryotic Exoso		1e-141
2vnu_D	760	Crystal Structure Of Sc Rrp44 Length = 760		1e-137
2ix0_A	663	Rnase Ii Length = 663		1e-24
2ix1_A	664	Rnase Ii D209n Mutant Length = 664		5e-24
2id0_A	644	Escherichia Coli Rnase Ii Length = 644		2e-18
2r7d_A	469	Crystal Structure Of Ribonuclease Ii Family Protein		3e-13

>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease Length = 977

Iteration: 1
 Score =  499 bits (1286), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 255/529 (48%), Positives = 348/529 (65%), Gaps = 19/529 (3%)
Query: 7   SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
           S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR +G I 
Sbjct: 392 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 451
Query: 67  DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
               E+E +L+++D++ RPFS +VL CLP              P +VS + L    R DL
Sbjct: 452 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 510
Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
           RD  + S+DPPGC DI+DALH   L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 511 RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 570
Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
           YLV++RIDMLP  L  D+CSL+  V+R AFSVIWEL   A I++  + KSVI+S  A SY
Sbjct: 571 YLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSY 630
Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
            +AQ R+DD    D LT  +R +  L+ K++Q+R+E GAL LAS EVK  +D+ET DP +
Sbjct: 631 EQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNE 690
Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
           + + ++   N +VEEFML AN+SVA +I   FP  ++LRRH   PS   E+L  +L T  
Sbjct: 691 VEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRK 750
Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
            + ++L+  SSKALADSLDR V  +DPYFN L+RI++TRCM  A YF SG  + P+F HY
Sbjct: 751 NMSISLE--SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHY 808
Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
           GLA  +YTHFTSPIRRY DVV HR L+ ++G   L    +D+ ++  I  N+N +HRNAQ
Sbjct: 809 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQ 868
Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
            A R S+E +     R   +     ++K+ +NG +V VPKFG+EG + L
Sbjct: 869 FAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 917

>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 1003

Iteration: 1
 Score =  499 bits (1285), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 255/529 (48%), Positives = 348/529 (65%), Gaps = 19/529 (3%)
Query: 7   SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
           S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR +G I 
Sbjct: 418 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 477
Query: 67  DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
               E+E +L+++D++ RPFS +VL CLP              P +VS + L    R DL
Sbjct: 478 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 536
Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
           RD  + S+DPPGC DI+DALH   L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 537 RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 596
Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
           YLV++RIDMLP  L  D+CSL+  V+R AFSVIWEL   A I++  + KSVI+S  A SY
Sbjct: 597 YLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSY 656
Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
            +AQ R+DD    D LT  +R +  L+ K++Q+R+E GAL LAS EVK  +D+ET DP +
Sbjct: 657 EQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNE 716
Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
           + + ++   N +VEEFML AN+SVA +I   FP  ++LRRH   PS   E+L  +L T  
Sbjct: 717 VEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRK 776
Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
            + ++L+  SSKALADSLDR V  +DPYFN L+RI++TRCM  A YF SG  + P+F HY
Sbjct: 777 NMSISLE--SSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHY 834
Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
           GLA  +YTHFTSPIRRY DVV HR L+ ++G   L    +D+ ++  I  N+N +HRNAQ
Sbjct: 835 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQ 894
Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
            A R S+E +     R   +     ++K+ +NG +V VPKFG+EG + L
Sbjct: 895 FAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 943

>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44 Length = 760

Iteration: 1
 Score =  484 bits (1247), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 252/529 (47%), Positives = 338/529 (63%), Gaps = 19/529 (3%)
Query: 7   SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIG 66
           S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR +G I 
Sbjct: 175 SSSTQNVFVILXDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIE 234
Query: 67  DRDTESEMVLIDNDIDARPFSTQVLACLPPL------------PWSVSSEDLANPIRLDL 114
               E+E +L+++D++ RPFS +VL CLP              P +VS + L    R DL
Sbjct: 235 SAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTK-RKDL 293
Query: 115 RDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSV 174
           RD  + S+DPPGC DI+DALH   L +GN+EVGVHIADVT+FV PGT LD E + RGTSV
Sbjct: 294 RDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSV 353
Query: 175 YLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY 234
           YLV++RID LP  L  D+CSL+  V+R AFSVIWEL   A I++  + KSVI+S  A SY
Sbjct: 354 YLVDKRIDXLPXLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFXKSVIRSREAFSY 413
Query: 235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 294
            +AQ R+DD    D LT   R +  L+ K++Q+R+E GAL LAS EVK   D+ET DP +
Sbjct: 414 EQAQLRIDDKTQNDELTXGXRALLKLSVKLKQKRLEAGALNLASPEVKVHXDSETSDPNE 473
Query: 295 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAA 351
           + + ++   N +VEEF L AN+SVA +I   FP  + LRRH   PS   E+L   L T  
Sbjct: 474 VEIKKLLATNSLVEEFXLLANISVARKIYDAFPQTAXLRRHAAPPSTNFEILNEXLNTRK 533
Query: 352 AVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHY 410
              ++L+  SSKALADSLDR V  +DPYFN L+RI +TRC   A YF SG  + P+F HY
Sbjct: 534 NXSISLE--SSKALADSLDRCVDPEDPYFNTLVRIXSTRCXXAAQYFYSGAYSYPDFRHY 591
Query: 411 GLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQ 470
           GLA  +YTHFTSPIRRY DVV HR L+ ++G   L    +D+ +   I  N+N +HRNAQ
Sbjct: 592 GLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKXDXICRNINRKHRNAQ 651
Query: 471 MASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 519
            A R S+E +     R   +     ++K+ +NG +V VPKFG+EG + L
Sbjct: 652 FAGRASIEYYVGQVXRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRL 700

>pdb|2IX0|A Chain A, Rnase Ii Length = 663

Iteration: 1
 Score =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 132/470 (28%), Positives = 198/470 (42%), Gaps = 54/470 (11%)
Query: 110 IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169
           +R DL  L   ++D    +D+DDAL   AL     ++ V IAD T ++  G+ LD  A  
Sbjct: 207 VREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKI 266
Query: 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKS 228
           R  + YL    I MLP+ L++D+CSLRA+  R   +    L+ +  I  +  +  + I+S
Sbjct: 267 RAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIES 326
Query: 229 CAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RGALTLASAEVKFQI 285
            A L Y +    ++++    P +  +     L  ++ QRR E     AL          I
Sbjct: 327 KAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFI 386
Query: 286 DTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEP 345
             E  + LDI     R AN++VEE M+AAN+  A ++LR      +   H        + 
Sbjct: 387 LGEKGEVLDIVAEPRRIANRIVEEAMIAANICAA-RVLRDKLGFGIYNVHMGFDPANADA 445
Query: 346 LLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILATRCMTQAVYFCSGD 401
           L       GL++D      L     L R +   P  + +  IR        Q+    S +
Sbjct: 446 LAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRF------QSFAEISTE 499
Query: 402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADN 461
             P    H+GL    Y  +TSPIR+Y D++ HRLL A      +      RPQ   I   
Sbjct: 500 PGP----HFGLGLEAYATWTSPIRKYGDMINHRLLKAV-----IKGETATRPQ-DEITVQ 549
Query: 462 LNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--ARIVKIR---------SNGFIV 506
           +  R R  +MA R   ++   +Y R    K  TDT   A IV I           NG I 
Sbjct: 550 MAERRRLNRMAER---DVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIA 606
Query: 507 FVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 556
           F+P      P     R      D  V  Q+   V++ G   Y V   +++
Sbjct: 607 FIP-----APFLHAVR------DELVCSQENGTVQIKGETVYKVTDVIDV 645

>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant Length = 664

Iteration: 1
 Score =  109 bits (272), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 131/470 (27%), Positives = 198/470 (42%), Gaps = 54/470 (11%)
Query: 110 IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169
           +R DL  L   ++D    +D++DAL   AL     ++ V IAD T ++  G+ LD  A  
Sbjct: 208 VREDLTALDFVTIDSASTEDMNDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKI 267
Query: 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKS 228
           R  + YL    I MLP+ L++D+CSLRA+  R   +    L+ +  I  +  +  + I+S
Sbjct: 268 RAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIES 327
Query: 229 CAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RGALTLASAEVKFQI 285
            A L Y +    ++++    P +  +     L  ++ QRR E     AL          I
Sbjct: 328 KAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFI 387
Query: 286 DTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEP 345
             E  + LDI     R AN++VEE M+AAN+  A ++LR      +   H        + 
Sbjct: 388 LGEKGEVLDIVAEPRRIANRIVEEAMIAANICAA-RVLRDKLGFGIYNVHMGFDPANADA 446
Query: 346 LLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILATRCMTQAVYFCSGD 401
           L       GL++D      L     L R +   P  + +  IR        Q+    S +
Sbjct: 447 LAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRF------QSFAEISTE 500
Query: 402 LTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADN 461
             P    H+GL    Y  +TSPIR+Y D++ HRLL A      +      RPQ   I   
Sbjct: 501 PGP----HFGLGLEAYATWTSPIRKYGDMINHRLLKAV-----IKGETATRPQ-DEITVQ 550
Query: 462 LNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--ARIVKIR---------SNGFIV 506
           +  R R  +MA R   ++   +Y R    K  TDT   A IV I           NG I 
Sbjct: 551 MAERRRLNRMAER---DVGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIA 607
Query: 507 FVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 556
           F+P      P     R      D  V  Q+   V++ G   Y V   +++
Sbjct: 608 FIP-----APFLHAVR------DELVCSQENGTVQIKGETVYKVTDVIDV 646

>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii Length = 644

Iteration: 1
 Score = 90.5 bits (223), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 132/488 (27%), Positives = 196/488 (40%), Gaps = 55/488 (11%)
Query: 98  PWSVSSEDLANP-IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNF 156
           P  V++E L    +R DL  L   ++D    +D DDAL   AL     ++ V IAD T +
Sbjct: 175 PDGVATEXLDEGLVREDLTALDFVTIDSASTEDXDDALFAKALPDDKLQLIVAIADPTAW 234
Query: 157 VHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEI 216
           +  G+ LD  A  R  + YL    I  LP+ L++D+CSLRA+  R   +    L+ +  I
Sbjct: 235 IAEGSKLDKAAKIRAFTNYLPGFNIPXLPRELSDDLCSLRANEVRPVLACRXTLSADGTI 294
Query: 217 I-STRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIE---RG 272
             +  +  + I+S A L Y +    ++++    P +  +     L  ++ QRR E     
Sbjct: 295 EDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNH 354
Query: 273 ALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLL 332
           AL          I  E  + LDI     R AN++VEE    A    A ++LR      + 
Sbjct: 355 ALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEE-AXIAANICAARVLRDKLGFGIY 413
Query: 333 RRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALAD--SLDRAVGDDP--YFNKLIRILAT 388
             H        + L       GL++D      L     L R +   P  + +  IR    
Sbjct: 414 NVHXGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRF-- 471
Query: 389 RCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSV 448
               Q+    S +  P    H+GL    Y  +TSPIR+Y D + HRLL A      +   
Sbjct: 472 ----QSFAEISTEPGP----HFGLGLEAYATWTSPIRKYGDXINHRLLKAV-----IKGE 518
Query: 449 FQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR----KRPTDTE--ARIVKIR-- 500
              RPQ   I      R R  + A R   ++   +Y R    K  TDT   A IV I   
Sbjct: 519 TATRPQ-DEITVQXAERRRLNRXAER---DVGDWLYARFLKDKAGTDTRFAAEIVDISRG 574
Query: 501 -------SNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQT 553
                   NG I F+P      P     R      D  V  Q+   V++ G   Y V   
Sbjct: 575 GXRVRLVDNGAIAFIP-----APFLHAVR------DELVCSQENGTVQIKGETVYKVTDV 623
Query: 554 VNIHMEVV 561
           +++ +  V
Sbjct: 624 IDVTIAEV 631

>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From Deinococcus Radiodurans, Triclinic Crystal Form. Northeast Structural Genomics Target Drr63 Length = 469

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 56/160 (35%), Positives = 82/160 (51%), Gaps = 7/160 (4%)
Query: 85  PFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNF 144
           P++ ++ A L  +   V   D A   RLDL  L  F++D  G +D DDA+    L  G  
Sbjct: 56  PYADRLRAALNAVELPVPDFDPAEE-RLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLT 114
Query: 145 EVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAF 204
            + VH+ADV   V P +PLD EA  RG ++YL +R I  LP  L         +V   A 
Sbjct: 115 RLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGXLPDELVAKAGLGLHEVSP-AL 173
Query: 205 SVIWELTPE--AEIISTRYTKSVIKSCAALSYVEAQARMD 242
           S+  +L P+  AE +    T+  ++    L+Y EAQAR++
Sbjct: 174 SICLDLDPDGNAEAVDVLLTRVKVQR---LAYQEAQARLE 210

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	575
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	0.0
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	0.0
2r7d_A	469	Ribonuclease II family protein; structural genomic	1e-135
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	1e-120
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-10

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 Length = 760

 Score =  766 bits (1979), Expect = 0.0
 Identities = 259/592 (43%), Positives = 362/592 (61%), Gaps = 19/592 (3%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
             +   S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR
Sbjct: 169 SSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVR 228

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPL--PWSVSSEDLANPI-------- 110
            +G I     E+E +L+++D++ RPFS +VL CLP     W   ++              
Sbjct: 229 DLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLT 288

Query: 111 -RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169
            R DLRD  + S+DPPGC DI+DALH   L +GN+EVGVHIADVT+FV PGT LD E + 
Sbjct: 289 KRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAA 348

Query: 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSC 229
           RGTSVYLV++RIDMLP  L  D+CSL+  V+R AFSVIWEL   A I++  + KSVI+S 
Sbjct: 349 RGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSR 408

Query: 230 AALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTET 289
            A SY +AQ R+DD    D LT  +R +  L+ K++Q+R+E GAL LAS EVK  +D+ET
Sbjct: 409 EAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSET 468

Query: 290 HDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRT 349
            DP ++ + ++   N +VEEFML AN+SVA +I   FP  ++LRRH +P     E L   
Sbjct: 469 SDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEM 528

Query: 350 A-AAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
                 +++ + SSKALADSLDR V  +DPYFN L+RI++TRCM  A YF SG  + P+F
Sbjct: 529 LNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDF 588

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHR 467
            HYGLA  +YTHFTSPIRRY DVV HR L+ ++G   L    +D+ ++  I  N+N +HR
Sbjct: 589 RHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHR 648

Query: 468 NAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGS 527
           NAQ A R S+E +     R   +     ++K+ +NG +V VPKFG+EG + L    +  +
Sbjct: 649 NAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPN 708

Query: 528 GDWYVDEQQQKIV----KMDGNLSYSVLQTVNIHMEVV-EPQPNRPKLQLTL 574
                DE + K+       D      V   V + +  V +P  ++ K +L L
Sbjct: 709 -SAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLL 759

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 977

 Score =  764 bits (1975), Expect = 0.0
 Identities = 259/592 (43%), Positives = 362/592 (61%), Gaps = 19/592 (3%)

Query: 1   MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
             +   S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR
Sbjct: 386 SSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVR 445

Query: 61  VIGEIGDRDTESEMVLIDNDIDARPFSTQVLACLPPL--PWSVSSEDLANPI-------- 110
            +G I     E+E +L+++D++ RPFS +VL CLP     W   ++              
Sbjct: 446 DLGTIESAQAETEALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLT 505

Query: 111 -RLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASK 169
            R DLRD  + S+DPPGC DI+DALH   L +GN+EVGVHIADVT+FV PGT LD E + 
Sbjct: 506 KRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAA 565

Query: 170 RGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSC 229
           RGTSVYLV++RIDMLP  L  D+CSL+  V+R AFSVIWEL   A I++  + KSVI+S 
Sbjct: 566 RGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSR 625

Query: 230 AALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTET 289
            A SY +AQ R+DD    D LT  +R +  L+ K++Q+R+E GAL LAS EVK  +D+ET
Sbjct: 626 EAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSET 685

Query: 290 HDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRT 349
            DP ++ + ++   N +VEEFML AN+SVA +I   FP  ++LRRH +P     E L   
Sbjct: 686 SDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEM 745

Query: 350 A-AAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
                 +++ + SSKALADSLDR V  +DPYFN L+RI++TRCM  A YF SG  + P+F
Sbjct: 746 LNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDF 805

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHR 467
            HYGLA  +YTHFTSPIRRY DVV HR L+ ++G   L    +D+ ++  I  N+N +HR
Sbjct: 806 RHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHR 865

Query: 468 NAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGS 527
           NAQ A R S+E +     R   +     ++K+ +NG +V VPKFG+EG + L    +  +
Sbjct: 866 NAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPN 925

Query: 528 GDWYVDEQQQKIV----KMDGNLSYSVLQTVNIHMEVV-EPQPNRPKLQLTL 574
                DE + K+       D      V   V + +  V +P  ++ K +L L
Sbjct: 926 -SAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLL 976

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A Length = 469

 Score =  399 bits (1028), Expect = e-135
 Identities = 110/470 (23%), Positives = 171/470 (36%), Gaps = 60/470 (12%)

Query: 51  SRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARP--FSTQVLACLPPLPWSVSSEDLAN 108
            R      +R +      +    ++L     D     ++ ++ A L  +   V   D A 
Sbjct: 20  GRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPAE 79

Query: 109 PIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEAS 168
             RLDL  L  F++D  G +D DDA+    L  G   + VH+ADV   V P +PLD EA 
Sbjct: 80  E-RLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEAR 138

Query: 169 KRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKS 228
            RG ++YL +R I MLP  L      L       A S+  +L P+    +     + +K 
Sbjct: 139 ARGATLYLPDRTIGMLPDELVAK-AGLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKV 197

Query: 229 CAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTE 288
              L+Y EAQAR++              +  LA+  R+ R   GAL++   EV+ + D  
Sbjct: 198 -QRLAYQEAQARLEAGE------EPFVTLARLARASRRLREGEGALSIDLPEVRVKADET 250

Query: 289 THDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLR 348
                 +      E   +V+E M  A    A        +         PT+E+    L 
Sbjct: 251 GA---SVFPLPKPEMRTVVQECMTLAGWGTAI-FADDNEIPLPFATQDYPTREVAGDTLP 306

Query: 349 TAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFH 408
              A                                    + + +  +       P    
Sbjct: 307 AMWAR----------------------------------RKTLARTRF------QPSPGP 326

Query: 409 HYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRN 468
           H+G+   LY   TSP+RRY D+VVH+ L A L      S       + +           
Sbjct: 327 HHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRDPLS----SKVMAAHIAESQMNADA 382

Query: 469 AQMASRGSVELHTLIYFRKRPTDT-EARIVKIRSNGFIVFVPKFGIEGPV 517
            + A R S   HTL +   +P    +A +V  R     + +P    +  V
Sbjct: 383 TRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFDVQV 432

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A Length = 644

 Score =  367 bits (945), Expect = e-120
 Identities = 123/556 (22%), Positives = 206/556 (37%), Gaps = 44/556 (7%)

Query: 16  VPKDRRIPK---IRIQTRQLGNLLDKRIIVA-VDSW-DCQSRYPFGHYVRVIGEIGDRDT 70
           VP    +      R          +    VA +        R  +    + I    D   
Sbjct: 100 VPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFV 159

Query: 71  ESEMVLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDI 130
              + L  ++++ +     V   +         ++     R DL  L   ++D    +D+
Sbjct: 160 PWWVTLARHNLE-KEAPDGVATEML--------DEGLV--REDLTALDFVTIDSASTEDM 208

Query: 131 DDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTE 190
           DDAL   AL     ++ V IAD T ++  G+ LD  A  R  + YL    I MLP+ L++
Sbjct: 209 DDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSD 268

Query: 191 DICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKSCAALSYVEAQA----RMDDSR 245
           D+CSLRA+  R   +    L+ +  I  +  +  + I+S A L Y +         D   
Sbjct: 269 DLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQP 328

Query: 246 LMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQ 305
             + +   +R +  + ++  + R     +     + +F +  E  + LDI     R AN+
Sbjct: 329 ESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILG-EKGEVLDIVAEPRRIANR 387

Query: 306 MVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKAL 365
           +VEE M+AAN+  A  +LR      +   H        + L       GL++D      L
Sbjct: 388 IVEEAMIAANICAAR-VLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTL 446

Query: 366 AD--SLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSP 423
                L R +   P     +     R  + A    S +  P    H+GL    Y  +TSP
Sbjct: 447 DGFCKLRRELDAQP--TGFLDSRIRRFQSFAEI--STEPGP----HFGLGLEAYATWTSP 498

Query: 424 IRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLI 483
           IR+Y D++ HRLL A +                 I   +  R R  +MA R   +     
Sbjct: 499 IRKYGDMINHRLLKAVIKGET------ATRPQDEITVQMAERRRLNRMAERDVGDWLYAR 552

Query: 484 YFRKRPTDT---EARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV 540
           + + +        A IV I   G  V +   G    +           D  V  Q+   V
Sbjct: 553 FLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLH--AVRDELVCSQENGTV 610

Query: 541 KMDGNLSYSVLQTVNI 556
           ++ G   Y V   +++
Sbjct: 611 QIKGETVYKVTDVIDV 626

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 76.8 bits (188), Expect = 1e-14
 Identities = 79/564 (14%), Positives = 158/564 (28%), Gaps = 185/564 (32%)

Query: 14  LFVPKDRRIPKIRIQTRQLGNLLDKRIIV--------------AVDSWDCQSRYPFG-HY 58
             V + +   K+R    +L     K +++                 S+  Q +  F   +
Sbjct: 129 YNVSRLQPYLKLRQALLELRP--AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 59  VRVIGEIGDRDTESEMVL-----IDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIR-- 111
           + +       +T  EM+      ID +  +R   +        L        +   +R  
Sbjct: 187 LNL-KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS----NIKLR----IHSIQAELRRL 237

Query: 112 ----------LDLRD------LRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTN 155
                     L L +         F++    CK          L++           VT+
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNL---SCK--------ILLTTRF-------KQVTD 279

Query: 156 FVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAE 215
           F+   T          T+   ++     L     + +     D          +L  E  
Sbjct: 280 FLSAAT----------TTHISLDHHSMTLTPDEVKSLLLKYLDCR------PQDLPREVL 323

Query: 216 IISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD-LRNMNSLAKKMRQRRIERGAL 274
             + R     +   A          + D       T D  +++N    K+    IE    
Sbjct: 324 TTNPR----RLSIIAES--------IRD----GLATWDNWKHVNC--DKL-TTIIESSLN 364

Query: 275 TLASAEVK--------FQIDTETHDPLDIGMYQIREA--NQMVEEFMLAANVSVAEQILR 324
            L  AE +        F           I    +       +++             ++ 
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSA------HI-PTILLSLIWFDVIKS--------DVMVVVN 409

Query: 325 QFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIR 384
           +    SL+ + P  +             + +        ++   L   + ++   ++   
Sbjct: 410 KLHKYSLVEKQPKEST------------ISIP-------SIYLELKVKLENEYALHR--S 448

Query: 385 ILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLG--I 442
           I+    + +   F S DL PP    Y      Y+H             H L +      +
Sbjct: 449 IVDHYNIPKT--FDSDDLIPPYLDQY-----FYSHI-----------GHHLKNIEHPERM 490

Query: 443 YKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVE--LHTLIYFRKRPTDTEA---RIV 497
                VF D      +   +  RH +    + GS+   L  L +++    D +    R+V
Sbjct: 491 TLFRMVFLD---FRFLEQKI--RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLV 545

Query: 498 KIRSNGFIVFVPKFGIEGPVYLTP 521
               N  + F+PK  IE  +  + 
Sbjct: 546 ----NAILDFLPK--IEENLICSK 563

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 62.2 bits (150), Expect = 3e-10
 Identities = 78/504 (15%), Positives = 162/504 (32%), Gaps = 132/504 (26%)

Query: 143 NFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLT----EDICSLRAD 198
           +FE G H     + +     + ++A         V+   DM    L+    + I   +  
Sbjct: 8   DFETGEHQYQYKDIL----SVFEDAFVDNFDCKDVQ---DMPKSILSKEEIDHIIMSKDA 60

Query: 199 VERLAFSVIWELTPEAEIISTRYTKSVIKS-----CAALSYVEAQARMDDSRLMDPLTTD 253
           V      + W L  + E +  ++ + V++       + +   E +     +R+       
Sbjct: 61  VSGTLR-LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT-EQRQPSMMTRMYIEQRDR 118

Query: 254 LRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFM-- 311
           L N N +  K    R++                   +  L   + ++R A  ++ + +  
Sbjct: 119 LYNDNQVFAKYNVSRLQ------------------PYLKLRQALLELRPAKNVLIDGVLG 160

Query: 312 -----LAANVSVAEQILRQFPL----CSLLRRH-PSPTKEMLEPLLRTAAAVGLNLDVSS 361
                +A +V ++ ++  +        +L   + P    EML+ LL        +    S
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220

Query: 362 SK------ALADSLDRAVGDDPYFNKLIRILATRCMTQAV-YF---C-----SGDLTPPE 406
           S       ++   L R +   PY N L+ +L      +A   F   C     +      +
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLL-VLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279

Query: 407 FHHYGLAAPLYTHFTSPIRRYADVVVHR----LLSASLGI--YKLPS-VFQDRPQLTS-I 458
           F    L+A   TH    +  ++  +       LL   L      LP  V    P+  S I
Sbjct: 280 F----LSAATTTHI--SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333

Query: 459 ADNL--------NYRHRNA---QMASRGSVELHTLIYFRKR-------PTDTEARIVKIR 500
           A+++        N++H N          S+ +     +RK        P         I 
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS-----AHIP 388

Query: 501 SNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQ------TV 554
           +    +                       W+   +   +V ++    YS+++      T+
Sbjct: 389 TILLSLI----------------------WFDVIKSDVMVVVNKLHKYSLVEKQPKESTI 426

Query: 555 NIH---MEVVEPQPNRPKLQLTLI 575
           +I    +E+     N   L  +++
Sbjct: 427 SIPSIYLELKVKLENEYALHRSIV 450

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	575
2vnu_D	760	Exosome complex exonuclease RRP44; hydrolase-RNA c	100.0
2wp8_J	977	Exosome complex exonuclease DIS3; nucleus, hydrola	100.0
2id0_A	644	Exoribonuclease 2; RNAse, exonuclease, hydrolyase,	100.0
2r7d_A	469	Ribonuclease II family protein; structural genomic	100.0
1luz_A	88	Protein K3, protein K2; stranded anti-parallel bet	98.85
4ayb_E	180	DNA-directed RNA polymerase; transferase, multi-su	98.82
2ckz_B	218	C25, DNA-directed RNA polymerase III 25 KD polypep	98.81
1kl9_A	182	Eukaryotic translation initiation factor 2 subuni;	98.69
1go3_E	187	DNA-directed RNA polymerase subunit E; transferase	98.66
2a19_A	175	EIF-2- alpha, eukaryotic translation initiation fa	98.65
2k52_A	80	Uncharacterized protein MJ1198; metal-binding, zin	98.65
2c35_B	172	Human RPB7, DNA-directed RNA polymerase II 19 kDa	98.64
3bzc_A	785	TEX; helix-turn-helix, helix-hairpin-helix, S1 dom	98.61
2k4k_A	130	GSP13, general stress protein 13; cytoplasm, stres	98.58
3ayh_B	203	DNA-directed RNA polymerase III subunit RPC8; tran	98.54
2cqo_A	119	Nucleolar protein of 40 kDa; S1 domain, OB-fold, s	98.52
2khi_A	115	30S ribosomal protein S1; acetylation, phosphoprot	98.51
2eqs_A	103	ATP-dependent RNA helicase DHX8; S1 domain, OB-fol	98.49
2b8k_G	215	B16, DNA-directed RNA polymerase II 19 kDa polypep	98.44
1y14_B	171	B16, RPB7, DNA-directed RNA polymerase II 19 kDa p	98.44
2khj_A	109	30S ribosomal protein S1; OB fold, acetylation, ph	98.39
3aev_A	275	Translation initiation factor 2 subunit alpha; pro	98.37
1q8k_A	308	Eukaryotic translation initiation factor 2 subunit	98.3
3h0g_G	172	DNA-directed RNA polymerase II subunit RPB7; trans	98.24
1wi5_A	119	RRP5 protein homolog; S1 domain, OB-fold, structur	98.02
3cw2_C	266	Translation initiation factor 2 subunit alpha; AIF	97.87
3psi_A	1219	Transcription elongation factor SPT6; nucleus; 3.3	97.77
4aid_A	726	Polyribonucleotide nucleotidyltransferase; transfe	97.69
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	97.68
1e3p_A	757	Guanosine pentaphosphate synthetase; polyribonucle	97.63
3psf_A	1030	Transcription elongation factor SPT6; nucleus; 2.5	97.55
3cdi_A	723	Polynucleotide phosphorylase; mRNA turnover, RNAse	97.46
3m7n_A	179	Putative uncharacterized protein AF_0206; exosome,	96.88
2nn6_I	209	3'-5' exoribonuclease CSL4 homolog; RNA, exosome,	96.64
2je6_I	251	RRP4, exosome complex RNA-binding protein 1; nucle	95.71
2ba0_A	229	Archeal exosome RNA binding protein RRP4; RNAse PH	95.67
1hh2_P	344	NUSA, N utilization substance protein A; transcrip	95.53
2z0s_A	235	Probable exosome complex RNA-binding protein 1; al	95.44
3go5_A	285	Multidomain protein with S1 RNA-binding domains; s	94.22
1k0r_A	366	NUSA; two component arrangement, S1 domain, two K-	94.06
2asb_A	251	Transcription elongation protein NUSA; protein-RNA	92.41
2ja9_A	175	Exosome complex exonuclease RRP40; RNA-binding pro	91.23
2bh8_A	101	1B11; transcription, molecular evolution, unique a	88.05
2bx2_L	517	Ribonuclease E, RNAse E; RNA-binding, RNA turnover	87.81
2rf4_A	214	DNA-directed RNA polymerase I subunit RPA4; transf	87.65
2nn6_H	308	Exosome complex exonuclease RRP4; RNA, exosome, PM	85.67

>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16

Probab=100.00  E-value=3e-128  Score=1098.66  Aligned_cols=563  Identities=46%  Similarity=0.775  Sum_probs=520.9

Q ss_pred             CCCccEEEEEeCCCCCCceEecCCccCcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCC
Q 008167            7 SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPF   86 (575)
Q Consensus         7 ~~~~~~~~~~P~d~r~p~i~i~~~~~~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f   86 (575)
                      |.+.+++||+|.|+|+|.|.|++++.+...|++|+|+|++||.++.+|.|+|+++||..+++++++++++.+|+|+..+|
T Consensus       175 ~~~~~~~~~~P~d~ri~~i~i~~~~~~~~~g~~vvv~i~~~p~~~~~p~G~i~~~LG~~~d~~~e~~~il~~~~l~~~~F  254 (760)
T 2vnu_D          175 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPF  254 (760)
T ss_dssp             CCSCEEEEEEESSTTSCCEEEEETTGGGGTTEEEEEEEEECCTTCSSCEEEEEEEEEESSCSHHHHHHHHHHTTCCCSCC
T ss_pred             cCccceEEEEECCCCCccEEEecccccccCCCEEEEEEeeccCCCCCCcEEEEEEeCCCCCchhHHHHHHHHCCCCCcCC
Confidence            44567889999999999999999988888899999999999999999999999999999999999999999999998679


Q ss_pred             cHHHHhcCCCC--CCCCCc----------c-ccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccc
Q 008167           87 STQVLACLPPL--PWSVSS----------E-DLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADV  153 (575)
Q Consensus        87 ~~~v~~~~~~~--~~~~~~----------~-~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADv  153 (575)
                      |++|++|++..  +|.+++          + +..  +|+|||++++|||||++|+||||||||+++++|+|+||||||||
T Consensus       255 ~~~vl~~~~~~~~~~~i~~~~~~~~~v~~~~~~~--~R~Dlr~l~~~TID~~~a~D~DDAvsie~~~~g~~~l~VHIADV  332 (760)
T 2vnu_D          255 SKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLT--KRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADV  332 (760)
T ss_dssp             CHHHHTTSCTTGGGCCCCSSTTCHHHHHHCGGGG--GSEECTTSCCEEEESSSCCCCCEEEEEEECTTSCEEEEEEEECH
T ss_pred             CHHHHHHHHhcccccccccccccccccccccchh--cccccccCeEEEEcCCCCCcccceEEEEEcCCCcEEEEEEeccH
Confidence            99999999887  787653          2 444  89999999999999999999999999999999999999999999


Q ss_pred             cccccCCCHHHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeC
Q 008167          154 TNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALS  233 (575)
Q Consensus       154 s~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~lt  233 (575)
                      |+||+|||+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+||++|+|++++|++|+|+|+++||
T Consensus       333 s~yV~~gs~LD~eA~~RgtSvYlp~rviPMLP~~Ls~~lcSL~p~~dRla~S~~~~id~~G~v~~~~~~~svI~s~~rlt  412 (760)
T 2vnu_D          333 THFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFS  412 (760)
T ss_dssp             HHHSCTTSHHHHHHHHHCBCEECSSCEECSSCHHHHTTTSSCCBTSEEEEEEEEEEECTTCCEEEEEEEEEEEEBSEEEE
T ss_pred             HHeeCCCCHHHHHHHHcCCcEecCCceEeCCChHHcccccccCCCCcEEEEEEEEEEcCCCCEEEEEEEEEEEEecceEc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHH
Q 008167          234 YVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA  313 (575)
Q Consensus       234 Y~~v~~~l~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~Mil  313 (575)
                      |++|+++|+++....++.++|..|+++|+.|+++|.++|+++|+.||++|.+|++.|.|.++.+.++.+||.|||||||+
T Consensus       413 Y~~v~~~l~~~~~~~~l~~~L~~L~~la~~lr~~R~~~Gai~~~~pe~~~~ld~e~g~~~~i~~~~~~~a~~lIeE~Mll  492 (760)
T 2vnu_D          413 YEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLL  492 (760)
T ss_dssp             HHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCCEEEEECSSSSCEEEEEECCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCceEEEEecCCCcEEEEEEcCCccHHHHHHHHHHH
Confidence            99999999987666788899999999999999999999999999999999999666889999999999999999999999


Q ss_pred             HHHHHHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHc-CCccCCCCHHHHHHHHHHHhC-CChhHHHHHHHHHHhhc
Q 008167          314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAV-GLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCM  391 (575)
Q Consensus       314 AN~~vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~-g~~~~~~~~~~l~~~l~~~~~-~~~~~~~~l~~~~~r~m  391 (575)
                      ||.+||+++.++++.|++||+|+.|+++++++|.+++..+ |+.++..++++++++|+++.+ .++.++.+++.+++|+|
T Consensus       493 AN~~vA~~l~~~~~~~~l~R~h~~P~~~~l~~l~~~~~~~~g~~l~~~~~~~l~~~l~~~~~~~~~~~~~ll~~~~~r~m  572 (760)
T 2vnu_D          493 ANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCM  572 (760)
T ss_dssp             HHHHHHHHHHHHCTTTCEEEEBCCCCGGGGHHHHHHHHHHHSCCCCCSCHHHHHHHHHTCCBTTBTTHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhCCCCeeEEecCCCCHHHHHHHHHHHHHccCCCcCCCCHHHHHHHHHHhhCCchHHHHHHHHHHHHHhh
Confidence            9999999999988899999999999999999999999999 999998899999999987655 55677888999999999


Q ss_pred             cCceecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 008167          392 TQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQM  471 (575)
Q Consensus       392 ~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~  471 (575)
                      ++|+|+++|..+.++.+|||||++.|||||||||||+||+|||||+++|.+++.+....+.+.|..+|.+||.++++|+.
T Consensus       573 ~~A~Y~~~g~~~~~~~~HfgLa~~~YtHfTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~~~~~~s~~er~A~~  652 (760)
T 2vnu_D          573 MAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQF  652 (760)
T ss_dssp             CCCEEEEGGGSCGGGGCBTTTTBSCCCCCSCTTTBHHHHHHHHHHHHHTTSSCCCGGGGCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hCccccccCcCCCCCCCceecCCCceeccCchHhhhHHHHHHHHHHHHHccCCCcccccCHHHHHHHHHHhhHHHHHHHH
Confidence            99999999988889999999999999999999999999999999999998765554445667899999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCCC--CCCCCcceecCCcEEEEeeCC----C
Q 008167          472 ASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRG--QKGSGDWYVDEQQQKIVKMDG----N  545 (575)
Q Consensus       472 a~r~~~~~~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~--~d~~~~~~~d~~~~~l~g~~~----~  545 (575)
                      |+|++.++|+|.||+++++.++|+|++|.++|++|.||++|+||+||++++.  ++|   |.||+.+++++|+++    +
T Consensus       653 aer~~~~~~~~~~l~~~~~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d~---~~fd~~~~~l~g~~~~~~~~  729 (760)
T 2vnu_D          653 AGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNS---AAFDEVEYKLTFVPTNSDKP  729 (760)
T ss_dssp             HHHHHHHHHHHHHHHTCCSEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGGG---CEEETTTTEEEECCTTCSSC
T ss_pred             HHHHHHHHHHHHHhhcCceEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCce---eEEcccccEEEEecCCCccC
Confidence            9999999999999999888999999999999999999999999999999996  665   899999999998775    6


Q ss_pred             eEEeeCcEEEEEEEEecCCCC-CCceEEEe
Q 008167          546 LSYSVLQTVNIHMEVVEPQPN-RPKLQLTL  574 (575)
Q Consensus       546 ~~~~lGD~V~V~V~~vd~~~~-~~~i~l~l  574 (575)
                      ++|++||+|+|+|.+++.+.+ ++||.|+|
T Consensus       730 ~~~~lGD~V~VkV~~vd~~~~~~~kI~lsl  759 (760)
T 2vnu_D          730 RDVYVFDKVEVQVRSVMDPITSKRKAELLL  759 (760)
T ss_dssp             EEEETTCEEEEEEC--------CCEEEC--
T ss_pred             cEEecCCEEEEEEEEEECccccCCcEEEEe
Confidence            999999999999999997532 48999987

>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.8e-127  Score=1103.21  Aligned_cols=563  Identities=46%  Similarity=0.774  Sum_probs=527.4

Q ss_pred             CCCccEEEEEeCCCCCCceEecCCccCcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCCCC
Q 008167            7 SGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDARPF   86 (575)
Q Consensus         7 ~~~~~~~~~~P~d~r~p~i~i~~~~~~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~~f   86 (575)
                      |.+.+++||+|.|+|+|.|.|++++.+...|++|+|+|++||.++.+|.|+|+++||..+++++++++++.+|||+..+|
T Consensus       392 g~~~~~~~~~P~D~ri~~i~I~~~~~~~~~g~~vvv~I~~wp~~~~~p~G~iv~~LG~~~d~~~e~~~il~~~~l~~~~F  471 (977)
T 2wp8_J          392 SSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYRPF  471 (977)
T ss_dssp             CCSCEEEEEEESSTTSCCEEEEETTTTGGGGEEEEEEEEECCTTCSSCEEEEEEEEEESSCSHHHHHHHHHHTTCCCSCC
T ss_pred             CCccceEEEEECCCCCccEEeccccccccCCCEEEEEEeeccCCCCCccEEEEEEeCCCCCcchhHHHHHHHcCCCcccC
Confidence            34557789999999999999999988888899999999999999999999999999999999999999999999998779


Q ss_pred             cHHHHhcCCCC--CCCCC----------cc-ccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccc
Q 008167           87 STQVLACLPPL--PWSVS----------SE-DLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADV  153 (575)
Q Consensus        87 ~~~v~~~~~~~--~~~~~----------~~-~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADv  153 (575)
                      |++|+++++..  +|.++          ++ +..  +|+|||++++|||||++|+||||||||+++++|+|+||||||||
T Consensus       472 p~~vl~~~~~~~~~~~i~~~~~~~~~v~~~~~~~--~R~Dlr~l~~~TID~~~akDlDDAvsie~~~~G~~~lgVHIADV  549 (977)
T 2wp8_J          472 SKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLT--KRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADV  549 (977)
T ss_dssp             CHHHHTTSCTTGGGCCCCSSTTCHHHHHHCGGGG--GCEECTTSCCEEEECTTCSCCCEEEEEEECTTSCEEEEEEEECH
T ss_pred             CHHHHHHHHhcccccccccccccccccccccccc--cceecccCcEEEECCCCCCcccceEEEEEcCCCcEEEEEEeccH
Confidence            99999999988  78765          22 444  89999999999999999999999999999999999999999999


Q ss_pred             cccccCCCHHHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeC
Q 008167          154 TNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALS  233 (575)
Q Consensus       154 s~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~lt  233 (575)
                      |+||+|||+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+||++|+|++++|++|+|+|+++||
T Consensus       550 s~yV~~gS~LD~eA~~RgtSvYLpdrviPMLP~~LS~~lcSL~pg~dRla~Sv~~~id~~G~i~~~~~~~svIrs~~rlt  629 (977)
T 2wp8_J          550 THFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFS  629 (977)
T ss_dssp             HHHSCSSSHHHHHHHHHCBCEEETTEEECSSCHHHHTTTSSCCBTSEEEEEEEEEEECTTSCEEEEEEEEEEEEBSEEEE
T ss_pred             HHeeCCCCHHHHHHHHcCCcEeCCCceEeCCChHHhccccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEEecceEc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHH
Q 008167          234 YVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLA  313 (575)
Q Consensus       234 Y~~v~~~l~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~Mil  313 (575)
                      |++|+++|+++....++.++|..|+++|+.|+++|.++|+++|+.||.+|.+|++.|.|.++.+.++.+||.|||||||+
T Consensus       630 Y~~v~~~l~~~~~~~~l~~~L~~L~~la~~Lr~~R~~~Gai~~~~pE~~~~ld~e~g~~~~i~~~~~~~a~~LIEE~Mll  709 (977)
T 2wp8_J          630 YEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLL  709 (977)
T ss_dssp             HHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHHHHHHTTTCCCCCSHHHHTTSCCTTCCCCCSSCCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCceEEEeccCCCceEEEEecCCCcHHHHHHHHHHH
Confidence            99999999987666788899999999999999999999999999999999999556789988888999999999999999


Q ss_pred             HHHHHHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHc-CCccCCCCHHHHHHHHHHHhC-CChhHHHHHHHHHHhhc
Q 008167          314 ANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAV-GLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCM  391 (575)
Q Consensus       314 AN~~vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~-g~~~~~~~~~~l~~~l~~~~~-~~~~~~~~l~~~~~r~m  391 (575)
                      ||++||+++.++++.|++||+|+.|++++++.|.++++.+ |+.++..++++++++|+++.+ .++.++.+++.+++|+|
T Consensus       710 AN~~vA~~l~~~~~~~~lyR~h~~P~~~kl~~l~~~~~~~~G~~l~~~~~~~l~~~L~~~~~~~~~~~~~ll~~~~lrsm  789 (977)
T 2wp8_J          710 ANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCM  789 (977)
T ss_dssp             HHHHHHHHHHHHCTTTCEEEEBCCCCGGGGHHHHHHHHHHHSCCCCCSSHHHHHHHHHHCCCSSCTTHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhCCCCeEEEeCCCCCHHHHHHHHHHHHHccCCCCCCCCHHHHHHHHHHhhCCchHHHHHHHHHHHHHhc
Confidence            9999999999988899999999999999999999999999 999998899999999998766 56777888999999999


Q ss_pred             cCceecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 008167          392 TQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQM  471 (575)
Q Consensus       392 ~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~  471 (575)
                      ++|+|+++|..++++.+|||||++.|||||||||||+||+|||||+++|.+++.+....+.+.|..+|.+||.++++|+.
T Consensus       790 ~~A~Y~~sg~~s~~~~gHfgLa~~~YtHfTSPIRRY~DLivHR~L~a~L~~~~~~~~~~~~~~l~~i~~~~s~~er~A~~  869 (977)
T 2wp8_J          790 MAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQF  869 (977)
T ss_dssp             CCCEEEEGGGSCGGGSCBTTTTBSSCCCCSCTTTBHHHHHHHHHHHHHTTSSCCCGGGGCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCceeecccccCCCCCCceecCCCCeeccCchHhhHHHHHHHHHHHHHhcCCCCcccccCHHHHHHHHHHhCHHHHHHHH
Confidence            99999999988889999999999999999999999999999999999998776544445678899999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCceeEEEEEEEecCeEEEEEcCCceEEEEEccCCC--CCCCCcceecCCcEEEEeeC----CC
Q 008167          472 ASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRG--QKGSGDWYVDEQQQKIVKMD----GN  545 (575)
Q Consensus       472 a~r~~~~~~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~--~d~~~~~~~d~~~~~l~g~~----~~  545 (575)
                      |+|++.++|++.||+.+.+.++|+|++|.++|++|.||++|+||+||++++.  ++|   |.||+.+++++|++    .+
T Consensus       870 aeR~~~~~~~~~~l~~~ge~~~g~V~~V~~~G~fV~L~~~giEGlVhis~L~~~~d~---y~fde~~~~L~g~~~~g~~~  946 (977)
T 2wp8_J          870 AGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNS---AAFDEVEYKLTFVPTNSDKP  946 (977)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEEEEECSSEEEEECTTTCCEEEEEGGGTCSCGGG---CEEETTTTEEEECCTTCCSC
T ss_pred             HHHHHHHHHHhhhhcccceEEEEEEEEEcCCeEEEEEcCCCeEEEEEeccccCCCce---eEEcccccEEEeecCCCccC
Confidence            9999999999999998878999999999999999999999999999999997  665   89999999999986    36


Q ss_pred             eEEeeCcEEEEEEEEecCCCC-CCceEEEe
Q 008167          546 LSYSVLQTVNIHMEVVEPQPN-RPKLQLTL  574 (575)
Q Consensus       546 ~~~~lGD~V~V~V~~vd~~~~-~~~i~l~l  574 (575)
                      ++|++||+|+|+|.+++.+.. ++||.|+|
T Consensus       947 ~~~~lGD~V~VkV~~vd~~~~~~~kI~Lsl  976 (977)
T 2wp8_J          947 RDVYVFDKVEVQVRSVMDPITSKRKAELLL  976 (977)
T ss_dssp             EEEETTCEEEEEECCCCCSSSCCCCCCEEE
T ss_pred             cEEccCCEEEEEEEEEcCcccCCCceEEEe
Confidence            999999999999999987544 48999987

>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR family, hydrolase; 2.35A {Escherichia coli} SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A

Probab=100.00  E-value=4.5e-118  Score=999.67  Aligned_cols=531  Identities=21%  Similarity=0.274  Sum_probs=476.0

Q ss_pred             ccEEEEEeCCCCCCceEecCCccCc-----CCCCEEEEEEeecCCCCCCc-ceEEEEeecCCCChhhHHHHHHhhCCCCC
Q 008167           10 VAHALFVPKDRRIPKIRIQTRQLGN-----LLDKRIIVAVDSWDCQSRYP-FGHYVRVIGEIGDRDTESEMVLIDNDIDA   83 (575)
Q Consensus        10 ~~~~~~~P~d~r~p~i~i~~~~~~~-----~~~~~~~v~i~~w~~~~~~p-~g~i~~~lG~~~~~~~~~~~il~~~~i~~   83 (575)
                      +..++++|.|++++. .|+.++...     ..|++|+|+|++||.++.+| .|+|+++||..+++++++.++|.+|||+.
T Consensus        94 ~~~~~v~pdd~~~~~-~i~~~~~~~~~~~~~~g~~v~v~i~~~p~~~~~p~~g~i~~~LG~~~d~~~e~~~~l~~~~l~~  172 (644)
T 2id0_A           94 NDRLAIVPDHPLLKD-AIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEK  172 (644)
T ss_dssp             TTEEEEEESSTTCCS-CEECCBCSSCCCCCCSSCEEEEEEEECGGGTCSSCEEEEEEEEECTTCTTHHHHHHHHHTTCCC
T ss_pred             CCEEEEEECCCCccc-cccccccccccccCCCCCEEEEEEecCcCCCCCCceEEEEEEeCCCCCccchHHHHHHHcCCCC
Confidence            346789999999988 888776654     37999999999999999899 99999999999999999999999999998


Q ss_pred             CCCcHHHHhcCCCCCCCCCccccCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHH
Q 008167           84 RPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPL  163 (575)
Q Consensus        84 ~~f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~L  163 (575)
                       .||+++.++       +++ +..  +|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||+|||+|
T Consensus       173 -~fp~~~~~~-------~~~-~~~--~R~Dlr~l~~~TID~~~a~D~DDAvsie~~~~g~~~l~VHIADVs~yV~~gs~L  241 (644)
T 2id0_A          173 -EAPDGVATE-------MLD-EGL--VREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKL  241 (644)
T ss_dssp             -SCCCCCCCC-------CCC-SCC--CCCCCCSSCCBEEECSSCSCCCEEEEECCCSSSCEEEEEEEECGGGTCCTTSHH
T ss_pred             -CCChHHhhc-------CCc-ccc--cceeccCCcEEEEcCCCCCcccceEEEEEcCCCCEEEEEEeccHHHeeCCCCHH
Confidence             588765433       222 223  899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEE-EEEEEEEEeecceeCHHHHHHHhc
Q 008167          164 DDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS-TRYTKSVIKSCAALSYVEAQARMD  242 (575)
Q Consensus       164 D~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~-~~~~~s~I~s~~~ltY~~v~~~l~  242 (575)
                      |+||++||||||||++++||||+.||+++|||+||++|+||||.|+||++|+|++ ++|++|+|+|+++|||++|+++|+
T Consensus       242 D~eA~~RgtSvYlp~~~iPMLP~~Ls~~lcSL~p~~dR~a~s~~~~id~~G~v~~~~~~~~svI~s~~rltY~~v~~~l~  321 (644)
T 2id0_A          242 DKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLE  321 (644)
T ss_dssp             HHHHHHHCBCEEETTEEECSSCHHHHTTTSSCCSSCEEEEEEEEEEECSSCCCSTTCCEEEEEEECCCEEEHHHHHHHTT
T ss_pred             HHHHHHhCCcEeCCCEEEeCCCHHHhcCcccCCCCCceEEEEEEEEEeCCCCEeeccEEEEEEEEeccccCHHHHHHHHh
Confidence            9999999999999999999999999999999999999999999999999999998 999999999999999999999998


Q ss_pred             CCCC----CCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHH
Q 008167          243 DSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSV  318 (575)
Q Consensus       243 ~~~~----~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~v  318 (575)
                      ++..    ..++.++|..|+++|+.|+++|.++|+++|+.||.+|.+|++ |.|.++.+.++++||.|||||||+||++|
T Consensus       322 ~~~~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gai~~~~pe~~~~ld~~-g~~~~i~~~~~~~a~~lIeE~MllAN~~v  400 (644)
T 2id0_A          322 NTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEK-GEVLDIVAEPRRIANRIVEEAMIAANICA  400 (644)
T ss_dssp             CCSSCCCSCHHHHHHHHHHHHHHHHHHHHHHHHSCCCCCCCCEEEEECTT-SCEEEEEECCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCccccccHHHHHHHHHHHHHHHHHHHHHHhCCCccccCCceEEEECCC-CCEEEEEEecCCcHHHHHHHHHHHHHHHH
Confidence            6531    235778999999999999999999999999999999999865 78999999999999999999999999999


Q ss_pred             HHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCccCCC---CHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCce
Q 008167          319 AEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS---SSKALADSLDRAVGDDPYFNKLIRILATRCMTQAV  395 (575)
Q Consensus       319 A~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~  395 (575)
                      |+++.++ ..|++||+|+.|+++++++|.++++.+|+.++..   ++..+++.++.+.+...  . +++.+++|+|++|.
T Consensus       401 A~~l~~~-~~~~lyR~h~~p~~~~l~~l~~~~~~~g~~l~~~~~~~~~~~~~l~~~~~~~~~--~-~l~~~l~r~~~~a~  476 (644)
T 2id0_A          401 ARVLRDK-LGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPT--G-FLDSRIRRFQSFAE  476 (644)
T ss_dssp             HHHHHHH-TSCCCEEEBCCBCTTTHHHHHHHHHHHTCCCCHHHHTSHHHHHHHHHHHHTSSS--S-HHHHHHTTSBCCCE
T ss_pred             HHHHHHc-CCCceeecCCCCCHHHHHHHHHHHHHcCCCCCCCcccCHHHHHHHHHHhcCChH--H-HHHHHHHHhccccc
Confidence            9999998 5799999999999999999999999999988643   34556666666655221  1 56778899999999


Q ss_pred             ecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHH
Q 008167          396 YFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRG  475 (575)
Q Consensus       396 Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~  475 (575)
                      |      ++++.+|||||++.|||||||||||+||+|||||+++|.+++.+.      ..+.+|.+||.++++|+.|+|+
T Consensus       477 y------s~~~~~HfgLa~~~YthfTSPIRRY~DLivHR~l~a~l~~~~~~~------~~~~~~~~~s~~er~a~~aer~  544 (644)
T 2id0_A          477 I------STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR------PQDEITVQMAERRRLNRMAERD  544 (644)
T ss_dssp             E------ESSCCCBTTTTBSSCBCCSCTTTBHHHHHHHHHHHHHTTC----C------CCTTHHHHHHHHHHHHHHHHHH
T ss_pred             c------cCCCCCchhcCCCceeeeCChhhcchHHHHHHHHHHHHcCCCCCc------cHHHHHHHHHHHHHHHHHHHHH
Confidence            9      678899999999999999999999999999999999998764331      1246788999999999999999


Q ss_pred             HHHHHHHHHHhcCC-c--eeEEEEEEEecCeEEEEEcCCceEEEEEccCCCC--CCCCcceecCCcEEEEeeCCCeEEee
Q 008167          476 SVELHTLIYFRKRP-T--DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQ--KGSGDWYVDEQQQKIVKMDGNLSYSV  550 (575)
Q Consensus       476 ~~~~~~~~~l~~~~-~--~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~--d~~~~~~~d~~~~~l~g~~~~~~~~l  550 (575)
                      +.++|+|.||+.++ +  +|+|+|++|+++|+||.|+++|++|+||++.+++  +|   |.||+...+++. +++..|++
T Consensus       545 ~~~~~~~~~l~~~vGe~~~f~g~V~~V~~~G~fV~L~~~gieGlVhis~l~~~~d~---~~~d~~~~~l~~-~~~~~~~l  620 (644)
T 2id0_A          545 VGDWLYARFLKDKAGTDTRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDE---LVCSQENGTVQI-KGETVYKV  620 (644)
T ss_dssp             HHHHHHHHHHGGGTTSCCCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCGGG---EEEETTTTEEEE-TTEEEEET
T ss_pred             HHHHHHHHHhhhccCCCceEEEEEEEEeCCceEEEEcCCcEEEEEEchhccCcCce---eEEcccccEEEe-cCCCEeCC
Confidence            99999999999887 5  8999999999999999999999999999999984  55   899988888754 77889999


Q ss_pred             CcEEEEEEEEecCCCCCCceEEEeC
Q 008167          551 LQTVNIHMEVVEPQPNRPKLQLTLI  575 (575)
Q Consensus       551 GD~V~V~V~~vd~~~~~~~i~l~l~  575 (575)
                      ||+|+|+|.++|.+  +++|.|+|+
T Consensus       621 GD~V~VkV~~vd~~--~~~I~~~l~  643 (644)
T 2id0_A          621 TDVIDVTIAEVRME--TRSIIARPV  643 (644)
T ss_dssp             TCEEEEEEEEEETT--TTEEEEEEC
T ss_pred             CCEEEEEEEEEeCC--CCEEEEEEc
Confidence            99999999999976  899999985

>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure initiative, northeast structural genomics consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5 b.40.4.16 PDB: 2r7f_A

Probab=100.00  E-value=1.9e-99  Score=817.76  Aligned_cols=427  Identities=25%  Similarity=0.314  Sum_probs=374.2

Q ss_pred             CCCcceEEEEeecCCCChhhHHHH-------------HHhhCCCCCCCCcHHHHhcCCCCCCCCCccccCCCCCccCCCC
Q 008167           51 SRYPFGHYVRVIGEIGDRDTESEM-------------VLIDNDIDARPFSTQVLACLPPLPWSVSSEDLANPIRLDLRDL  117 (575)
Q Consensus        51 ~~~p~g~i~~~lG~~~~~~~~~~~-------------il~~~~i~~~~f~~~v~~~~~~~~~~~~~~~~~~~~R~Dlr~~  117 (575)
                      +..|.|+|+++||..++++.+.+.             ++.+|+++. .||     +++   ..  +.+.. .+|+|||++
T Consensus        20 ~~~~~g~i~~~LG~~~~~~~~~~lL~~~G~~~~~~~~~~~~~~lp~-~fp-----~l~---~~--~~~~~-~~R~Dlr~l   87 (469)
T 2r7d_A           20 GRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAAL-NAV-----ELP---VP--DFDPA-EERLDLTHL   87 (469)
T ss_dssp             TSCSCCHHHHHTTCCCSHHHHHHHHHHHTSSCTTCCCHHHHTTCCC-SCC-----CCC---CC--CCCTT-SCCEECTTS
T ss_pred             CCCcceeEeeecCCCCChhhHHHHHHhcCCCCchhhHHHHHcCCCC-CCc-----ccC---CC--Ccccc-cCceecccC
Confidence            467999999999999999999865             455789988 588     121   11  22220 279999999


Q ss_pred             eEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHhCCCceEcCCccccCCChhhhccccCCCC
Q 008167          118 RVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRA  197 (575)
Q Consensus       118 ~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~  197 (575)
                      ++|||||++|+|+||||||+++++|+|+|||||||||+||+|||+||+||++||||||||++++||||+.| +++|||+|
T Consensus        88 ~~~TID~~~a~D~DDAvsve~~~~g~~~l~VHIADVs~~V~~gs~LD~eA~~RgtSvYlp~~~ipMLP~~L-~~~cSL~p  166 (469)
T 2r7d_A           88 PTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDEL-VAKAGLGL  166 (469)
T ss_dssp             CEEEEECTTCCCCCEEEEEEECSTTCEEEEEEEECGGGTCCTTSHHHHHHHHHCBCEECSSCEECSSCHHH-HHHHSTTS
T ss_pred             CEEEEcCCCCCCccceEEEEEeCCCCEEEEEEeccHhheeCCCCHHHHHHHHhCceEecCCceEcCCChHH-hcccCCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999 89999999


Q ss_pred             CCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhcCCcccc
Q 008167          198 DVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLA  277 (575)
Q Consensus       198 ~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~  277 (575)
                      |++|+||||.|+||++|+|++++|++|+|+|+ +|||++|+++|+++      .++|..|+++|+.|+++|.++|+++|+
T Consensus       167 g~dr~als~~~~id~~G~i~~~~~~~svI~s~-rltY~~v~~~l~~~------~~~L~~L~~la~~lr~~R~~~Gai~~~  239 (469)
T 2r7d_A          167 HEVSPALSICLDLDPDGNAEAVDVLLTRVKVQ-RLAYQEAQARLEAG------EEPFVTLARLARASRRLREGEGALSID  239 (469)
T ss_dssp             SSSEEEEEEEEEECTTSCEEEEEEEEEEECEE-EEEHHHHHHHHHTT------CTTHHHHHHHHHHHHHHHHHTTCCCCC
T ss_pred             CCceEEEEEEEEEcCCCCEeeeEEEEEEEEec-cccHHHHHHHHhCC------cHHHHHHHHHHHHHHHHHHhCCCcccC
Confidence            99999999999999999999999999999999 99999999999875      146999999999999999999999999


Q ss_pred             CcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHcCCcc
Q 008167          278 SAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNL  357 (575)
Q Consensus       278 ~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~g~~~  357 (575)
                      .||.+|.+|++   +..+...++++|+.|||||||+||++||+++.++ +.|++||+|+.|+.+++              
T Consensus       240 ~pe~~i~~d~~---~~~i~~~~~~~a~~lIeE~MilAN~~vA~~l~~~-~ip~~yR~h~~p~~~~~--------------  301 (469)
T 2r7d_A          240 LPEVRVKADET---GASVFPLPKPEMRTVVQECMTLAGWGTAIFADDN-EIPLPFATQDYPTREVA--------------  301 (469)
T ss_dssp             CCCEEEEEETT---EEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHT-TCCCCEEEECCCSSCCC--------------
T ss_pred             CCceEEEECCC---cceEEecCCCcHHHHHHHHHHHHHHHHHHHHHHc-CCCeeEeeCCCCCcccC--------------
Confidence            99999999864   7788888999999999999999999999999987 88999999999987653              


Q ss_pred             CCCCHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHH
Q 008167          358 DVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLS  437 (575)
Q Consensus       358 ~~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~  437 (575)
                      .                ...    +++.+++|+|++|.|      +..|.+|||||++.|||||||||||+||+|||||+
T Consensus       302 ~----------------~~~----~~~~~l~r~m~~a~y------~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~  355 (469)
T 2r7d_A          302 G----------------DTL----PAMWARRKTLARTRF------QPSPGPHHGMGLDLYAQATSPMRRYLDLVVHQQLR  355 (469)
T ss_dssp             C----------------CSH----HHHHHHHHHCCCEEE------ESSCCCBTTTTBSCCCCCSCTTTBHHHHHHHHHHH
T ss_pred             c----------------chH----HHHHHHHHhcccccc------cCCCCCchhhCccceeeECCcccccHHHHHHHHHH
Confidence            0                011    244567899999999      45689999999999999999999999999999999


Q ss_pred             HHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEE
Q 008167          438 ASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGP  516 (575)
Q Consensus       438 ~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~  516 (575)
                      ++|.+++ +   ++.++|+.+|.+||.+++.|++|||++.++|++.||+++. ++|+|+|+.+...+..|.++++|.+  
T Consensus       356 a~l~~~~-~---~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~~l~~~~g~~f~g~vv~l~~~~glV~v~~l~~d--  429 (469)
T 2r7d_A          356 AFLAGRD-P---LSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQPERVWDAVVVDRRGAQATLLIPDLAFD--  429 (469)
T ss_dssp             HHHTTCC-C---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCEEEEEEEEETTEEEEEEGGGTEE--
T ss_pred             HHHcCCC-C---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCEEEEEEEEEeCcEEEEEECCCCeE--
Confidence            9998762 2   3467899999999999999999999999999999999876 7899999876544444444444433  


Q ss_pred             EEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCceEEEe
Q 008167          517 VYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTL  574 (575)
Q Consensus       517 v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~i~l~l  574 (575)
                                          .     +.++.|++||+|+|+|.+||..  +++|.|++
T Consensus       430 --------------------~-----~~~~~~~lGd~V~V~v~~vd~~--~~~i~f~~  460 (469)
T 2r7d_A          430 --------------------V-----QVNTPAAPGTALQVQFADIDLP--QMRVRARS  460 (469)
T ss_dssp             --------------------E-----EEECCCCTTCEEEEEEEEEETT--TTEEEEEE
T ss_pred             --------------------E-----ecCCcCCCCCEEEEEEEEEccC--CCEEEEEE
Confidence                                0     1135799999999999999976  89999976

>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5

Probab=98.85  E-value=9.4e-10  Score=91.17  Aligned_cols=74  Identities=9%  Similarity=0.110  Sum_probs=60.6

Q ss_pred             HHHhcCC-ceeEEEEEEEecCeEEEEEcCC-ceEEEEEcc-CCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEE
Q 008167          483 IYFRKRP-TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLT-PRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME  559 (575)
Q Consensus       483 ~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~-~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~  559 (575)
                      .|+..+. +.++|+|+ +.++|+||.|+++ |++|+||++ ++++++   +.+.           ...+ +||+|+|+|.
T Consensus         5 ~y~~~~vG~~~~G~V~-v~~fG~FVel~~~~~~eGLvhis~el~~~~---~~~~-----------~~~~-~Gd~V~VkV~   68 (88)
T 1luz_A            5 CYSLPNAGDVIKGRVY-EKDYALYIYLFDYPHFEAILAESVKMHMDR---YVEY-----------RDKL-VGKTVKVKVI   68 (88)
T ss_dssp             CSCCCCTTCEEEEEEE-EETTEEEEEETTCTTSEEEEGGGSSCCHHH---HHHH-----------HHHH-TTCEEEEEEE
T ss_pred             EecCCCCCCEEEEEEE-EEccEEEEEECCCCCeEEEEEeeHHhCccc---ccCH-----------hHEe-CCCEEEEEEE
Confidence            3555554 78999999 9999999999886 899999999 997653   3322           2456 9999999999


Q ss_pred             EecCCCCCCceEEEe
Q 008167          560 VVEPQPNRPKLQLTL  574 (575)
Q Consensus       560 ~vd~~~~~~~i~l~l  574 (575)
                      ++|.+  ++||+|++
T Consensus        69 ~vd~~--~~kI~lsl   81 (88)
T 1luz_A           69 RVDYT--KGYIDVNY   81 (88)
T ss_dssp             EEETT--TTEEEEEE
T ss_pred             EEECC--CCEEEEEE
Confidence            99976  89999986

>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E 4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E

Probab=98.82  E-value=8.4e-09  Score=97.25  Aligned_cols=80  Identities=15%  Similarity=0.188  Sum_probs=69.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCC--CC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQP--NR  567 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~--~~  567 (575)
                      +.++|+|++++++|+||.+.  +++|++|.+++.+++   |.||+....+.|++++..|++||+|+|+|.+++.+.  ..
T Consensus        83 ev~~G~V~~v~~~G~fv~l~--~~~glvh~s~l~~d~---~~~d~~~~~~~g~~~~~~~~~Gd~VrvkV~~v~~~~~~~~  157 (180)
T 4ayb_E           83 EVVEGEVLQVDNYGVFVNLG--PMDGLVHISQITDDT---LKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTGRL  157 (180)
T ss_dssp             CEEEEEEEEEETTEEEEECS--SSEEEEEGGGSCSSC---EEECSSSCCEEETTTCCCCCTTCEEEEEEEEECC------
T ss_pred             CEEEEEEeeeccceEEEEEC--CccceEEeeecCCCc---cccchhcceEEEeccCeEECCCCEEEEEEEEEeCCCCccc
Confidence            78999999999999999986  589999999999987   899999999999999999999999999999999753  24


Q ss_pred             CceEEEe
Q 008167          568 PKLQLTL  574 (575)
Q Consensus       568 ~~i~l~l  574 (575)
                      .||.||+
T Consensus       158 ~rI~ls~  164 (180)
T 4ayb_E          158 PRIALTM  164 (180)
T ss_dssp             -CEEEEC
T ss_pred             CcEEEEc
Confidence            5788875

>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=98.81  E-value=2.6e-09  Score=103.40  Aligned_cols=81  Identities=12%  Similarity=0.080  Sum_probs=71.4

Q ss_pred             HHHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEe---eCCCeEEeeCcEEE
Q 008167          480 HTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK---MDGNLSYSVLQTVN  555 (575)
Q Consensus       480 ~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g---~~~~~~~~lGD~V~  555 (575)
                      +.|.||+.+. ++++|+|++|+++|+||.|+. .++|+++.+.+.+++   |.||+..+.++|   +++++.|++||+|+
T Consensus        72 fk~~~f~p~vGEv~~G~Is~Vt~fGifVeL~g-~~eglv~~s~l~~d~---~~fd~~~~~~vg~~~e~t~~~~~~Gd~Vr  147 (218)
T 2ckz_B           72 FRAVVFKPFLGEIVTGWISKCTAEGIKVSLLG-IFDDIFIPQNMLFEG---CYYTPEESAWIWPMDEETKLYFDVNEKIR  147 (218)
T ss_dssp             EEEEEECCCTTCEEEEEEEEEETTEEEEECTT-SCCCEEEETTTSCTT---CEEETTTTEEEEECC--CEEEECTTCEEE
T ss_pred             EEEEEecCCCCCEEEEEEEEEccCcEEEEccC-ccceEEEcHHHCCCC---cEEcCcCceEEeeccccCCcEEcCCCEEE
Confidence            3567888876 889999999999999999976 589999999998887   899999999999   77889999999999


Q ss_pred             EEEEEecCC
Q 008167          556 IHMEVVEPQ  564 (575)
Q Consensus       556 V~V~~vd~~  564 (575)
                      |+|.+++..
T Consensus       148 vrV~~v~~~  156 (218)
T 2ckz_B          148 FRIEREVFV  156 (218)
T ss_dssp             EEEEEEEEC
T ss_pred             EEEEEEEcc
Confidence            999999975

>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5

Probab=98.69  E-value=2e-08  Score=94.30  Aligned_cols=77  Identities=13%  Similarity=0.128  Sum_probs=57.4

Q ss_pred             HHHHhc---CC-ceeEEEEEEEecCeEEEEEcC-CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167          482 LIYFRK---RP-TDTEARIVKIRSNGFIVFVPK-FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI  556 (575)
Q Consensus       482 ~~~l~~---~~-~~~~g~V~~v~~~g~~V~l~~-~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V  556 (575)
                      |+||++   .. ..+.|+|++|.++|+||.|++ .|++|+||+++++.++    .          .+....|++||.|+|
T Consensus         5 ~~~~~~~~p~~G~iv~G~V~~I~~fGaFV~L~e~~g~eGLvhiSels~~~----v----------~~~~~~~~vGd~V~V   70 (182)
T 1kl9_A            5 CRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRR----I----------RSINKLIRIGRNECV   70 (182)
T ss_dssp             CCSSSSSSCCTTCEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC--------------------------CTTCEEEE
T ss_pred             eEeccccCCCCCCEEEEEEEEEeccEEEEEEccCCCcEEEEEHHHCCCcc----c----------CCHHHhcCCCCEEEE
Confidence            667765   22 789999999999999999953 4899999999997543    1          135678999999999


Q ss_pred             EEEEecCCCCCCceEEEe
Q 008167          557 HMEVVEPQPNRPKLQLTL  574 (575)
Q Consensus       557 ~V~~vd~~~~~~~i~l~l  574 (575)
                      +|.++|.+  +++|+||+
T Consensus        71 kVl~vD~~--~~rI~LSl   86 (182)
T 1kl9_A           71 VVIRVDKE--KGYIDLSK   86 (182)
T ss_dssp             EEEEEETT--TTEEEEES
T ss_pred             EEEEEECC--CCEEEEEE
Confidence            99999975  89999987

>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1

Probab=98.66  E-value=8.2e-08  Score=91.00  Aligned_cols=80  Identities=14%  Similarity=0.171  Sum_probs=68.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC---
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN---  566 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~---  566 (575)
                      +.++|+|+++.++|+||.|.  +++|++|.+++.+++   +.||+...++++++....|++||.|+|+|.+++.+..   
T Consensus        83 ev~~G~V~~v~~~G~fV~l~--~~eglvhis~l~~~~---~~~d~~~~~~~~~~~~~~~~~Gd~V~vkV~~vd~~~~~p~  157 (187)
T 1go3_E           83 ELIEGEVVDVVEFGSFVRLG--PLDGLIHVSQIMDDY---VSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKR  157 (187)
T ss_dssp             CEEEEEEEEEETTEEEEECS--SSEEEEEGGGSCSSC---EEECCC--CEEETTTCCEECTTCEEEEEEEEEECCC----
T ss_pred             CEEEEEEEEEeCcEEEEEEc--CccEEEEhHHhCCCc---ceECCccceEEecCCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence            78999999999999999995  489999999998775   7899988999988888999999999999999997532   


Q ss_pred             CCceEEEe
Q 008167          567 RPKLQLTL  574 (575)
Q Consensus       567 ~~~i~l~l  574 (575)
                      ..+|.||+
T Consensus       158 ~~~I~lS~  165 (187)
T 1go3_E          158 GSKIALTM  165 (187)
T ss_dssp             -CEEEEEC
T ss_pred             ccEEEEEE
Confidence            23888886

>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha; transferase, protein biosynthesis, protein synthesis transferase complex; HET: TPO ANP; 2.50A {Saccharomyces cerevisiae} PDB: 2a1a_A* 1q46_A

Probab=98.65  E-value=2.7e-08  Score=93.03  Aligned_cols=77  Identities=13%  Similarity=0.092  Sum_probs=59.6

Q ss_pred             HHHHhcC---C-ceeEEEEEEEecCeEEEEEcC-CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167          482 LIYFRKR---P-TDTEARIVKIRSNGFIVFVPK-FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI  556 (575)
Q Consensus       482 ~~~l~~~---~-~~~~g~V~~v~~~g~~V~l~~-~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V  556 (575)
                      |+|+++.   . ..+.|+|++|.++|+||.|++ .|++|+||+++++.++    .          .+....|++||.|+|
T Consensus         5 ~~~~~~~~p~~G~iv~G~V~~i~~fGaFV~L~e~~gveGLvhiSels~~~----v----------~~~~~~~~vGd~V~v   70 (175)
T 2a19_A            5 CRFYENKYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRR----I----------RSIQKLIRVGKNDVA   70 (175)
T ss_dssp             CCSSSSSSCCTTCEEEEEEEEEETTEEEEEETTTTTCEEEEECC----------------------CCCCCCCTTSEEEE
T ss_pred             eEEhhhcCCCCCCEEEEEEEEEecceEEEEEcCCCCcEEEEEHHHcCCcc----c----------CCHHHcCCCCCEEEE
Confidence            4566665   3 789999999999999999963 4899999999997542    1          245678999999999


Q ss_pred             EEEEecCCCCCCceEEEe
Q 008167          557 HMEVVEPQPNRPKLQLTL  574 (575)
Q Consensus       557 ~V~~vd~~~~~~~i~l~l  574 (575)
                      +|.++|.+  +++|.||+
T Consensus        71 kVl~vd~~--~~~I~LSl   86 (175)
T 2a19_A           71 VVLRVDKE--KGYIDLSK   86 (175)
T ss_dssp             EEEEEETT--TTEEEEES
T ss_pred             EEEEEECC--CCeEEEEE
Confidence            99999975  89999986

>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii}

Probab=98.65  E-value=6.6e-08  Score=78.51  Aligned_cols=65  Identities=11%  Similarity=0.138  Sum_probs=57.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +.+.|.|+++.++|+||.|++ +++|+||++++..++   +               ..|++||+|+|+|.++|.+  ++|
T Consensus         7 ~iv~G~V~~v~~~G~fV~l~~-~~~Gllh~sel~~~~---~---------------~~~~~Gd~V~v~V~~vd~~--~~~   65 (80)
T 2k52_A            7 KFYKGVVTRIEKYGAFINLNE-QVRGLLRPRDMISLR---L---------------ENLNVGDEIIVQAIDVRPE--KRE   65 (80)
T ss_dssp             CEEEEEEEEEETTEEEEEEET-TEEEEECGGGCSSCC---G---------------GGCCTTCEEEEEEEEEETT--TTE
T ss_pred             CEEEEEEEEEeCCEEEEEECC-CCEEEEEHHHCCccc---c---------------eeeCCCCEEEEEEEEEECC--CCE
Confidence            679999999999999999987 899999999987542   1               4599999999999999975  799


Q ss_pred             eEEEeC
Q 008167          570 LQLTLI  575 (575)
Q Consensus       570 i~l~l~  575 (575)
                      |.|++.
T Consensus        66 i~lsl~   71 (80)
T 2k52_A           66 IDFKYI   71 (80)
T ss_dssp             EEEEEC
T ss_pred             EEEEEe
Confidence            999973

>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: b.40.4.5 d.230.1.1

Probab=98.64  E-value=7.6e-08  Score=89.97  Aligned_cols=76  Identities=11%  Similarity=0.099  Sum_probs=64.6

Q ss_pred             HHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCc--EEEEeeCCCeEEeeCcEEEEEEE
Q 008167          483 IYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQ--QKIVKMDGNLSYSVLQTVNIHME  559 (575)
Q Consensus       483 ~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~--~~l~g~~~~~~~~lGD~V~V~V~  559 (575)
                      .+++... +.++|+|++++++|+||.|.  ..+|+||++.+++.    |.||+..  .+|+|++++..|++||.|+|+|.
T Consensus        75 ~~~~~~~Gev~~G~V~~v~~fG~fV~l~--~~~glvhis~l~~~----~~~d~~~~~~~~~~~~~~~~~~~Gd~V~vkV~  148 (172)
T 2c35_B           75 IVFRPFKGEVVDAVVTQVNKVGLFTEIG--PMSCFISRHSIPSE----MEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIV  148 (172)
T ss_dssp             EEECCCTTCEEEEEEEEEETTEEEEEET--TEEEEEEGGGSCTT----EEEESSSSSCEEEETTSCSEEETTCEEEEEEE
T ss_pred             EEeeCCCCCEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHCCCC----cEECCCCCccEEEeCCCCEEECCCCEEEEEEE
Confidence            3455555 78999999999999999995  57899999999643    6777766  78898888899999999999999


Q ss_pred             EecCC
Q 008167          560 VVEPQ  564 (575)
Q Consensus       560 ~vd~~  564 (575)
                      ++|.+
T Consensus       149 ~vd~~  153 (172)
T 2c35_B          149 GTRVD  153 (172)
T ss_dssp             EEEEE
T ss_pred             EEEcC
Confidence            99975

>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain, transcription, RNA binding protein; 2.27A {Pseudomonas aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5 c.55.3.13 PDB: 3bzk_A 2oce_A

Probab=98.61  E-value=1.5e-08  Score=114.50  Aligned_cols=166  Identities=14%  Similarity=0.157  Sum_probs=108.1

Q ss_pred             hhhHHHHHHHHHHcCCcc--CC--CCHHHHH---HHHHHHhCCChhHHHHH-HHHHHhhccCceecccCCCCCCCCCccc
Q 008167          340 KEMLEPLLRTAAAVGLNL--DV--SSSKALA---DSLDRAVGDDPYFNKLI-RILATRCMTQAVYFCSGDLTPPEFHHYG  411 (575)
Q Consensus       340 ~~~~~~l~~~~~~~g~~~--~~--~~~~~l~---~~l~~~~~~~~~~~~~l-~~~~~r~m~~a~Y~~~~~~~~~~~~H~g  411 (575)
                      +..++.+..++.-.|...  +.  ..+.+++   +.+..+ +. + ...++ +...+|+|.+|.|      +.   .|||
T Consensus       548 ~k~~ekl~~FL~i~G~~~pLD~t~VHPEsY~~a~kil~~~-g~-~-~e~li~~~~~Lrsl~~a~Y------a~---~hfG  615 (785)
T 3bzc_A          548 EKTFEQAAGFLRVMNGDNPLDASAVHPETYPLVQRIAADT-ER-D-IRSLIGDSAFLKRLDPKKF------TD---ETFG  615 (785)
T ss_dssp             HHHHHHHGGGEECTTSSCGGGGSSCCGGGHHHHHHHHHHH-TC-C-HHHHTTCHHHHHHSCGGGT------CC---SSSC
T ss_pred             HHHHHHhhheEEECCcccccccCcCCHHHHHHHHHHHHHc-CC-C-HHHHhhhHHHHHhcCHHHH------hh---hcCC
Confidence            445555555555555432  21  2455554   555554 32 2 23444 5567899999999      31   4999


Q ss_pred             cCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CC-
Q 008167          412 LAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRK-RP-  489 (575)
Q Consensus       412 L~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~~l~~-~~-  489 (575)
                      |+                 .+||+++.++....-+...+....+   +              ++.      .-+++ ++ 
T Consensus       616 l~-----------------tl~rIi~eL~kpg~d~R~~~~~~~~---~--------------~~v------e~~~~l~vG  655 (785)
T 3bzc_A          616 LP-----------------TVTDILKELDKPGRDPRPEFKTAEF---Q--------------EGV------ESLKDLKPG  655 (785)
T ss_dssp             HH-----------------HHHHHHHHHHSTTCCCSCCCCTTTT---C--------------CCC------CSSTTCCTT
T ss_pred             cH-----------------HHHHHHHHHhccCCChhhhcccchh---h--------------hcc------cchhhcCCC
Confidence            76                 8999999988543212111111111   0              000      00112 22 


Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      .+++|+|++|.+||+||.|. .+++|+||++++++.    |.++          .+..|++||.|+|+|.+||.+  +++
T Consensus       656 ~iv~G~V~~V~~fGaFV~l~-~~~eGLVhiS~Lsd~----~v~d----------~~~~~~vGd~V~VkVi~VD~~--~~r  718 (785)
T 3bzc_A          656 MVLEGVVTNVTNFGAFVDIG-VHQDGLVHISALSEK----FVKD----------PYEVVKAGDIVKVKVMEVDIP--RNR  718 (785)
T ss_dssp             CBCCCEEEEEETTEEEEECS-SSSEEEEETTTSCSS----CCSC----------HHHHCCTTCCCCCBEEEEETT--TTE
T ss_pred             CEEEEEEEEEecCCeEEEeC-CCcEEEEEHHHcCcc----ccCC----------hhheeCCCCEEEEEEEEEECC--CCE
Confidence            68999999999999999996 489999999999864    4443          357799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       719 I~LSl  723 (785)
T 3bzc_A          719 VGLSM  723 (785)
T ss_dssp             EEECC
T ss_pred             EEEEE
Confidence            99986

>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis}

Probab=98.58  E-value=1.1e-07  Score=84.57  Aligned_cols=68  Identities=18%  Similarity=0.226  Sum_probs=58.7

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|++|.++|+||.|++ |++|+||++++.+++    ..          +....|++||.|+|+|..+|.+  +++
T Consensus         9 ~iv~G~V~~i~~~G~FV~l~~-~~~Glihisel~~~~----~~----------~~~~~~~vGd~V~vkV~~vd~~--~~k   71 (130)
T 2k4k_A            9 SVYTGKVTGLQAYGAFVALDE-ETQGLVHISEVTHGF----VK----------DINEHLSVGDEVQVKVLAVDEE--KGK   71 (130)
T ss_dssp             CEEEEEEEEEETTEEEEEEET-TEEEEEEGGGTSSSC----CS----------CGGGTCCTTCEEEEEEEEEETT--TTE
T ss_pred             CEEEEEEEEEeCCeEEEEECC-CcEEEEEHHHCCccc----cc----------CccccCCCCCEEEEEEEEEeCC--CCE
Confidence            678999999999999999986 899999999998653    21          2356799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        72 I~LSl   76 (130)
T 2k4k_A           72 ISLSI   76 (130)
T ss_dssp             EEEES
T ss_pred             EEEEE
Confidence            99986

>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=98.54  E-value=2.2e-08  Score=96.01  Aligned_cols=79  Identities=13%  Similarity=0.075  Sum_probs=70.2

Q ss_pred             HHHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEe--------eCCCeEEeeC
Q 008167          481 TLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK--------MDGNLSYSVL  551 (575)
Q Consensus       481 ~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g--------~~~~~~~~lG  551 (575)
                      .+.||+.+. ++++|+|++++++|+||.|.  .++|.+|.+++.+++   |.||+....++|        +++++.|++|
T Consensus        73 k~~~f~p~~GEv~~G~Vs~vt~~GifV~lg--~~eglv~~~~l~~d~---~~fd~~~~~~v~~~~~~~~~~~~~~~~~~G  147 (203)
T 3ayh_B           73 RLIIFRPFRGEVMLGKIKSCSEEGIRVTIS--FFDDIFIPKDMLFDP---CVFRPDERAWVWKIEGEDGSEGTELYFDID  147 (203)
T ss_dssp             EEEEECCCTTCEEEEEEEEEETTEEEEECS--SCCCEEEEGGGBCTT---EEEEGGGTEEEEEECCCTTSCCEEEECCTT
T ss_pred             EEEEEccCCCCEEEEEEEEEeccEEEEEEe--CceEEEEcHHhCCCC---ceECccCceEEeecccccccccCCcEEcCC
Confidence            456777776 88999999999999999994  689999999998876   899999999998        7778999999


Q ss_pred             cEEEEEEEEecCC
Q 008167          552 QTVNIHMEVVEPQ  564 (575)
Q Consensus       552 D~V~V~V~~vd~~  564 (575)
                      |+|+|+|.+++..
T Consensus       148 d~VrvrV~~v~~~  160 (203)
T 3ayh_B          148 EEIRFQIESEDFV  160 (203)
T ss_dssp             CEEEEEEEEEEEC
T ss_pred             CEEEEEEEEEEcc
Confidence            9999999999873

>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.52  E-value=5e-08  Score=85.46  Aligned_cols=71  Identities=17%  Similarity=0.113  Sum_probs=58.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|++|.++|+||.|+.++.+|+||++++.+++    .          .+....|++||.|+|+|..+|.+..+++
T Consensus        24 ~iv~G~V~~I~~fGaFV~l~g~~~~Glvhisel~~~~----~----------~~~~~~~~~Gd~V~VkV~~vd~~~~~~~   89 (119)
T 2cqo_A           24 TIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCR----V----------DKPSEIVDVGDKVWVKLIGREMKNDRIK   89 (119)
T ss_dssp             CEEEEEEEEEETTEEEEECTTCSSCEEEEHHHHCSSC----C----------SCHHHHCCTTCEEEEEEEEEEECSSCEE
T ss_pred             CEEEEEEEEEeCceEEEEECCCcEEEEEEHHHCCccc----c----------cChhhcCCCCCEEEEEEEEEeccccCce
Confidence            6899999999999999999866689999999987653    1          1345679999999999999997522469


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus        90 i~LSl   94 (119)
T 2cqo_A           90 VSLSM   94 (119)
T ss_dssp             EEEES
T ss_pred             EEEEE
Confidence            99986

>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=98.51  E-value=1.4e-07  Score=82.16  Aligned_cols=69  Identities=19%  Similarity=0.290  Sum_probs=58.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|+|+++.++|+||.|++ |++|+||++++..+.   +.          .+....|++||.|+|+|..+|.+  +++
T Consensus        32 ~~~~G~V~~v~~~G~FV~l~~-~~~Glvhisel~~~~---~~----------~~~~~~~~vGd~V~vkV~~vd~~--~~r   95 (115)
T 2khi_A           32 TKLTGRVTNLTDYGCFVEIEE-GVEGLVHVSEMDWTN---KN----------IHPSKVVNVGDVVEVMVLDIDEE--RRR   95 (115)
T ss_dssp             CEEEEEEEEEETTEEEEECST-TCEEEEETTSSSCSS---TT----------CSSTTTCCTTCEEEEEEEEEETT--TTE
T ss_pred             CEEEEEEEEEECCEEEEEECC-CCEEEEEHHHCCccc---cc----------cCcccEECCCCEEEEEEEEEECC--CCE
Confidence            689999999999999999975 899999999886421   11          24566799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus        96 I~lsl  100 (115)
T 2khi_A           96 ISLGL  100 (115)
T ss_dssp             EEECC
T ss_pred             EEEEE
Confidence            99986

>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.49  E-value=1.3e-07  Score=80.62  Aligned_cols=68  Identities=18%  Similarity=0.146  Sum_probs=57.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC--ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF--GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR  567 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~--gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~  567 (575)
                      +.+.|.|++|.++|+||.|.++  +++|+||++++.+++   +.          .+....|++||.|+|+|..+|.    
T Consensus        14 ~i~~G~V~~v~~fG~FV~l~~~~~~~~Glvhisel~~~~---~~----------~~~~~~~~~Gd~V~VkV~~vd~----   76 (103)
T 2eqs_A           14 DIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREG---RV----------ANVADVVSKGQRVKVKVLSFTG----   76 (103)
T ss_dssp             CEEEEEEEEECSSCEEEEECSSSSCCEEEECGGGTSSSS---CC----------CCHHHHCCTTCEEEEEEEEEET----
T ss_pred             CEEEEEEEEEeccEEEEEEcCCCCCeEEEEEHHHCCCCc---cc----------CCcccEeCCCCEEEEEEEEEEC----
Confidence            6899999999999999999875  899999999995442   11          2345679999999999999994    


Q ss_pred             CceEEEe
Q 008167          568 PKLQLTL  574 (575)
Q Consensus       568 ~~i~l~l  574 (575)
                      .||.||+
T Consensus        77 ~~i~LSl   83 (103)
T 2eqs_A           77 TKTSLSM   83 (103)
T ss_dssp             TEEEEES
T ss_pred             CeeEEEE
Confidence            5899886

>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent RNA polymerase, cellular RNA polymerase; 4.15A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1

Probab=98.44  E-value=3.2e-07  Score=88.47  Aligned_cols=73  Identities=14%  Similarity=0.108  Sum_probs=60.8

Q ss_pred             HHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcE--EEEeeCCCeEEeeCcEEEEEEEE
Q 008167          484 YFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQ--KIVKMDGNLSYSVLQTVNIHMEV  560 (575)
Q Consensus       484 ~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~--~l~g~~~~~~~~lGD~V~V~V~~  560 (575)
                      +++... ++++|+|+++.++|+||.|..  ++|+||++.+++.    |.||+...  .+.+++  +.|++||.|+|+|.+
T Consensus        78 ~~~p~vGev~~G~V~~vt~fG~FVelg~--~dGlVhiS~l~d~----~~~d~~~~~w~~~~~~--~~~~~Gd~VrVkV~~  149 (215)
T 2b8k_G           78 VFKPFKGEVVDGTVVSCSQHGFEVQVGP--MKVFVTKHLMPQD----LTFNAGSNPPSYQSSE--DVITIKSRIRVKIEG  149 (215)
T ss_dssp             EECCCTTEEEEEEEEEEETTEEEEECTT--SEEEEEGGGSCSS----CCCBSSCSSCEEECSS--CEEETTCEEEEEEEE
T ss_pred             eeccCCCCEEEEEEEEEecceEEEEecC--cEEEEEHHHCCcc----ceeccccccceeeccc--cEECCCCEEEEEEEE
Confidence            455555 789999999999999999964  8999999999653    67777655  677654  679999999999999


Q ss_pred             ecCC
Q 008167          561 VEPQ  564 (575)
Q Consensus       561 vd~~  564 (575)
                      +|.+
T Consensus       150 vd~~  153 (215)
T 2b8k_G          150 CISQ  153 (215)
T ss_dssp             EEEE
T ss_pred             EEcC
Confidence            9975

>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G 1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G* 2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H 3hou_G* 3hov_G* ...

Probab=98.44  E-value=4e-07  Score=84.90  Aligned_cols=75  Identities=13%  Similarity=0.113  Sum_probs=59.3

Q ss_pred             HHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcE--EEEeeCCCeEEeeCcEEEEEE
Q 008167          482 LIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQ--KIVKMDGNLSYSVLQTVNIHM  558 (575)
Q Consensus       482 ~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~--~l~g~~~~~~~~lGD~V~V~V  558 (575)
                      +.+++... +.++|+|++++++|+||.+..  .+|+||++.+++.    |.||+...  ++.+++  +.|++||.|+|+|
T Consensus        76 ~~~~~~~~Gev~~G~V~~v~~fG~FV~l~~--~dglvhis~l~~~----~~~d~~~~~~~~~~~~--~~~~~Gd~V~vkV  147 (171)
T 1y14_B           76 AVVFKPFKGEVVDGTVVSCSQHGFEVQVGP--MKVFVTKHLMPQD----LTFNAGSNPPSYQSSE--DVITIKSRIRVKI  147 (171)
T ss_dssp             EEEECCCTTCEEEEEEEEEETTEEEEEETT--EEEEEEGGGSCTT----CEECC-----CEECSS--CEECTTCEEEEEE
T ss_pred             EEEccCCCCCEEEEEEEEEecCEEEEEecC--eEEEEEHHHCCCC----ceECcccCceEEeccc--eEECCCCEEEEEE
Confidence            33445544 789999999999999999974  9999999999753    67877655  566544  6799999999999


Q ss_pred             EEecCC
Q 008167          559 EVVEPQ  564 (575)
Q Consensus       559 ~~vd~~  564 (575)
                      .++|.+
T Consensus       148 ~~vd~~  153 (171)
T 1y14_B          148 EGCISQ  153 (171)
T ss_dssp             EEEEEE
T ss_pred             EEEEcC
Confidence            999975

>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli}

Probab=98.39  E-value=2.9e-07  Score=79.34  Aligned_cols=68  Identities=18%  Similarity=0.278  Sum_probs=58.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|+||.|++ |++|+||.+++.+++    .          .+....|++||+|+|+|..+|.+  +++
T Consensus        33 ~iv~G~V~~v~~~G~fV~l~~-~~~Gll~~sel~~~~----~----------~~~~~~~~vGd~V~v~V~~vd~~--~~k   95 (109)
T 2khj_A           33 AIVTGKVTAVDAKGATVELAD-GVEGYLRASEASRDR----V----------EDATLVLSVGDEVEAKFTGVDRK--NRA   95 (109)
T ss_dssp             SEEEEEEEEECSSCEEEECST-TCBCCBCTTCCCSSS----S----------SSGGGSCCTTCEEEEEEEEEETT--TTE
T ss_pred             CEEEEEEEEEECCeEEEEECC-CCEEEEEHHHcCccc----c----------cChhhccCCCCEEEEEEEEEECC--CCE
Confidence            789999999999999999986 899999999987653    1          13456799999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        96 i~LS~  100 (109)
T 2khj_A           96 ISLSV  100 (109)
T ss_dssp             EEEET
T ss_pred             EEEEE
Confidence            99986

>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A

Probab=98.37  E-value=6.5e-07  Score=89.49  Aligned_cols=76  Identities=17%  Similarity=0.159  Sum_probs=61.0

Q ss_pred             HHHhcCC---ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEE
Q 008167          483 IYFRKRP---TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHM  558 (575)
Q Consensus       483 ~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V  558 (575)
                      .|++..+   ..+.|.|+++.++|+||.|+++ |++|+||+++++.++    ..          +....|++||.|+|+|
T Consensus         3 ~~~~~~p~~Gdiv~G~V~~I~~fGaFV~L~e~~gieGlIhiSels~~~----v~----------~~~~~~kvGd~V~vkV   68 (275)
T 3aev_A            3 RKAREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTW----VR----------NIRDYLKEGQKVVAKV   68 (275)
T ss_dssp             ----CCCCTTCEEEEEEEEEETTEEEEEETTSTTCEEEEEGGGSCSSC----CS----------CGGGTCCTTCEEEEEE
T ss_pred             cccccCCCCCCEEEEEEEEEECcEEEEEECCCCCeEEEEEHHHcCccc----cc----------CHHhccCCCCEEEEEE
Confidence            3555553   6899999999999999999874 999999999997653    11          2356799999999999


Q ss_pred             EEecCCCCCCceEEEe
Q 008167          559 EVVEPQPNRPKLQLTL  574 (575)
Q Consensus       559 ~~vd~~~~~~~i~l~l  574 (575)
                      ..+|.+  +++|.||+
T Consensus        69 i~vD~~--~~~I~LSl   82 (275)
T 3aev_A           69 IRVDPR--KGHIDLSL   82 (275)
T ss_dssp             EEEETT--TTEEEEES
T ss_pred             EEEECC--CCEEEEEE
Confidence            999975  89999986

>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1

Probab=98.30  E-value=4.2e-07  Score=92.11  Aligned_cols=77  Identities=13%  Similarity=0.149  Sum_probs=63.8

Q ss_pred             HHHHhcC---C-ceeEEEEEEEecCeEEEEEcC-CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEE
Q 008167          482 LIYFRKR---P-TDTEARIVKIRSNGFIVFVPK-FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI  556 (575)
Q Consensus       482 ~~~l~~~---~-~~~~g~V~~v~~~g~~V~l~~-~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V  556 (575)
                      |+|+.+.   . ..+.|.|++|.++|+||.|.+ .|++|+||+++++.++    .          ++....|++||.|+|
T Consensus         3 ~~f~~~~~~~vG~iv~G~V~~I~~fGaFV~L~ey~gveGLvhiSels~~~----i----------~~~~~~~kvGd~V~V   68 (308)
T 1q8k_A            3 CRFYQHKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRR----I----------RSINKLIRIGRNECV   68 (308)
T ss_dssp             CCSSSSCCCSSCCEEEEEEEEEETTEEEEESCTTTSCCEEECGGGTSCSS----C----------SCCTTTCSSSCEEEE
T ss_pred             eEehhhcCCCCCCEEEEEEEEEeCcEEEEEECCCCCeEEEEEhHHcCccc----c----------cCHHHhcCCCCEEEE
Confidence            4566554   2 689999999999999999986 4899999999997542    1          245677999999999


Q ss_pred             EEEEecCCCCCCceEEEe
Q 008167          557 HMEVVEPQPNRPKLQLTL  574 (575)
Q Consensus       557 ~V~~vd~~~~~~~i~l~l  574 (575)
                      +|..+|.+  +++|.||+
T Consensus        69 kVl~vD~~--~~rI~LSl   84 (308)
T 1q8k_A           69 KVIRVDKE--KGYIDLSK   84 (308)
T ss_dssp             EEEEEETT--TTEEEEEC
T ss_pred             EEEEEeCC--CCEEEEEE
Confidence            99999975  89999986

>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=98.24  E-value=4.8e-07  Score=84.43  Aligned_cols=75  Identities=9%  Similarity=0.048  Sum_probs=61.4

Q ss_pred             HHHHhcCC-ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC--CcEEEEeeCCCeEEeeCcEEEEEE
Q 008167          482 LIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQTVNIHM  558 (575)
Q Consensus       482 ~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~--~~~~l~g~~~~~~~~lGD~V~V~V  558 (575)
                      +.+++... +.++|+|++++++|+||.+.  .++|+||.+++++.    |.||+  ...++  ++++..|++||+|+|+|
T Consensus        77 ~ivf~p~~Gev~~G~V~~v~~fG~FV~l~--~~~glVh~s~l~~~----~~~d~~~~~~~~--~~~~~~~~~Gd~VrvkV  148 (172)
T 3h0g_G           77 AVLWRPFRGEVVDAIVTTVNKMGFFANIG--PLNVFVSSHLVPPD----MKFDPTANPPNY--SGEDQVIEKGSNVRLKI  148 (172)
T ss_dssp             EEEECCCTTCEEECCCCEEETTEEECCBT--TBCCEEEGGGSCTT----CCCBSSSSSCBE--ESSSCEECSSCCEEEEE
T ss_pred             EeeeccCCCCEEEEEEEEEEcceEEEEeC--CeEEEEEHHHCCCc----cccCcccccceE--ecCCcEECCCCEEEEEE
Confidence            44555555 78999999999999999995  57899999999654    56665  44555  56788999999999999


Q ss_pred             EEecCC
Q 008167          559 EVVEPQ  564 (575)
Q Consensus       559 ~~vd~~  564 (575)
                      .+++.+
T Consensus       149 ~~vd~~  154 (172)
T 3h0g_G          149 VGTRTD  154 (172)
T ss_dssp             EEEEES
T ss_pred             EEEECC
Confidence            999986

>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: b.40.4.5

Probab=98.02  E-value=2.7e-06  Score=74.40  Aligned_cols=70  Identities=16%  Similarity=0.114  Sum_probs=54.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +.++|.|++|.++|+||.|...+.+|+++.+.. .+|   +.++         ..+..|++||.|+|+|.++|.+  +++
T Consensus        23 ~i~~G~V~~v~~fG~fV~l~~~~~~~l~~~~~~-~~~---~~~~---------~~~~~~~~Gd~V~vkV~~vd~~--~~~   87 (119)
T 1wi5_A           23 MLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKA-QEY---IRQK---------NKGAKLKVGQYLNCIVEKVKGN--GGV   87 (119)
T ss_dssp             CEEEEEEEEECSSEEEEECCCSSCEEEEEHHHH-HHH---HHHH---------SSSCCCCTTCEEEEEEEECCTT--SCE
T ss_pred             CEEEEEEEEEeCceEEEEECCCCeEEEEEEecc-ccc---cccc---------CccCEeCCCCEEEEEEEEEeCC--CCE
Confidence            689999999999999999984467777665543 222   3332         2357899999999999999975  789


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|++
T Consensus        88 i~Lsl   92 (119)
T 1wi5_A           88 VSLSV   92 (119)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            99986

>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2, initiation factor 2 alpha subunit, initiation factor 2 beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B 3v11_B*

Probab=97.87  E-value=3.9e-06  Score=83.64  Aligned_cols=69  Identities=12%  Similarity=0.041  Sum_probs=58.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcC-CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPK-FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~-~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|.|++|.++|+||.|++ .|++|+||+++++.++    .          .+....+++||.|+|+|..+|.+  ++
T Consensus        13 ~iv~G~V~~I~~~GaFV~l~e~~~~~GlihiSels~~~----v----------~~~~~~~~vGd~V~VkVi~vd~~--~g   76 (266)
T 3cw2_C           13 EILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKW----V----------KNIRDVLKENRKVIVKVIRVDRR--KG   76 (266)
T ss_dssp             CEEEEEEEECCSSSBEEEETTTTSEECBBCGGGSSCSS----C----------CCHHHHSCTTCEEEEEECCCCSS--SC
T ss_pred             CEEEEEEEEEeccEEEEEEcCCCCeEEEEEhHHcCccc----c----------cCHHHhCcCCCEEEEEEEEEeCC--CC
Confidence            689999999999999999975 4899999999997653    1          12456799999999999999864  78


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|.||+
T Consensus        77 ~I~LSl   82 (266)
T 3cw2_C           77 TVDVSL   82 (266)
T ss_dssp             CCBEES
T ss_pred             EEEEEE
Confidence            999986

>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae}

Probab=97.77  E-value=1.7e-05  Score=93.52  Aligned_cols=69  Identities=13%  Similarity=0.085  Sum_probs=59.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      .+++|+|++|.++|+||.|. .|++|+||++++++++   |..+          ....|++||.|+|+|..||.+  +++
T Consensus       904 ~iv~G~V~~V~~fGaFV~L~-~gveGLVHiSelsd~~---~v~~----------p~~v~kvGd~V~vkVl~VD~~--~~r  967 (1219)
T 3psi_A          904 SIIPVRVERFWHNDIICTTN-SEVECVVNAQRHAGAQ---LRRP----------ANEIYEIGKTYPAKVIYIDYA--NIT  967 (1219)
T ss_dssp             CEEEEEEEEECSSCEEEECT-TSCEEEECTTSSSSTT---SCSC----------STTTSCTTCEEEEEEEEEEGG--GTE
T ss_pred             CEEEEEEEEEecceEEEEeC-CCceEEEEHHHcCCCc---ccCC----------HHHcCCCCCEEEEEEEEEECC--CCE
Confidence            57899999999999999995 5999999999998763   2333          346799999999999999975  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       968 I~LSl  972 (1219)
T 3psi_A          968 AEVSL  972 (1219)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            99987

>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A

Probab=97.69  E-value=7.1e-06  Score=91.93  Aligned_cols=67  Identities=16%  Similarity=0.135  Sum_probs=0.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|+|++|.++|+||.|.. |++|+||++++.+++   +           .+....|++||+|+|+|.++|.   ++|
T Consensus       639 ~v~~G~V~~I~~fGaFVel~~-g~eGLvHiSels~~r---v-----------~~~~d~~kvGD~V~VkVi~iD~---~gr  700 (726)
T 4aid_A          639 KIYDGKVVKVVDFGAFVNFFG-AKDGLVHVSQISNER---V-----------AKPSDVLKEGQMVKVKLLGFDD---RGK  700 (726)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cEEEEEEEEEeccEEEEEECC-CcEEEEEHHHcCccc---c-----------cCccccCCCCCEEEEEEEEECC---CCc
Confidence            689999999999999999976 899999999998653   1           1356789999999999999995   578


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       701 I~LS~  705 (726)
T 4aid_A          701 TKLSM  705 (726)
T ss_dssp             -----
T ss_pred             EEEEE
Confidence            88875

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=97.68  E-value=7e-05  Score=75.24  Aligned_cols=60  Identities=15%  Similarity=0.155  Sum_probs=53.2

Q ss_pred             ceeEEEEEEEecCeEEE-EEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIV-FVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V-~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..++|+|.+++++|+|| .+.+ |++|+||.+++..                      .+++||+|+|+|..++.+  ++
T Consensus       154 ~~V~g~V~~i~~~G~fV~~i~~-g~~Glih~SEl~~----------------------~l~~Gd~v~~~V~~id~~--d~  208 (285)
T 3go5_A          154 QNWPAIVYRLKLSGTFVYLPEN-NMLGFIHPSERYA----------------------EPRLGQVLDARVIGFREV--DR  208 (285)
T ss_dssp             CEEEEEEEEEETTEEEEEETTT-TEEEEECGGGCSS----------------------CCCTTCEEEEEEEEEETT--TT
T ss_pred             CEEEEEEEEEeCCcEEEEEeCC-CeEEEEEHHHccc----------------------cCCCCCEEEEEEEEEECC--CC
Confidence            68999999999999999 7754 9999999997742                      379999999999999975  79


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      ||+|||
T Consensus       209 kI~LSl  214 (285)
T 3go5_A          209 TLNLSL  214 (285)
T ss_dssp             EEEEEC
T ss_pred             eEEEEe
Confidence            999997

>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A

Probab=97.63  E-value=2.9e-06  Score=95.78  Aligned_cols=137  Identities=16%  Similarity=0.137  Sum_probs=48.3

Q ss_pred             CCCccccccccccchhHHHHH--HHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-c
Q 008167          414 APLYTHFTSPIRRYADVVVHR--LLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-T  490 (575)
Q Consensus       414 ~~~YthfTSPIRRY~DlvvHr--~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~~l~~~~-~  490 (575)
                      .|-..+|+.|..++.|++-+.  .++.+.......   .+-+. +.. -+++.....+.++.++..+... ...+-.. .
T Consensus       596 ap~~~~~~I~~~ki~~vIG~gGk~Ik~I~~~~G~~---IdI~~-dG~-v~Is~~~~~~~~~a~~~i~~i~-~p~~~~vG~  669 (757)
T 1e3p_A          596 APRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAE---ITIED-DGT-IYIGAADGPAAEAARATINGIA-NPTSPEVGE  669 (757)
T ss_dssp             SCBCCCC------------------CTTCCCCCSC---C----------CCCBSSHHHHCC-------------------
T ss_pred             CceeEEEEEChHHeehcccccceeeehhhHhhCCE---EEecC-Cce-EEEecCCHHHHHHHHHHHHHhc-chhhccccc
Confidence            478889999999999999776  666554332111   00000 000 0111111111111111111111 1111122 6


Q ss_pred             eeEEEEEEEecCeEEEEEcCCceEEEEEccCC----CCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC
Q 008167          491 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPR----GQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN  566 (575)
Q Consensus       491 ~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l----~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~  566 (575)
                      .++|+|+++.+||+||.|.. |++|+||++++    .+++    .          ++....|++||+|+|+|..+|.   
T Consensus       670 i~~G~V~~i~~fGaFV~l~~-g~eGLvHiSel~~~~s~~r----v----------~~~~~~~~vGd~V~VkVi~vd~---  731 (757)
T 1e3p_A          670 RILGSVVKTTTFGAFVSLLP-GKDGLLHISQIRKLAGGKR----V----------ENVEDVLGVGQKVQVEIAEIDS---  731 (757)
T ss_dssp             ---CBEEECC-CSCEECCC----CCCCC---------------------------------CCSSCBCCCCCCCCCS---
T ss_pred             EEEEEEEEccccEEEEEEcC-CcEEEEEhHHhccccCCCc----c----------cCcccccCCCCEEEEEEEEECC---
Confidence            89999999999999999975 89999999998    5442    1          2456789999999999999985   


Q ss_pred             CCceEEEe
Q 008167          567 RPKLQLTL  574 (575)
Q Consensus       567 ~~~i~l~l  574 (575)
                      ++||.|++
T Consensus       732 ~grI~LS~  739 (757)
T 1e3p_A          732 RGKLSLIP  739 (757)
T ss_dssp             SCC-----
T ss_pred             CCCEEEEE
Confidence            68888886

>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae}

Probab=97.55  E-value=1.1e-05  Score=93.64  Aligned_cols=69  Identities=13%  Similarity=0.085  Sum_probs=0.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|+|++|.++|+||.|. .|++|+||++++++++   |..          +....|++||.|+|+|..||.+  +++
T Consensus       907 ~iv~G~V~~V~~fGaFV~L~-~gveGLVHiSelsd~~---~v~----------~~~~v~kvGd~V~vkVl~VD~~--~~r  970 (1030)
T 3psf_A          907 SIIPVRVERFWHNDIICTTN-SEVECVVNAQRHAGAQ---LRR----------PANEIYEIGKTYPAKVIYIDYA--NIT  970 (1030)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CEEEEEEEEEccCeEEEEeC-CCcEEEEEHHHcCCCc---ccC----------CHHHcCCCCCEEEEEEEEEECC--CCE
Confidence            56899999999999999995 5999999999998653   232          2457899999999999999975  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       971 I~LSl  975 (1030)
T 3psf_A          971 AEVSL  975 (1030)
T ss_dssp             -----
T ss_pred             EEEEe
Confidence            99986

>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A

Probab=97.46  E-value=1.7e-05  Score=89.18  Aligned_cols=67  Identities=18%  Similarity=0.207  Sum_probs=0.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..++|+|+++.++|+||.|.. |.+|+||++++.+++    .          ++....|++||+|+|+|..+|.   ++|
T Consensus       629 ~i~~G~V~~i~~fGaFVel~~-g~eGLvHiSel~~~~----v----------~~~~~~~~vGd~V~VkVi~vd~---~gr  690 (723)
T 3cdi_A          629 RVYTGKVTRIVDFGAFVAIGG-GKEGLVHISQIADKR----V----------EKVTDYLQMGQEVPVKVLEVDR---QGR  690 (723)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cEEEEEEEEEecceEEEEeCC-CceEEEEHHHcCCcc----c----------cCcccccCCCCEEEEEEEEECC---CCc
Confidence            689999999999999999975 899999999997543    1          2456789999999999999995   688


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus       691 I~LS~  695 (723)
T 3cdi_A          691 IRLSI  695 (723)
T ss_dssp             -----
T ss_pred             EEEEE
Confidence            88876

>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A

Probab=96.88  E-value=0.0014  Score=61.21  Aligned_cols=65  Identities=12%  Similarity=0.042  Sum_probs=53.2

Q ss_pred             CceeEEEEEEEecCeEEEEEcCC---------ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEE
Q 008167          489 PTDTEARIVKIRSNGFIVFVPKF---------GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME  559 (575)
Q Consensus       489 ~~~~~g~V~~v~~~g~~V~l~~~---------gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~  559 (575)
                      ...+.|.|++|.++|++|.|...         +++|+||++++...+    .          .+....|++||.|+++|.
T Consensus        58 GdiV~G~V~~V~~~ga~V~I~~v~~~~~~~~~~~~Gll~isei~~~~----~----------~~~~~~~~~GD~V~akVi  123 (179)
T 3m7n_A           58 GDVVLGRVVDLRNSIALIEVSSKKGENRGPSNRGIGILHVSNVDEGY----V----------KEISEAVGYLDILKARVI  123 (179)
T ss_dssp             TCEEEEEEEEECSSEEEEEEEEETTCCSCCTTCEEEEEEGGGTTSSC----C----------SSGGGTCCTTCEEEEEEE
T ss_pred             CCEEEEEEEEEeCCcEEEEEccccCcccccccCeeEEEEHHHcCcch----h----------hCHhhcCCCCCEEEEEEE
Confidence            57899999999999999999764         899999999987642    1          134577999999999999


Q ss_pred             EecCCCCCCceEEEe
Q 008167          560 VVEPQPNRPKLQLTL  574 (575)
Q Consensus       560 ~vd~~~~~~~i~l~l  574 (575)
                      +       +++.||+
T Consensus       124 ~-------~~i~LS~  131 (179)
T 3m7n_A          124 G-------DNLRLST  131 (179)
T ss_dssp             E-------TTTEEEC
T ss_pred             C-------CeEEEEE
Confidence            7       5677664

>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2

Probab=96.64  E-value=0.0016  Score=62.34  Aligned_cols=71  Identities=14%  Similarity=0.060  Sum_probs=55.3

Q ss_pred             ceeEEEEEEEecCeEEEEEc-------CCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167          490 TDTEARIVKIRSNGFIVFVP-------KFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE  562 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~-------~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd  562 (575)
                      ..+.|.|+++.++|++|.|.       ..+++|.||++++...+    . +.       .+....|++||.|+++|.+++
T Consensus        83 DvV~G~V~~v~~~~a~V~I~~v~~~~L~~~~~GlIhisei~~~~----~-~~-------~~~~~~l~~GD~V~akVisi~  150 (209)
T 2nn6_I           83 AIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIRKEDVRATE----K-DK-------VEIYKSFRPGDIVLAKVISLG  150 (209)
T ss_dssp             CEEEEEEEEECSSEEEEEEEESSSSCCCCSSCSCEEEEGGGTCS----S-CC-------CCGGGTCCSSSEEEEEEEEEE
T ss_pred             CEEEEEEEEEECceEEEEECccccccccCCceeEEEHHHccccc----c-cc-------cchhhhcCCCCEEEEEEEEEe
Confidence            68999999999999999985       23779999999887542    1 10       023566999999999999998


Q ss_pred             CCCCCCceEEEe
Q 008167          563 PQPNRPKLQLTL  574 (575)
Q Consensus       563 ~~~~~~~i~l~l  574 (575)
                      ..  +.++.||+
T Consensus       151 ~~--~~~i~LS~  160 (209)
T 2nn6_I          151 DA--QSNYLLTT  160 (209)
T ss_dssp             TT--TTEEEEEC
T ss_pred             CC--CCeEEEEE
Confidence            54  45788875

>2je6_I RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 PDB: 2jea_I* 2jeb_I* 3l7z_C

Probab=95.71  E-value=0.0081  Score=59.03  Aligned_cols=70  Identities=11%  Similarity=-0.002  Sum_probs=55.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.|.. +.+|+||++++.+.+   .+.+        .+....|++||.|+++|.+++.+   .+
T Consensus        76 DiV~G~V~~v~~~ga~VdI~~-~~~GlL~isei~~~~---~~~~--------~~~~~~l~vGD~V~arVi~v~~~---~~  140 (251)
T 2je6_I           76 DIVIGLVEDVEIYGWVVDIKA-PYKAYLPASNLLGRS---INVG--------EDLRRYLDVGDYVIARIENFDRS---ID  140 (251)
T ss_dssp             CEEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSC---CCTT--------CCCSSSCCTTCEEEEEEEEEETT---EE
T ss_pred             CEEEEEEEEEeCceEEEEcCC-CeEEEEEHHHhcCCc---cccc--------cchhhcCCCCCEEEEEEEEECCC---Cc
Confidence            689999999999999999975 789999999877542   1111        13456799999999999999863   57


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus       141 i~LS~  145 (251)
T 2je6_I          141 PVLSV  145 (251)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            87774

>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=95.67  E-value=0.019  Score=55.66  Aligned_cols=68  Identities=13%  Similarity=0.111  Sum_probs=54.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.|.. +.+|.||++++....   +.          .+....|++||.|.++|.+++.+   .+
T Consensus        59 DiV~G~V~~v~~~~a~V~I~~-~~~g~l~isev~~~~---~~----------~~~~~~l~~GD~V~arVi~v~~~---~~  121 (229)
T 2ba0_A           59 DVVIGIIREVAANGWAVDIYS-PYQAFLPVSENPEMK---PN----------KKPNEVLDIGDAIIAKVLNIDPK---MK  121 (229)
T ss_dssp             CEEEEEEEEECSSEEEEECSS-SSCEEEEGGGCTTCC---TT----------SCGGGTCCTTCEEEEEEEEECTT---CC
T ss_pred             CEEEEEEEEEeCCeEEEEeCC-CeEEEEEHHHccccc---cc----------cchhcccCCCCEEEEEEEEECCC---Cc
Confidence            689999999999999999975 689999999887421   11          13456799999999999999864   57


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus       122 i~LS~  126 (229)
T 2ba0_A          122 VTLTM  126 (229)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            77774

>1hh2_P NUSA, N utilization substance protein A; transcription regulation, termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A

Probab=95.53  E-value=0.018  Score=58.86  Aligned_cols=62  Identities=13%  Similarity=0.057  Sum_probs=50.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ....|+|..+.++|++|.+.  ++||++|.++..                    .+..|++||+|+|.|..++.+....+
T Consensus       136 eIV~G~V~ri~~~~v~VDlG--k~EgiLp~sE~i--------------------p~E~~~vGD~Vkv~V~~V~~~~kg~~  193 (344)
T 1hh2_P          136 TVTTAEVIRVMGEWADIRIG--KLETRLPKKEWI--------------------PGEEIKAGDLVKVYIIDVVKTTKGPK  193 (344)
T ss_dssp             CEEEEEEEEECSSEEEEEET--TEEEEEEGGGSC--------------------TTCCCCTTCEEEEEEEEEEEETTEEE
T ss_pred             CEEEEEEEEEecCcEEEEeC--CeEEEEeHHHcC--------------------CCcCCCCCCEEEEEEEEEEcCCCCcE
Confidence            68999999999999999996  899999998653                    23579999999999999986533346


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.||
T Consensus       194 I~LS  197 (344)
T 1hh2_P          194 ILVS  197 (344)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            6665

>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta protein, cytoplasm, structural genomics, NPPSFA; 3.20A {Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1

Probab=95.44  E-value=0.011  Score=57.50  Aligned_cols=71  Identities=8%  Similarity=-0.054  Sum_probs=55.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.|.. +.+|.||++++.+..   ...+.       .+....|++||.|+++|.+++.+   .+
T Consensus        68 DiV~G~V~~v~~~~~~V~I~~-~~~g~l~isei~~~~---~~~~~-------~~~~~~l~~GD~V~a~Vi~v~~~---~~  133 (235)
T 2z0s_A           68 DVVIGLIQSVGIMNWFVDINS-PYVAVLSVQDFLGRP---FNPAV-------DDMQSLLKVGDYIKAKVVAFDKT---RS  133 (235)
T ss_dssp             CCEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSC---CCTTT-------TCCTTSSCTTCEEEEEEEEECTT---SC
T ss_pred             CEEEEEEEEEeCCeEEEEeCC-CeEEEEEHHHhCCCc---cccch-------hhHhhcCCCCCEEEEEEEEECCC---Cc
Confidence            678999999999999999975 789999999876421   11111       12356799999999999999863   47


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.||+
T Consensus       134 i~LS~  138 (235)
T 2z0s_A          134 PLLTV  138 (235)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            87774

>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae}

Probab=94.22  E-value=0.076  Score=53.05  Aligned_cols=62  Identities=18%  Similarity=0.067  Sum_probs=47.3

Q ss_pred             ceeEEEEEEEe-cCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCC
Q 008167          490 TDTEARIVKIR-SNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR  567 (575)
Q Consensus       490 ~~~~g~V~~v~-~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~  567 (575)
                      +...|.|++++ ++|+||.+. . |.+|+||+++++..      .            ...+++||+|.|.+ .+|.   +
T Consensus        71 ~~~~g~V~~v~~~~GaFVdiG-~~~~d~lvp~sel~~~------~------------~~~~~~Gd~v~v~l-~iD~---~  127 (285)
T 3go5_A           71 QFGWGRVTEVRKDLGVFVDTG-LPDKEIVVSLDILPEL------K------------ELWPKKGDQLYIRL-EVDK---K  127 (285)
T ss_dssp             SCEEEEEEEEETTTEEEEECS-CTTCCEEEEGGGSCSS------G------------GGSCCTTCEEEEEE-EECT---T
T ss_pred             CEEEEEEEEEccCceEEEEEC-CCCcEEEEEHHHCCcc------c------------ccccCCCCEEEEEE-EECC---C
Confidence            67899999999 799999994 4 68999999988621      1            12358899998775 5664   4


Q ss_pred             CceEEEe
Q 008167          568 PKLQLTL  574 (575)
Q Consensus       568 ~~i~l~l  574 (575)
                      +||.+++
T Consensus       128 ~Ri~ls~  134 (285)
T 3go5_A          128 DRIWGLL  134 (285)
T ss_dssp             SCEEEEE
T ss_pred             CcEEEEe
Confidence            6888875

>1k0r_A NUSA; two component arrangement, S1 domain, two K-homology domains., structural genomics, PSI, protein structure initiative; 1.70A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 d.202.1.1

Probab=94.06  E-value=0.063  Score=55.13  Aligned_cols=65  Identities=14%  Similarity=0.044  Sum_probs=51.9

Q ss_pred             CceeEEEEEE----EecCeEEEEEcC--CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167          489 PTDTEARIVK----IRSNGFIVFVPK--FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE  562 (575)
Q Consensus       489 ~~~~~g~V~~----v~~~g~~V~l~~--~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd  562 (575)
                      .+.+.|+|..    +.+.+++|.|..  -++||.++.++..                    ++..|+.||+|+|.|..|+
T Consensus       131 GeIVtG~V~r~~~~v~~~~v~VdLG~~~~k~EgiLP~~Eqi--------------------P~E~~~~GDrVkvyV~~V~  190 (366)
T 1k0r_A          131 GEIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQV--------------------PGESYEHGNRLRCYVVGVT  190 (366)
T ss_dssp             TCEEEEEEECCHHHHHTTCEEEEECCSSSCEEEEECGGGSC--------------------TTCCCCTTCEEEEEEEEEE
T ss_pred             CCEEEEEEEEccccccCCeEEEEeCCCccceEEEEcHHHcC--------------------CCccCCCCCEEEEEEEEEe
Confidence            3789999999    999999999953  1499999987643                    2467999999999999999


Q ss_pred             CCCCCCceEEE
Q 008167          563 PQPNRPKLQLT  573 (575)
Q Consensus       563 ~~~~~~~i~l~  573 (575)
                      .+....+|.||
T Consensus       191 ~~~kgpqI~LS  201 (366)
T 1k0r_A          191 RGAREPLITLS  201 (366)
T ss_dssp             CCSSSCEEEEE
T ss_pred             cCCCccEEEEE
Confidence            76545666665

>2asb_A Transcription elongation protein NUSA; protein-RNA complex, transcription/RNA complex; 1.50A {Mycobacterium tuberculosis} SCOP: b.40.4.5 d.52.3.1 d.52.3.1 PDB: 2atw_A

Probab=92.41  E-value=0.2  Score=48.67  Aligned_cols=64  Identities=14%  Similarity=0.050  Sum_probs=51.4

Q ss_pred             CceeEEEEEE----EecCeEEEEEcCC---ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEe
Q 008167          489 PTDTEARIVK----IRSNGFIVFVPKF---GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV  561 (575)
Q Consensus       489 ~~~~~g~V~~----v~~~g~~V~l~~~---gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~v  561 (575)
                      .+.+.|+|..    +.+..++|.|. .   +.||.++.++..                    .+..|+.||+|+|.|..|
T Consensus         8 GeIVtG~V~r~~~~v~~~~ViVdlG-~~~~k~EgiLP~~Eqi--------------------p~E~~~~GDrIkayV~~V   66 (251)
T 2asb_A            8 GEIVAGVIQRDSRANARGLVVVRIG-TETKASEGVIPAAEQV--------------------PGESYEHGNRLRCYVVGV   66 (251)
T ss_dssp             TCEEEEEEECCHHHHHTTCEEEEEC-SSSSCEEEEECGGGSC--------------------TTCCCCTTCEEEEEEEEE
T ss_pred             CCEEEEEEEEccccccCCeEEEEeC-CCCcceEEEEcHHHcC--------------------CCccCCCCCEEEEEEEEE
Confidence            4789999999    78888999985 3   489999877542                    245799999999999999


Q ss_pred             cCCCCCCceEEE
Q 008167          562 EPQPNRPKLQLT  573 (575)
Q Consensus       562 d~~~~~~~i~l~  573 (575)
                      +......+|.||
T Consensus        67 ~~~~~gpqIiLS   78 (251)
T 2asb_A           67 TRGAREPLITLS   78 (251)
T ss_dssp             ECCSSSCEEEEE
T ss_pred             EcCCCCCEEEEE
Confidence            976445778776

>2ja9_A Exosome complex exonuclease RRP40; RNA-binding protein, RNA, S1 domain, KH domain, hydrolase, RNA-binding, nuclear protein; 2.20A {Saccharomyces cerevisiae} SCOP: b.40.4.5 d.51.1.1

Probab=91.23  E-value=0.55  Score=43.24  Aligned_cols=66  Identities=11%  Similarity=0.042  Sum_probs=52.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++..++++|.|......|.+|+++.++..               ++....|++||-|..+|.+++.+   .+
T Consensus         9 DvViG~V~~v~~~~~~VdI~~~~~~a~L~~s~~~g~~---------------k~~r~~l~~GDlV~ArV~~~~~~---~~   70 (175)
T 2ja9_A            9 DFVIGVIIGTFSDSYKVSLQNFSSSVSLSYMAFPNAS---------------KKNRPTLQVGDLVYARVCTAEKE---LE   70 (175)
T ss_dssp             CEEEEEEEEECSSEEEEESSTTSCCEEEETTSSTTCC---------------SSSCCCCCTTCEEEEEEEECCTT---SC
T ss_pred             CEEEEEEEEEECcEEEEEECCCCccEEEEHHHCCchh---------------hhhhccCCCCCEEEEEEEEecCC---Cc
Confidence            6789999999999999999754588999998765320               24567899999999999998853   45


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      +.|+
T Consensus        71 ~~Lt   74 (175)
T 2ja9_A           71 AEIE   74 (175)
T ss_dssp             CEEE
T ss_pred             eEEE
Confidence            5555

>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli}

Probab=88.05  E-value=0.2  Score=41.79  Aligned_cols=33  Identities=27%  Similarity=0.387  Sum_probs=30.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRG  523 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~  523 (575)
                      +.+++.|..+.++|++|.|+. +++|+||+++++
T Consensus        63 e~V~g~V~~i~~fG~fv~l~~-~~eGlvhis~i~   95 (101)
T 2bh8_A           63 DRVEGKIKSITDFGIFIGLDG-GIDGLVHLSDIS   95 (101)
T ss_dssp             CEEEEEEEECCSEEEEECTTS-CEEEEEEEEEEE
T ss_pred             CEEEEEEEEeCCcEEEEEcCC-CceEEEEHHHCc
Confidence            789999999999999999976 899999999875

>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonu nuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A

Probab=87.81  E-value=0.77  Score=49.43  Aligned_cols=67  Identities=12%  Similarity=-0.008  Sum_probs=47.7

Q ss_pred             ceeEEEEEEEecC--eEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEe-eCCCeEEeeCcEEEEEEEEecC
Q 008167          490 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK-MDGNLSYSVLQTVNIHMEVVEP  563 (575)
Q Consensus       490 ~~~~g~V~~v~~~--g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g-~~~~~~~~lGD~V~V~V~~vd~  563 (575)
                      ..+.|.|.+|.++  |+||.+.. |-+|++|++++...+   +. +...  ..+ .+....++.||.|.|+|.....
T Consensus        47 nIY~GkV~rv~p~~~aAFVdiG~-gk~gfLhisei~~~~---~~-~~~~--~~~~~~i~d~lk~Gq~VlVQV~Ke~~  116 (517)
T 2bx2_L           47 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREY---FP-ANYS--AHGRPNIKDVLREGQEVIVQIDKEER  116 (517)
T ss_dssp             CEEEEEEEEEETTTTEEEEESSS-SSCEEEEGGGSCGGG---CC----------CCCGGGTCCTTCEEEEEEEECCC
T ss_pred             CEEEEEEEEeccCCceEEEEeCC-CcEEEEEHHHcChhh---hc-cccc--cccccchhhhccCCCEEEEEEEeecc
Confidence            5799999999998  99999985 999999999985331   11 1000  000 1123558999999999998664

>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA, DNA-binding, phosphorylation, POL I, POLI, rpoli, nuclear protein; 3.10A {Saccharomyces cerevisiae}

Probab=87.65  E-value=1.2  Score=42.41  Aligned_cols=80  Identities=10%  Similarity=0.074  Sum_probs=54.9

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecC---CcEEEEeeCCCeEEeeCcEEEEEEEEecCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE---QQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN  566 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~---~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~  566 (575)
                      ++.+|+|..+++.|+.+.+-. -+..+|+-..++.+|  .|+.++   ....|+...+.   ++|++|+.+|.+++...+
T Consensus       131 evL~G~V~~~s~~~Ig~~~~G-~Fn~~Ip~~~ip~~~--~f~~~~~~~~~~~wv~~~~~---~ig~~IRFrV~~~~~~~~  204 (214)
T 2rf4_A          131 DVLEGYIFIQSASHIGLLIHD-AFNASIKKNNIPVDW--TFVHNDGNRSLGHWVDSNGE---PIDGKLRFTVRNVHTTGR  204 (214)
T ss_dssp             CEEEEEECCCCSSCEEEEETT-TEEEEECSTTSCSSC--BCCCCSCC-CCCCCBCSSCC---BCCSEEEEEEEEEECCSS
T ss_pred             CEEEEEEEEECCCcEEEEEeC-CEEEEEcHHHCCCcc--cccccccccCCCceEcCCCC---CCCCEEEEEEEEEEecCC
Confidence            678999999999999886533 356799999998875  244333   11344433332   369999999999997644


Q ss_pred             CCceEEEeC
Q 008167          567 RPKLQLTLI  575 (575)
Q Consensus       567 ~~~i~l~l~  575 (575)
                      --.|..+|+
T Consensus       205 ~lsI~Gsll  213 (214)
T 2rf4_A          205 VVSVDGTLI  213 (214)
T ss_dssp             SCEEEEECC
T ss_pred             EEEEEEEec
Confidence            555665553

>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1

Probab=85.67  E-value=0.43  Score=48.05  Aligned_cols=77  Identities=9%  Similarity=0.046  Sum_probs=50.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.+++++|.|.. ..++.++++.+..+.   +.... .....+.+....|++||.|.++|.+++.   ..+
T Consensus        97 DvViG~Vt~V~~~~a~VdI~s-~~~~~l~iS~v~f~g---g~iR~-~~~~D~~~m~~~l~vGDlV~ArVisv~~---~~~  168 (308)
T 2nn6_H           97 DIVVGRITEVQQKRWKVETNS-RLDSVLLLSSMNLPG---GELRR-RSAEDELAMRGFLQEGDLISAEVQAVFS---DGA  168 (308)
T ss_dssp             BCCCEEEEEEETTEEEEECSS-SSCEEEESSCCC-----------------CHHHHHHSCSSCEECCEEEEEET---TTE
T ss_pred             CEEEEEEEEEeCceEEEEECC-CcCCceechhhcccc---ceeec-ccchhhhhhhccCCCCCEEEEEEEEcCC---CCC
Confidence            678999999999999999974 467889988764321   11000 0000011234679999999999999984   356


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|+.
T Consensus       169 i~LSt  173 (308)
T 2nn6_H          169 VSLHT  173 (308)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            77653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	575
d2vnud4	416	b.40.4.16 (D:495-910) Exosome complex exonuclease	1e-107
d2ix0a4	385	b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Esch	1e-84
d2r7da2	401	b.40.4.16 (A:3-403) Ribonuclease II family protein	2e-68
d2vnud1	95	b.40.4.5 (D:400-494) Exosome complex exonuclease R	9e-25
d2vnud2	88	b.40.4.5 (D:911-998) Exosome complex exonuclease R	4e-22

>d2vnud4 b.40.4.16 (D:495-910) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Length = 416

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score =  327 bits (838), Expect = e-107
 Identities = 204/414 (49%), Positives = 267/414 (64%), Gaps = 13/414 (3%)

Query: 86  FSTQVLACLPP--LPWSVSSEDLANPI---------RLDLRDLRVFSVDPPGCKDIDDAL 134
           FS +VL CLP     W   ++               R DLRD  + S+DPPGC DI+DAL
Sbjct: 1   FSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDAL 60

Query: 135 HCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICS 194
           H   L +GN+EVGVHIADVT+FV PGT LD E + RGTSVYLV++RIDMLP  L  D+CS
Sbjct: 61  HAKKLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCS 120

Query: 195 LRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDL 254
           L+  V+R AFSVIWEL   A I++  + KSVI+S  A SY +AQ R+DD    D LT  +
Sbjct: 121 LKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGM 180

Query: 255 RNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAA 314
           R +  L+ K++Q+R+E GAL LAS EVK  +D+ET DP ++ + ++   N +VEEFML A
Sbjct: 181 RALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLA 240

Query: 315 NVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVG-LNLDVSSSKALADSLDRAV 373
           N+SVA +I   FP  ++LRRH +P     E L         +++ + SSKALADSLDR V
Sbjct: 241 NISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCV 300

Query: 374 G-DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVV 432
             +DPYFN L+RI++TRCM  A YF SG  + P+F HYGLA  +YTHFTSPIRRY DVV 
Sbjct: 301 DPEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVA 360

Query: 433 HRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR 486
           HR L+ ++G   L    +D+ ++  I  N+N +HRNAQ A R S+E +     R
Sbjct: 361 HRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMR 414

>d2ix0a4 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 385

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

 Score =  266 bits (681), Expect = 1e-84
 Identities = 99/397 (24%), Positives = 163/397 (41%), Gaps = 20/397 (5%)

Query: 98  PWSVSSEDL-ANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNF 156
           P  V++E L    +R DL  L   ++D    +D+DDAL   AL     ++ V IAD T +
Sbjct: 3   PDGVATEMLDEGLVREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAW 62

Query: 157 VHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEI 216
           +  G+ LD  A  R  + YL    I MLP+ L++D+CSLRA+  R   +    L+ +  I
Sbjct: 63  IAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTI 122

Query: 217 IST-RYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTD----LRNMNSLAKKMRQRRIER 271
                +  + I+S A L Y +    ++++    P +      +R +  + ++  + R   
Sbjct: 123 EDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNH 182

Query: 272 GALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSL 331
             +     + +F +  E  + LDI     R AN++VEE M+AAN+  A  +LR      +
Sbjct: 183 ALVFKDRPDYRFILG-EKGEVLDIVAEPRRIANRIVEEAMIAANICAAR-VLRDKLGFGI 240

Query: 332 LRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCM 391
              H        + L       GL++D      L          D      +     R  
Sbjct: 241 YNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQ 300

Query: 392 TQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQD 451
           + A              H+GL    Y  +TSPIR+Y D++ HRLL A +           
Sbjct: 301 SFAEIS------TEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR---- 350

Query: 452 RPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKR 488
                 I   +  R R  +MA R   +     + + +
Sbjct: 351 --PQDEITVQMAERRRLNRMAERDVGDWLYARFLKDK 385

>d2r7da2 b.40.4.16 (A:3-403) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]} Length = 401

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Ribonuclease II family protein DR0020
species: Deinococcus radiodurans [TaxId: 1299]

 Score =  224 bits (572), Expect = 2e-68
 Identities = 105/442 (23%), Positives = 161/442 (36%), Gaps = 59/442 (13%)

Query: 50  QSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDA--RPFSTQVLACLPPLPWSVSSEDLA 107
           + R      +R +      +    ++L     D    P++ ++ A L  +   V   D A
Sbjct: 17  RGRADKSRVLRDLKLPETPEAAHALLLRLGVWDEARTPYADRLRAALNAVELPVPDFDPA 76

Query: 108 NPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEA 167
              RLDL  L  F++D  G +D DDA+    L  G   + VH+ADV   V P +PLD EA
Sbjct: 77  EE-RLDLTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEA 135

Query: 168 SKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIK 227
             RG ++YL +R I MLP  L      L       A S+  +L P+    +     + +K
Sbjct: 136 RARGATLYLPDRTIGMLPDELVAKAG-LGLHEVSPALSICLDLDPDGNAEAVDVLLTRVK 194

Query: 228 SCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDT 287
               L+Y EAQAR++              +  LA+  R+ R   GAL++   EV+ + D 
Sbjct: 195 VQ-RLAYQEAQARLEAGEEPF------VTLARLARASRRLREGEGALSIDLPEVRVKADE 247

Query: 288 ETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLL 347
                         E   +V+E M  A    A        +         PT+E+    L
Sbjct: 248 TGASV---FPLPKPEMRTVVQECMTLAGWGTAI-FADDNEIPLPFATQDYPTREVAGDTL 303

Query: 348 RTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEF 407
                                                    + + +  +       P   
Sbjct: 304 PAM----------------------------------WARRKTLARTRF------QPSPG 323

Query: 408 HHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHR 467
            H+G+   LY   TSP+RRY D+VVH+ L A L      S       + +          
Sbjct: 324 PHHGMGLDLYAQATSPMRRYLDLVVHQQLRAFLAGRDPLS----SKVMAAHIAESQMNAD 379

Query: 468 NAQMASRGSVELHTLIYFRKRP 489
             + A R S   HTL +   +P
Sbjct: 380 ATRQAERLSRRHHTLRFIAAQP 401

>d2vnud1 b.40.4.5 (D:400-494) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Length = 95

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 96.1 bits (239), Expect = 9e-25
 Identities = 32/85 (37%), Positives = 54/85 (63%)

Query: 1  MPMPAGSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVR 60
            +   S S  +   +  D+ +PK+RI+TR+   LLDKRI++++DSW    +YP GH+VR
Sbjct: 11 SSVDPQSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVR 70

Query: 61 VIGEIGDRDTESEMVLIDNDIDARP 85
           +G I     E+E +L+++D++ RP
Sbjct: 71 DLGTIESAQAETEALLLEHDVEYRP 95

>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Length = 88

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

 Score = 88.3 bits (219), Expect = 4e-22
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 4/87 (4%)

Query: 490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV---KMDGNL 546
           +     ++K+ +NG +V VPKFG+EG + L    +  +   + + + +        D   
Sbjct: 2   STETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPR 61

Query: 547 SYSVLQTVNIHMEVV-EPQPNRPKLQL 572
              V   V + +  V +P  ++ K +L
Sbjct: 62  DVYVFDKVEVQVRSVMDPITSKRKAEL 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	575
d2vnud4	416	Exosome complex exonuclease RRP44 {Saccharomyces c	100.0
d2ix0a4	385	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	100.0
d2r7da2	401	Ribonuclease II family protein DR0020 {Deinococcus	100.0
d2vnud1	95	Exosome complex exonuclease RRP44 {Saccharomyces c	99.61
d2ix0a3	87	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.42
d1go3e1	106	C-terminal domain of RNA polymerase II subunit RBP	99.24
d2ix0a1	90	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	99.09
d2vnud2	88	Exosome complex exonuclease RRP44 {Saccharomyces c	99.06
d1y14b1	91	C-terminal domain of RNA polymerase II subunit RBP	98.99
d2c35b1	94	C-terminal domain of RNA polymerase II subunit RBP	98.95
d1kl9a2	86	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.87
d2ahob2	84	Eukaryotic initiation factor 2alpha, eIF2alpha, N-	98.7
d1sroa_	76	S1 RNA-binding domain of polyribonucleotide phosph	98.55
d3bzka4	94	Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]	98.4
d2ba0a1	83	S1-domain of exosome complex RNA-binding protein 1	98.24
d2je6i1	87	S1-domain of exosome complex RNA-binding protein 1	98.1
d2z0sa1	88	S1-domain of exosome complex RNA-binding protein 1	98.06
d1e3pa2	62	S1 RNA-binding domain of polyribonucleotide phosph	98.05
d1wi5a_	119	S1-domain of RRP5 protein homolog (PDCD11, KIAA018	97.86
d2nn6h1	95	S1-domain of Ribosomal RNA-processing protein 4, R	97.37
d1hh2p1	72	S1 domain of NusA {Thermotoga maritima [TaxId: 233	96.42
d2nn6g1	88	S1-domain of exosome component 3 (RRP40) {Human (H	95.76
d2asba1	76	S1 domain of NusA {Mycobacterium tuberculosis [Tax	92.41
d2ja9a1	90	S1-domain of exosome component 3 (RRP40) {Saccharo	90.91
d1smxa_	87	S1-domain of Ribonuclease E {Escherichia coli [Tax	82.19
d2ix0a2	79	Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5	81.08

>d2vnud4 b.40.4.16 (D:495-910) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=100.00  E-value=1.4e-91  Score=751.13  Aligned_cols=403  Identities=51%  Similarity=0.828  Sum_probs=370.3

Q ss_pred             CcHHHHhcCCCC--CCCCCccc---------cCCCCCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEecccc
Q 008167           86 FSTQVLACLPPL--PWSVSSED---------LANPIRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVT  154 (575)
Q Consensus        86 f~~~v~~~~~~~--~~~~~~~~---------~~~~~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs  154 (575)
                      ||++|+++++..  +|.++++.         ....+|+|||++++|||||++|+|+||||||+++++|+|+|||||||||
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~R~Dl~~l~~~tID~~~a~d~DDAisi~~~~~g~~~l~VHIADva   80 (416)
T d2vnud4           1 FSKKVLECLPAEGHDWKAPTKLDDPEAVSKDPLLTKRKDLRDKLICSIDPPGCVDINDALHAKKLPNGNWEVGVHIADVT   80 (416)
T ss_dssp             CCHHHHTTSCTTGGGCCCCSSTTCHHHHHHCGGGGGSEECTTSCCEEEESSSCCCCCEEEEEEECTTSCEEEEEEEECHH
T ss_pred             CCHHHHhhcccccCcccCchhhhhhhhccCchhhcCCccCCCCCEEEEcCCCCccccceEEEEEeCCCcEEEEEEEccHH
Confidence            788899988864  55553221         1123899999999999999999999999999999999999999999999


Q ss_pred             ccccCCCHHHHHHHhCCCceEcCCccccCCChhhhccccCCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCH
Q 008167          155 NFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSY  234 (575)
Q Consensus       155 ~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~cSL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY  234 (575)
                      +||++||+||++|++||+|+|||++++||||+.||+++|||.||++|+|+||.+++|.+|+|.+++|++|+|+|.++|||
T Consensus        81 ~~v~~~s~Ld~~A~~R~~t~Ylp~~~~pMLP~~ls~~~~SL~~~~~r~a~s~~~~~~~~g~i~~~~~~~s~I~~~~~ltY  160 (416)
T d2vnud4          81 HFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSY  160 (416)
T ss_dssp             HHSCTTSHHHHHHHHHCBCEECSSCEECSSCHHHHTTTSSCCBTSEEEEEEEEEEECTTCCEEEEEEEEEEEEBSEEEEH
T ss_pred             HhhCCCCHHHHHHHHhCeeEeCCCCccccCCHHHhhhhhcccCCcceeeEEeeeeeccccccccceeehhhhccccccch
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHH
Q 008167          235 VEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAA  314 (575)
Q Consensus       235 ~~v~~~l~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilA  314 (575)
                      ++|+++|++.....++.+.|..|+++++.|+++|.++|++.++.++.++.+|.+.+.+..+.......||.|||||||+|
T Consensus       161 ~ev~~~l~~~~~~~~~~~~l~~L~~~a~~l~~~R~~~g~l~~~~~~~~~~~d~~~~~~~~~~~~~~~~s~~lVeE~Mi~A  240 (416)
T d2vnud4         161 EQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLA  240 (416)
T ss_dssp             HHHHHHHHCTTCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCCEEEEECSSSSCEEEEEECCCCHHHHHHHHHHHHH
T ss_pred             hhHHHHhccccccccchhHHHHHHHHHHHHHHHHHhcCCcccCCCceEEEeccccccccccceeecccchhhHHHHhhhh
Confidence            99999999887778888999999999999999999999999999999999987767777777778899999999999999


Q ss_pred             HHHHHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHc-CCccCCCCHHHHHHHHHHHhC-CChhHHHHHHHHHHhhcc
Q 008167          315 NVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAV-GLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILATRCMT  392 (575)
Q Consensus       315 N~~vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~-g~~~~~~~~~~l~~~l~~~~~-~~~~~~~~l~~~~~r~m~  392 (575)
                      |.+||+++.++++.+++||+|+.|+.++++.+.+++... |+.++..+...+.+.+..+.+ .++....+++..++|+|.
T Consensus       241 N~~vA~~l~~~~~~~~~~R~h~~p~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~i~~~~~~~~~  320 (416)
T d2vnud4         241 NISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMSTRCMM  320 (416)
T ss_dssp             HHHHHHHHHHHCTTTCEEEEBCCCCGGGGHHHHHHHHHHHSCCCCCSCHHHHHHHHHTCCBTTBTTHHHHHHHHHHTTSC
T ss_pred             hHHHHHHHHHhCCCCCccceeCCCCHHHHHHHHHHHHHhcccCcCccchhhHHHHHHHHhCccCchHHHHHHHHHHHHHH
Confidence            999999999888899999999999999999999888754 767777788888888887665 566677788888999999


Q ss_pred             CceecccCCCCCCCCCccccCCCCccccccccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHH
Q 008167          393 QAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMA  472 (575)
Q Consensus       393 ~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a  472 (575)
                      +|.|+.++.++.++.+|||||++.|||||||||||+||+|||||+++|.+++.++...+.++|..+|.+||.+++.|++|
T Consensus       321 ~a~~~~~~~~s~~~~~H~gLgl~~YthfTSPIRRY~DLv~hrqL~a~l~~~~~~~~~~~~e~l~~i~~~~~~~e~~a~~a  400 (416)
T d2vnud4         321 AAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFA  400 (416)
T ss_dssp             CCEEEEGGGSCGGGGCBTTTTBSCCCCCSCTTTBHHHHHHHHHHHHHTTSSCCCGGGGCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhccccCCCCccCcHhhCcccccccCcHHhhHHHHHHHHHHHHHHcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999887766666788999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcC
Q 008167          473 SRGSVELHTLIYFRKR  488 (575)
Q Consensus       473 ~r~~~~~~~~~~l~~~  488 (575)
                      ||++.++|+|+||+++
T Consensus       401 er~~~~~~~~~~lk~~  416 (416)
T d2vnud4         401 GRASIEYYVGQVMRNN  416 (416)
T ss_dssp             HHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHhCC
Confidence            9999999999999874

>d2ix0a4 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=8.9e-87  Score=706.82  Aligned_cols=362  Identities=25%  Similarity=0.356  Sum_probs=324.1

Q ss_pred             CCccCCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHhCCCceEcCCccccCCChhhh
Q 008167          110 IRLDLRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLT  189 (575)
Q Consensus       110 ~R~Dlr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls  189 (575)
                      .|+|||++++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|+
T Consensus        16 ~R~Dl~~l~~~tID~~~a~d~DDAisie~~~~~~~~l~VHIADva~~v~~~s~Ld~~A~~R~~S~Ylp~~~~pMLP~~ls   95 (385)
T d2ix0a4          16 VREDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELS   95 (385)
T ss_dssp             CCEECTTSCCBEEECSSCCCCCEEEEEEEEGGGEEEEEEEECCGGGTSCTTSHHHHHHHHHCBCEEETTEEECSSCHHHH
T ss_pred             CcccCCCCCEEEEcCCCCccccceEEEEEeCCCcEEEEEEECCHHHHhCCCCHHHHHHHHhCCcEECCCCCCCCCChhhh
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCeeeEEEEEEEEcCCCcEE-EEEEEEEEEeecceeCHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHH
Q 008167          190 EDICSLRADVERLAFSVIWELTPEAEII-STRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKM  264 (575)
Q Consensus       190 ~~~cSL~~~~~r~a~s~~~~i~~~G~i~-~~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~L~~L~~la~~l  264 (575)
                      +++|||.||++|+|+||.+++|.+|+|. ++++++|+|+|+++|||++|+++|++...    .......|..|+++++.+
T Consensus        96 ~~~~SL~~~~~r~a~s~~~~l~~~g~i~~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~~~~~~~~~l~~L~~~~~~l  175 (385)
T d2ix0a4          96 DDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRR  175 (385)
T ss_dssp             HTTSSCCTTCEEEEEEEEEEECTTCCBCSCCEEEEEEEECCCEEEHHHHHHHHTTCSSCCCSSHHHHHHHHHHHHHHHHH
T ss_pred             hhhcccccccceeEEEEEEEEccCcceeccceEEeEEEEecCcCcHHHHHHHHhcccccccchhhhHHHHHHHHHHHHHH
Confidence            9999999999999999999999999985 58999999999999999999999987532    234667899999999999


Q ss_pred             HHHHHhcCCccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHHhCCCceeeeeCCCCChhhHH
Q 008167          265 RQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLE  344 (575)
Q Consensus       265 r~~R~~~Gal~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~~~~~~~~~R~h~~P~~~~~~  344 (575)
                      +++|..+|++.++.++.++.++++ +.+..+.......|+.||||+||+||.+||+++.++ +.|++||+|+.|++.+++
T Consensus       176 r~~R~~~g~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~s~~lieE~MilaN~~va~~l~~~-~~~~i~R~~~~p~~~~~~  253 (385)
T d2ix0a4         176 GEWRHNHALVFKDRPDYRFILGEK-GEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDK-LGFGIYNVHMGFDPANAD  253 (385)
T ss_dssp             HHHHHHHSCCCCCCCEEEEEECTT-SCEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHH-TSCCCEEEBCCSCGGGHH
T ss_pred             HHHHhhcCccccccchheeecccc-cccceEEEeeccHHHHHHHHHHHHhhHHHHHHHHHc-cCCCccccccccChHHHH
Confidence            999999999999999999999875 567777778889999999999999999999999987 678999999999999999


Q ss_pred             HHHHHHHHcCCccCCCCHHHH---HHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCCCccccCCCCccccc
Q 008167          345 PLLRTAAAVGLNLDVSSSKAL---ADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFT  421 (575)
Q Consensus       345 ~l~~~~~~~g~~~~~~~~~~l---~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~gL~~~~YthfT  421 (575)
                      ++.++++.+|+.++.....++   ............   ..++.++.|+|.+|.|      +..+.+|||||++.|||||
T Consensus       254 ~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~r~~~~a~y------s~~~~~H~gLgl~~YthfT  324 (385)
T d2ix0a4         254 ALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPT---GFLDSRIRRFQSFAEI------STEPGPHFGLGLEAYATWT  324 (385)
T ss_dssp             HHHHHHHHTTCCCCTTGGGSHHHHHHHHHHHHHSSS---SHHHHHTGGGCCCCEE------ESSCCCBTTTTBSCCBCCS
T ss_pred             HHHHHHHHhccccCcccccchhhHHHHhhhcccccc---hHHHHHHHHHhhhhcc------CCCCCCchhhCcccceeeC
Confidence            999999999999876644333   322222211111   1345667899999999      6788999999999999999


Q ss_pred             cccccchhHHHHHHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 008167          422 SPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKR  488 (575)
Q Consensus       422 SPIRRY~DlvvHr~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~~l~~~  488 (575)
                      ||||||+||+|||||+++|.+++.++      ..+++|.+||.+++.++.|||++.++|+|.||+++
T Consensus       325 SPIRRY~DLivhrqL~a~L~~~~~~~------~~~ei~~~~~~~~~~a~~aer~~~~~~~~~~lk~~  385 (385)
T d2ix0a4         325 SPIRKYGDMINHRLLKAVIKGETATR------PQDEITVQMAERRRLNRMAERDVGDWLYARFLKDK  385 (385)
T ss_dssp             CTTTBHHHHHHHHHHHHHHHTCCCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGG
T ss_pred             cHHhhHHHHHHHHHHHHHHcCCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999876553      23568999999999999999999999999999864

>d2r7da2 b.40.4.16 (A:3-403) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNB domain-like
domain: Ribonuclease II family protein DR0020
species: Deinococcus radiodurans [TaxId: 1299]

Probab=100.00  E-value=3.8e-86  Score=700.90  Aligned_cols=390  Identities=27%  Similarity=0.369  Sum_probs=338.0

Q ss_pred             CEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCC---CCCCcHHHHhcCCCCCCCCCccc-cCCCCCcc
Q 008167           38 KRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDID---ARPFSTQVLACLPPLPWSVSSED-LANPIRLD  113 (575)
Q Consensus        38 ~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~---~~~f~~~v~~~~~~~~~~~~~~~-~~~~~R~D  113 (575)
                      ++|.|++..+   +..|.|+|+++||..++++.+.+.++ +.|+.   ..+||+++.+++....+.++..+ .+  +|+|
T Consensus         8 ~~v~ve~~~~---~~~~~~~i~~~lg~~~~~~~~~~~l~-~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~R~D   81 (401)
T d2r7da2           8 QRTEVELLAR---GRADKSRVLRDLKLPETPEAAHALLL-RLGVWDEARTPYADRLRAALNAVELPVPDFDPAE--ERLD   81 (401)
T ss_dssp             HHHHHHHHHT---TSCSCCHHHHHTTCCCSHHHHHHHHH-HHTSSCTTCCCHHHHTTCCCSCCCCCCCCCCTTS--CCEE
T ss_pred             CEEEEEEccc---CCCCCccchhhcCCCCCcchHHHHHH-HhCCCcccccCCcHHHHHHHhhccCCCCCccccc--cccc
Confidence            4455555443   46899999999999999999887665 45542   23578888887776666554332 33  7999


Q ss_pred             CCCCeEEEECCCCCCCcCceEEEEEecCCcEEEEEEeccccccccCCCHHHHHHHhCCCceEcCCccccCCChhhhcccc
Q 008167          114 LRDLRVFSVDPPGCKDIDDALHCTALSSGNFEVGVHIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDIC  193 (575)
Q Consensus       114 lr~~~~~tID~~~a~D~DDAisi~~~~~g~~~l~VHIADvs~~v~~~s~LD~eA~~R~~SvYlp~~~~pMLP~~Ls~~~c  193 (575)
                      ||++++|||||++|+|+||||||+++++|.|+|||||||||+||++||+||+||++||||+|||++++||||+.|++. |
T Consensus        82 lr~l~~~tID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~v~~~s~Ld~eA~~R~tSvYlp~~~~pMLP~~ls~~-~  160 (401)
T d2r7da2          82 LTHLPTFAIDDEGNQDPDDAVGVEDLGGGLTRLWVHVADVAALVAPDSPLDLEARARGATLYLPDRTIGMLPDELVAK-A  160 (401)
T ss_dssp             CTTSCEEEEECTTCCCCCEEEEEEECSTTCEEEEEEEECGGGTCCTTSHHHHHHHHHCBCEECSSCEECSSCHHHHHH-H
T ss_pred             cccCcEEEECCCCCcccccceeEEEcCCCcEEEEEeecchhhhccCCChHHHHHHHhCccccCCCCeeecCcHHHhcc-c
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999985 9


Q ss_pred             CCCCCCeeeEEEEEEEEcCCCcEEEEEEEEEEEeecceeCHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhcCC
Q 008167          194 SLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGA  273 (575)
Q Consensus       194 SL~~~~~r~a~s~~~~i~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~~~~~L~~L~~la~~lr~~R~~~Ga  273 (575)
                      ||.||++|+||||.+++|.+|+|.+++|++|+|++ ++|||++|++++++..      +.|..+..+++.+++.|.++|+
T Consensus       161 SL~~~~~r~als~~~~ld~~g~i~~~~~~~s~I~~-~~ltY~~v~~~~~~~~------~~l~~l~~~~~~l~~~R~~~ga  233 (401)
T d2r7da2         161 GLGLHEVSPALSICLDLDPDGNAEAVDVLLTRVKV-QRLAYQEAQARLEAGE------EPFVTLARLARASRRLREGEGA  233 (401)
T ss_dssp             STTSSSSEEEEEEEEEECTTSCEEEEEEEEEEECE-EEEEHHHHHHHHHTTC------TTHHHHHHHHHHHHHHHHHTTC
T ss_pred             ccccCccccccceEEEEccCCCcccceEEEEEEEE-eeccHHHHHHHhhccc------hhHHHHHHHHHHHHHHHHhcCC
Confidence            99999999999999999999999999999999999 5899999999998753      3578899999999999999999


Q ss_pred             ccccCcceEEEecCCCCCeeeEEEeecchHHHHHHHHHHHHHHHHHHHHHHhCCCceeeeeCCCCChhhHHHHHHHHHHc
Q 008167          274 LTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAV  353 (575)
Q Consensus       274 l~~~~~e~~~~~d~~~~~~~~v~~~~~~~s~~lVeE~MilAN~~vA~~l~~~~~~~~~~R~h~~P~~~~~~~l~~~~~~~  353 (575)
                      +.|+.++.++.+|++ +  ..+...+..+|+.|||||||+||.++|+++.++ +.|++||+|+.|..+...         
T Consensus       234 l~~~~~~~~~~~d~~-~--~~~~~~~~~~s~~lVeE~MilAN~~~A~~l~~~-~~p~iyR~~~~p~~~~~~---------  300 (401)
T d2r7da2         234 LSIDLPEVRVKADET-G--ASVFPLPKPEMRTVVQECMTLAGWGTAIFADDN-EIPLPFATQDYPTREVAG---------  300 (401)
T ss_dssp             CCCCCCCEEEEEETT-E--EEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHT-TCCCCEEEECCCSSCCCC---------
T ss_pred             cccccccceeeeccC-C--cccceeeccchhhhhHhHhhhcchhHHHHHhhc-cCCccccccCCCchhhhh---------
Confidence            999999999999875 2  345556778999999999999999999999987 789999999999765321         


Q ss_pred             CCccCCCCHHHHHHHHHHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCCCccccCCCCccccccccccchhHHHH
Q 008167          354 GLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVH  433 (575)
Q Consensus       354 g~~~~~~~~~~l~~~l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~gL~~~~YthfTSPIRRY~DlvvH  433 (575)
                                            +. ...+  ....|+|.+|.|      +..+.+|||||++.|||||||||||+||+||
T Consensus       301 ----------------------~~-l~~~--~~~~~~~~~a~y------s~~~~~H~gLgl~~YthfTSPIRRY~DLivh  349 (401)
T d2r7da2         301 ----------------------DT-LPAM--WARRKTLARTRF------QPSPGPHHGMGLDLYAQATSPMRRYLDLVVH  349 (401)
T ss_dssp             ----------------------CS-HHHH--HHHHHHCCCEEE------ESSCCCBTTTTBSCCCCCSCTTTBHHHHHHH
T ss_pred             ----------------------cc-HHHH--HHhhhhcceeeE------cCCCCcChhccCCceeeeCChhhhhHHHHHH
Confidence                                  00 1111  123578999999      5678999999999999999999999999999


Q ss_pred             HHHHHHhCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 008167          434 RLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP  489 (575)
Q Consensus       434 r~L~~~l~~~~~~~~~~~~~~l~~~~~~~n~~~~~a~~a~r~~~~~~~~~~l~~~~  489 (575)
                      |||+++|.+++ +   .+.+++..+|.+||.+++.++++||++.++|++.||++++
T Consensus       350 rqL~a~L~~~~-~---~~~~~l~~~~~~~~~~~~~~~~~er~~~~~~~~~yl~~~p  401 (401)
T d2r7da2         350 QQLRAFLAGRD-P---LSSKVMAAHIAESQMNADATRQAERLSRRHHTLRFIAAQP  401 (401)
T ss_dssp             HHHHHHHTTCC-C---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCT
T ss_pred             HHHHHHHcCCC-C---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            99999998864 2   3467999999999999999999999999999999999875

>d2vnud1 b.40.4.5 (D:400-494) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.61  E-value=9.6e-16  Score=127.04  Aligned_cols=79  Identities=39%  Similarity=0.812  Sum_probs=75.0

Q ss_pred             CCCCccEEEEEeCCCCCCceEecCCccCcCCCCEEEEEEeecCCCCCCcceEEEEeecCCCChhhHHHHHHhhCCCCCC
Q 008167            6 GSGSVAHALFVPKDRRIPKIRIQTRQLGNLLDKRIIVAVDSWDCQSRYPFGHYVRVIGEIGDRDTESEMVLIDNDIDAR   84 (575)
Q Consensus         6 ~~~~~~~~~~~P~d~r~p~i~i~~~~~~~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG~~~~~~~~~~~il~~~~i~~~   84 (575)
                      .+.+.++++|+|.|+|+|.|.|++++.+.+.|++|+|+|++||..+.+|.|+|+++||..+++++|+++||.+|+|+++
T Consensus        16 ~~~~~~~~~v~P~d~rip~i~I~~~~~~~~~g~~Vvv~I~~w~~~~~~P~G~i~~vLG~~gd~~~e~~~il~~~~ip~~   94 (95)
T d2vnud1          16 QSSSTQNVFVILMDKCLPKVRIRTRRAAELLDKRIVISIDSWPTTHKYPLGHFVRDLGTIESAQAETEALLLEHDVEYR   94 (95)
T ss_dssp             TCCSCEEEEEEESSTTSCCEEEEETTGGGGTTEEEEEEEEECCTTCSSCEEEEEEEEEESSCSHHHHHHHHHHTTCCCS
T ss_pred             CCCCcceEEEEECCCCCCceeccccchhHhCCCEEEEEEeecCCCCCCCCEEEEEEecCCCCcHHHHHHHHHHcCCCCC
Confidence            4567789999999999999999999888889999999999999999999999999999999999999999999999975

>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=99.42  E-value=3e-13  Score=109.78  Aligned_cols=80  Identities=18%  Similarity=0.116  Sum_probs=69.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEE-EeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKI-VKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l-~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ++|+|+|++|+++|+||.|+++++||+||++.+++|+   |.||....++ .++++++.|++||+|+|+|..+|++  ++
T Consensus         5 ~~F~g~Is~v~~~GifV~L~e~~~eGlI~~s~L~~d~---y~~d~~~~~l~~~~~~~~~~~~Gd~V~V~v~~vd~~--~r   79 (87)
T d2ix0a3           5 TRFAAEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVR---DELVCSQENGTVQIKGETVYKVTDVIDVTIAEVRME--TR   79 (87)
T ss_dssp             CCEEEEEEEEETTEEEEEETTTCCEEEEEGGGTCSCG---GGEEEETTTTEEEETTEEEEETTCEEEEEEEEEETT--TT
T ss_pred             CEEEEEEEEEEcCeEEEEEecCCcEEEEEehhCCCce---EEEeccceEEEEEEcccEEEECCCEEEEEEEEEecc--cC
Confidence            6899999999999999999999999999999999886   7777554443 3456678899999999999999976  89


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|.++-
T Consensus        80 ~I~~~P   85 (87)
T d2ix0a3          80 SIIARP   85 (87)
T ss_dssp             EEEEEE
T ss_pred             eEEEEE
Confidence            998864

>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.24  E-value=8.5e-12  Score=105.24  Aligned_cols=75  Identities=11%  Similarity=0.117  Sum_probs=65.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +.++|+|++|.++|+||.|.  +++|+||++.+++++   |.+++..++++|++.++.|++||+|+|+|.+||.+  +++
T Consensus         5 ei~~g~V~~v~~~G~FVel~--~ieGlv~~s~l~~~~---~~~~~~~~~~~~~~~~~~~~~Gd~v~vkV~~vd~~--~~~   77 (106)
T d1go3e1           5 ELIEGEVVDVVEFGSFVRLG--PLDGLIHVSQIMDDY---VSYDPKREAIIGKETGKVLEIGDYVRARIVAISLK--AER   77 (106)
T ss_dssp             CEEEEEEEEEETTEEEEECS--SSEEEEEGGGSCSSC---EEECCC--CEEETTTCCEECTTCEEEEEEEEEECC--C--
T ss_pred             CEEEEEEEEEeeeEEEEEee--CeEEEEEeecccCce---eeeccceeEEeecccccceeecceEEEEEEEEchh--hcc
Confidence            68999999999999999995  799999999999887   89999999999999999999999999999999976  565


Q ss_pred             eE
Q 008167          570 LQ  571 (575)
Q Consensus       570 i~  571 (575)
                      +.
T Consensus        78 ~~   79 (106)
T d1go3e1          78 KR   79 (106)
T ss_dssp             --
T ss_pred             cc
Confidence            43

>d2ix0a1 b.40.4.5 (A:83-172) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=99.09  E-value=1.6e-10  Score=94.02  Aligned_cols=74  Identities=8%  Similarity=0.010  Sum_probs=64.3

Q ss_pred             CccEEEEEeCCCCCC-ceEecCCcc---CcCCCCEEEEEEeecCCCCC-CcceEEEEeecCCCChhhHHHHHHhhCCCC
Q 008167            9 SVAHALFVPKDRRIP-KIRIQTRQL---GNLLDKRIIVAVDSWDCQSR-YPFGHYVRVIGEIGDRDTESEMVLIDNDID   82 (575)
Q Consensus         9 ~~~~~~~~P~d~r~p-~i~i~~~~~---~~~~~~~~~v~i~~w~~~~~-~p~g~i~~~lG~~~~~~~~~~~il~~~~i~   82 (575)
                      ..++++++|.|+|++ .|.|+....   +...|++|+|+|++||.... .+.|+|+++||..+|+++++.++|++|+||
T Consensus        11 ~~~~~fVvPd~~ri~~~I~I~~~~~~~~~ak~Gd~Vvvei~~~P~~~~~~~~g~I~evlG~~~Dp~~e~~~~la~~~Lp   89 (90)
T d2ix0a1          11 KNDRLAIVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLE   89 (90)
T ss_dssp             CSSSEEEEESCTTCCSCEEEEECTTCCCCCCTTCEEEEEEEECGGGTCSSCEEEEEEECCCTTCTTHHHHHHHHHTTCC
T ss_pred             eCCEEEEEeCCCcccccccccccccccccCCCCCEEEEEEEeCCCCCCCCceEEEEEEEecCCCCCCcHHHHHHHcCCC
Confidence            456899999999998 599987653   34479999999999997654 568999999999999999999999999997

>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exosome complex exonuclease RRP44
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=99.06  E-value=1.1e-10  Score=93.50  Aligned_cols=81  Identities=27%  Similarity=0.457  Sum_probs=60.1

Q ss_pred             eeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEe----eCCCeEEeeCcEEEEEEEEe-cCCC
Q 008167          491 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK----MDGNLSYSVLQTVNIHMEVV-EPQP  565 (575)
Q Consensus       491 ~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g----~~~~~~~~lGD~V~V~V~~v-d~~~  565 (575)
                      .-+|.|+.|.++|+.|.+|.||+||.|++++..++ ...+.||+..+.++-    .....+++++|+|+|+|.++ +...
T Consensus         3 ~EegyV~~Vr~NGivVfVPkyGiEG~v~l~~~~~~-~~~~~~De~~~~l~~~~~~~~~~~~~~vFD~V~V~is~vkd~~~   81 (88)
T d2vnud2           3 TETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTED-PNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPIT   81 (88)
T ss_dssp             EEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSC-GGGCEEETTTTEEEECCTTCSSCEEEETTCEEEEEEC-------
T ss_pred             eeEEEEEEEecccEEEEEeccceeEEEEEeccCCC-CcceEEcchheEEEEecccCCCcEEEEecceEEEEEEEEECCcC
Confidence            46899999999999999999999999999887654 234678877766641    12367999999999999988 5556


Q ss_pred             CCCceEE
Q 008167          566 NRPKLQL  572 (575)
Q Consensus       566 ~~~~i~l  572 (575)
                      ++||++|
T Consensus        82 ~k~k~~l   88 (88)
T d2vnud2          82 SKRKAEL   88 (88)
T ss_dssp             -CCEEEC
T ss_pred             CCccccC
Confidence            7888764

>d1y14b1 b.40.4.5 (B:81-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.99  E-value=6.8e-10  Score=90.70  Aligned_cols=74  Identities=12%  Similarity=0.073  Sum_probs=62.7

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ++++|+|++++++|+||.+.  .++|+||.+.++++    |.||+....+.++++++.|++||.|+|+|.+++.+  +++
T Consensus         5 ev~~g~I~~v~~~G~fv~lg--~~eg~i~~~~l~~~----~~~d~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~--~~~   76 (91)
T d1y14b1           5 EVVDGTVVSCSQHGFEVQVG--PMKVFVTKHLMPQD----LTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQ--VSS   76 (91)
T ss_dssp             CEEEEEEEEEETTEEEEEET--TEEEEEEGGGSCTT----CEECC-----CEECSSCEECTTCEEEEEEEEEEEE--TTE
T ss_pred             CEEEEEEEEEEeeEEEEEEc--CeEEEEEhhhcCcc----eEEccccceeEecccCeEEeCCCEEEEEEEEEecc--cCc
Confidence            68999999999999999996  57999999999877    68999999999999999999999999999999976  666


Q ss_pred             eE
Q 008167          570 LQ  571 (575)
Q Consensus       570 i~  571 (575)
                      |.
T Consensus        77 i~   78 (91)
T d1y14b1          77 IH   78 (91)
T ss_dssp             EE
T ss_pred             cE
Confidence            64

>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=1.4e-09  Score=89.42  Aligned_cols=76  Identities=5%  Similarity=0.063  Sum_probs=68.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ++++|+|+++.++|++|.+.  .++|+||.+.+++++  .|++++....|.+++++..|++||.|+|+|.+++.+  .++
T Consensus         6 ev~~g~V~~v~~~G~fv~lg--~~~~~v~~~~l~~d~--~y~~~~~~~~~~~~~~~~~~~~Gd~VrvkV~~v~~~--~~~   79 (94)
T d2c35b1           6 EVVDAVVTQVNKVGLFTEIG--PMSCFISRHSIPSEM--EFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVD--KND   79 (94)
T ss_dssp             CEEEEEEEEEETTEEEEEET--TEEEEEEGGGSCTTE--EEESSSSSCEEEETTSCSEEETTCEEEEEEEEEEEE--TTE
T ss_pred             CEEEEEEEEEEeeEEEEEec--CceEEEEhhhcCcce--eecccccceEEEcccceEEEeCCCEEEEEEEEEecC--cCc
Confidence            78999999999999999995  479999999999874  377899999999999999999999999999999986  566


Q ss_pred             eE
Q 008167          570 LQ  571 (575)
Q Consensus       570 i~  571 (575)
                      |.
T Consensus        80 I~   81 (94)
T d2c35b1          80 IF   81 (94)
T ss_dssp             EE
T ss_pred             ce
Confidence            64

>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.87  E-value=1.6e-09  Score=87.39  Aligned_cols=69  Identities=14%  Similarity=0.149  Sum_probs=53.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|.|+++.++|+||.|+++ |++|+||.+++++++    .          .+....|++||.|+|+|.++|.+  ++
T Consensus        15 ~iv~G~V~~i~~~G~fV~l~~~~~i~G~i~~sels~~~----~----------~~~~~~~~~Gd~v~~kV~~vd~~--~~   78 (86)
T d1kl9a2          15 DVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRR----I----------RSINKLIRIGRNECVVVIRVDKE--KG   78 (86)
T ss_dssp             CEEEEEEEEECSSEEEEEETTTTTEEEEEEGGGC--------------------------CTTCEEEEEEEEEETT--TT
T ss_pred             CEEEEEEEEEeCCeEEEEEecCCCEEEEEEeeeccccc----c----------ccceEEeecccEEEEEEEEEECC--CC
Confidence            6899999999999999999875 799999999997542    1          13457799999999999999976  89


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      ||.||+
T Consensus        79 ki~LS~   84 (86)
T d1kl9a2          79 YIDLSK   84 (86)
T ss_dssp             EEEEES
T ss_pred             EEEEEe
Confidence            999996

>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.70  E-value=6e-09  Score=83.61  Aligned_cols=69  Identities=12%  Similarity=0.091  Sum_probs=57.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCC-ceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCC
Q 008167          490 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP  568 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~-gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~  568 (575)
                      ..+.|.|.++.++|+||.|+++ |++|+||.++++.++    .          .+....|++||+|+|+|.++|.+  ++
T Consensus        13 ~iv~G~V~~v~~~G~fV~l~~~~gi~Gli~~sels~~~----~----------~~~~~~~~~G~~v~~kV~~vd~~--~~   76 (84)
T d2ahob2          13 EILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKW----V----------KNIRDVLKENRKVIVKVIRVDRR--KG   76 (84)
T ss_dssp             CCCEEEEEEEETTEEEEEETTTTTEEEEECGGGCC-------------------CHHHHTCSSCEEECEEEEEETT--TT
T ss_pred             CEEEEEEEEEECCEEEEEECCcCCEEEEEEcccccccc----c----------cccceEeecccEEEEEEEEEECC--CC
Confidence            5789999999999999999875 799999999987653    1          13356799999999999999976  89


Q ss_pred             ceEEEe
Q 008167          569 KLQLTL  574 (575)
Q Consensus       569 ~i~l~l  574 (575)
                      +|.||+
T Consensus        77 ~i~LS~   82 (84)
T d2ahob2          77 TVDVSL   82 (84)
T ss_dssp             EEEEES
T ss_pred             EEEEEE
Confidence            999986

>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Escherichia coli [TaxId: 562]

Probab=98.55  E-value=2.2e-08  Score=78.59  Aligned_cols=67  Identities=18%  Similarity=0.207  Sum_probs=56.8

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|.++.++|+||.|+. |++|+||.++++.++    .          .+....|++||+|+|+|.++|.   ++|
T Consensus         7 ~iv~G~V~~v~~~G~fV~l~~-~~~Glv~~sels~~~----~----------~~~~~~~~~G~~v~v~Vi~id~---~~r   68 (76)
T d1sroa_           7 RVYTGKVTRIVDFGAFVAIGG-GKEGLVHISQIADKR----V----------EKVTDYLQMGQEVPVKVLEVDR---QGR   68 (76)
T ss_dssp             SEEEEEEEEEETTEEEEECSS-SCCCBCCTTSSCSSC----C----------SCHHHHCCTTCEEEEEEEECCT---TCC
T ss_pred             CEEEEEEEEEeCcEEEEEeCC-CCEEEEEhHHhCccc----c----------CCHHHccCCCCEEEEEEEEECC---CCC
Confidence            678999999999999999976 899999999998653    1          1345679999999999999985   357


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        69 i~LS~   73 (76)
T d1sroa_          69 IRLSI   73 (76)
T ss_dssp             CEEEE
T ss_pred             EEEEE
Confidence            99986

>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Tex S1-domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=98.40  E-value=1.6e-07  Score=76.75  Aligned_cols=68  Identities=16%  Similarity=0.140  Sum_probs=59.1

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|.++.++|++|.|.. |++|+||.+++++++    .          .+....|++||.|+|+|..+|.+  +++
T Consensus        20 ~iv~g~V~~v~~~G~~V~l~~-~i~G~i~~~~ls~~~----~----------~~~~~~~~vGq~v~~~V~~id~~--~~~   82 (94)
T d3bzka4          20 MVLEGVVTNVTNFGAFVDIGV-HQDGLVHISALSEKF----V----------KDPYEVVKAGDIVKVKVMEVDIP--RNR   82 (94)
T ss_dssp             CEEEEEEEEEETTEEEEECSS-SSCEEEEGGGGCSSC----C----------SCHHHHCCTTCEEEEEEEEEETT--TTE
T ss_pred             CEEEEEEEEEECcEEEEEeCC-CceEEeehhhhhccc----c----------cChhhhhccCcEEEEEEEEEECC--CCE
Confidence            688999999999999999976 999999999998653    2          12346799999999999999976  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        83 i~LS~   87 (94)
T d3bzka4          83 VGLSM   87 (94)
T ss_dssp             EEEES
T ss_pred             EEEEE
Confidence            99986

>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.24  E-value=9.6e-07  Score=70.12  Aligned_cols=68  Identities=13%  Similarity=0.117  Sum_probs=56.3

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|.++.++|++|.|.. +++|++|+++++++.   ..          .+....|++||.|+|+|.++|.   .++
T Consensus         7 d~V~G~V~~v~~~g~~V~i~~-~~~g~l~~se~s~~~---~~----------~~~~~~~~vGd~V~~kV~~vd~---~~~   69 (83)
T d2ba0a1           7 DVVIGIIREVAANGWAVDIYS-PYQAFLPVSENPEMK---PN----------KKPNEVLDIGDAIIAKVLNIDP---KMK   69 (83)
T ss_dssp             CEEEEEEEEECSSEEEEECSS-SSCEEEEGGGCTTCC---TT----------SCGGGTCCTTCEEEEEEEEECT---TCC
T ss_pred             CEEEEEEEEEECCEEEEecCC-CeeEEEecccccccc---cc----------cChhhhcccccEEEEEEEEECC---CCC
Confidence            678999999999999999986 899999999987542   11          1234569999999999999985   367


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        70 i~LS~   74 (83)
T d2ba0a1          70 VTLTM   74 (83)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            99986

>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.10  E-value=9e-07  Score=70.97  Aligned_cols=70  Identities=10%  Similarity=-0.036  Sum_probs=57.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.|.. +++|++|++++.+++    ..+.       .+....|++||.|+++|.++|.   .++
T Consensus         9 div~G~V~~i~~~g~fV~i~~-~~~gll~~s~~~~~~----~~~~-------~~~~~~~~~Gd~v~~kV~~vd~---~~~   73 (87)
T d2je6i1           9 DIVIGLVEDVEIYGWVVDIKA-PYKAYLPASNLLGRS----INVG-------EDLRRYLDVGDYVIARIENFDR---SID   73 (87)
T ss_dssp             CEEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSC----CCTT-------CCCSSSCCTTCEEEEEEEEEET---TEE
T ss_pred             CEEEEEEEEEECCEEEEEeCC-CEEEEEehHHhCCce----eccc-------cccchhhcccceEEEEEEEECC---CCC
Confidence            689999999999999999986 899999999987542    1111       1234679999999999999995   468


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        74 i~LS~   78 (87)
T d2je6i1          74 PVLSV   78 (87)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            99886

>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome complex RNA-binding protein 1, ECR1
species: Aeropyrum pernix [TaxId: 56636]

Probab=98.06  E-value=1.1e-06  Score=70.61  Aligned_cols=71  Identities=8%  Similarity=-0.055  Sum_probs=57.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|+++.++|++|.|.. +.+|+||++++.+++   +..+.       .+..+.|++||.|+++|.++|.   .++
T Consensus         9 dvV~G~V~~v~~~g~fV~i~~-~~~g~l~~se~~~~~---~~~~~-------~~~~~~~~vGd~V~~kV~~vd~---~~~   74 (88)
T d2z0sa1           9 DVVIGLIQSVGIMNWFVDINS-PYVAVLSVQDFLGRP---FNPAV-------DDMQSLLKVGDYIKAKVVAFDK---TRS   74 (88)
T ss_dssp             CCEEEEEEEECSSEEEEECSS-SSCEEEEHHHHHTSC---CCTTT-------TCCTTSSCTTCEEEEEEEEECT---TSC
T ss_pred             CEEEEEEEEEECCeEEEEeCC-CeEEEEehHHhCccc---ccccc-------cchhhhcccCcEEEEEEEEECC---CCC
Confidence            678999999999999999976 889999999887653   22111       1234679999999999999995   367


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        75 i~Ls~   79 (88)
T d2z0sa1          75 PLLTV   79 (88)
T ss_dssp             EEEEC
T ss_pred             EEEEE
Confidence            99986

>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
species: Streptomyces antibioticus [TaxId: 1890]

Probab=98.05  E-value=6.1e-08  Score=72.75  Aligned_cols=60  Identities=15%  Similarity=0.138  Sum_probs=34.9

Q ss_pred             EEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCC
Q 008167          494 ARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ  564 (575)
Q Consensus       494 g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~  564 (575)
                      |.|++|.++|+||.|+. |++|+||+++++.++.  +.+-        .+....|++||+|+|+|.++|.+
T Consensus         1 G~V~~i~~fG~FV~l~~-g~~Glihiseis~~~~--~~~v--------~~~~~~~~~G~~V~vkV~~iD~~   60 (62)
T d1e3pa2           1 GSVVKTTTFGAFVSLLP-GKDGLLHISQIRKLAG--GKRV--------ENVEDVLGVGQKVQVEIAEIDSR   60 (62)
T ss_dssp             CBEEECC-CSCEECCC----CCCCC-----------------------------CCSSCBCCCCCCCCCSS
T ss_pred             CEEEEEEeceEEEEecC-CceEEEEHHHcccccc--cccc--------cCHHHhcCCCCEEEEEEEEEcCC
Confidence            68999999999999986 9999999999975420  1110        13467799999999999999964

>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of RRP5 protein homolog (PDCD11, KIAA0185)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.86  E-value=3.5e-06  Score=71.56  Aligned_cols=70  Identities=14%  Similarity=0.099  Sum_probs=57.2

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|+|..|.++|++|.|..-+++|+||++++.++    +..         .+....|++||.|+|+|..++..  +++
T Consensus        23 ~iv~G~V~~i~~~G~~V~lg~~~~~G~l~~~els~~----~~~---------~~~~~~~~vGq~v~~~V~~vd~~--~~~   87 (119)
T d1wi5a_          23 MLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEY----IRQ---------KNKGAKLKVGQYLNCIVEKVKGN--GGV   87 (119)
T ss_dssp             CEEEEEEEEECSSEEEEECCCSSCEEEEEHHHHHHH----HHH---------HSSSCCCCTTCEEEEEEEECCTT--SCE
T ss_pred             CEEEEEEEEEeccEEEEEEeccccceEEeHHHhccc----ccc---------CCHHHhcccceEEEEEEEEEeCC--CCE
Confidence            678999999999999999943489999999988643    111         12346799999999999999965  899


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.||+
T Consensus        88 i~LS~   92 (119)
T d1wi5a_          88 VSLSV   92 (119)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            99986

>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribosomal RNA-processing protein 4, RRP4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.37  E-value=4.1e-05  Score=61.99  Aligned_cols=77  Identities=9%  Similarity=0.051  Sum_probs=53.4

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+.|.|+++.++|++|.|.. +.+|+||++++...+   +... +.......+....|++||.|.|+|.+++.   ..+
T Consensus        10 diV~G~V~~v~~~g~~V~I~~-~~~g~l~is~i~~~~---~~~r-r~~~~~~~~~~~~~~~Gd~V~~kV~~v~~---dg~   81 (95)
T d2nn6h1          10 DIVVGRITEVQQKRWKVETNS-RLDSVLLLSSMNLPG---GELR-RRSAEDELAMRGFLQEGDLISAEVQAVFS---DGA   81 (95)
T ss_dssp             BCCCEEEEEEETTEEEEECSS-SSCEEEESSCCC-----------------CHHHHHHSCSSCEECCEEEEEET---TTE
T ss_pred             CEEEEEEEEEecCcEEEEeCC-CceEEEEHHHccccc---cccc-cccchhhhhhhhhcccccEEEEEEEEECC---CCC
Confidence            568999999999999999975 689999999886432   1111 10000011224569999999999999996   367


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      |.|+.
T Consensus        82 i~Ls~   86 (95)
T d2nn6h1          82 VSLHT   86 (95)
T ss_dssp             EEEEC
T ss_pred             EEEEe
Confidence            88874

>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Thermotoga maritima [TaxId: 2336]

Probab=96.42  E-value=0.0039  Score=47.09  Aligned_cols=62  Identities=13%  Similarity=0.057  Sum_probs=50.6

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      +...|+|..+.+..+.|.|.  ++||.++-++.-                    .+..|+.||+|+|.|..|+......+
T Consensus        10 eiv~G~V~r~~~~~~~Vdlg--~~eaiLp~~eqi--------------------p~E~~~~Gdrik~~i~~V~~~~kgpq   67 (72)
T d1hh2p1          10 TVTTAEVIRVMGEWADIRIG--KLETRLPKKEWI--------------------PGEEIKAGDLVKVYIIDVVKTTKGPK   67 (72)
T ss_dssp             CEEEEEEEEECSSEEEEEET--TEEEEEEGGGSC--------------------TTCCCCTTCEEEEEEEEEEEETTEEE
T ss_pred             cEEEEEEEEEcCCCEEEEEC--CcEEECCHHHcC--------------------CCCCCCCCCEEEEEEEEEEEcCCCCe
Confidence            78899999999999999996  799999976432                    35679999999999999987654556


Q ss_pred             eEEE
Q 008167          570 LQLT  573 (575)
Q Consensus       570 i~l~  573 (575)
                      |.||
T Consensus        68 I~lS   71 (72)
T d1hh2p1          68 ILVS   71 (72)
T ss_dssp             EEEE
T ss_pred             EEEe
Confidence            6655

>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.76  E-value=0.0091  Score=46.87  Aligned_cols=66  Identities=8%  Similarity=-0.067  Sum_probs=52.5

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+-|.|+++..++++|.|-. +.+|++|+++++..     .          .+....+++||.|-++|.+++..   .+
T Consensus         8 D~ViG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~g~-----~----------k~~r~~l~~GD~V~arV~~v~~~---~~   68 (88)
T d2nn6g1           8 DHVIGIVTAKSGDIFKVDVGG-SEPASLSYLSFEGA-----T----------KRNRPNVQVGDLIYGQFVVANKD---ME   68 (88)
T ss_dssp             EEEEEEEEEEETTEEEEECSS-SSCCCEESCSSSCC-----S----------SCSSSSSCTTCEEEEEEEECCTT---SC
T ss_pred             CEEEEEEEEEeCCeEEEEcCC-CeeEEEeHHHcCcc-----c----------cccCcccCCCCEEEEEEEEeCCC---CC
Confidence            567899999999999999976 68899999887532     1          13455699999999999999864   56


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|+.
T Consensus        69 ~~Lsc   73 (88)
T d2nn6g1          69 PEMVC   73 (88)
T ss_dssp             CEEEC
T ss_pred             EEEEE
Confidence            66664

>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1 domain of NusA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.41  E-value=0.1  Score=39.33  Aligned_cols=64  Identities=14%  Similarity=0.074  Sum_probs=47.5

Q ss_pred             ceeEEEEEEEecCe----EEEEEcC--CceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecC
Q 008167          490 TDTEARIVKIRSNG----FIVFVPK--FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEP  563 (575)
Q Consensus       490 ~~~~g~V~~v~~~g----~~V~l~~--~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~  563 (575)
                      +...|+|..+....    +.|.|..  -++||.++-++.                    -.+..|+.||+|++.|..|+.
T Consensus         6 eiv~G~V~r~~~~~~~~~v~vdlG~~~~~~EaiLp~~eq--------------------ip~E~y~~Gdrik~~i~~V~~   65 (76)
T d2asba1           6 EIVAGVIQRDSRANARGLVVVRIGTETKASEGVIPAAEQ--------------------VPGESYEHGNRLRCYVVGVTR   65 (76)
T ss_dssp             CEEEEEEECCHHHHHTTCEEEEECSSSSCEEEEECGGGS--------------------CTTCCCCTTCEEEEEEEEEEC
T ss_pred             eEEEEEEEEEecCCCceEEEEECCCCCCCEEEECCHHHc--------------------CCCcccCCCCEEEEEEEEEEe
Confidence            67789998875432    5677742  369999976542                    135679999999999999998


Q ss_pred             CCCCCceEEE
Q 008167          564 QPNRPKLQLT  573 (575)
Q Consensus       564 ~~~~~~i~l~  573 (575)
                      .....+|.||
T Consensus        66 ~~kGp~IilS   75 (76)
T d2asba1          66 GAREPLITLS   75 (76)
T ss_dssp             CSSSCEEEEE
T ss_pred             cCCCCEEEEe
Confidence            7767777765

>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of exosome component 3 (RRP40)
species: Saccharomyces cerevisiae [TaxId: 4932]

Probab=90.91  E-value=0.29  Score=38.00  Aligned_cols=67  Identities=9%  Similarity=-0.058  Sum_probs=49.0

Q ss_pred             ceeEEEEEEEecCeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEecCCCCCCc
Q 008167          490 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK  569 (575)
Q Consensus       490 ~~~~g~V~~v~~~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd~~~~~~~  569 (575)
                      ..+-|.|+++..++++|.|-. ...|.++.+..-...       .       ++....+++||-|-++|.+++.+   .+
T Consensus         9 D~ViG~V~~~~~~~~~vdI~~-~~~~~L~~~~~f~g~-------~-------k~~r~~l~~GDlV~arV~~v~~~---~~   70 (90)
T d2ja9a1           9 DFVIGVIIGTFSDSYKVSLQN-FSSSVSLSYMAFPNA-------S-------KKNRPTLQVGDLVYARVCTAEKE---LE   70 (90)
T ss_dssp             CEEEEEEEEECSSEEEEESST-TSCCEEEETTSSTTC-------C-------SSSCCCCCTTCEEEEEEEECCTT---SC
T ss_pred             CEEEEEEEEEeCCcEEEEcCC-cchhhhhhhhccCcc-------c-------cccCCccCCCCEEEEEEEEECCC---CC
Confidence            578899999999999999964 457777755322111       1       23456699999999999999864   56


Q ss_pred             eEEEe
Q 008167          570 LQLTL  574 (575)
Q Consensus       570 i~l~l  574 (575)
                      +.|+.
T Consensus        71 ~~Lsc   75 (90)
T d2ja9a1          71 AEIEC   75 (90)
T ss_dssp             CEEES
T ss_pred             EEEEE
Confidence            66654

>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: S1-domain of Ribonuclease E
species: Escherichia coli [TaxId: 562]

Probab=82.19  E-value=0.39  Score=36.94  Aligned_cols=66  Identities=12%  Similarity=0.019  Sum_probs=45.8

Q ss_pred             eeEEEEEEEec--CeEEEEEcCCceEEEEEccCCCCCCCCcceecCCcEEEEeeCCCeEEeeCcEEEEEEEEec
Q 008167          491 DTEARIVKIRS--NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE  562 (575)
Q Consensus       491 ~~~g~V~~v~~--~g~~V~l~~~gleg~v~~~~l~~d~~~~~~~d~~~~~l~g~~~~~~~~lGD~V~V~V~~vd  562 (575)
                      .+.|.|.+|.+  +++||.+.. +-.|++|++++..++   +..+....  ........++.||.|-|+|..-.
T Consensus         3 IY~G~V~~V~pgl~AAFVDiG~-~k~gFL~~~di~~~~---~~~~~~~~--~~~~i~~~l~~G~~ilVQV~Ke~   70 (87)
T d1smxa_           3 IYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREY---FPANYSAH--GRPNIKDVLREGQEVIVQIDKEE   70 (87)
T ss_dssp             CEEEEEEEEEGGGTEEEEESSS-SSCEEEEGGGSCGGG---CSSCCCSS--SCCCGGGTCCTTCEEEEEEEECC
T ss_pred             cEEEEEEEecCCceEEEEEeCC-CccceeEecccceee---eccccccc--cccchhhhccCCCeEEEEEeecc
Confidence            57899999976  689999975 889999999876542   11111000  00123466899999999998743

>d2ix0a2 b.40.4.5 (A:4-82) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Exoribonuclease 2, RNB
species: Escherichia coli [TaxId: 562]

Probab=81.08  E-value=0.83  Score=34.33  Aligned_cols=51  Identities=12%  Similarity=0.094  Sum_probs=36.8

Q ss_pred             CCccEEEEEeCCCCCCceEecCCccC-cCCCCEEEEEEeecCCCCCCcceEEEEeec
Q 008167            8 GSVAHALFVPKDRRIPKIRIQTRQLG-NLLDKRIIVAVDSWDCQSRYPFGHYVRVIG   63 (575)
Q Consensus         8 ~~~~~~~~~P~d~r~p~i~i~~~~~~-~~~~~~~~v~i~~w~~~~~~p~g~i~~~lG   63 (575)
                      .++.+.+++|.|.  ..|.|+..+.. ...|++|.|+|...  . ..|.|+|+++|-
T Consensus        26 ~~~G~GFv~~d~~--~DifI~~~~~~~A~~GD~V~v~i~~~--~-~r~eg~I~~ilE   77 (79)
T d2ix0a2          26 TEKGFGFLEVDAQ--KSYFIPPPQMKKVMHGDRIIAVIHSE--K-ERESAEPEELVE   77 (79)
T ss_dssp             CC--CEEEEEETT--EEEEECHHHHTTCCTTCEEEEEEECC-----CCEEEEEEEEE
T ss_pred             eCCCcEEEEECCC--CcEEECHHHHcCCCCCCEEEEEEEeC--C-CcEEEEEEEEec
Confidence            4566788899874  46999988765 45799999999743  2 458999999873