Citrus Sinensis ID: 008899

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-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------55
MIDLLEDCVSQYHIYVEKLEEREDCNVNQSEEKECRKETEGSKGECKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGAESLTSTNQRGKTTLCYDKDGETYREERSTATDSEAAADPMFNSTLNRLTLTFRKLLS
ccccccccHHHHHHHHHHHHHHHHccccccHHHHHHccccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHcccccEEEEEcccccccccccccccccEEEEEcccccHHHHHHHccccccccEEEEEccccccccccccHHHHHccccccHHHHHHccccccccccccccccHHHHHccHHHHHcccccccccccccccccccccccccccEEEEEcccccEEccccccccHHHHHHHHHHHHHHHHHHccccccccEEEEccHHHHHHHHHHHHHHHHcccccccEEEccccccccccccEEEEEcccccccccEEEcccccccHHHHcccccEEEEEcccccccccHHHHHHHHHHHHHcccEEEccccHHHHHHHHHHccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccc
ccHHHcccHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHccccccEEEEccHHHHHHHHHHHHHHccccEEEEEEccHHcccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHcccEEEEEEccccccHHHccccccEEEEEcHHHccccccEEEEEcccccEEEEEcccccccHHHHHHHHHHcccccHHHHHHHHcccccEEEEEEEcccccHccccccHHHcccccccccccHcccccccccccccccEEEEEEccccccccccccHcHHHHHHHHHHHHHHHHHcccccccEEEEEEccHHHHHHHHHHHHHccccccccEEEEEEEEccccccccEEEEEEEEEEcccccEEEcccccHHHHEHHEccEEEEEEccHHHHHcccHHHHHHHHHHHHcccEEEccccHHHHHHHHHcccccccccccccccccccccEEEEEccccccHHHHHHccccHHHcccccccHHHHHHHHHHHHHcc
MIDLLEDCVSQYHIYVEKleeredcnvnqseekecrketegskgeckpFLKYVKERFKRAVVPLRNCIFIFCThlpksyisensFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSvdegissafVGKRYLLQLHQRRSECLSVLRNLWNsldelnlpcttskLLLEDFCFKRASLffstasssyklhsveikplnFLVIDEAAQlkesestiplqlaGINHAVligdecqlpAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQyrmhpsislfpnlqfyrnqildganvksksyekhylpgtelgpysfINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVgskqkvsigvvsPYTAQAVAIRKKIGseyenkdgftVKVKsidgfqggeedIIIISTVRcnaggsigfiskpqRVNVALTRARHCLWILGNERTLISSESIWGALVCDAkarqcffnadedRNVAKARLDIGKELVEIGAESltstnqrgkttlcydkdgetyreerstatdseaaadpmfnSTLNRLTLTFRKLLS
MIDLLEDCVSQYHIyvekleeredcnvnqseekecrketegskgeckpfLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFShsvdegissaFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYlpgtelgpYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVgskqkvsigvvspytAQAVAIRKKigseyenkdgftvKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGaesltstnqrgkttlcydkdgetyreerstatdseaaadpmfnstlnrlTLTFRKLLS
MIDLLEDCVSQYHIYVEKLEEREDCNVNQSEEKECRKETEGSKGECKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGAESLTSTNQRGKTTLCYDKDGETYREERSTATDSEAAADPMFNSTLNRLTLTFRKLLS
***LLEDCVSQYHIYVEKL**************************CKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGA*************LC******************************************
MIDLLEDCVSQYHIYV*****************************CKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGT*****************************************************************KLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINI***************VEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNV*************************************************************************
MIDLLEDCVSQYHIYVEKLEER**********************ECKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGAESLTSTNQRGKTTLCYDKDGE************EAAADPMFNSTLNRLTLTFRKLLS
MIDLLEDCVSQYHIYVEKLEER**C*****************KGECKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGAESLTSTNQRGKTTLCYDKDGETYREERSTATDSEAAADPMFNSTLNRLTLTFRKLLS
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MIDLLEDCVSQYHIYVEKLEEREDCNVNQSEEKECRKETEGSKGECKPFLKYVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEELEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINIIGGSEEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAKARLDIGKELVEIGAESLTSTNQRGKTTLCYDKDGETYREERSTATDSEAAADPMFNSTLNRLTLTFRKLLS
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 ?
Query549 2.2.26 [Sep-21-2011]
Q00416 2231 Helicase SEN1 OS=Saccharo yes no 0.469 0.115 0.380 3e-43
O943871944 Uncharacterized ATP-depen yes no 0.475 0.134 0.388 3e-43
B6SFA4818 Probable helicase MAGATAM no no 0.544 0.365 0.323 4e-41
Q923551687 Helicase sen1 OS=Schizosa no no 0.482 0.157 0.357 2e-40
Q86AS0967 Probable helicase DDB_G02 no no 0.542 0.308 0.337 2e-40
Q9HEH1 1093 Regulator of nonsense tra N/A no 0.469 0.236 0.370 6e-37
Q9FJR0 1254 Regulator of nonsense tra no no 0.477 0.208 0.365 1e-36
P30771971 ATP-dependent helicase NA no no 0.488 0.276 0.342 1e-36
Q9EPU0 1124 Regulator of nonsense tra yes no 0.460 0.225 0.362 2e-35
Q92900 1129 Regulator of nonsense tra yes no 0.460 0.224 0.362 2e-35
>sp|Q00416|SEN1_YEAST Helicase SEN1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SEN1 PE=1 SV=2 Back     alignment and function desciption
 Score =  177 bits (448), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 105/276 (38%), Positives = 160/276 (57%), Gaps = 18/276 (6%)

Query: 201  LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSL 260
            ++IDEA Q  E  S IPL+  G    +++GD  QLP  V S  +    + +SLF R+   
Sbjct: 1587 VIIDEACQCTELSSIIPLRYGG-KRCIMVGDPNQLPPTVLSGAASNFKYNQSLFVRMEK- 1644

Query: 261  NHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGA--NVKSKSYEKHYLPGTELGPYSFIN 318
            N S +LL+VQYRMHPSIS FP+ +FY+ ++ DG   ++ +K       P   L PY F +
Sbjct: 1645 NSSPYLLDVQYRMHPSISKFPSSEFYQGRLKDGPGMDILNKRPWHQLEP---LAPYKFFD 1701

Query: 319  IIGGSEE--FIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVS----IGVVSPYTAQAVA 372
            II G +E      S  NM E+ V I+++  L++ +     K+     IG++SPY  Q   
Sbjct: 1702 IISGRQEQNAKTMSYTNMEEIRVAIELVDYLFRKF---DNKIDFTGKIGIISPYREQMQK 1758

Query: 373  IRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRC-NAGGSIGFISKPQRVNVAL 431
            +RK+    +      ++   +IDGFQG E++II+IS VR  +   S+GF+   +R+NVAL
Sbjct: 1759 MRKEFARYFGGMINKSIDFNTIDGFQGQEKEIILISCVRADDTKSSVGFLKDFRRMNVAL 1818

Query: 432  TRARHCLWILGNERTLISSESIWGALVCDAKARQCF 467
            TRA+  +W+LG++R+L  S+ +W  L+ DAK R C 
Sbjct: 1819 TRAKTSIWVLGHQRSLAKSK-LWRDLIEDAKDRSCL 1853
ATP-dependent 5'->3' DNA/RNA helicase required for the expression and maturation of diverse classes of non-protein-coding RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription termination on snoRNAs as well as on several short protein-coding genes. May also play a role in transcription-coupled nucleotide excision repair.
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -
>sp|O94387|YGSA_SCHPO Uncharacterized ATP-dependent helicase C29A10.10c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC29A10.10c PE=3 SV=1 Back     alignment and function description
>sp|B6SFA4|MAA3_ARATH Probable helicase MAGATAMA 3 OS=Arabidopsis thaliana GN=MAA3 PE=2 SV=1 Back     alignment and function description
>sp|Q92355|SEN1_SCHPO Helicase sen1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=sen1 PE=1 SV=1 Back     alignment and function description
>sp|Q86AS0|Y4399_DICDI Probable helicase DDB_G0274399 OS=Dictyostelium discoideum GN=DDB_G0274399 PE=3 SV=1 Back     alignment and function description
>sp|Q9HEH1|RENT1_NEUCR Regulator of nonsense transcripts 1 homolog OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=2E4.130 PE=3 SV=1 Back     alignment and function description
>sp|Q9FJR0|RENT1_ARATH Regulator of nonsense transcripts 1 homolog OS=Arabidopsis thaliana GN=UPF1 PE=1 SV=2 Back     alignment and function description
>sp|P30771|NAM7_YEAST ATP-dependent helicase NAM7 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NAM7 PE=1 SV=1 Back     alignment and function description
>sp|Q9EPU0|RENT1_MOUSE Regulator of nonsense transcripts 1 OS=Mus musculus GN=Upf1 PE=1 SV=2 Back     alignment and function description
>sp|Q92900|RENT1_HUMAN Regulator of nonsense transcripts 1 OS=Homo sapiens GN=UPF1 PE=1 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 ?
Query549
359473527 2788 PREDICTED: uncharacterized protein LOC10 0.885 0.174 0.604 1e-168
359473525 2792 PREDICTED: uncharacterized protein LOC10 0.888 0.174 0.608 1e-168
255555527 2820 conserved hypothetical protein [Ricinus 0.887 0.172 0.589 1e-166
147865014 2676 hypothetical protein VITISV_037587 [Viti 0.877 0.180 0.6 1e-164
356510822 2812 PREDICTED: uncharacterized protein LOC10 0.883 0.172 0.566 1e-154
297738288 2562 unnamed protein product [Vitis vinifera] 0.808 0.173 0.578 1e-153
449445371 2710 PREDICTED: uncharacterized protein LOC10 0.907 0.183 0.541 1e-145
449526710 2474 PREDICTED: uncharacterized protein LOC10 0.907 0.201 0.541 1e-145
297738290 6100 unnamed protein product [Vitis vinifera] 0.763 0.068 0.549 1e-142
449498392 1064 PREDICTED: uncharacterized protein LOC10 0.868 0.448 0.522 1e-140
>gi|359473527|ref|XP_002263192.2| PREDICTED: uncharacterized protein LOC100243095 [Vitis vinifera] Back     alignment and taxonomy information
 Score =  598 bits (1541), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 302/500 (60%), Positives = 371/500 (74%), Gaps = 14/500 (2%)

Query: 1   MIDLLEDCVSQYHIYVEKLEEREDCNVNQ--SEEKECRKETEGSKGECKP-------FLK 51
           MID LEDCVS Y I++E    +E    N+  S ++E   + E S  EC+        F++
Sbjct: 388 MIDFLEDCVSHYRIFLENESRKEKSCSNKGGSTKEEVFMKNELSSNECESTKKVDISFIE 447

Query: 52  YVKERFKRAVVPLRNCIFIFCTHLPKSYISENSFQDMVALKILLHTFGTLLFKDNVVSEE 111
           + ++RF+    PLR C+ IFCTHLPKS+I + +FQ+MV L  LL +F +LL KD+VV EE
Sbjct: 448 FARDRFRATAGPLRRCVRIFCTHLPKSFILKQNFQNMVYLIQLLDSFESLLSKDDVVPEE 507

Query: 112 LEKLFSHSVDEGISSAFVGKRYLLQLHQRRSECLSVLRNLWNSLDELNLPCTTSKLLLED 171
           LE+LFSH   E +  ++     LL +H  R ECLSVL+ L +SL+ELNLP   +K L++ 
Sbjct: 508 LERLFSHQ--EAVRDSYSDSSDLLYVH--RGECLSVLKTLRSSLNELNLPSAMNKGLIKQ 563

Query: 172 FCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGD 231
           FCFK ASL F TASSSY+L+ V +KPL+ LVIDEAAQLKE ES IPLQL  I HA+LIGD
Sbjct: 564 FCFKMASLIFCTASSSYQLYRVNMKPLDLLVIDEAAQLKECESVIPLQLPDIRHAILIGD 623

Query: 232 ECQLPAMVASKISDEAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQIL 291
           ECQLPAMV+SK+S EAGFGRSLFERL+SL H KHLLNVQYRMHPSIS FPN +FY NQIL
Sbjct: 624 ECQLPAMVSSKVSKEAGFGRSLFERLSSLGHFKHLLNVQYRMHPSISFFPNSKFYFNQIL 683

Query: 292 DGANVKSKSYEKHYLPGTELGPYSFINIIGGSE-EFIYHSCRNMVEVSVVIKILQKLYKA 350
           D  NVKSKSY KHYL G   G YSFIN+ G  E + +  S +NM+EV++VIKI+  LYK 
Sbjct: 684 DAPNVKSKSYTKHYLSGPMFGSYSFINVRGKEEHDDVGKSRKNMIEVAIVIKIVGNLYKE 743

Query: 351 WVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTV 410
           W GS QK+SIGV+SPY AQ VA++  +G +YEN D F VKVK++DGFQ GEEDIII+STV
Sbjct: 744 WSGSNQKLSIGVISPYAAQVVAVQDNLGEKYENLDNFAVKVKTVDGFQAGEEDIIIMSTV 803

Query: 411 RCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNA 470
           R N+ GSIGF+S PQR NVALTRARHCLWILGNERTL  SES+W  LVCDAK R+ FFNA
Sbjct: 804 RANSHGSIGFLSNPQRTNVALTRARHCLWILGNERTLAKSESVWEDLVCDAKRRKRFFNA 863

Query: 471 DEDRNVAKARLDIGKELVEI 490
           DED+++AKA L+I  E  ++
Sbjct: 864 DEDKDMAKAILEIKTEFDQL 883

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359473525|ref|XP_003631315.1| PREDICTED: uncharacterized protein LOC100265010 [Vitis vinifera] Back     alignment and taxonomy information
>gi|255555527|ref|XP_002518800.1| conserved hypothetical protein [Ricinus communis] gi|223542181|gb|EEF43725.1| conserved hypothetical protein [Ricinus communis] Back     alignment and taxonomy information
>gi|147865014|emb|CAN78970.1| hypothetical protein VITISV_037587 [Vitis vinifera] Back     alignment and taxonomy information
>gi|356510822|ref|XP_003524133.1| PREDICTED: uncharacterized protein LOC100802419 [Glycine max] Back     alignment and taxonomy information
>gi|297738288|emb|CBI27489.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449445371|ref|XP_004140446.1| PREDICTED: uncharacterized protein LOC101212468 [Cucumis sativus] Back     alignment and taxonomy information
>gi|449526710|ref|XP_004170356.1| PREDICTED: uncharacterized protein LOC101229717 [Cucumis sativus] Back     alignment and taxonomy information
>gi|297738290|emb|CBI27491.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449498392|ref|XP_004160526.1| PREDICTED: uncharacterized protein LOC101225988 [Cucumis sativus] 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 ?
Query549
TAIR|locus:2018561 1050 AT1G65810 [Arabidopsis thalian 0.608 0.318 0.573 6.7e-100
TAIR|locus:2166163692 AT5G37140 [Arabidopsis thalian 0.642 0.510 0.488 8.9e-94
TAIR|locus:2173033676 AT5G52090 [Arabidopsis thalian 0.652 0.529 0.491 1.8e-93
TAIR|locus:2166173839 AT5G37150 [Arabidopsis thalian 0.652 0.426 0.491 3.8e-93
TAIR|locus:2166183871 AT5G37160 [Arabidopsis thalian 0.606 0.382 0.522 2.7e-92
TAIR|locus:2018536 1065 AT1G65780 [Arabidopsis thalian 0.848 0.437 0.432 3.9e-92
TAIR|locus:2135472689 AT4G05540 [Arabidopsis thalian 0.564 0.449 0.549 9e-90
TAIR|locus:2152627638 AT5G37030 [Arabidopsis thalian 0.555 0.478 0.536 1.4e-80
DICTYBASE|DDB_G0268914 4540 DDB_G0268914 [Dictyostelium di 0.520 0.062 0.382 4.9e-46
DICTYBASE|DDB_G0268662 2523 DDB_G0268662 "DNA2/NAM7 helica 0.491 0.107 0.380 8.8e-45
TAIR|locus:2018561 AT1G65810 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 957 (341.9 bits), Expect = 6.7e-100, Sum P(2) = 6.7e-100
 Identities = 195/340 (57%), Positives = 244/340 (71%)

Query:   140 RRSECLSVLRNLWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLN 199
             R  +CL +L ++  S+    LP   SK  L+  C   A L F TASSS +LH     P+ 
Sbjct:   500 RTQDCLEMLTSISMSI---KLPDFISKFELQKLCLDNAYLLFCTASSSARLHMSS--PIQ 554

Query:   200 FLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTS 259
              LVIDEAAQLKE ES IPLQL G+ HA+LIGDE QLPAM+ S I+ EA  GRSLFERL  
Sbjct:   555 LLVIDEAAQLKECESAIPLQLRGLQHAILIGDEKQLPAMIKSNIASEADLGRSLFERLVL 614

Query:   260 LNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINI 319
             L H+K LLN+QYRMHPSIS+FPN +FY  +ILD  +V+ +SYEK +LP    GPYSFINI
Sbjct:   615 LGHNKQLLNMQYRMHPSISIFPNREFYDMKILDAPSVRLRSYEKKFLPEKMYGPYSFINI 674

Query:   320 IGGSEEFIY-HSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIG 378
               G E+F   +S +N+VEVSVV +I+ KLY     + + +S+GV+SPY AQ  AI+++IG
Sbjct:   675 AYGREQFGEGYSSKNLVEVSVVAEIVSKLYSVSRKTGRTISVGVISPYKAQVFAIQERIG 734

Query:   379 SEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCL 438
              +Y  +  FTV V+S+DGFQGGEEDIIIISTVR N  G+IGF+S  QR NVALTRAR+CL
Sbjct:   735 EKYNTEGTFTVSVRSVDGFQGGEEDIIIISTVRSNGNGAIGFLSNQQRTNVALTRARYCL 794

Query:   439 WILGNERTLISSESIWGALVCDAKARQCFFNADEDRNVAK 478
             WILGNE TL ++ S+W  LV DAKAR CF NA+ED ++A+
Sbjct:   795 WILGNEATLTNNRSVWRQLVDDAKARNCFHNAEEDESLAQ 834
GO:0005737 "cytoplasm" evidence=ISM
GO:0008150 "biological_process" evidence=ND
GO:0048451 "petal formation" evidence=RCA
GO:0048453 "sepal formation" evidence=RCA
TAIR|locus:2166163 AT5G37140 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2173033 AT5G52090 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2166173 AT5G37150 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2166183 AT5G37160 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2018536 AT1G65780 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2135472 AT4G05540 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2152627 AT5G37030 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0268914 DDB_G0268914 [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
DICTYBASE|DDB_G0268662 DDB_G0268662 "DNA2/NAM7 helicase family protein" [Dictyostelium discoideum (taxid:44689)] 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 Layer3.6.4LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
GSVIVG00021285001
SubName- Full=Chromosome chr1 scaffold_22, whole genome shotgun sequence; Flags- Fragment; (1776 aa)
(Vitis vinifera)
Predicted Functional Partners:
 
Sorry, there are no predicted associations at the current settings.
 

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 ?
Query549
pfam13087195 pfam13087, AAA_12, AAA domain 9e-72
COG1112767 COG1112, COG1112, Superfamily I DNA and RNA helica 1e-40
TIGR00376637 TIGR00376, TIGR00376, DNA helicase, putative 2e-40
pfam13086220 pfam13086, AAA_11, AAA domain 3e-14
>gnl|CDD|221913 pfam13087, AAA_12, AAA domain Back     alignment and domain information 
 Score =  227 bits (581), Expect = 9e-72
 Identities = 79/197 (40%), Positives = 118/197 (59%), Gaps = 6/197 (3%)

Query: 249 FGRSLFERL-TSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLP 307
             RSLFERL  +   +  +L+ QYRMHP IS FP+  FY  ++ DG +V  +     +  
Sbjct: 1   LDRSLFERLQEAGPEAVVMLDTQYRMHPDISEFPSELFYGGKLKDGESVAERPLPWDFHL 60

Query: 308 GTELGPYSFINIIGGSEEF-IYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPY 366
              LGP  FI++ G  EE     S  N  E  +V+++++KL K+    ++   IG+++PY
Sbjct: 61  PDPLGPLVFIDVDGSEEEEEKSTSYSNEAEAELVVQLVEKLLKSGP--EKNKDIGIITPY 118

Query: 367 TAQAVAIRKKIGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQR 426
            AQ   I+K +  ++       ++V ++DGFQG E+D+II STVR N  G IGF+S P+R
Sbjct: 119 RAQVRLIKKLLKRKF--GGEPDIEVNTVDGFQGREKDVIIFSTVRSNEKGGIGFLSDPRR 176

Query: 427 VNVALTRARHCLWILGN 443
           +NVALTRA+  L I+GN
Sbjct: 177 LNVALTRAKRGLIIVGN 193

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. Length = 195
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative Back     alignment and domain information
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 549
KOG1802935 consensus RNA helicase nonsense mRNA reducing fact 100.0
KOG1803649 consensus DNA helicase [Replication, recombination 100.0
TIGR00376637 DNA helicase, putative. The gene product may repre 100.0
KOG1801827 consensus tRNA-splicing endonuclease positive effe 100.0
KOG18051100 consensus DNA replication helicase [Replication, r 100.0
KOG18071025 consensus Helicases [Replication, recombination an 100.0
COG1112767 Superfamily I DNA and RNA helicases and helicase s 100.0
PF13087200 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP 100.0
KOG1804775 consensus RNA helicase [RNA processing and modific 99.98
KOG18061320 consensus DEAD box containing helicases [Replicati 99.93
PRK11054684 helD DNA helicase IV; Provisional 99.59
TIGR01447586 recD exodeoxyribonuclease V, alpha subunit. This f 99.56
TIGR01448720 recD_rel helicase, putative, RecD/TraA family. Thi 99.55
PF13086236 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV 99.54
PRK10875615 recD exonuclease V subunit alpha; Provisional 99.49
TIGR02768744 TraA_Ti Ti-type conjugative transfer relaxase TraA 99.38
PRK13909 910 putative recombination protein RecB; Provisional 99.37
TIGR02785 1232 addA_Gpos recombination helicase AddA, Firmicutes 99.31
TIGR01073 726 pcrA ATP-dependent DNA helicase PcrA. Designed to 99.3
PF01443234 Viral_helicase1: Viral (Superfamily 1) RNA helicas 99.3
COG1074 1139 RecB ATP-dependent exoDNAse (exonuclease V) beta s 99.3
PRK13826 1102 Dtr system oriT relaxase; Provisional 99.29
TIGR02784 1141 addA_alphas double-strand break repair helicase Ad 99.29
TIGR00609 1087 recB exodeoxyribonuclease V, beta subunit. All pro 99.27
PRK10876 1181 recB exonuclease V subunit beta; Provisional 99.22
PRK13889 988 conjugal transfer relaxase TraA; Provisional 99.21
PRK11773 721 uvrD DNA-dependent helicase II; Provisional 99.19
TIGR01075 715 uvrD DNA helicase II. Designed to identify uvrD me 99.19
PRK10919 672 ATP-dependent DNA helicase Rep; Provisional 99.11
COG3973747 Superfamily I DNA and RNA helicases [General funct 98.94
COG0507696 RecD ATP-dependent exoDNAse (exonuclease V), alpha 98.75
PRK13709 1747 conjugal transfer nickase/helicase TraI; Provision 98.58
PRK14712 1623 conjugal transfer nickase/helicase TraI; Provision 98.56
KOG1804 775 consensus RNA helicase [RNA processing and modific 98.53
PF13538104 UvrD_C_2: UvrD-like helicase C-terminal domain; PD 98.36
PF13604196 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL 98.33
TIGR02760 1960 TraI_TIGR conjugative transfer relaxase protein Tr 98.33
PF09848352 DUF2075: Uncharacterized conserved protein (DUF207 98.23
TIGR01074 664 rep ATP-dependent DNA helicase Rep. Designed to id 97.91
PF13361351 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 97.86
COG0210 655 UvrD Superfamily I DNA and RNA helicases [DNA repl 97.16
COG3972660 Superfamily I DNA and RNA helicases [General funct 97.08
TIGR01074664 rep ATP-dependent DNA helicase Rep. Designed to id 96.96
PF05970364 PIF1: PIF1-like helicase; InterPro: IPR010285 This 96.74
TIGR02760 1960 TraI_TIGR conjugative transfer relaxase protein Tr 96.26
KOG2108853 consensus 3'-5' DNA helicase [Replication, recombi 95.49
COG0210655 UvrD Superfamily I DNA and RNA helicases [DNA repl 95.48
PRK10536262 hypothetical protein; Provisional 95.06
PF00580315 UvrD-helicase: UvrD/REP helicase N-terminal domain 94.43
PF13361351 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 94.39
PF02562205 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH 92.44
TIGR02773 1158 addB_Gpos ATP-dependent nuclease subunit B. DNA re 91.92
COG1875436 NYN ribonuclease and ATPase of PhoH family domains 87.97
PRK13709 1747 conjugal transfer nickase/helicase TraI; Provision 80.15
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification] Back     alignment and domain information 
Probab=100.00  E-value=6.8e-63  Score=523.52  Aligned_cols=299  Identities=35%  Similarity=0.488  Sum_probs=264.2

Q ss_pred             HHHHHHHHhcCCcEEEEccccchhhcccCCCCCCEEEEEcCCCCChhHHhHhhhhcCCCeEEEEcCCCCCCccccccccc
Q 008899          166 KLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISD  245 (549)
Q Consensus       166 ~~~i~~~~l~~a~vI~~T~~sa~~l~~~~~~~fd~VIVDEAsq~~e~e~lipL~l~~~~~vILvGD~~QLpPiv~s~~~~  245 (549)
                      .+..++.++..|+||||||.+|+.. .+....|..|+||||.|++||++++|+.+ |++++||||||+||+|++..+.++
T Consensus       538 k~~~e~ell~~AdVIccTcv~Agd~-rl~~~kfr~VLiDEaTQatEpe~LiPlvl-G~kq~VlVGDh~QLgpvi~~kK~a  615 (935)
T KOG1802|consen  538 KRAAEKELLNQADVICCTCVGAGDR-RLSKFKFRTVLIDEATQATEPECLIPLVL-GAKQLVLVGDHKQLGPVIMCKKAA  615 (935)
T ss_pred             HHHHHHHHHhhcCEEEEecccccch-hhccccccEEEEecccccCCcchhhhhhh-cceeEEEeccccccCceeeeHHHH
Confidence            4566789999999999999999973 33346899999999999999999999987 999999999999999999999999


Q ss_pred             cccCcccHHHHHHhcCCCcccceeccccCccccccCcccccccccccCcccccccccccCCCCC-CCCCeEEEEcCCCcc
Q 008899          246 EAGFGRSLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGT-ELGPYSFINIIGGSE  324 (549)
Q Consensus       246 ~~~~~~SLfeRl~~~~~~~~~L~~qYRmhp~I~~f~n~~fY~g~L~~~~~v~~~~~~~~~l~~~-~~~~~~fidv~~g~e  324 (549)
                      .+|+.+||||||+..|..+++|.+||||||.|++|||..||+|.|+++....++......+|-+ ...|+.|... .|.|
T Consensus       616 ~Agl~qsLferli~lg~~P~~L~vQYRmhP~lSefpsn~fY~G~LqnGVT~~~R~~~g~~~pwp~p~~pl~fy~~-~g~e  694 (935)
T KOG1802|consen  616 TAGLSQSLFERLISLGIKPIRLQVQYRMHPALSEFPSNMFYEGELQNGVTEIERSPLGVDFPWPQPDKPLFFYVC-YGQE  694 (935)
T ss_pred             HhHHHHHHHHHHHhccCCceEEEEeeeeChhhhhcchhhhccchhhcCcchhhhccCCCCCCCCCCCCccceEEe-ccce
Confidence            9999999999999999999999999999999999999999999999998877765543333322 2346666666 6666


Q ss_pred             cc--cccccCCHHHHHHHHHHHHHHHHhhcCCCCCccEEEEccchHHHHHHHHHHhhhhc--CCCCCeEEEecccCCCCc
Q 008899          325 EF--IYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYE--NKDGFTVKVKSIDGFQGG  400 (549)
Q Consensus       325 ~~--~~~S~~N~~Ea~~V~~lv~~L~~~~~~~~~~~sIgIITPY~aQ~~~I~~~L~~~~~--~~~~~~v~V~TVd~fQG~  400 (549)
                      +.  .|+|+.|..||..+..++..|++.+....   .|||||||.+|+..|-+.+...-.  ..-...|.|.|||+|||+
T Consensus       695 eisasGtSf~Nr~Ea~~~ekii~~l~~~gv~~~---qIGVITpYegQr~~i~~ym~~~gsl~~~ly~~veVasVDaFQGr  771 (935)
T KOG1802|consen  695 EISASGTSFLNRTEAANCEKIITKLLKSGVKPS---QIGVITPYEGQRSYIVNYMQTNGSLHKDLYKEVEVASVDAFQGR  771 (935)
T ss_pred             eeeccccceecHHHHHHHHHHHHHHHHcCCCHH---HeeeecccchhHHHHHHHHHhcCccccchhheeEEEeeccccCc
Confidence            66  88999999999999999999999987654   699999999999999998855322  111246899999999999


Q ss_pred             cccEEEEEccccCCCCCcccCCCCCcceeeccccccceEEEeehhhhhccchHHHHHHHHHHhCCceecCC
Q 008899          401 EEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNAD  471 (549)
Q Consensus       401 E~DiVIlS~vrs~~~~~~GFl~d~~RlNVAlTRAR~~LiIiGn~~tL~~~~~~w~~li~~~~~~g~~~~~~  471 (549)
                      |+|+||+||||+|....+||+.|+||||||+||||++|+||||+..|++ +++|.++|.+++++++++..+
T Consensus       772 EKdfIIlSCVRsn~~qgIGFl~d~RRlNVaLTRaK~glvivGN~~~L~k-~~LW~~li~h~~eke~l~eg~  841 (935)
T KOG1802|consen  772 EKDFIILSCVRSNEHQGIGFLNDPRRLNVALTRAKYGLVIVGNPKVLRK-HPLWGHLITHYKEKEVLVEGP  841 (935)
T ss_pred             ccceEEEEEeecccccccccccCchhhhhhhhhcccceEEecCHHHhhh-chHHHHHHHHhhcccceeecc
Confidence            9999999999999999999999999999999999999999999999998 899999999999999999854

>KOG1803 consensus DNA helicase [Replication, recombination and repair] Back     alignment and domain information
>TIGR00376 DNA helicase, putative Back     alignment and domain information
>KOG1801 consensus tRNA-splicing endonuclease positive effector (SEN1) [RNA processing and modification] Back     alignment and domain information
>KOG1805 consensus DNA replication helicase [Replication, recombination and repair] Back     alignment and domain information
>KOG1807 consensus Helicases [Replication, recombination and repair] Back     alignment and domain information
>COG1112 Superfamily I DNA and RNA helicases and helicase subunits [DNA replication, recombination, and repair] Back     alignment and domain information
>PF13087 AAA_12: AAA domain; PDB: 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A 2XZL_A Back     alignment and domain information
>KOG1804 consensus RNA helicase [RNA processing and modification] Back     alignment and domain information
>KOG1806 consensus DEAD box containing helicases [Replication, recombination and repair] Back     alignment and domain information
>PRK11054 helD DNA helicase IV; Provisional Back     alignment and domain information
>TIGR01447 recD exodeoxyribonuclease V, alpha subunit Back     alignment and domain information
>TIGR01448 recD_rel helicase, putative, RecD/TraA family Back     alignment and domain information
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A Back     alignment and domain information
>PRK10875 recD exonuclease V subunit alpha; Provisional Back     alignment and domain information
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA Back     alignment and domain information
>PRK13909 putative recombination protein RecB; Provisional Back     alignment and domain information
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type Back     alignment and domain information
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA Back     alignment and domain information
>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases Back     alignment and domain information
>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13826 Dtr system oriT relaxase; Provisional Back     alignment and domain information
>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type Back     alignment and domain information
>TIGR00609 recB exodeoxyribonuclease V, beta subunit Back     alignment and domain information
>PRK10876 recB exonuclease V subunit beta; Provisional Back     alignment and domain information
>PRK13889 conjugal transfer relaxase TraA; Provisional Back     alignment and domain information
>PRK11773 uvrD DNA-dependent helicase II; Provisional Back     alignment and domain information
>TIGR01075 uvrD DNA helicase II Back     alignment and domain information
>PRK10919 ATP-dependent DNA helicase Rep; Provisional Back     alignment and domain information
>COG3973 Superfamily I DNA and RNA helicases [General function prediction only] Back     alignment and domain information
>COG0507 RecD ATP-dependent exoDNAse (exonuclease V), alpha subunit - helicase superfamily I member [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional Back     alignment and domain information
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional Back     alignment and domain information
>KOG1804 consensus RNA helicase [RNA processing and modification] Back     alignment and domain information
>PF13538 UvrD_C_2: UvrD-like helicase C-terminal domain; PDB: 1W36_G 3K70_G 3DMN_A 3UPU_B 3GPL_A 3E1S_A 3GP8_A Back     alignment and domain information
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI Back     alignment and domain information
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function Back     alignment and domain information
>TIGR01074 rep ATP-dependent DNA helicase Rep Back     alignment and domain information
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A Back     alignment and domain information
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] Back     alignment and domain information
>COG3972 Superfamily I DNA and RNA helicases [General function prediction only] Back     alignment and domain information
>TIGR01074 rep ATP-dependent DNA helicase Rep Back     alignment and domain information
>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins Back     alignment and domain information
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI Back     alignment and domain information
>KOG2108 consensus 3'-5' DNA helicase [Replication, recombination and repair] Back     alignment and domain information
>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10536 hypothetical protein; Provisional Back     alignment and domain information
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA Back     alignment and domain information
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A Back     alignment and domain information
>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli [] Back     alignment and domain information
>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B Back     alignment and domain information
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only] Back     alignment and domain information
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional 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 ?
Query549
2xzl_A802 Upf1-Rna Complex Length = 802 1e-37
2wjv_A800 Crystal Structure Of The Complex Between Human Nons 6e-37
2gjk_A624 Structural And Functional Insights Into The Human U 7e-37
2xzo_A623 Upf1 Helicase - Rna Complex Length = 623 8e-37
4b3g_A646 Crystal Structure Of Ighmbp2 Helicase In Complex Wi 2e-25
4b3f_X646 Crystal Structure Of 1ghmbp2 Helicase Length = 646 3e-25
>pdb|2XZL|A Chain A, Upf1-Rna Complex Length = 802 Back     alignment and structure 
Iteration: 1

 Score =  154 bits (389), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 95/277 (34%), Positives = 147/277 (53%), Gaps = 9/277 (3%)
Query: 201 LVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGRSLFERLTSL 260
           ++IDE+ Q  E E  IP+ + G    +L+GD  QL  ++  + + +AG  +SLFERL SL
Sbjct: 521 VLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISL 579
Query: 261 NHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTELGPYSFINII 320
            H    L VQYRM+P +S FP+  FY   + +G  ++ ++      P    G        
Sbjct: 580 GHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWAN 639
Query: 321 GGSEEFIYH--SCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRK--K 376
            G EE   +  S  N +E     +I+ KL++  V  +Q   IGV++PY  Q   I +  +
Sbjct: 640 YGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQRAYILQYMQ 696
Query: 377 IGSEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARH 436
           +    +      V+V S+D FQG E+D II+S VR N   +IGF+  P+R+NV LTRA++
Sbjct: 697 MNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKY 756
Query: 437 CLWILGNERTLISSESIWGALVCDAKARQCFFNADED 473
            L ILGN R+L +  ++W  L+   + + C      D
Sbjct: 757 GLVILGNPRSL-ARNTLWNHLLIHFREKGCLVEGTLD 792
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense Mediated Decay Factors Upf1 And Upf2 Length = 800 Back     alignment and structure
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1 Helicase Core Length = 624 Back     alignment and structure
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex Length = 623 Back     alignment and structure
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna Length = 646 Back     alignment and structure
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase Length = 646 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 ?
Query549
2xzl_A802 ATP-dependent helicase NAM7; hydrolase-RNA complex 1e-103
2gk6_A624 Regulator of nonsense transcripts 1; UPF1, helicas 3e-99
2wjy_A800 Regulator of nonsense transcripts 1; nonsense medi 1e-95
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 8e-18
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 9e-07
3vkw_A446 Replicase large subunit; alpha/beta domain, helica 2e-07
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Length = 802 Back     alignment and structure
 Score =  328 bits (843), Expect = e-103
 Identities = 104/346 (30%), Positives = 162/346 (46%), Gaps = 15/346 (4%)

Query: 136 QLHQRRSECLSVLRNLWNSLDELNLPCT----TSKLLLEDFCFKRASLFFSTASSSYKLH 191
            + +     L  L  L + + EL+   T          E     +A +   T   +    
Sbjct: 454 LVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAG--D 511

Query: 192 SVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISDEAGFGR 251
                    ++IDE+ Q  E E  IP+ + G    +L+GD  QL  ++  + + +AG  +
Sbjct: 512 KRLDTKFRTVLIDESTQASEPECLIPI-VKGAKQVILVGDHQQLGPVILERKAADAGLKQ 570

Query: 252 SLFERLTSLNHSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKHYLPGTEL 311
           SLFERL SL H    L VQYRM+P +S FP+  FY   + +G  ++ ++      P    
Sbjct: 571 SLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIR 630

Query: 312 GPYSFINIIGGSEEFIY--HSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQ 369
           G         G EE      S  N +E     +I+ KL++  V  +Q   IGV++PY  Q
Sbjct: 631 GIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQ---IGVITPYEGQ 687

Query: 370 AVAIRKKIG--SEYENKDGFTVKVKSIDGFQGGEEDIIIISTVRCNAGGSIGFISKPQRV 427
              I + +      +      V+V S+D FQG E+D II+S VR N   +IGF+  P+R+
Sbjct: 688 RAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRL 747

Query: 428 NVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADED 473
           NV LTRA++ L ILGN R+L +  ++W  L+   + + C      D
Sbjct: 748 NVGLTRAKYGLVILGNPRSL-ARNTLWNHLLIHFREKGCLVEGTLD 792
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Length = 624 Back     alignment and structure
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Length = 800 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
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus} Length = 446 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query549
4b3f_X646 DNA-binding protein smubp-2; hydrolase, helicase; 100.0
2gk6_A624 Regulator of nonsense transcripts 1; UPF1, helicas 100.0
2wjy_A800 Regulator of nonsense transcripts 1; nonsense medi 100.0
2xzl_A802 ATP-dependent helicase NAM7; hydrolase-RNA complex 100.0
3e1s_A574 Exodeoxyribonuclease V, subunit RECD; alpha and be 99.73
3vkw_A446 Replicase large subunit; alpha/beta domain, helica 99.61
3upu_A459 ATP-dependent DNA helicase DDA; RECA-like domain, 99.56
1w36_D608 RECD, exodeoxyribonuclease V alpha chain; recombin 99.56
3lfu_A 647 DNA helicase II; SF1 helicase, ATP-binding, DNA da 99.53
3dmn_A174 Putative DNA helicase; APC89291.2, lactobacillus p 99.44
1pjr_A 724 PCRA; DNA repair, DNA replication, SOS response, h 99.37
1uaa_A 673 REP helicase, protein (ATP-dependent DNA helicase 99.34
3u4q_A 1232 ATP-dependent helicase/nuclease subunit A; helicas 99.04
1w36_B 1180 RECB, exodeoxyribonuclease V beta chain; recombina 98.98
3u4q_B 1166 ATP-dependent helicase/deoxyribonuclease subunit; 96.61
3u4q_B 1166 ATP-dependent helicase/deoxyribonuclease subunit; 89.87
1w36_C 1122 RECC, exodeoxyribonuclease V gamma chain; recombin 89.48
2l8b_A189 Protein TRAI, DNA helicase I; RECD, hydrolase; NMR 80.69
>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A Back     alignment and structure
Probab=100.00  E-value=9e-58  Score=514.13  Aligned_cols=293  Identities=30%  Similarity=0.356  Sum_probs=248.9

Q ss_pred             HHHHHhcCCcEEEEccccchhh---cccCCCCCCEEEEEcCCCCChhHHhHhhhhcCCCeEEEEcCCCCCCccccccccc
Q 008899          169 LEDFCFKRASLFFSTASSSYKL---HSVEIKPLNFLVIDEAAQLKESESTIPLQLAGINHAVLIGDECQLPAMVASKISD  245 (549)
Q Consensus       169 i~~~~l~~a~vI~~T~~sa~~l---~~~~~~~fd~VIVDEAsq~~e~e~lipL~l~~~~~vILvGD~~QLpPiv~s~~~~  245 (549)
                      .....+..+++|++|+++++..   .......||+||||||+|++|+++++|+.  +++++||||||+||||++.+..+.
T Consensus       335 ~~~~~l~~~~vv~~t~~~a~~~~~~~~~~~~~Fd~vIIDEAsQ~~e~~~lipL~--~~~~~ILVGD~~QLpP~v~~~~a~  412 (646)
T 4b3f_X          335 AMLESLTSANVVLATNTGASADGPLKLLPESYFDVVVIDECAQALEASCWIPLL--KARKCILAGDHKQLPPTTVSHKAA  412 (646)
T ss_dssp             HHHHHHHHCSEEEEETTTTCSSSGGGGSCTTCCSEEEETTGGGSCHHHHTTTGG--GSSEEEEEECTTSCCCCCSCHHHH
T ss_pred             HHHHHHhhcceeeeehhhhhhhhHHHhhhhccCCEEEEcCccccchHHHHhhcc--ccceEEEcCCccccCceecchhhh
Confidence            3445688999999999988752   22345689999999999999999999986  569999999999999999999999


Q ss_pred             cccCcccHHHHHHhcC--CCcccceeccccCccccccCcccccccccccCccccccccccc---CCCCCCCCCeEEEEcC
Q 008899          246 EAGFGRSLFERLTSLN--HSKHLLNVQYRMHPSISLFPNLQFYRNQILDGANVKSKSYEKH---YLPGTELGPYSFINII  320 (549)
Q Consensus       246 ~~~~~~SLfeRl~~~~--~~~~~L~~qYRmhp~I~~f~n~~fY~g~L~~~~~v~~~~~~~~---~l~~~~~~~~~fidv~  320 (549)
                      ..|++.|+|+|+....  .+.++|++||||||.|+.|+|..||+|+|.+++++..+.....   ........|+.|+|+.
T Consensus       413 ~~gl~~SlferL~~~~~~~~v~~L~~qYRmhp~I~~f~n~~fY~g~L~~~~~~~~~~~~~lp~~~~~~~~~~p~~f~d~~  492 (646)
T 4b3f_X          413 LAGLSLSLMERLAEEYGARVVRTLTVQYRMHQAIMRWASDTMYLGQLTAHSSVARHLLRDLPGVAATEETGVPLLLVDTA  492 (646)
T ss_dssp             HTTTTCCHHHHHHHHHGGGTEEECCEESSSCHHHHHHHHHHHSTTCCEECTTTTTCCGGGSTTCCCCTTTTCSEEEEECT
T ss_pred             hccccchHHHHHHHhcCCceeeecccccCCcHHHHhhhHHhhcCCccccCcchhhhhhccccccccccccCCceEEEecC
Confidence            9999999999998753  4456899999999999999999999999999888765533211   1112234589999996


Q ss_pred             CCc----ccccccccCCHHHHHHHHHHHHHHHHhhcCCCCCccEEEEccchHHHHHHHHHHhhhhcCCCCCeEEEecccC
Q 008899          321 GGS----EEFIYHSCRNMVEVSVVIKILQKLYKAWVGSKQKVSIGVVSPYTAQAVAIRKKIGSEYENKDGFTVKVKSIDG  396 (549)
Q Consensus       321 ~g~----e~~~~~S~~N~~Ea~~V~~lv~~L~~~~~~~~~~~sIgIITPY~aQ~~~I~~~L~~~~~~~~~~~v~V~TVd~  396 (549)
                      +..    ++..+.|+.|..||..|+.++..|++.+...   .+|||||||++|+.+|++.|.+.     ...++|+|||+
T Consensus       493 g~~~~~~~~~~~~s~~N~~EA~~V~~~v~~L~~~gv~~---~dIgVItpYraQ~~~l~~~l~~~-----~~~i~v~TVd~  564 (646)
T 4b3f_X          493 GCGLFELEEEDEQSKGNPGEVRLVSLHIQALVDAGVPA---RDIAVVSPYNLQVDLLRQSLVHR-----HPELEIKSVDG  564 (646)
T ss_dssp             TSSCCCCC-----CCCCHHHHHHHHHHHHHHHHHTCCG---GGEEEEESCHHHHHHHHHHHTTT-----CTTCEEEEGGG
T ss_pred             CCccccccccCCccccCHHHHHHHHHHHHHHHhcCCCc---CcEEEECCCHHHHHHHHHHHHHh-----CCCCEECChhh
Confidence            542    2226789999999999999999999887653   48999999999999999999764     23689999999


Q ss_pred             CCCccccEEEEEccccCCCCCcccCCCCCcceeeccccccceEEEeehhhhhccchHHHHHHHHHHhCCceecCCc
Q 008899          397 FQGGEEDIIIISTVRCNAGGSIGFISKPQRVNVALTRARHCLWILGNERTLISSESIWGALVCDAKARQCFFNADE  472 (549)
Q Consensus       397 fQG~E~DiVIlS~vrs~~~~~~GFl~d~~RlNVAlTRAR~~LiIiGn~~tL~~~~~~w~~li~~~~~~g~~~~~~~  472 (549)
                      |||+|+|+||+|+||+|..+.+||+.|++|+|||+||||++||||||..+|.+ ++.|++|+++++++|+++.+.+
T Consensus       565 fQG~E~dvII~S~vrsn~~~~iGFl~~~rRlNVAlTRAk~~liivGn~~~l~~-~~~~~~li~~~~~~g~~~~~~e  639 (646)
T 4b3f_X          565 FQGREKEAVILSFVRSNRKGEVGFLAEDRRINVAVTRARRHVAVICDSRTVNN-HAFLKTLVEYFTQHGEVRTAFE  639 (646)
T ss_dssp             GTTCCEEEEEEECCCCCTTCCCCSTTCHHHHHHHHHTEEEEEEEEECHHHHTT-SHHHHHHHHHHHHSSEEEEGGG
T ss_pred             cccccCCEEEEEeccCCCCCCccccCCcCcEEeEhhhhhCeEEEEEchHHhcC-CHHHHHHHHHHHHCCCEeeHHH
Confidence            99999999999999999999999999999999999999999999999999986 7899999999999999987643
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A Back     alignment and structure
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A Back     alignment and structure
>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae} Back     alignment and structure
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* Back     alignment and structure
>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus} Back     alignment and structure
>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4} Back     alignment and structure
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D* Back     alignment and structure
>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A* Back     alignment and structure
>3dmn_A Putative DNA helicase; APC89291.2, lactobacillus plantarum WCFS1, STR genomics, PSI-2, midwest center for structural genomics; HET: MSE; 1.66A {Lactobacillus plantarum} Back     alignment and structure
>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B* Back     alignment and structure
>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 Back     alignment and structure
>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A* Back     alignment and structure
>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B* Back     alignment and structure
>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B* Back     alignment and structure
>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B* Back     alignment and structure
>1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.25 PDB: 3k70_C* Back     alignment and structure
>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli} 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 549
d1w36d1359 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha c 0.003
>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Length = 359 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

 Score = 37.6 bits (86), Expect = 0.003
 Identities = 26/117 (22%), Positives = 45/117 (38%), Gaps = 7/117 (5%)

Query: 151 LWNSLDELNLPCTTSKLLLEDFCFKRASLFFSTASSSYKLHSVEIKPLNFLVIDEAAQLK 210
           L  +L +L L     K + ED       L     S   + H+     L+ LV+DEA+ + 
Sbjct: 215 LGKALRQLPLTDEQKKRIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID 274

Query: 211 ESESTIPLQLAGIN-HAVLIGDECQLPAMVASKI------SDEAGFGRSLFERLTSL 260
               +  +     +   + +GD  QL ++ A  +         AGF      +L+ L
Sbjct: 275 LPMMSRLIDALPDHARVIFLGDRDQLASVEAGAVLGDICAYANAGFTAERARQLSRL 331

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query549
g1qhh.1623 DEXX box DNA helicase {Bacillus stearothermophilus 99.14
d1w36d1359 Exodeoxyribonuclease V alpha chain (RecD) {Escheri 98.48
d1uaaa1306 DEXX box DNA helicase {Escherichia coli, RepD [Tax 98.26
d1w36d2246 Exodeoxyribonuclease V alpha chain (RecD) {Escheri 98.22
d1w36b1485 Exodeoxyribonuclease V beta chain (RecB), N-termin 98.01
d1w36b2395 Exodeoxyribonuclease V beta chain (RecB), N-termin 97.98
d1pjra1318 DEXX box DNA helicase {Bacillus stearothermophilus 97.91
d1uaaa2333 DEXX box DNA helicase {Escherichia coli, RepD [Tax 97.61
d1pjra2333 DEXX box DNA helicase {Bacillus stearothermophilus 97.31
d1w36c2470 Exodeoxyribonuclease V gamma chain (RecC), N-termi 94.91
>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]} Back     information, alignment and structure
>d1w36d2 c.37.1.19 (D:361-606) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1w36b2 c.37.1.19 (B:486-880) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]} Back     information, alignment and structure
>d1uaaa2 c.37.1.19 (A:308-640) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]} Back     information, alignment and structure
>d1pjra2 c.37.1.19 (A:319-651) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]} Back     information, alignment and structure
>d1w36c2 c.37.1.19 (C:348-817) Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure