Citrus Sinensis ID: 013634

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------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-------44
MKLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
cccccccEEEEEEEcccccccccccHHHHHHHHccccEEEccccccccccccccccccccccccEEEEEEEEEEccccEEEEEEEEccEEEccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEEEcccccccEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHccccEEEcccccccHHHHHHHHHHHHHcccEEccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEEEEccEEEEEEccccEEEEEEcccccccccccEEEcccccEEEEEccccEEEEccEEEEEEEEEcccccccEEEEEEc
cccccccEEEEEEEEEEEEEEcccccHHHHHHHccccEEccccccccccHHcccccccccccccEEEEEEEEEEcccccEEEEEEEHHHHcccHHccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccEEEEEEccccccccEEEEEccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccHHHHHHHHHHHHHcccEEccccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHEEEccccccccccccccccHHHHHccccHHccccHHHHHHHHHHHHHccccccccccHHHHHHHHHHccHHHHHHHHHHHcHHHHHHHHHHHHccccccEEEEEEcccEEEEEcccccEEEEEEEEccccccccEEEEcHHHcEEEEccccEEEEEccEEEEEEEEEEcccccccEEEEEc
mklqysslMFQLdiadvtnfvhpgtplddeaskrgtsVYLVERRidmlpkpltediCSLRADVERLAFSVIWeltpeaeiisTRYTKSVIKSCAALSYVEAQArmddsrlmdpltTDLRNMNSLAKKMRQRRIERGALTLASAEVKFqidtethdpldigmYQIREANQMVEEFMLAANVSVAEQILRQfplcsllrrhpsptkemLEPLLRTAAAVGLNLDVSSSKALADSldravgddpyfNKLIRILATRCMTQAvyfcsgdltppefhhyglaaplythftspirRYADVVVHRLLSASlgiyklpsvfqdrpqltsiadnlnyrhrnaqmasrgsvELHTLIYfrkrptdteARIVKIRsngfivfvpkfgiegpvyltprgqkgsgdwyvdEQQQKIVkmdgnlsySVLQTVNIHMevvepqpnrpklqltli
MKLQYSSLMFQLDIADVTNFVHpgtplddeaskrgtSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIweltpeaeiistrytkSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADsldravgddpYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAqmasrgsvelhtliyfrkrptdteariVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHmevvepqpnrpklqltli
MKLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
******SLMFQLDIADVTNFVHPGT*********GTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQ*********************************GALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRR********LEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV**************
MKLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSV*QDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
MKLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
**LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
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MKLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query439 2.2.26 [Sep-21-2011]
Q9CSH3958 Exosome complex exonuclea yes no 0.968 0.443 0.479 1e-116
Q9Y2L1958 Exosome complex exonuclea yes no 0.968 0.443 0.484 1e-116
Q17632961 Probable exosome complex yes no 0.961 0.439 0.473 1e-111
P37202970 Exosome complex exonuclea yes no 0.835 0.378 0.509 1e-107
Q081621001 Exosome complex exonuclea yes no 0.865 0.379 0.489 1e-100
Q8CI75870 DIS3-like exonuclease 2 O no no 0.826 0.417 0.409 4e-75
A0JN801053 DIS3-like exonuclease 1 O no no 0.890 0.371 0.389 4e-75
Q5U2P01054 DIS3-like exonuclease 1 O no no 0.968 0.403 0.368 1e-74
A2RV181057 DIS3-like exonuclease 1 O no no 0.879 0.365 0.389 2e-74
Q8C0S11053 DIS3-like exonuclease 1 O no no 0.993 0.414 0.358 2e-74
>sp|Q9CSH3|RRP44_MOUSE Exosome complex exonuclease RRP44 OS=Mus musculus GN=Dis3 PE=2 SV=4 Back     alignment and function desciption
 Score =  419 bits (1077), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 211/440 (47%), Positives = 297/440 (67%), Gaps = 15/440 (3%)

Query: 2   KLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRA 61
           +L   +L   + IADV++F+ PG  LD E+++RGT+VYL E+RIDM+P+ L+ ++CSLR+
Sbjct: 494 ELSNGNLEVGVHIADVSHFIRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLRS 553

Query: 62  DVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNM 121
           +V+RLAFS IWE+   AEI+ TR+TKSVI S A+L+Y EAQ R+D + + D +TT LR +
Sbjct: 554 NVDRLAFSCIWEMNHNAEILKTRFTKSVINSKASLTYAEAQMRIDSAAMNDDITTSLRGL 613

Query: 122 NSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVS 181
           N LAK +++ RIE+GALTL+S E++F +D+ETHDP+D+   ++RE N MVEEFML AN+S
Sbjct: 614 NQLAKILKKGRIEKGALTLSSPEIRFHMDSETHDPIDLQTKELRETNSMVEEFMLLANIS 673

Query: 182 VAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDD- 240
           VA++I  +F   +LLR+HP+P     + L++ A +  L +   ++K+LADSLDRA   D 
Sbjct: 674 VAKKIHEEFSEHALLRKHPAPPPSNYDILVKAAKSKNLQIKTDTAKSLADSLDRAESPDF 733

Query: 241 PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLL 300
           PY N L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++VHRLL
Sbjct: 734 PYLNTLLRILATRCMMQAVYFCSG--MDNDFHHYGLASPIYTHFTSPIRRYADIIVHRLL 791

Query: 301 SASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEAR 359
           + ++G         D+ +L+ I  NLN+RH+ AQ A R SV  HT ++F+ +     EA 
Sbjct: 792 AVAIGADCTYPELTDKHKLSDICKNLNFRHKMAQYAQRASVAFHTQLFFKSKGIVSEEAY 851

Query: 360 IVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE-----------QQQKIVKMDG 408
           I+ +R N  +V +PK+G+EG V+   + +      Y DE                VK+  
Sbjct: 852 ILFVRKNAIVVLIPKYGLEGTVFFEEKDKPKPRLAYDDEIPSLRIEGTVFHVFDKVKVKI 911

Query: 409 NLSYSVLQTVNIHMEVVEPQ 428
            L  S LQ   I M +VEPQ
Sbjct: 912 TLDSSNLQHQKIRMALVEPQ 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 Back     alignment and function description
>sp|Q17632|RRP44_CAEEL Probable exosome complex exonuclease RRP44 OS=Caenorhabditis elegans GN=dis-3 PE=3 SV=2 Back     alignment and function description
>sp|P37202|DIS3_SCHPO Exosome complex exonuclease dis3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=dis3 PE=1 SV=1 Back     alignment and function description
>sp|Q08162|RRP44_YEAST Exosome complex exonuclease DIS3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DIS3 PE=1 SV=1 Back     alignment and function description
>sp|Q8CI75|DI3L2_MOUSE DIS3-like exonuclease 2 OS=Mus musculus GN=Dis3l2 PE=1 SV=1 Back     alignment and function description
>sp|A0JN80|DI3L1_BOVIN DIS3-like exonuclease 1 OS=Bos taurus GN=DIS3L PE=2 SV=2 Back     alignment and function description
>sp|Q5U2P0|DI3L1_RAT DIS3-like exonuclease 1 OS=Rattus norvegicus GN=Dis3l PE=2 SV=2 Back     alignment and function description
>sp|A2RV18|DI3L1_DANRE DIS3-like exonuclease 1 OS=Danio rerio GN=dis3l PE=2 SV=1 Back     alignment and function description
>sp|Q8C0S1|DI3L1_MOUSE DIS3-like exonuclease 1 OS=Mus musculus GN=Dis3l PE=2 SV=2 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query439
225438440 899 PREDICTED: exosome complex exonuclease R 0.972 0.474 0.906 0.0
255561455 934 mitotic control protein dis3, putative [ 0.995 0.467 0.883 0.0
225438438 937 PREDICTED: exosome complex exonuclease R 0.970 0.454 0.906 0.0
297836470 933 ribonuclease II family protein [Arabidop 0.970 0.456 0.906 0.0
356516247 934 PREDICTED: exosome complex exonuclease R 0.968 0.455 0.910 0.0
224071355 935 predicted protein [Populus trichocarpa] 0.970 0.455 0.892 0.0
334184269 1012 exosome complex exonuclease DIS3/RRP44 [ 0.970 0.420 0.884 0.0
357517627 1045 Exosome complex exonuclease [Medicago tr 0.970 0.407 0.884 0.0
18398450 933 exosome complex exonuclease DIS3/RRP44 [ 0.970 0.456 0.884 0.0
356509070 934 PREDICTED: exosome complex exonuclease R 0.968 0.455 0.896 0.0
>gi|225438440|ref|XP_002276909.1| PREDICTED: exosome complex exonuclease RRP44 isoform 1 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  820 bits (2117), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 387/427 (90%), Positives = 412/427 (96%)

Query: 13  DIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIW 72
           DIADVTNFVHPGTPLDDEA++RGTSVYLVERRIDMLPKPLTEDICSLR+DVERLAFSVIW
Sbjct: 471 DIADVTNFVHPGTPLDDEAAQRGTSVYLVERRIDMLPKPLTEDICSLRSDVERLAFSVIW 530

Query: 73  ELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRR 132
           E+TP+AEIIST+YTKS+IKSCAALSY+EAQARMDDSRLMDPLT DLRNMN+LAK MR RR
Sbjct: 531 EMTPQAEIISTKYTKSIIKSCAALSYIEAQARMDDSRLMDPLTMDLRNMNALAKVMRLRR 590

Query: 133 IERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPL 192
           IERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAE+IL+ FPL
Sbjct: 591 IERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEKILKHFPL 650

Query: 193 CSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDDPYFNKLIRILAT 252
           CSLLRRHPSPT+EMLEPLLRTAAAVGLNLDVSSSKALADSLD AVGDDPYFNKLIRILAT
Sbjct: 651 CSLLRRHPSPTREMLEPLLRTAAAVGLNLDVSSSKALADSLDHAVGDDPYFNKLIRILAT 710

Query: 253 RCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSV 312
           RCMTQAVYFCSGDL+PPEFHHYGLAAPLYTHFTSPIRRYADV+VHRLL+ASLG+YKLP++
Sbjct: 711 RCMTQAVYFCSGDLSPPEFHHYGLAAPLYTHFTSPIRRYADVIVHRLLAASLGLYKLPTI 770

Query: 313 FQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFV 372
           FQD  QLTS ADNLNYRHRNAQMA R SVELHTLIYFRKRPTDTEARIVKIRSNGFIVFV
Sbjct: 771 FQDNAQLTSTADNLNYRHRNAQMAGRASVELHTLIYFRKRPTDTEARIVKIRSNGFIVFV 830

Query: 373 PKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432
           PK+GIEGPVYLTPRG+KG G+W VDEQQQK+ KMDG++SYSVLQTV IHMEVVEPQPNRP
Sbjct: 831 PKYGIEGPVYLTPRGEKGGGEWVVDEQQQKVKKMDGSISYSVLQTVMIHMEVVEPQPNRP 890

Query: 433 KLQLTLI 439
           KL+L LI
Sbjct: 891 KLELALI 897

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

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] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>gi|356516247|ref|XP_003526807.1| PREDICTED: exosome complex exonuclease RRP44-like [Glycine max] Back     alignment and taxonomy information
>gi|224071355|ref|XP_002303419.1| predicted protein [Populus trichocarpa] gi|222840851|gb|EEE78398.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>gi|357517627|ref|XP_003629102.1| Exosome complex exonuclease [Medicago truncatula] gi|355523124|gb|AET03578.1| Exosome complex exonuclease [Medicago truncatula] Back     alignment and taxonomy information
>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] Back     alignment and taxonomy information
>gi|356509070|ref|XP_003523275.1| PREDICTED: exosome complex exonuclease RRP44-like [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query439
ZFIN|ZDB-GENE-080213-3950 dis3 "DIS3 mitotic control hom 0.965 0.446 0.478 5.8e-105
UNIPROTKB|E1BXX6963 DIS3 "Uncharacterized protein" 0.968 0.441 0.472 9.5e-105
UNIPROTKB|E2RNY6958 DIS3 "Uncharacterized protein" 0.968 0.443 0.484 9.5e-105
UNIPROTKB|G3V1J5796 DIS3 "Exosome complex exonucle 0.968 0.533 0.484 9.5e-105
UNIPROTKB|Q9Y2L1958 DIS3 "Exosome complex exonucle 0.968 0.443 0.484 9.5e-105
MGI|MGI:1919912958 Dis3 "DIS3 mitotic control hom 0.968 0.443 0.481 9.5e-105
UNIPROTKB|F1RHF7752 DIS3 "Uncharacterized protein" 0.968 0.565 0.484 8.6e-104
DICTYBASE|DDB_G02936141006 DDB_G0293614 "putative exoribo 0.965 0.421 0.461 1.4e-101
WB|WBGene00001001961 dis-3 [Caenorhabditis elegans 0.961 0.439 0.473 3.4e-100
POMBASE|SPBC26H8.10970 dis3 "3'-5' exoribonuclease su 0.965 0.437 0.462 1.7e-98
ZFIN|ZDB-GENE-080213-3 dis3 "DIS3 mitotic control homolog (S. cerevisiae)" [Danio rerio (taxid:7955)] Back     alignment and assigned GO terms
 Score = 1020 (364.1 bits), Expect = 5.8e-105, Sum P(2) = 5.8e-105
 Identities = 210/439 (47%), Positives = 299/439 (68%)

Query:     2 KLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRA 61
             +L+  +L   + IADV++F+ PG  LD EA+ RGT+VYL  +RIDM+P+ L+ ++CSLR+
Sbjct:   491 ELENGNLEVGVHIADVSHFIRPGNALDQEAANRGTTVYLCGKRIDMVPELLSSNLCSLRS 550

Query:    62 DVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNM 121
             +VERLAFS IWE+  +AEII T +TKSVI S A+L+Y EAQ R+DD+ + D +T  LR +
Sbjct:   551 NVERLAFSCIWEMNHKAEIIKTHFTKSVINSKASLTYAEAQMRIDDTTMNDDITKSLRGL 610

Query:   122 NSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVS 181
             N LAK ++ +RI++GALTL+S EV+F ID+ETHDP+D+   ++ E N MVEEFML AN+S
Sbjct:   611 NKLAKILKAQRIDKGALTLSSPEVRFHIDSETHDPIDLQTKELMETNSMVEEFMLLANIS 670

Query:   182 VAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVGDD- 240
             VA++I  +F  C+LLR+HP+P     + L++ A +  L +   S+KALADSL+ A  ++ 
Sbjct:   671 VAQKIYDEFSECALLRKHPAPPPSNYDILIKAAKSRDLEIHTDSAKALADSLNNATIENF 730

Query:   241 PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLL 300
              YFN L+RILATRCM QAVYFCSG     +FHHYGLA+P+YTHFTSPIRRYAD++VHRLL
Sbjct:   731 AYFNTLLRILATRCMMQAVYFCSG--MDSDFHHYGLASPIYTHFTSPIRRYADIIVHRLL 788

Query:   301 SASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPT-DTEAR 359
             + ++          D+ + +++ +N+NYRH+ AQ A R SV  HT ++F+ +   + E  
Sbjct:   789 AVAINADSTYPDLMDKHKQSALCNNINYRHKMAQYAQRASVAFHTQLFFKNKGIINEEGF 848

Query:   360 IVKIRSNGFIVFVPKFGIEGPVYL------TPR-GQKGSGDWY-VDEQQQKI---VKMDG 408
             I+ +R N  I+ +PKFG+EG V+       +PR      G    V+E   +I   VK+  
Sbjct:   849 ILFVRKNAIIILIPKFGLEGTVFFENKDKPSPRLSFDTEGPTLKVEEHTFRIFDRVKVTI 908

Query:   409 NLSYSVLQTVNIHMEVVEP 427
             +L  S LQ   I M + EP
Sbjct:   909 SLDASNLQHQRIRMALTEP 927
GO:0003723 "RNA binding" evidence=IEA
GO:0004540 "ribonuclease activity" evidence=IEA
UNIPROTKB|E1BXX6 DIS3 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E2RNY6 DIS3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|G3V1J5 DIS3 "Exosome complex exonuclease RRP44" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|Q9Y2L1 DIS3 "Exosome complex exonuclease RRP44" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
MGI|MGI:1919912 Dis3 "DIS3 mitotic control homolog (S. cerevisiae)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|F1RHF7 DIS3 "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0293614 DDB_G0293614 "putative exoribonuclease" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
WB|WBGene00001001 dis-3 [Caenorhabditis elegans (taxid:6239)] Back     alignment and assigned GO terms
POMBASE|SPBC26H8.10 dis3 "3'-5' exoribonuclease subunit Dis3 (predicted)" [Schizosaccharomyces pombe (taxid:4896)] Back     alignment and assigned GO terms

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 LevelEC numberConfidence of Prediction
3rd Layer3.1.13LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query439
COG0557706 COG0557, VacB, Exoribonuclease R [Transcription] 1e-103
pfam00773322 pfam00773, RNB, RNB domain 1e-93
TIGR02063709 TIGR02063, RNase_R, ribonuclease R 1e-82
smart00955286 smart00955, RNB, This domain is the catalytic doma 7e-81
TIGR00358654 TIGR00358, 3_prime_RNase, VacB and RNase II family 2e-54
PRK11642813 PRK11642, PRK11642, exoribonuclease R; Provisional 1e-36
TIGR02062639 TIGR02062, RNase_B, exoribonuclease II 2e-27
COG4776645 COG4776, Rnb, Exoribonuclease II [Transcription] 2e-26
PRK05054644 PRK05054, PRK05054, exoribonuclease II; Provisiona 6e-26
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription] Back     alignment and domain information 
 Score =  322 bits (827), Expect = e-103
 Identities = 138/397 (34%), Positives = 207/397 (52%), Gaps = 17/397 (4%)

Query: 14  IADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWE 73
           IADV+++V PG+ LD EA KRGTSVYL +R I MLP+ L+  +CSL   V+RLA S    
Sbjct: 287 IADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEALSNGLCSLNPGVDRLALSCEMT 346

Query: 74  LTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRL--MDPLTTDLRNMNSLAKKMRQR 131
           L  E  +       SVIKS A L+Y E QA +D        PL   L  +  LAK ++++
Sbjct: 347 LDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKYAPLLDSLLELLELAKILKKK 406

Query: 132 RIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFP 191
           R+ RGA+   + E K  +D E   P++I + +  +A +++EEFML AN +VAE + +   
Sbjct: 407 RLSRGAIDFDTPEAKIVLD-EEGRPVEIEIRERLDAEKLIEEFMLLANETVAEHLEKHKI 465

Query: 192 LCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAV--GDDPYFNKLIRI 249
              L R H  P+ E L+ L      +GL L +  SK         +          +++ 
Sbjct: 466 P-LLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPLEAVLQT 524

Query: 250 LATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKL 309
           L  R M QA Y      +P    H+GLA   YTHFTSPIRRY D++VHR L A L    +
Sbjct: 525 LLLRSMKQAEY------SPDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPI 578

Query: 310 PSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDT-EARIVKIRSNGF 368
           P       +L  +A +++   R AQ A R  ++L    Y +KR  +  +  +  + S GF
Sbjct: 579 PEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGF 638

Query: 369 IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK 405
            V +P+ G+EG V+++        D+Y  +++ + + 
Sbjct: 639 FVELPELGLEGLVHIS----SLPDDYYHFDERGQALV 671

Length = 706
>gnl|CDD|216112 pfam00773, RNB, RNB domain Back     alignment and domain information
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R Back     alignment and domain information
>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of ribonuclease II Back     alignment and domain information
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5' exoribonucleases Back     alignment and domain information
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional Back     alignment and domain information
>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II Back     alignment and domain information
>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription] Back     alignment and domain information
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 439
TIGR00358654 3_prime_RNase VacB and RNase II family 3'-5' exori 100.0
PRK11642813 exoribonuclease R; Provisional 100.0
TIGR02063709 RNase_R ribonuclease R. This family consists of an 100.0
PRK05054644 exoribonuclease II; Provisional 100.0
TIGR02062639 RNase_B exoribonuclease II. This family consists o 100.0
COG0557706 VacB Exoribonuclease R [Transcription] 100.0
KOG2102941 consensus Exosomal 3'-5' exoribonuclease complex, 100.0
PF00773325 RNB: RNB domain CAUTION: The Prosite pattern does 100.0
COG4776645 Rnb Exoribonuclease II [Transcription] 100.0
cd0447183 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domai 99.27
cd0568673 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding dom 98.84
cd0569769 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a t 98.76
cd0446099 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. 98.74
cd0569069 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal p 98.71
cd0568972 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal p 98.62
cd0570673 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a 98.61
cd0569671 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a t 98.6
cd0570373 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: R 98.58
cd0570768 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a 98.57
cd0570574 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a 98.56
cd0569870 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp 98.53
cd0570877 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a 98.53
PF0057574 S1: S1 RNA binding domain; InterPro: IPR003029 Rib 98.52
cd0568479 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal 98.51
cd0446183 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp 98.5
COG1098129 VacB Predicted RNA binding protein (contains ribos 98.5
PRK08582139 hypothetical protein; Provisional 98.49
PRK07252120 hypothetical protein; Provisional 98.49
PTZ00248 319 eukaryotic translation initiation factor 2 subunit 98.48
cd0445276 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of tr 98.46
cd0569566 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a t 98.43
cd0568568 S1_Tex S1_Tex: The C-terminal S1 domain of a trans 98.41
PHA0294588 interferon resistance protein; Provisional 98.35
TIGR00448179 rpoE DNA-directed RNA polymerase (rpoE), archaeal 98.35
cd0570472 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a 98.33
cd0569173 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal p 98.29
cd0447268 S1_PNPase S1_PNPase: Polynucleotide phosphorylase 98.23
cd0569269 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal p 98.22
cd0568868 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal p 98.21
PRK05807136 hypothetical protein; Provisional 98.2
PRK08059123 general stress protein 13; Validated 98.18
cd0447377 S1_RecJ_like S1_RecJ_like: The S1 domain of the ar 98.14
cd0569474 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp 98.14
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.14
PRK03987 262 translation initiation factor IF-2 subunit alpha; 98.13
PLN00207891 polyribonucleotide nucleotidyltransferase; Provisi 98.11
COG1095183 RPB7 DNA-directed RNA polymerase, subunit E' [Tran 98.08
cd0568770 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Rib 98.05
COG0539 541 RpsA Ribosomal protein S1 [Translation, ribosomal 98.05
smart0031672 S1 Ribosomal protein S1-like RNA-binding domain. 98.05
PRK08563187 DNA-directed RNA polymerase subunit E'; Provisiona 98.02
cd0016465 S1_like S1_like: Ribosomal protein S1-like RNA-bin 97.97
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 97.97
cd0446567 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Rib 97.88
cd05693100 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp 97.82
COG1093 269 SUI2 Translation initiation factor 2, alpha subuni 97.79
PRK12269863 bifunctional cytidylate kinase/ribosomal protein S 97.75
PRK07899 486 rpsA 30S ribosomal protein S1; Reviewed 97.74
PRK07400318 30S ribosomal protein S1; Reviewed 97.73
PRK13806 491 rpsA 30S ribosomal protein S1; Provisional 97.7
PRK13806491 rpsA 30S ribosomal protein S1; Provisional 97.69
cd0570270 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: R 97.68
PRK11824693 polynucleotide phosphorylase/polyadenylase; Provis 97.67
TIGR02696719 pppGpp_PNP guanosine pentaphosphate synthetase I/p 97.66
PRK12269 863 bifunctional cytidylate kinase/ribosomal protein S 97.63
cd0578986 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. 97.62
cd0445388 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-lik 97.54
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 97.51
PRK06676390 rpsA 30S ribosomal protein S1; Reviewed 97.43
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 97.42
cd0445567 S1_NusA S1_NusA: N-utilizing substance A protein ( 97.41
PRK00087647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 97.33
PTZ00162176 DNA-directed RNA polymerase II subunit 7; Provisio 97.32
TIGR00717516 rpsA ribosomal protein S1. This model provides tru 97.32
TIGR03591684 polynuc_phos polyribonucleotide nucleotidyltransfe 97.32
PRK07400 318 30S ribosomal protein S1; Reviewed 97.26
PRK06676 390 rpsA 30S ribosomal protein S1; Reviewed 97.18
PRK06299 565 rpsA 30S ribosomal protein S1; Reviewed 97.17
cd0446288 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA poly 97.13
cd0445482 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA- 97.1
COG1185692 Pnp Polyribonucleotide nucleotidyltransferase (pol 96.87
COG2183780 Tex Transcriptional accessory protein [Transcripti 96.78
PRK09202 470 nusA transcription elongation factor NusA; Validat 96.72
PRK00087 647 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 96.52
PRK12327 362 nusA transcription elongation factor NusA; Provisi 96.39
PHA0285886 EIF2a-like PKR inhibitor; Provisional 96.19
TIGR01953 341 NusA transcription termination factor NusA. This m 96.02
PRK09521189 exosome complex RNA-binding protein Csl4; Provisio 96.0
PRK04163235 exosome complex RNA-binding protein Rrp4; Provisio 95.67
cd0569972 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a t 95.34
KOG1067760 consensus Predicted RNA-binding polyribonucleotide 94.82
TIGR0000868 infA translation initiation factor IF-1. This fami 93.48
KOG3298170 consensus DNA-directed RNA polymerase subunit E' [ 93.39
KOG1070 1710 consensus rRNA processing protein Rrp5 [RNA proces 93.09
PRK12329 449 nusA transcription elongation factor NusA; Provisi 92.41
PRK1244287 translation initiation factor IF-1; Reviewed 92.24
cd0579192 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. 91.22
PF08292122 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; I 91.14
PRK12328 374 nusA transcription elongation factor NusA; Provisi 91.01
COG2996287 Predicted RNA-bindining protein (contains S1 and H 90.77
KOG1070 1710 consensus rRNA processing protein Rrp5 [RNA proces 90.64
COG1107 715 Archaea-specific RecJ-like exonuclease, contains D 88.3
COG036175 InfA Translation initiation factor 1 (IF-1) [Trans 87.56
TIGR00757 414 RNaseEG ribonuclease, Rne/Rng family. The C-termin 84.46
cd0579086 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domai 81.14
PF1350961 S1_2: S1 domain; PDB: 3GO5_A. 80.53
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases Back     alignment and domain information 
Probab=100.00  E-value=6.1e-99  Score=804.92  Aligned_cols=422  Identities=27%  Similarity=0.434  Sum_probs=387.4

Q ss_pred             ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634            3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS   82 (439)
Q Consensus         3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~   82 (439)
                      +++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|.+
T Consensus       222 ~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~~~id~~G~i~~  301 (654)
T TIGR00358       222 LPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITD  301 (654)
T ss_pred             eCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccCCCCcceEEEEEEEECCCCCEeE
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeEEecCceecHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeee
Q 013634           83 TRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD  158 (439)
Q Consensus        83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~  158 (439)
                      ++|++|+|+|+++|||++|+++|++++.    ..++.++|..|+++|++|+++|.++|++.|+.|+.+|.+|++ |.+..
T Consensus       302 ~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~lr~~R~~~Gai~~~~~e~~~~~d~~-g~~~~  380 (654)
T TIGR00358       302 NEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEE-GRVID  380 (654)
T ss_pred             EEEEEEEEEECcEEcHHHHHHHHcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceeEEECCC-CCeeE
Confidence            9999999999999999999999987632    245778999999999999999999999999999999999865 78888


Q ss_pred             eEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCC-----CHHHHHHHH
Q 013634          159 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS-----SSKALADSL  233 (439)
Q Consensus       159 v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~-----~~~~l~~~l  233 (439)
                      +.....++||.|||||||+||++||+|+.++ ++|++||+|++|++++++++.+++..+|+.++..     ++.+++..|
T Consensus       381 i~~~~~~~a~~lIeE~MilAN~~vA~~~~~~-~~p~iyR~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l  459 (654)
T TIGR00358       381 IVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWL  459 (654)
T ss_pred             EEeccCcHHHHHHHHHHHHHHHHHHHHHHHc-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCcCCCChHHHHHHH
Confidence            8888899999999999999999999999997 8999999999999999999999999999986432     356788888


Q ss_pred             HHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCC-CC
Q 013634          234 DRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLP-SV  312 (439)
Q Consensus       234 ~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~-~~  312 (439)
                      .++.+ .+ ...+++.+++|+|++|+|      +..|.+|||||++.|||||||||||+||+|||||+++|.+++.. ..
T Consensus       460 ~~~~~-~~-~~~~l~~~llr~m~~A~y------~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~~~~  531 (654)
T TIGR00358       460 REVKD-RP-EYEILVTRLLRSLSQAEY------SPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTER  531 (654)
T ss_pred             HHhhC-CC-HHHHHHHHHHHhhccccc------CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCcccc
Confidence            87754 23 234778889999999999      67899999999999999999999999999999999999876432 22


Q ss_pred             CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCC
Q 013634          313 FQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGS  391 (439)
Q Consensus       313 ~~~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~  391 (439)
                      .++.++|..+|++||.+++.+++|||++.++|.|.||+++. ++|+|+|+++.++|+||+|+++|+||+||++++.++  
T Consensus       532 ~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d--  609 (654)
T TIGR00358       532 YQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHND--  609 (654)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCc--
Confidence            24567899999999999999999999999999999999987 889999999999999999999999999999999987  


Q ss_pred             CceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEeC
Q 013634          392 GDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI  439 (439)
Q Consensus       392 ~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l~  439 (439)
                       +|.+|+.+.++++++.++.|++||+|+|+|.+||..  +++|+|+|+
T Consensus       610 -~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~--~~~I~f~l~  654 (654)
T TIGR00358       610 -YYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME--TRSIIFELV  654 (654)
T ss_pred             -ceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc--cCeEEEEEC
Confidence             699999999999888889999999999999999976  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 Back     alignment and domain information
>TIGR02063 RNase_R ribonuclease R Back     alignment and domain information
>PRK05054 exoribonuclease II; Provisional Back     alignment and domain information
>TIGR02062 RNase_B exoribonuclease II Back     alignment and domain information
>COG0557 VacB Exoribonuclease R [Transcription] Back     alignment and domain information
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam Back     alignment and domain information
>COG4776 Rnb Exoribonuclease II [Transcription] Back     alignment and domain information
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain Back     alignment and domain information
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain Back     alignment and domain information
>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 Back     alignment and domain information
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain Back     alignment and domain information
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK08582 hypothetical protein; Provisional Back     alignment and domain information
>PRK07252 hypothetical protein; Provisional Back     alignment and domain information
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional Back     alignment and domain information
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain Back     alignment and domain information
>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 Back     alignment and domain information
>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 Back     alignment and domain information
>PHA02945 interferon resistance protein; Provisional Back     alignment and domain information
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form Back     alignment and domain information
>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 Back     alignment and domain information
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain Back     alignment and domain information
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>PRK05807 hypothetical protein; Provisional Back     alignment and domain information
>PRK08059 general stress protein 13; Validated Back     alignment and domain information
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease Back     alignment and domain information
>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 Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated Back     alignment and domain information
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional Back     alignment and domain information
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription] Back     alignment and domain information
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional Back     alignment and domain information
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain Back     alignment and domain information
>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 Back     alignment and domain information
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>PRK13806 rpsA 30S ribosomal protein S1; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional Back     alignment and domain information
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase Back     alignment and domain information
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional Back     alignment and domain information
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain Back     alignment and domain information
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional Back     alignment and domain information
>TIGR00717 rpsA ribosomal protein S1 Back     alignment and domain information
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase Back     alignment and domain information
>PRK07400 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed Back     alignment and domain information
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain Back     alignment and domain information
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain Back     alignment and domain information
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG2183 Tex Transcriptional accessory protein [Transcription] Back     alignment and domain information
>PRK09202 nusA transcription elongation factor NusA; Validated Back     alignment and domain information
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed Back     alignment and domain information
>PRK12327 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PHA02858 EIF2a-like PKR inhibitor; Provisional Back     alignment and domain information
>TIGR01953 NusA transcription termination factor NusA Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>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 Back     alignment and domain information
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] Back     alignment and domain information
>TIGR00008 infA translation initiation factor IF-1 Back     alignment and domain information
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription] Back     alignment and domain information
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>PRK12329 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>PRK12442 translation initiation factor IF-1; Reviewed Back     alignment and domain information
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain Back     alignment and domain information
>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 Back     alignment and domain information
>PRK12328 nusA transcription elongation factor NusA; Provisional Back     alignment and domain information
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only] Back     alignment and domain information
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification] Back     alignment and domain information
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair] Back     alignment and domain information
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family Back     alignment and domain information
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain Back     alignment and domain information
>PF13509 S1_2: S1 domain; PDB: 3GO5_A Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query439
2wp8_J977 Yeast Rrp44 Nuclease Length = 977 1e-102
4ifd_J1003 Crystal Structure Of An 11-subunit Eukaryotic Exoso 1e-102
2vnu_D760 Crystal Structure Of Sc Rrp44 Length = 760 1e-97
2ix1_A664 Rnase Ii D209n Mutant Length = 664 1e-18
2ix0_A663 Rnase Ii Length = 663 1e-18
2id0_A644 Escherichia Coli Rnase Ii Length = 644 2e-12
2r7d_A469 Crystal Structure Of Ribonuclease Ii Family Protein 2e-05
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease Length = 977 Back     alignment and structure 
Iteration: 1

 Score =  367 bits (941), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 189/386 (48%), Positives = 255/386 (66%), Gaps = 6/386 (1%)
Query: 2   KLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRA 61
           KL   +    + IADVT+FV PGT LD E + RGTSVYLV++RIDMLP  L  D+CSL+ 
Sbjct: 534 KLPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKP 593
Query: 62  DVERLAFSVIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNM 121
            V+R AFSVIWEL   A I++  + KSVI+S  A SY +AQ R+DD    D LT  +R +
Sbjct: 594 YVDRFAFSVIWELDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRAL 653
Query: 122 NSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVS 181
             L+ K++Q+R+E GAL LAS EVK  +D+ET DP ++ + ++   N +VEEFML AN+S
Sbjct: 654 LKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANIS 713
Query: 182 VAEQILRQFPLCSLLRRH---PSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVG 238
           VA +I   FP  ++LRRH   PS   E+L  +L T   + ++L+  SSKALADSLDR V 
Sbjct: 714 VARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLE--SSKALADSLDRCVD 771
Query: 239 -DDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVH 297
            +DPYFN L+RI++TRCM  A YF SG  + P+F HYGLA  +YTHFTSPIRRY DVV H
Sbjct: 772 PEDPYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAH 831
Query: 298 RLLSASLGIYKLPSVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTE 357
           R L+ ++G   L    +D+ ++  I  N+N +HRNAQ A R S+E +     R   +   
Sbjct: 832 RQLAGAIGYEPLSLTHRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTET 891
Query: 358 ARIVKIRSNGFIVFVPKFGIEGPVYL 383
             ++K+ +NG +V VPKFG+EG + L
Sbjct: 892 GYVIKVFNNGIVVLVPKFGVEGLIRL 917
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome Complex Bound To Rna Length = 1003 Back     alignment and structure
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44 Length = 760 Back     alignment and structure
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant Length = 664 Back     alignment and structure
>pdb|2IX0|A Chain A, Rnase Ii Length = 663 Back     alignment and structure
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii Length = 644 Back     alignment and structure
>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 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query439
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 0.0
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 0.0
2r7d_A469 Ribonuclease II family protein; structural genomic 1e-103
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 2e-94
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 5e-10
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 2e-08
>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 Back     alignment and structure
 Score =  580 bits (1496), Expect = 0.0
 Identities = 194/432 (44%), Positives = 267/432 (61%), Gaps = 8/432 (1%)

Query: 14  IADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWE 73
           IADVT+FV PGT LD E + RGTSVYLV++RIDMLP  L  D+CSL+  V+R AFSVIWE
Sbjct: 329 IADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWE 388

Query: 74  LTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRI 133
           L   A I++  + KSVI+S  A SY +AQ R+DD    D LT  +R +  L+ K++Q+R+
Sbjct: 389 LDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRL 448

Query: 134 ERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLC 193
           E GAL LAS EVK  +D+ET DP ++ + ++   N +VEEFML AN+SVA +I   FP  
Sbjct: 449 EAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQT 508

Query: 194 SLLRRHPSPTKEMLEPLLRTA-AAVGLNLDVSSSKALADSLDRAVG-DDPYFNKLIRILA 251
           ++LRRH +P     E L         +++ + SSKALADSLDR V  +DPYFN L+RI++
Sbjct: 509 AMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMS 568

Query: 252 TRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPS 311
           TRCM  A YF SG  + P+F HYGLA  +YTHFTSPIRRY DVV HR L+ ++G   L  
Sbjct: 569 TRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 628

Query: 312 VFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVF 371
             +D+ ++  I  N+N +HRNAQ A R S+E +     R   +     ++K+ +NG +V 
Sbjct: 629 THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVL 688

Query: 372 VPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIV----KMDGNLSYSVLQTVNIHMEVV-E 426
           VPKFG+EG + L    +  +     DE + K+       D      V   V + +  V +
Sbjct: 689 VPKFGVEGLIRLDNLTEDPN-SAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMD 747

Query: 427 PQPNRPKLQLTL 438
           P  ++ K +L L
Sbjct: 748 PITSKRKAELLL 759
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Length = 977 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query439
2vnu_D760 Exosome complex exonuclease RRP44; hydrolase-RNA c 100.0
2wp8_J977 Exosome complex exonuclease DIS3; nucleus, hydrola 100.0
2id0_A644 Exoribonuclease 2; RNAse, exonuclease, hydrolyase, 100.0
2r7d_A469 Ribonuclease II family protein; structural genomic 100.0
1luz_A88 Protein K3, protein K2; stranded anti-parallel bet 98.92
1kl9_A182 Eukaryotic translation initiation factor 2 subuni; 98.79
2k52_A80 Uncharacterized protein MJ1198; metal-binding, zin 98.77
2a19_A175 EIF-2- alpha, eukaryotic translation initiation fa 98.76
2ckz_B218 C25, DNA-directed RNA polymerase III 25 KD polypep 98.74
4ayb_E180 DNA-directed RNA polymerase; transferase, multi-su 98.73
1go3_E187 DNA-directed RNA polymerase subunit E; transferase 98.7
2k4k_A130 GSP13, general stress protein 13; cytoplasm, stres 98.68
2c35_B172 Human RPB7, DNA-directed RNA polymerase II 19 kDa 98.64
2khi_A115 30S ribosomal protein S1; acetylation, phosphoprot 98.62
2cqo_A119 Nucleolar protein of 40 kDa; S1 domain, OB-fold, s 98.62
3bzc_A785 TEX; helix-turn-helix, helix-hairpin-helix, S1 dom 98.6
2eqs_A103 ATP-dependent RNA helicase DHX8; S1 domain, OB-fol 98.58
2b8k_G215 B16, DNA-directed RNA polymerase II 19 kDa polypep 98.48
2khj_A109 30S ribosomal protein S1; OB fold, acetylation, ph 98.48
3aev_A 275 Translation initiation factor 2 subunit alpha; pro 98.47
3ayh_B203 DNA-directed RNA polymerase III subunit RPC8; tran 98.47
1y14_B171 B16, RPB7, DNA-directed RNA polymerase II 19 kDa p 98.46
1q8k_A 308 Eukaryotic translation initiation factor 2 subunit 98.4
3h0g_G172 DNA-directed RNA polymerase II subunit RPB7; trans 98.24
1wi5_A119 RRP5 protein homolog; S1 domain, OB-fold, structur 98.24
3cw2_C 266 Translation initiation factor 2 subunit alpha; AIF 98.02
3go5_A285 Multidomain protein with S1 RNA-binding domains; s 97.85
3psi_A 1219 Transcription elongation factor SPT6; nucleus; 3.3 97.84
4aid_A726 Polyribonucleotide nucleotidyltransferase; transfe 97.83
3psf_A1030 Transcription elongation factor SPT6; nucleus; 2.5 97.65
3cdi_A723 Polynucleotide phosphorylase; mRNA turnover, RNAse 97.61
1e3p_A757 Guanosine pentaphosphate synthetase; polyribonucle 97.35
3m7n_A179 Putative uncharacterized protein AF_0206; exosome, 97.09
2nn6_I209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, 96.92
1hh2_P 344 NUSA, N utilization substance protein A; transcrip 96.31
2je6_I 251 RRP4, exosome complex RNA-binding protein 1; nucle 96.01
2ba0_A 229 Archeal exosome RNA binding protein RRP4; RNAse PH 95.94
2z0s_A235 Probable exosome complex RNA-binding protein 1; al 95.88
3go5_A 285 Multidomain protein with S1 RNA-binding domains; s 95.37
1k0r_A 366 NUSA; two component arrangement, S1 domain, two K- 95.14
2asb_A 251 Transcription elongation protein NUSA; protein-RNA 93.66
2bx2_L 517 Ribonuclease E, RNAse E; RNA-binding, RNA turnover 92.77
2ja9_A175 Exosome complex exonuclease RRP40; RNA-binding pro 91.74
2bh8_A101 1B11; transcription, molecular evolution, unique a 91.63
2nn6_H 308 Exosome complex exonuclease RRP4; RNA, exosome, PM 85.22
>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 Back     alignment and structure
Probab=100.00  E-value=1.1e-103  Score=853.33  Aligned_cols=433  Identities=45%  Similarity=0.712  Sum_probs=399.8

Q ss_pred             ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634            3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS   82 (439)
Q Consensus         3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~   82 (439)
                      +++|+|+|||||||||+||+|||+||+||++||||||||++++||||+.||+++|||+||++|+||||.|+||++|+|++
T Consensus       318 ~~~g~~~l~VHIADVs~yV~~gs~LD~eA~~RgtSvYlp~rviPMLP~~Ls~~lcSL~p~~dRla~S~~~~id~~G~v~~  397 (760)
T 2vnu_D          318 LPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVN  397 (760)
T ss_dssp             CTTSCEEEEEEEECHHHHSCTTSHHHHHHHHHCBCEECSSCEECSSCHHHHTTTSSCCBTSEEEEEEEEEEECTTCCEEE
T ss_pred             cCCCcEEEEEEeccHHHeeCCCCHHHHHHHHcCCcEecCCceEeCCChHHcccccccCCCCcEEEEEEEEEEcCCCCEEE
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeEEecCceecHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeeeeEee
Q 013634           83 TRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMY  162 (439)
Q Consensus        83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~v~~~  162 (439)
                      ++|++|+|+|+++|||++|+++|+++...+++.++|..|+++|+.|+++|.++|+++|+.|+++|.+|++.|.|.++.+.
T Consensus       398 ~~~~~svI~s~~rltY~~v~~~l~~~~~~~~l~~~L~~L~~la~~lr~~R~~~Gai~~~~pe~~~~ld~e~g~~~~i~~~  477 (760)
T 2vnu_D          398 VNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIK  477 (760)
T ss_dssp             EEEEEEEEEBSEEEEHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCCEEEEECSSSSCEEEEEEC
T ss_pred             EEEEEEEEEecceEcHHHHHHHHhCCCcchHHHHHHHHHHHHHHHHHHHHHhCCCcccCCCceEEEEecCCCcEEEEEEc
Confidence            99999999999999999999999987767788899999999999999999999999999999999999666889999999


Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHc-CCcccCCCHHHHHHHHHHHhC-CC
Q 013634          163 QIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAV-GLNLDVSSSKALADSLDRAVG-DD  240 (439)
Q Consensus       163 ~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~-g~~~~~~~~~~l~~~l~~~~~-~~  240 (439)
                      +..+||.|||||||+||.+||+|+.++++.|++||+|+.|++++++.|.+++..+ |+.++..++++++++|+.+.+ .+
T Consensus       478 ~~~~a~~lIeE~MllAN~~vA~~l~~~~~~~~l~R~h~~P~~~~l~~l~~~~~~~~g~~l~~~~~~~l~~~l~~~~~~~~  557 (760)
T 2vnu_D          478 KLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPED  557 (760)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHCTTTCEEEEBCCCCGGGGHHHHHHHHHHHSCCCCCSCHHHHHHHHHTCCBTTB
T ss_pred             CCccHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEecCCCCHHHHHHHHHHHHHccCCCcCCCCHHHHHHHHHHhhCCch
Confidence            9999999999999999999999999988899999999999999999999999999 999998899999999997654 56


Q ss_pred             hhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCCCCCCChhHHH
Q 013634          241 PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLT  320 (439)
Q Consensus       241 ~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~~~~~~~~~l~  320 (439)
                      +.+..+++.+++|+|++|+|+++|+.+.++.+|||||++.|||||||||||+||+|||||+++|.+++.+...++.+.|.
T Consensus       558 ~~~~~ll~~~~~r~m~~A~Y~~~g~~~~~~~~HfgLa~~~YtHfTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~~~l~  637 (760)
T 2vnu_D          558 PYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMD  637 (760)
T ss_dssp             TTHHHHHHHHHHTTSCCCEEEEGGGSCGGGGCBTTTTBSCCCCCSCTTTBHHHHHHHHHHHHHTTSSCCCGGGGCHHHHH
T ss_pred             HHHHHHHHHHHHHhhhCccccccCcCCCCCCCceecCCCceeccCchHhhhHHHHHHHHHHHHHccCCCcccccCHHHHH
Confidence            67778889899999999999999988889999999999999999999999999999999999998776655555678899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCC--CCCCCceeecC
Q 013634          321 SIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRG--QKGSGDWYVDE  398 (439)
Q Consensus       321 ~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~--~~~~~~~~~d~  398 (439)
                      .+|.+||.+++.|+.|+|++.++|.|.||+++.+.++|+|++|.++|++|+||++|+||+||++++.  ++   +|.+++
T Consensus       638 ~~~~~~s~~er~A~~aer~~~~~~~~~~l~~~~~~~~g~V~~V~~~G~fV~l~~~giEGlVhis~L~~~~d---~~~fd~  714 (760)
T 2vnu_D          638 MICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPN---SAAFDE  714 (760)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCSEEEEEEEEEETTEEEEEETTTTEEEEEEHHHHCSCGG---GCEEET
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHHhhcCceEEEEEEEEEECCeEEEEEeCCCcEEEEEeccccCCCc---eeEEcc
Confidence            9999999999999999999999999999999888999999999999999999999999999999996  55   789999


Q ss_pred             CeEEEEeeCC----ceEEeeCceEEEEEEEecCCCC-CCceeEEe
Q 013634          399 QQQKIVKMDG----NLSYSVLQTVNIHMEVVEPQPN-RPKLQLTL  438 (439)
Q Consensus       399 ~~~~l~~~~~----~~~~~iGd~V~V~v~~vd~~~~-~~~i~l~l  438 (439)
                      .+.+++++++    ++.|++||+|+|+|.++|.+.+ ++||.|+|
T Consensus       715 ~~~~l~g~~~~~~~~~~~~lGD~V~VkV~~vd~~~~~~~kI~lsl  759 (760)
T 2vnu_D          715 VEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDPITSKRKAELLL  759 (760)
T ss_dssp             TTTEEEECCTTCSSCEEEETTCEEEEEEC--------CCEEEC--
T ss_pred             cccEEEEecCCCccCcEEecCCEEEEEEEEEECccccCCcEEEEe
Confidence            9899988764    6999999999999999997543 48999986
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding, exonucle binding, mitochondrion, rRNA processing; 3.00A {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>1luz_A Protein K3, protein K2; stranded anti-parallel beta barrel, viral protein; 1.80A {Vaccinia virus} SCOP: b.40.4.5 Back     alignment and structure
>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 Back     alignment and structure
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger, structural genomics, PSI-2, protein structure initiative; NMR {Methanocaldococcus jannaschii} Back     alignment and structure
>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 Back     alignment and structure
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: b.40.4.5 d.230.1.1 Back     alignment and structure
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA binding protein; NMR {Bacillus subtilis} Back     alignment and structure
>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 Back     alignment and structure
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>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} Back     alignment and structure
>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 Back     alignment and structure
>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} Back     alignment and structure
>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 Back     alignment and structure
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein, ribonucleoprotein, RNA-binding; NMR {Escherichia coli} Back     alignment and structure
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex, 16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB: 1yz6_A Back     alignment and structure
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A {Schizosaccharomyces pombe} Back     alignment and structure
>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* ... Back     alignment and structure
>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 Back     alignment and structure
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>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 Back     alignment and structure
>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* Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces cerevisiae} Back     alignment and structure
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A 4am3_A Back     alignment and structure
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces cerevisiae} Back     alignment and structure
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Back     alignment and structure
>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 Back     alignment and structure
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.40A {Streptococcus pneumoniae} Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>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 Back     alignment and structure
>2bh8_A 1B11; transcription, molecular evolution, unique architecture, transcription regulation, phosphorylation; 1.9A {Escherichia coli} Back     alignment and structure
>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 Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 439
d2vnud4416 b.40.4.16 (D:495-910) Exosome complex exonuclease 4e-80
d2ix0a4385 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Esch 2e-60
d2r7da2401 b.40.4.16 (A:3-403) Ribonuclease II family protein 7e-43
d2vnud288 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 Back     information, alignment and structure

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 =  251 bits (642), Expect = 4e-80
 Identities = 171/339 (50%), Positives = 226/339 (66%), Gaps = 2/339 (0%)

Query: 14  IADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWE 73
           IADVT+FV PGT LD E + RGTSVYLV++RIDMLP  L  D+CSL+  V+R AFSVIWE
Sbjct: 76  IADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWE 135

Query: 74  LTPEAEIISTRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRI 133
           L   A I++  + KSVI+S  A SY +AQ R+DD    D LT  +R +  L+ K++Q+R+
Sbjct: 136 LDDSANIVNVNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRL 195

Query: 134 ERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLC 193
           E GAL LAS EVK  +D+ET DP ++ + ++   N +VEEFML AN+SVA +I   FP  
Sbjct: 196 EAGALNLASPEVKVHMDSETSDPNEVEIKKLLATNSLVEEFMLLANISVARKIYDAFPQT 255

Query: 194 SLLRRHPSPTKEMLEPLLRTAAAVG-LNLDVSSSKALADSLDRAVG-DDPYFNKLIRILA 251
           ++LRRH +P     E L         +++ + SSKALADSLDR V  +DPYFN L+RI++
Sbjct: 256 AMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMS 315

Query: 252 TRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPS 311
           TRCM  A YF SG  + P+F HYGLA  +YTHFTSPIRRY DVV HR L+ ++G   L  
Sbjct: 316 TRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 375

Query: 312 VFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFR 350
             +D+ ++  I  N+N +HRNAQ A R S+E +     R
Sbjct: 376 THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMR 414
>d2ix0a4 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Length = 385 Back     information, alignment and structure
>d2r7da2 b.40.4.16 (A:3-403) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]} Length = 401 Back     information, alignment and structure
>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Length = 88 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query439
d2vnud4416 Exosome complex exonuclease RRP44 {Saccharomyces c 100.0
d2ix0a4385 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 100.0
d2r7da2401 Ribonuclease II family protein DR0020 {Deinococcus 100.0
d2ix0a387 Exoribonuclease 2, RNB {Escherichia coli [TaxId: 5 99.44
d1go3e1106 C-terminal domain of RNA polymerase II subunit RBP 99.28
d2vnud288 Exosome complex exonuclease RRP44 {Saccharomyces c 99.05
d1y14b191 C-terminal domain of RNA polymerase II subunit RBP 98.98
d1kl9a286 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 98.97
d2c35b194 C-terminal domain of RNA polymerase II subunit RBP 98.96
d2ahob284 Eukaryotic initiation factor 2alpha, eIF2alpha, N- 98.77
d1sroa_76 S1 RNA-binding domain of polyribonucleotide phosph 98.64
d3bzka494 Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287] 98.55
d2ba0a183 S1-domain of exosome complex RNA-binding protein 1 98.34
d1e3pa262 S1 RNA-binding domain of polyribonucleotide phosph 98.22
d2je6i187 S1-domain of exosome complex RNA-binding protein 1 98.22
d2z0sa188 S1-domain of exosome complex RNA-binding protein 1 98.17
d1wi5a_119 S1-domain of RRP5 protein homolog (PDCD11, KIAA018 98.08
d2nn6h195 S1-domain of Ribosomal RNA-processing protein 4, R 97.56
d1hh2p172 S1 domain of NusA {Thermotoga maritima [TaxId: 233 96.69
d2nn6g188 S1-domain of exosome component 3 (RRP40) {Human (H 96.25
d2asba176 S1 domain of NusA {Mycobacterium tuberculosis [Tax 93.58
d2ja9a190 S1-domain of exosome component 3 (RRP40) {Saccharo 92.27
d1smxa_87 S1-domain of Ribonuclease E {Escherichia coli [Tax 84.91
d1ah9a_71 Translational initiation factor 1, IF1 {Escherichi 82.94
>d2vnud4 b.40.4.16 (D:495-910) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
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=4.2e-82  Score=644.69  Aligned_cols=350  Identities=49%  Similarity=0.790  Sum_probs=326.3

Q ss_pred             ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634            3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS   82 (439)
Q Consensus         3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~   82 (439)
                      +++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.||+++|||.||++|+|+|+.+++|.+|+|.+
T Consensus        65 ~~~g~~~l~VHIADva~~v~~~s~Ld~~A~~R~~t~Ylp~~~~pMLP~~ls~~~~SL~~~~~r~a~s~~~~~~~~g~i~~  144 (416)
T d2vnud4          65 LPNGNWEVGVHIADVTHFVKPGTALDAEGAARGTSVYLVDKRIDMLPMLLGTDLCSLKPYVDRFAFSVIWELDDSANIVN  144 (416)
T ss_dssp             CTTSCEEEEEEEECHHHHSCTTSHHHHHHHHHCBCEECSSCEECSSCHHHHTTTSSCCBTSEEEEEEEEEEECTTCCEEE
T ss_pred             eCCCcEEEEEEEccHHHhhCCCCHHHHHHHHhCeeEeCCCCccccCCHHHhhhhhcccCCcceeeEEeeeeecccccccc
Confidence            56889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEEeEEecCceecHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeeeeEee
Q 013634           83 TRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMY  162 (439)
Q Consensus        83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~v~~~  162 (439)
                      ++|++|+|+|.++|||++|+++|++.....++.+.|..|++++++|+++|.++|++.++.++..+.+|.+.+.+..+...
T Consensus       145 ~~~~~s~I~~~~~ltY~ev~~~l~~~~~~~~~~~~l~~L~~~a~~l~~~R~~~g~l~~~~~~~~~~~d~~~~~~~~~~~~  224 (416)
T d2vnud4         145 VNFMKSVIRSREAFSYEQAQLRIDDKTQNDELTMGMRALLKLSVKLKQKRLEAGALNLASPEVKVHMDSETSDPNEVEIK  224 (416)
T ss_dssp             EEEEEEEEEBSEEEEHHHHHHHHHCTTCCCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCCEEEEECSSSSCEEEEEEC
T ss_pred             ceeehhhhccccccchhhHHHHhccccccccchhHHHHHHHHHHHHHHHHHhcCCcccCCCceEEEecccccccccccee
Confidence            99999999999999999999999998888888999999999999999999999999999999999998776777777777


Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHc-CCcccCCCHHHHHHHHHHHhC-CC
Q 013634          163 QIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAV-GLNLDVSSSKALADSLDRAVG-DD  240 (439)
Q Consensus       163 ~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~-g~~~~~~~~~~l~~~l~~~~~-~~  240 (439)
                      ....||.|||||||+||.+||+++.++++.|++||+|+.|+.++++.+.+++... |+.++.++...+.+.|+.+.+ .+
T Consensus       225 ~~~~s~~lVeE~Mi~AN~~vA~~l~~~~~~~~~~R~h~~p~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~l~~~~~~~~  304 (416)
T d2vnud4         225 KLLATNSLVEEFMLLANISVARKIYDAFPQTAMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPED  304 (416)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHHHHHCTTTCEEEEBCCCCGGGGHHHHHHHHHHHSCCCCCSCHHHHHHHHHTCCBTTB
T ss_pred             ecccchhhHHHHhhhhhHHHHHHHHHhCCCCCccceeCCCCHHHHHHHHHHHHHhcccCcCccchhhHHHHHHHHhCccC
Confidence            8889999999999999999999999888899999999999999999998887643 667777788888888887654 56


Q ss_pred             hhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCCCCCCChhHHH
Q 013634          241 PYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDRPQLT  320 (439)
Q Consensus       241 ~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~~~~~~~~~l~  320 (439)
                      +....+++...+++|..|.|+.++.++.++.+|||||++.|||||||||||+||+|||||+++|.+++.+....+.++|.
T Consensus       305 ~~~~~~i~~~~~~~~~~a~~~~~~~~s~~~~~H~gLgl~~YthfTSPIRRY~DLv~hrqL~a~l~~~~~~~~~~~~e~l~  384 (416)
T d2vnud4         305 PYFNTLVRIMSTRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSLTHRDKNKMD  384 (416)
T ss_dssp             TTHHHHHHHHHHTTSCCCEEEEGGGSCGGGGCBTTTTBSCCCCCSCTTTBHHHHHHHHHHHHHTTSSCCCGGGGCHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHhhccccCCCCccCcHhhCcccccccCcHHhhHHHHHHHHHHHHHHcCCCCCCChhhHHHHH
Confidence            66777888888999999999999999999999999999999999999999999999999999999988777666778899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 013634          321 SIADNLNYRHRNAQMASRGSVELHTLIYFRKR  352 (439)
Q Consensus       321 ~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~  352 (439)
                      .+|.+||.+++.+++|||++.++|+|+||+++
T Consensus       385 ~i~~~~~~~e~~a~~aer~~~~~~~~~~lk~~  416 (416)
T d2vnud4         385 MICRNINRKHRNAQFAGRASIEYYVGQVMRNN  416 (416)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            99999999999999999999999999999874
>d2ix0a4 b.40.4.16 (A:173-557) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2r7da2 b.40.4.16 (A:3-403) Ribonuclease II family protein DR0020 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2ix0a3 b.40.4.5 (A:558-644) Exoribonuclease 2, RNB {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1go3e1 b.40.4.5 (E:79-184) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d2vnud2 b.40.4.5 (D:911-998) Exosome complex exonuclease RRP44 {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>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]} Back     information, alignment and structure
>d1kl9a2 b.40.4.5 (A:3-88) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2c35b1 b.40.4.5 (B:78-171) C-terminal domain of RNA polymerase II subunit RBP7 (RpoE) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d1sroa_ b.40.4.5 (A:) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d3bzka4 b.40.4.5 (A:637-730) Tex S1-domain {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d2ba0a1 b.40.4.5 (A:53-135) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1e3pa2 b.40.4.5 (A:656-717) S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase {Streptomyces antibioticus [TaxId: 1890]} Back     information, alignment and structure
>d2je6i1 b.40.4.5 (I:66-152) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Sulfolobus solfataricus [TaxId: 2287]} Back     information, alignment and structure
>d2z0sa1 b.40.4.5 (A:60-147) S1-domain of exosome complex RNA-binding protein 1, ECR1 {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
>d1wi5a_ b.40.4.5 (A:) S1-domain of RRP5 protein homolog (PDCD11, KIAA0185) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2nn6h1 b.40.4.5 (H:73-167) S1-domain of Ribosomal RNA-processing protein 4, RRP4 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1hh2p1 b.40.4.5 (P:127-198) S1 domain of NusA {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2nn6g1 b.40.4.5 (G:107-194) S1-domain of exosome component 3 (RRP40) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2asba1 b.40.4.5 (A:108-183) S1 domain of NusA {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d2ja9a1 b.40.4.5 (A:62-151) S1-domain of exosome component 3 (RRP40) {Saccharomyces cerevisiae [TaxId: 4932]} Back     information, alignment and structure
>d1smxa_ b.40.4.5 (A:) S1-domain of Ribonuclease E {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ah9a_ b.40.4.5 (A:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure