Citrus Sinensis ID: 008209

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-------550-------560-------570----

MSLCFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQCEAKRVLERLYRKREKERENNRK

cccccccccEEEEccHHHHHHHHHcccccccccEEEEEccccccHHHHHHHHHHHHHHHHcccccEEEEcccccHHHHHcccccccEEEEccccccEEEEEcccccHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHHHHHHHHHHcccccccEEEEEEcccccHHHHHccccccccccccccccccEEEEEEcccccccccccEEEEEcccccccccccccccccEEEEccccHHHHHHHccccccccccEEEEcccHHHHHccccccccccHHHcccHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHccccccccccHHHHHHHccccccccHHHHHHccccccHHHHHHHHHHHcccccEEcccHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccccHHHHcccHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHcccccccccEEEcccccEEEEcccccccccccEEEEEHHHHcccccccccEEEcccHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHccc

ccccccHccEEEEcccHHHHHHHHccccHHHcEEEEEccHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccHHHHHHHHccccEEEcccccccEEEEEccccHHHHHHHHHHHHHHHHcccccccEEEEEccHHHHHHHHHHHHHHHHHHccccccEEEEEEEccccHHHHHHHccccccccccccccccEEEEEEEEEEEEEEEccEEEEEcccccccccccccccccEEEEccHcHHHHHHHcccccccccccEEEEEcHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccEEEEcccccccHHHHHHHHHHHHHHHHccccccccHHHHHHccccccHHHHHHHHHcccccccHHHHHHHHHHccccEEEccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEcccccHHHHHHHHHHHHHHHHHHHHHccccccEEEEEcccEEEEccccHccccccEEEEEEEEEEcHHHHHHHccccHHHHHHHcHHHcccccccccHHHHHHHHHHHHHHcccccccc

MSLCFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVlknrpdlkLVVMSATLEAEKfqgyfygaplmkvpgrlhpveifytqepERDYLEAAIRTVVQIhmcepsgdiLVFLTGEEEIEDACRKITKEITnmgdqvgpvkvvplystlppamqqkifepapppskeggppgrkivvstniaetsltidgivyvidpgfakqkvynprvrvesllvspiskasahqrsgragrtqpgkcfrlyteksfnndlqpqtypeiLRSNLANTVLTLKKlgiddlvhfdfmdppapETLMRALEVLNYLgaldddgnltemgekmsefpldpqmskmlvespkyncsneILSISAMlsvpncfvrpreAQKAADEAKARfghidgdhlTLLNVYHAYkqnnedpswcydnfvnhralksADNVRQQLVRIMARFNLKlcsndfnsrDYYVNIRKAMLAGYFMQVAHLertgqyltvkdnqvvhlhpsncldhkpewviYNEYVLTSRNFIRTVTDVRGEWLIdiaphyydlsnfpqCEAKRVLERLYRKREKERENNRK

MSLCFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEitnmgdqvgpvKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVspiskasahqrsgragrtqpgKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFnlklcsndfnSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLhpsncldhkpeWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPhyydlsnfpqCEAKRVLERLYrkrekerennrk

MSLCFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEpapppskeggppgRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQCEAkrvlerlyrkrekerennrk

**LCFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYST**************************IVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLV*********************KCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDD****************************KYNCSNEILSISAMLSVPNCFVRP*********AKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQCEAKRVLERLY************

***CFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITK********VGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFV***************FGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKL*****NSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYY******************************

MSLCFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPA*********PGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPI***************QPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPR*********KARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQCEAKRVLERLYRK**********

***CFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKAS***********QPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQCEAKRVLERLYRKREK*******

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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
Query		574	2.2.26 [Sep-21-2011]
O22899		729	Probable pre-mRNA-splicin	no	no	0.980	0.772	0.909	0.0
O43143		795	Putative pre-mRNA-splicin	yes	no	0.961	0.694	0.743	0.0
O35286		795	Putative pre-mRNA-splicin	yes	no	0.961	0.694	0.743	0.0
Q5RAZ4		795	Putative pre-mRNA-splicin	yes	no	0.961	0.694	0.743	0.0
Q20875		739	Putative pre-mRNA-splicin	yes	no	0.951	0.738	0.704	0.0
O42945		735	Probable pre-mRNA-splicin	yes	no	0.977	0.763	0.654	0.0
P53131		767	Pre-mRNA-splicing factor	yes	no	0.961	0.719	0.646	0.0
Q54NJ4		727	Putative pre-mRNA-splicin	yes	no	0.940	0.742	0.648	0.0
O17438		455	Putative pre-mRNA-splicin	no	no	0.789	0.995	0.762	0.0
Q54F05		1160	ATP-dependent RNA helicas	no	no	0.944	0.467	0.522	1e-172

>sp\|O22899\|DHX15_ARATH Probable pre-mRNA-splicing factor ATP-dependent RNA helicase OS=Arabidopsis thaliana GN=At2g47250 PE=2 SV=1	Back alignment and function desciption

 Score = 1091 bits (2821), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 514/565 (90%), Positives = 544/565 (96%), Gaps = 2/565 (0%)

Query: 12  RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71
           +YLTDGMLLREAM DPLLERYKVI+LDEAHERTLATDVLFGLLKEVL+NRPDLKLVVMSA
Sbjct: 165 KYLTDGMLLREAMADPLLERYKVIILDEAHERTLATDVLFGLLKEVLRNRPDLKLVVMSA 224

Query: 72  TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131
           TLEAEKFQ YF GAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEP GDILV
Sbjct: 225 TLEAEKFQEYFSGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPPGDILV 284

Query: 132 FLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPP 191
           FLTGEEEIEDACRKI KE++N+GDQVGPVKVVPLYSTLPPAMQQKIF+PAP P  EGGP 
Sbjct: 285 FLTGEEEIEDACRKINKEVSNLGDQVGPVKVVPLYSTLPPAMQQKIFDPAPVPLTEGGPA 344

Query: 192 GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRA 251
           GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPR+RVESLLVSPISKASAHQRSGRA
Sbjct: 345 GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRIRVESLLVSPISKASAHQRSGRA 404

Query: 252 GRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP 311
           GRT+PGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP
Sbjct: 405 GRTRPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP 464

Query: 312 ETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAM 371
           ETLMRALEVLNYLGALDD+GNLT+ GE MSEFPLDPQMSKML+ SP++NCSNEILS+SAM
Sbjct: 465 ETLMRALEVLNYLGALDDEGNLTKTGEIMSEFPLDPQMSKMLIVSPEFNCSNEILSVSAM 524

Query: 372 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRA 431
           LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP+WC++NFVN+RA
Sbjct: 525 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPNWCFENFVNNRA 584

Query: 432 LKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTV 491
           +KSADNVRQQLVRIM+RFNLK+CS DFNSRDYYVNIRKAMLAGYFMQVAHLERTG YLTV
Sbjct: 585 MKSADNVRQQLVRIMSRFNLKMCSTDFNSRDYYVNIRKAMLAGYFMQVAHLERTGHYLTV 644

Query: 492 KDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQ 551
           KDNQVVHLHPSNCLDHKPEWVIYNEYVLT+RNFIRTVTD+RGEWL+D+A HYYDLSNFP 
Sbjct: 645 KDNQVVHLHPSNCLDHKPEWVIYNEYVLTTRNFIRTVTDIRGEWLVDVAQHYYDLSNFPN 704

Query: 552 CEAKRVLERLYRKREKER--ENNRK 574
           CEAKR LE+LY+KRE+E+    NRK
Sbjct: 705 CEAKRALEKLYKKREREKNESKNRK 729

Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp\|O43143\|DHX15_HUMAN Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 OS=Homo sapiens GN=DHX15 PE=1 SV=2	Back alignment and function description

>sp\|O35286\|DHX15_MOUSE Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 OS=Mus musculus GN=Dhx15 PE=2 SV=2	Back alignment and function description

>sp\|Q5RAZ4\|DHX15_PONAB Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 OS=Pongo abelii GN=DHX15 PE=2 SV=2	Back alignment and function description

>sp\|Q20875\|DHX15_CAEEL Putative pre-mRNA-splicing factor ATP-dependent RNA helicase F56D2.6 OS=Caenorhabditis elegans GN=F56D2.6 PE=2 SV=1	Back alignment and function description

>sp\|O42945\|DHX15_SCHPO Probable pre-mRNA-splicing factor ATP-dependent RNA helicase prp43 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=prp43 PE=3 SV=1	Back alignment and function description

>sp\|P53131\|PRP43_YEAST Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PRP43 PE=1 SV=1	Back alignment and function description

>sp\|Q54NJ4\|DHX15_DICDI Putative pre-mRNA-splicing factor ATP-dependent RNA helicase dhx15 OS=Dictyostelium discoideum GN=dhx15 PE=3 SV=1	Back alignment and function description

>sp\|O17438\|DHX15_STRPU Putative pre-mRNA-splicing factor ATP-dependent RNA helicase PRP1 (Fragment) OS=Strongylocentrotus purpuratus GN=PRP1 PE=2 SV=1	Back alignment and function description

>sp\|Q54F05\|DHX8_DICDI ATP-dependent RNA helicase dhx8 OS=Dictyostelium discoideum GN=dhx8 PE=3 SV=1	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
Query		574
357442187		721	ATP-dependent RNA helicase-like protein	0.979	0.779	0.946	0.0
356499785		722	PREDICTED: probable pre-mRNA-splicing fa	0.959	0.763	0.961	0.0
356572813		713	PREDICTED: probable pre-mRNA-splicing fa	0.959	0.772	0.960	0.0
356572811		721	PREDICTED: probable pre-mRNA-splicing fa	0.959	0.764	0.960	0.0
356505645		720	PREDICTED: probable pre-mRNA-splicing fa	0.959	0.765	0.960	0.0
225437618		728	PREDICTED: probable pre-mRNA-splicing fa	0.979	0.771	0.937	0.0
222624808		707	hypothetical protein OsJ_10612 [Oryza sa	0.979	0.794	0.932	0.0
449436399		732	PREDICTED: probable pre-mRNA-splicing fa	0.979	0.767	0.928	0.0
255548377		731	ATP-dependent RNA helicase, putative [Ri	0.980	0.770	0.927	0.0
108707810		722	Pre-mRNA splicing factor ATP-dependent R	0.979	0.778	0.932	0.0

>gi\|357442187\|ref\|XP_003591371.1\| ATP-dependent RNA helicase-like protein [Medicago truncatula] gi\|355480419\|gb\|AES61622.1\| ATP-dependent RNA helicase-like protein [Medicago truncatula]	Back alignment and taxonomy information

 Score = 1128 bits (2918), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 532/562 (94%), Positives = 552/562 (98%)

Query: 12  RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71
           +YLTDGMLLREAMTDPLLERYKVI+LDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA
Sbjct: 157 KYLTDGMLLREAMTDPLLERYKVIILDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 216

Query: 72  TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131
           TLEAEKFQGYF+GAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEP+GDILV
Sbjct: 217 TLEAEKFQGYFFGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPAGDILV 276

Query: 132 FLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPP 191
           FLTGEEEIEDACRKI+KE+ NMGDQVGPVK VPLYSTLPPAMQQKIFEPAPPP KEGGPP
Sbjct: 277 FLTGEEEIEDACRKISKEVANMGDQVGPVKAVPLYSTLPPAMQQKIFEPAPPPVKEGGPP 336

Query: 192 GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRA 251
           GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRA
Sbjct: 337 GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRA 396

Query: 252 GRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP 311
           GRTQPGKCFRLYTE+SFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP
Sbjct: 397 GRTQPGKCFRLYTERSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP 456

Query: 312 ETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAM 371
           ETLMRALEVLNYLGALDD+GNLT++GE MSEFPLDPQMSKMLV SP++NCSNEILSISAM
Sbjct: 457 ETLMRALEVLNYLGALDDEGNLTKLGEIMSEFPLDPQMSKMLVVSPEFNCSNEILSISAM 516

Query: 372 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRA 431
           LSVPNCF+RPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNED SWCYDNFVN+RA
Sbjct: 517 LSVPNCFIRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDASWCYDNFVNNRA 576

Query: 432 LKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTV 491
           LKSADNVRQQLVRIMARFNLKLCS DFNSRDYYVNIRKAMLAGYFMQVAHLERTG YLTV
Sbjct: 577 LKSADNVRQQLVRIMARFNLKLCSTDFNSRDYYVNIRKAMLAGYFMQVAHLERTGHYLTV 636

Query: 492 KDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQ 551
           KDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTD+RGEWL+DIAPHYYDLSNFPQ
Sbjct: 637 KDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDIRGEWLVDIAPHYYDLSNFPQ 696

Query: 552 CEAKRVLERLYRKREKERENNR 573
           CEAKRVLE+LY+KREKE++  R
Sbjct: 697 CEAKRVLEKLYKKREKEKDEAR 718

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356499785\|ref\|XP_003518717.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase-like [Glycine max]	Back alignment and taxonomy information

>gi\|356572813\|ref\|XP_003554560.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase-like isoform 2 [Glycine max]	Back alignment and taxonomy information

>gi\|356572811\|ref\|XP_003554559.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase-like isoform 1 [Glycine max]	Back alignment and taxonomy information

>gi\|356505645\|ref\|XP_003521600.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase-like [Glycine max]	Back alignment and taxonomy information

>gi\|225437618\|ref\|XP_002278247.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase [Vitis vinifera] gi\|147787427\|emb\|CAN64445.1\| hypothetical protein VITISV_036050 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|222624808\|gb\|EEE58940.1\| hypothetical protein OsJ_10612 [Oryza sativa Japonica Group]	Back alignment and taxonomy information

>gi\|449436399\|ref\|XP_004135980.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase-like [Cucumis sativus] gi\|449515243\|ref\|XP_004164659.1\| PREDICTED: probable pre-mRNA-splicing factor ATP-dependent RNA helicase-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255548377\|ref\|XP_002515245.1\| ATP-dependent RNA helicase, putative [Ricinus communis] gi\|223545725\|gb\|EEF47229.1\| ATP-dependent RNA helicase, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|108707810\|gb\|ABF95605.1\| Pre-mRNA splicing factor ATP-dependent RNA helicase, putative, expressed [Oryza sativa Japonica Group]	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
Query		574
TAIR\|locus:2065210		729	AT2G47250 [Arabidopsis thalian	0.945	0.744	0.906	2e-271
TAIR\|locus:2095989		726	AT3G62310 [Arabidopsis thalian	0.945	0.747	0.900	6.6e-271
FB\|FBgn0033160		729	CG11107 [Drosophila melanogast	0.944	0.743	0.759	3.3e-230
UNIPROTKB\|F1NHI3		762	DHX15 "Uncharacterized protein	0.944	0.711	0.737	2.8e-224
UNIPROTKB\|A5D7D9		795	DHX15 "Uncharacterized protein	0.944	0.681	0.735	3.6e-224
UNIPROTKB\|E2R2U3		795	DHX15 "Uncharacterized protein	0.944	0.681	0.735	3.6e-224
UNIPROTKB\|O43143		795	DHX15 "Putative pre-mRNA-splic	0.944	0.681	0.735	3.6e-224
UNIPROTKB\|F1S5A8		795	DHX15 "Uncharacterized protein	0.944	0.681	0.735	3.6e-224
MGI\|MGI:1099786		795	Dhx15 "DEAH (Asp-Glu-Ala-His)	0.944	0.681	0.735	3.6e-224
RGD\|1308072		795	Dhx15 "DEAH (Asp-Glu-Ala-His)	0.944	0.681	0.735	3.6e-224

TAIR\|locus:2065210 AT2G47250 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2610 (923.8 bits), Expect = 2.0e-271, P = 2.0e-271
 Identities = 492/543 (90%), Positives = 518/543 (95%)

Query:    12 RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71
             +YLTDGMLLREAM DPLLERYKVI+LDEAHERTLATDVLFGLLKEVL+NRPDLKLVVMSA
Sbjct:   165 KYLTDGMLLREAMADPLLERYKVIILDEAHERTLATDVLFGLLKEVLRNRPDLKLVVMSA 224

Query:    72 TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131
             TLEAEKFQ YF GAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEP GDILV
Sbjct:   225 TLEAEKFQEYFSGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPPGDILV 284

Query:   132 FLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEXXXXXXXXXXXX 191
             FLTGEEEIEDACRKI KE++N+GDQVGPVKVVPLYSTLPPAMQQKIF+            
Sbjct:   285 FLTGEEEIEDACRKINKEVSNLGDQVGPVKVVPLYSTLPPAMQQKIFDPAPVPLTEGGPA 344

Query:   192 XRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSGRA 251
              RKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPR+RVESLLVSPISKASAHQRSGRA
Sbjct:   345 GRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRIRVESLLVSPISKASAHQRSGRA 404

Query:   252 GRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP 311
             GRT+PGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP
Sbjct:   405 GRTRPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAP 464

Query:   312 ETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAM 371
             ETLMRALEVLNYLGALDD+GNLT+ GE MSEFPLDPQMSKML+ SP++NCSNEILS+SAM
Sbjct:   465 ETLMRALEVLNYLGALDDEGNLTKTGEIMSEFPLDPQMSKMLIVSPEFNCSNEILSVSAM 524

Query:   372 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRA 431
             LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP+WC++NFVN+RA
Sbjct:   525 LSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPNWCFENFVNNRA 584

Query:   432 LKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERTGQYLTV 491
             +KSADNVRQQLVRIM+RFNLK+CS DFNSRDYYVNIRKAMLAGYFMQVAHLERTG YLTV
Sbjct:   585 MKSADNVRQQLVRIMSRFNLKMCSTDFNSRDYYVNIRKAMLAGYFMQVAHLERTGHYLTV 644

Query:   492 KDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQ 551
             KDNQVVHLHPSNCLDHKPEWVIYNEYVLT+RNFIRTVTD+RGEWL+D+A HYYDLSNFP 
Sbjct:   645 KDNQVVHLHPSNCLDHKPEWVIYNEYVLTTRNFIRTVTDIRGEWLVDVAQHYYDLSNFPN 704

Query:   552 CEA 554
             CEA
Sbjct:   705 CEA 707

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008026 "ATP-dependent helicase activity" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

TAIR\|locus:2095989 AT3G62310 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

FB\|FBgn0033160 CG11107 [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NHI3 DHX15 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|A5D7D9 DHX15 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R2U3 DHX15 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|O43143 DHX15 "Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1S5A8 DHX15 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

MGI\|MGI:1099786 Dhx15 "DEAH (Asp-Glu-Ala-His) box polypeptide 15" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1308072 Dhx15 "DEAH (Asp-Glu-Ala-His) box polypeptide 15" [Rattus norvegicus (taxid:10116)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q20875	DHX15_CAEEL	3, ., 6, ., 4, ., 1, 3	0.7043	0.9512	0.7388	yes	no
Q54NJ4	DHX15_DICDI	3, ., 6, ., 4, ., 1, 3	0.6485	0.9407	0.7427	yes	no
Q5RAZ4	DHX15_PONAB	3, ., 6, ., 4, ., 1, 3	0.7436	0.9616	0.6943	yes	no
O35286	DHX15_MOUSE	3, ., 6, ., 4, ., 1, 3	0.7436	0.9616	0.6943	yes	no
P53131	PRP43_YEAST	3, ., 6, ., 4, ., 1, 3	0.6462	0.9616	0.7196	yes	no
O43143	DHX15_HUMAN	3, ., 6, ., 4, ., 1, 3	0.7436	0.9616	0.6943	yes	no
O22899	DHX15_ARATH	3, ., 6, ., 4, ., 1, 3	0.9097	0.9808	0.7722	no	no
O42945	DHX15_SCHPO	3, ., 6, ., 4, ., 1, 3	0.6543	0.9773	0.7632	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	0.914
3rd Layer	3.6.4	0.921

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00028144001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_42, whole genome shotgun sequence); (728 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00021307001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (586 aa)	•	•	•	0.449
	GSVIVG00034559001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (840 aa)	•	•	•	0.427
	GSVIVG00037695001	SubName- Full=Chromosome undetermined scaffold_91, whole genome shotgun sequence; (245 aa)	•	•	•	0.404

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
Query		574
COG1643		845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	0.0
TIGR01967		1283	TIGR01967, DEAH_box_HrpA, ATP-dependent helicase H	1e-128
PRK11131		1294	PRK11131, PRK11131, ATP-dependent RNA helicase Hrp	1e-114
TIGR01970		819	TIGR01970, DEAH_box_HrpB, ATP-dependent helicase H	6e-75
PRK11664		812	PRK11664, PRK11664, ATP-dependent RNA helicase Hrp	9e-68
pfam04408		91	pfam04408, HA2, Helicase associated domain (HA2)	1e-39
pfam07717		109	pfam07717, OB_NTP_bind, Oligonucleotide/oligosacch	7e-34
smart00847		82	smart00847, HA2, Helicase associated domain (HA2)	2e-30
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-13
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	2e-11
PHA02653		675	PHA02653, PHA02653, RNA helicase NPH-II; Provision	2e-10
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-10
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-09
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	5e-09

>gnl\|CDD\|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

 Score =  591 bits (1526), Expect = 0.0
 Identities = 228/611 (37%), Positives = 327/611 (53%), Gaps = 68/611 (11%)

Query: 12  RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRP-DLKLVVMS 70
           + +TDG+LLRE   DPLL  Y V+++DEAHER+L TD+L GLLK++L  R  DLKL++MS
Sbjct: 143 KVMTDGILLREIQNDPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMS 202

Query: 71  ATLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDY-LEAAIRTVVQIHMCEPSGDI 129
           ATL+AE+F  YF  AP++++ GR +PVEI Y  E E DY L  AI   V IH+ E SG I
Sbjct: 203 ATLDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSI 262

Query: 130 LVFLTGEEEIEDACRKITKEITNMGDQVGP-VKVVPLYSTLPPAMQQKIFEPAPPPSKEG 188
           LVFL G+ EIE     +         ++G  ++++PLY  L    Q ++FEPAP      
Sbjct: 263 LVFLPGQREIERTAEWL------EKAELGDDLEILPLYGALSAEEQVRVFEPAPGGK--- 313

Query: 189 GPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRS 248
               RK+V++TNIAETSLTI GI YVID G AK+K Y+PR  +  L   PISKASA QR+
Sbjct: 314 ----RKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRA 369

Query: 249 GRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGID-DLVHFDFMD 307
           GRAGRT PG C+RLY+E+ F       T PEILR++L+  VL LK LGI  D+  F F+D
Sbjct: 370 GRAGRTGPGICYRLYSEEDF-LAFPEFTLPEILRTDLSGLVLQLKSLGIGQDIAPFPFLD 428

Query: 308 PPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILS 367
           PP    +  AL +L  LGALDD G LT +G++MS  PLDP++++ML+ +P+  C  E  +
Sbjct: 429 PPPEAAIQAALTLLQELGALDDSGKLTPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAAT 488

Query: 368 ISAMLSVPNC------FVRPREAQKAADEAK-ARF---GHIDGDHLTLLNVYHAYKQNNE 417
           I++MLS  +        V+ R+ + A D  K  +        GDHL LL  +        
Sbjct: 489 IASMLSEQDRESDFSRDVKLRKQRTAQDLLKRLKRRNAADPRGDHLLLLEAFPDRIARKR 548

Query: 418 DP------SWCYDNFVNHRALKSADNVRQQLVRIMAR-FNLKLCSNDFNSRD-------- 462
                   + C       +AL  A  +   L+   +      L + + +  +        
Sbjct: 549 AKGEYLRANGCRAMLFPTKALSRAPWIIAALLVQTSALAGRILAAAEIDEDEWAAQHLPE 608

Query: 463 ------YYVNIRKAMLAGYFMQVAHLE-RTGQYLTVKDNQVVHLHPSNCLD--HKPEWVI 513
                  + +IR A+ AG  + +A L+     Y+T+ DN  V  HPS+        EW+ 
Sbjct: 609 HCYSEPIWDDIRGALAAGRKLNIAQLQLDGRPYVTLSDNTPVFAHPSSVRLGLVLLEWIK 668

Query: 514 YNEYVLTSRNFIR-----------TVTDVRGEWLIDIAP---HYYDLSNFPQCEAKRVLE 559
           Y E++ T + ++R           T+ ++   WL +          L+     +A   L 
Sbjct: 669 YAEFLRTRKGYLREGRGERWPDVQTLIELLKLWLKEQVKGLRGLDGLTKAAMKQALPDLL 728

Query: 560 R--LYRKREKE 568
              L +  ++ 
Sbjct: 729 PWDLTQLLDER 739

Length = 845

>gnl\|CDD\|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA	Back alignment and domain information

>gnl\|CDD\|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional	Back alignment and domain information

>gnl\|CDD\|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB	Back alignment and domain information

>gnl\|CDD\|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional	Back alignment and domain information

>gnl\|CDD\|218070 pfam04408, HA2, Helicase associated domain (HA2)	Back alignment and domain information

>gnl\|CDD\|219532 pfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding (OB)-fold	Back alignment and domain information

>gnl\|CDD\|214852 smart00847, HA2, Helicase associated domain (HA2) Add an annotation	Back alignment and domain information

>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Back alignment and domain information

>gnl\|CDD\|197757 smart00490, HELICc, helicase superfamily c-terminal domain	Back alignment and domain information

>gnl\|CDD\|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional	Back alignment and domain information

>gnl\|CDD\|238005 cd00046, DEXDc, DEAD-like helicases superfamily	Back alignment and domain information

>gnl\|CDD\|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain	Back alignment and domain information

>gnl\|CDD\|214692 smart00487, DEXDc, DEAD-like helicases superfamily	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		574
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	100.0
KOG0925		699	consensus mRNA splicing factor ATP-dependent RNA h	100.0
KOG0924		1042	consensus mRNA splicing factor ATP-dependent RNA h	100.0
KOG0923		902	consensus mRNA splicing factor ATP-dependent RNA h	100.0
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	100.0
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	100.0
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	100.0
KOG0921		1282	consensus Dosage compensation complex, subunit MLE	100.0
PHA02653		675	RNA helicase NPH-II; Provisional	100.0
PRK01172		674	ski2-like helicase; Provisional	100.0
PRK02362		737	ski2-like helicase; Provisional	100.0
PRK00254		720	ski2-like helicase; Provisional	99.97
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	99.96
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	99.96
COG1202		830	Superfamily II helicase, archaea-specific [General	99.96
PTZ00110		545	helicase; Provisional	99.96
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.95
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	99.95
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	99.95
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	99.95
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	99.95
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	99.94
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	99.94
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	99.94
PTZ00424		401	helicase 45; Provisional	99.94
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.94
COG1204		766	Superfamily II helicase [General function predicti	99.94
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.93
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	99.93
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.93
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	99.93
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	99.93
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	99.93
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	99.92
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	99.92
KOG0343		758	consensus RNA Helicase [RNA processing and modific	99.91
PRK13767		876	ATP-dependent helicase; Provisional	99.91
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.91
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	99.91
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	99.91
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.9
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	99.9
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	99.9
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.89
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	99.89
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	99.89
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	99.88
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	99.88
PRK10689		1147	transcription-repair coupling factor; Provisional	99.88
KOG0341		610	consensus DEAD-box protein abstrakt [RNA processin	99.87
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	99.87
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	99.86
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.86
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.86
COG1201		814	Lhr Lhr-like helicases [General function predictio	99.86
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	99.85
KOG0347		731	consensus RNA helicase [RNA processing and modific	99.84
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.84
KOG0346		569	consensus RNA helicase [RNA processing and modific	99.83
KOG4284		980	consensus DEAD box protein [Transcription]	99.83
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	99.83
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.82
KOG0327		397	consensus Translation initiation factor 4F, helica	99.82
PF07717		114	OB_NTP_bind: Oligonucleotide/oligosaccharide-bindi	99.81
KOG0334		997	consensus RNA helicase [RNA processing and modific	99.8
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	99.79
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.79
PRK13766		773	Hef nuclease; Provisional	99.76
PF04408		102	HA2: Helicase associated domain (HA2); InterPro: I	99.76
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.76
PRK09694		878	helicase Cas3; Provisional	99.75
PHA02558		501	uvsW UvsW helicase; Provisional	99.73
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	99.73
COG1205		851	Distinct helicase family with a unique C-terminal	99.73
KOG0950		1008	consensus DNA polymerase theta/eta, DEAD-box super	99.71
KOG0354		746	consensus DEAD-box like helicase [General function	99.71
smart00847		92	HA2 Helicase associated domain (HA2) Add an annota	99.68
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	99.68
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	99.67
KOG0349		725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.66
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	99.65
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	99.64
PRK09401		1176	reverse gyrase; Reviewed	99.64
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	99.62
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	99.62
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	99.62
TIGR00595		505	priA primosomal protein N'. All proteins in this f	99.61
PRK14701		1638	reverse gyrase; Provisional	99.59
PRK09200		790	preprotein translocase subunit SecA; Reviewed	99.58
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	99.57
KOG0921		1282	consensus Dosage compensation complex, subunit MLE	99.57
PRK05580		679	primosome assembly protein PriA; Validated	99.56
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	99.55
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	99.54
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	99.53
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	99.52
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	99.49
PRK05298		652	excinuclease ABC subunit B; Provisional	99.47
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	99.47
KOG0353		695	consensus ATP-dependent DNA helicase [General func	99.47
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.46
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	99.44
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	99.42
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.41
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	99.39
PRK04914		956	ATP-dependent helicase HepA; Validated	99.27
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.27
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.23
KOG4150		1034	consensus Predicted ATP-dependent RNA helicase [RN	99.23
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	99.1
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.07
PRK12904		830	preprotein translocase subunit SecA; Reviewed	99.06
PRK13107		908	preprotein translocase subunit SecA; Reviewed	99.05
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	99.0
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	98.94
KOG0953		700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.86
COG4096		875	HsdR Type I site-specific restriction-modification	98.7
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	98.64
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	98.62
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	98.59
COG1198		730	PriA Primosomal protein N' (replication factor Y)	98.57
PRK12326		764	preprotein translocase subunit SecA; Reviewed	98.54
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	98.42
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	98.36
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	98.29
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	98.27
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	98.24
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.17
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.1
CHL00122		870	secA preprotein translocase subunit SecA; Validate	98.06
KOG0387		923	consensus Transcription-coupled repair protein CSB	98.03
KOG1123		776	consensus RNA polymerase II transcription initiati	97.93
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	97.88
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.87
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	97.85
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	97.79
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	97.69
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	97.61
PF06862		442	DUF1253: Protein of unknown function (DUF1253); In	97.34
PRK14873		665	primosome assembly protein PriA; Provisional	97.33
smart00487		201	DEXDc DEAD-like helicases superfamily.	97.27
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.26
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	97.2
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	97.16
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	97.05
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	97.01
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	96.86
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	96.83
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	96.81
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	96.61
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	96.06
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	96.04
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	95.5
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	95.32
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	95.14
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	95.04
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	94.46
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	93.15
COG4889		1518	Predicted helicase [General function prediction on	92.27
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	89.47
PRK05580		679	primosome assembly protein PriA; Validated	89.04
PRK14873		665	primosome assembly protein PriA; Provisional	88.76
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	88.42
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	88.39
TIGR00595		505	priA primosomal protein N'. All proteins in this f	87.5
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	87.01
KOG2340		698	consensus Uncharacterized conserved protein [Funct	86.8
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	86.76
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	86.5
KOG0347		731	consensus RNA helicase [RNA processing and modific	85.07
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	84.21
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	84.16
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	83.82
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	83.73
PRK04914		956	ATP-dependent helicase HepA; Validated	83.22
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	80.88
PF13871		278	Helicase_C_4: Helicase_C-like	80.52
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	80.29

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]	Back alignment and domain information

Probab=100.00  E-value=2.5e-133  Score=1046.35  Aligned_cols=531  Identities=54%  Similarity=0.946  Sum_probs=507.7

Q ss_pred             ccccCCCeEEEchHHHHHHHhcCCCCCCccEEEEecCCCCCcchHHHHHHHHHHHhhCCCccEEEEccCCCHHHHHhhhC
Q 008209            4 CFCVLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFY   83 (574)
Q Consensus         4 ~~~~~~~I~~~T~g~Ll~~l~~~~~L~~~~~vIiDE~HeR~~~~d~ll~~lk~~~~~~~~~klvlmSATl~~~~~~~~f~   83 (574)
                      +.|..|.|+|||||+|||+++.||.|++|++|||||||||++++|+++++||+++++|+++|+|+||||+|+++|++||.
T Consensus       136 ~ts~~TrikymTDG~LLRE~l~Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R~~LklIimSATlda~kfS~yF~  215 (674)
T KOG0922|consen  136 STSKDTRIKYMTDGMLLREILKDPLLSKYSVIILDEAHERSLHTDILLGLLKKILKKRPDLKLIIMSATLDAEKFSEYFN  215 (674)
T ss_pred             cCCCceeEEEecchHHHHHHhcCCccccccEEEEechhhhhhHHHHHHHHHHHHHhcCCCceEEEEeeeecHHHHHHHhc
Confidence            44556999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEeCCeeeceeEEeecCCchhHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHHHHhhcCCCCCCeEEE
Q 008209           84 GAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVV  163 (574)
Q Consensus        84 ~~~~i~~~gr~~~v~~~y~~~~~~~~~~~~~~~~~~i~~~~~~g~iLVFl~~~~ei~~~~~~L~~~~~~~~~~~~~~~v~  163 (574)
                      +||++.++||.|||+++|.+.+..||+++++.++++||.++++|+|||||+|++||+.+++.|.+....+....+. .++
T Consensus       216 ~a~i~~i~GR~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe~~~~~l~e~~~~~~~~~~~-~~l  294 (674)
T KOG0922|consen  216 NAPILTIPGRTFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIEAACELLRERAKSLPEDCPE-LIL  294 (674)
T ss_pred             CCceEeecCCCCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHHHHHHHHHHHhhhccccCcc-eee
Confidence            9999999999999999999999999999999999999999999999999999999999999999987776554444 789


Q ss_pred             EcCCCCCHHHHhhhcCCCCCCCCCCCCCCcEEEEecccccccccCCCeEEEEcCCcccceeecCCCCcceeeeeeccHhh
Q 008209          164 PLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKAS  243 (574)
Q Consensus       164 ~lhs~l~~~~q~~v~~~~~~g~~~~~~~~~kvivaT~iae~gitip~v~~VID~g~~k~~~y~~~~~~~~l~~~~is~~~  243 (574)
                      |+||+||.++|.+||++.+.|.       ||||+||||||||||||||+||||+|++|++.|||.+|++.|...|||+++
T Consensus       295 ply~aL~~e~Q~rvF~p~p~g~-------RKvIlsTNIAETSlTI~GI~YVVDsG~vK~~~y~p~~g~~~L~v~~ISkas  367 (674)
T KOG0922|consen  295 PLYGALPSEEQSRVFDPAPPGK-------RKVILSTNIAETSLTIDGIRYVVDSGFVKQKKYNPRTGLDSLIVVPISKAS  367 (674)
T ss_pred             eecccCCHHHhhccccCCCCCc-------ceEEEEcceeeeeEEecceEEEEcCCceEEEeeccccCccceeEEechHHH
Confidence            9999999999999999999999       999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcccCCCCCCCeEEeeccccccccccCCCCcchhccCCchhhHHHHhhcCCCCccccCCCCCCcHHHHHHHHHHHHH
Q 008209          244 AHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNY  323 (574)
Q Consensus       244 ~~QR~GRaGR~~~G~~~rl~t~~~~~~~l~~~~~pei~~~~l~~~~L~l~~~~~~~~~~~~~l~~P~~~~l~~al~~L~~  323 (574)
                      +.||+|||||++||+|||||++++| +.|++.+.|||+|++|+..+|+||++|++|+..|+|+|||+++++..|++.|+.
T Consensus       368 A~QRaGRAGRt~pGkcyRLYte~~~-~~~~~~~~PEI~R~~Ls~~vL~Lkalgi~d~l~F~f~d~P~~~~l~~AL~~L~~  446 (674)
T KOG0922|consen  368 ANQRAGRAGRTGPGKCYRLYTESAY-DKMPLQTVPEIQRVNLSSAVLQLKALGINDPLRFPFIDPPPPEALEEALEELYS  446 (674)
T ss_pred             HhhhcccCCCCCCceEEEeeeHHHH-hhcccCCCCceeeechHHHHHHHHhcCCCCcccCCCCCCCChHHHHHHHHHHHh
Confidence            9999999999999999999999999 799999999999999999999999999999999999999999999999999999


Q ss_pred             cCCccCCCCcCh-hhhhhccCCCCHHHHHHHHhccCCCCchhhHhHHhhccCCCcccCChhHHHH-HHHHHHhhCCCCCc
Q 008209          324 LGALDDDGNLTE-MGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREAQKA-ADEAKARFGHIDGD  401 (574)
Q Consensus       324 lgald~~~~lT~-lG~~~~~lpl~p~~~~~ll~~~~~~c~~~~~~i~a~ls~~~~f~~~~~~~~~-~~~~~~~~~~~~sD  401 (574)
                      +||||++|.||. +|+.|+++|++|.++|||+.+..+||.+|+++|+||||++++|.+|.+.+.+ ++..+.+|.+.+||
T Consensus       447 lgald~~g~lt~p~G~~ma~~Pl~p~lsk~ll~s~~~gc~~e~l~i~a~Lsv~~~f~~p~~~~~~~a~~~~~kf~~~eGD  526 (674)
T KOG0922|consen  447 LGALDDRGKLTSPLGRQMAELPLEPHLSKMLLKSSELGCSEEILTIAAMLSVQSVFSRPKDKKAEDADRKRAKFANPEGD  526 (674)
T ss_pred             cCcccCcCCcCchHHhhhhhcCCCcchhhhhhhccccCCcchhhhheeeeeccceecCccchhhhhhhHHHHhhcCcccC
Confidence            999999999998 9999999999999999999999999999999999999999999999988776 89999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCchhHhhhcCCHHHHHHHHHHHHHHHHHHHHcCCcccCCCCCCchhHHHHHHHHHhccccceee
Q 008209          402 HLTLLNVYHAYKQNNEDPSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAH  481 (574)
Q Consensus       402 ~l~~l~~~~~~~~~~~~~~~c~~~~l~~~~l~~~~~ir~qL~~~l~~~~~~~~~~~~~~~~~~~~i~~~l~~g~~~niA~  481 (574)
                      |++++++|+.|.+++..++||++|+||++.|++|.++|+||.+++.+.+++..++.    .+.+.|++||++|||.|+|+
T Consensus       527 h~tlL~vy~~~~~~~~~~~wC~en~i~~r~l~~a~~ir~QL~~i~~~~~~~~~s~~----~d~~~i~k~l~aGff~N~A~  602 (674)
T KOG0922|consen  527 HLTLLNVYESWKENGTSKKWCKENFINARSLKRAKDIRKQLRRILDKFGLPVSSCG----GDMEKIRKCLCAGFFRNVAE  602 (674)
T ss_pred             HHHHHHHHHHHHhcCChhhHHHHhcccHHHHHHHHHHHHHHHHHHHHcCCCccCCC----CCHHHHHHHHHHHHHHHHHH
Confidence            99999999999998889999999999999999999999999999999988875432    33578999999999999999


Q ss_pred             ec-CCCcEEEeecCeEEEEcCCCCCC-CCCcEEEEEEecccchhhcccccccCHHHHHhHcCccccccc
Q 008209          482 LE-RTGQYLTVKDNQVVHLHPSNCLD-HKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSN  548 (574)
Q Consensus       482 ~~-~~~~y~~~~~~~~~~ihpsS~l~-~~~~~ivy~e~~~t~k~~i~~vt~I~~~wl~~~~~~~~~~~~  548 (574)
                      +. .+| |+++.+|+.++|||||+++ .+|+||||+|++.|+|.|||+||+|+++||.+++|++++...
T Consensus       603 ~~~~~~-Yrti~~~~~v~IHPSS~l~~~~p~~viy~el~~Ttk~Y~r~Vt~i~~~wL~e~ap~~~~~~~  670 (674)
T KOG0922|consen  603 RDYQDG-YRTIRGGQPVYIHPSSVLFRRKPEWVIYHELLQTTKEYMRNVTAIDPEWLLELAPHFFKQSD  670 (674)
T ss_pred             hhcCCC-eEEccCCcEEEEechHHhhcCCCCEEEEEEEeecchHhHhheeecCHHHHHHhCchHhhccc
Confidence            98 446 9999999999999999998 568999999999999999999999999999999999976543

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0923 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional	Back alignment and domain information

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA	Back alignment and domain information

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]	Back alignment and domain information

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB	Back alignment and domain information

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional	Back alignment and domain information

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]	Back alignment and domain information

>PHA02653 RNA helicase NPH-II; Provisional	Back alignment and domain information

>PRK01172 ski2-like helicase; Provisional	Back alignment and domain information

>PRK02362 ski2-like helicase; Provisional	Back alignment and domain information

>PRK00254 ski2-like helicase; Provisional	Back alignment and domain information

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional	Back alignment and domain information

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]	Back alignment and domain information

>PTZ00110 helicase; Provisional	Back alignment and domain information

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional	Back alignment and domain information

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional	Back alignment and domain information

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional	Back alignment and domain information

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase	Back alignment and domain information

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]	Back alignment and domain information

>COG1204 Superfamily II helicase [General function prediction only]	Back alignment and domain information

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family	Back alignment and domain information

>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional	Back alignment and domain information

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]	Back alignment and domain information

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional	Back alignment and domain information

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK09751 putative ATP-dependent helicase Lhr; Provisional	Back alignment and domain information

>KOG0343 consensus RNA Helicase [RNA processing and modification]	Back alignment and domain information

>PRK13767 ATP-dependent helicase; Provisional	Back alignment and domain information

>TIGR01389 recQ ATP-dependent DNA helicase RecQ	Back alignment and domain information

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype	Back alignment and domain information

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>TIGR00580 mfd transcription-repair coupling factor (mfd)	Back alignment and domain information

>PRK10689 transcription-repair coupling factor; Provisional	Back alignment and domain information

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]	Back alignment and domain information

>TIGR01587 cas3_core CRISPR-associated helicase Cas3	Back alignment and domain information

>PRK10917 ATP-dependent DNA helicase RecG; Provisional	Back alignment and domain information

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type	Back alignment and domain information

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>COG1201 Lhr Lhr-like helicases [General function prediction only]	Back alignment and domain information

>TIGR00643 recG ATP-dependent DNA helicase RecG	Back alignment and domain information

>KOG0347 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0346 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG4284 consensus DEAD box protein [Transcription]	Back alignment and domain information

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF07717 OB_NTP_bind: Oligonucleotide/oligosaccharide-binding (OB)-fold; InterPro: IPR011709 This domain is found towards the C terminus of the DEAD-box helicases (IPR011545 from INTERPRO)	Back alignment and domain information

>KOG0334 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length	Back alignment and domain information

>KOG0947 consensus Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

>PHA02558 uvsW UvsW helicase; Provisional	Back alignment and domain information

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]	Back alignment and domain information

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>KOG0354 consensus DEAD-box like helicase [General function prediction only]	Back alignment and domain information

>smart00847 HA2 Helicase associated domain (HA2) Add an annotation	Back alignment and domain information

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]	Back alignment and domain information

>PRK12898 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]	Back alignment and domain information

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]	Back alignment and domain information

>TIGR00595 priA primosomal protein N'	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>PRK09200 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]	Back alignment and domain information

>PRK05580 primosome assembly protein PriA; Validated	Back alignment and domain information

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

>TIGR03714 secA2 accessory Sec system translocase SecA2	Back alignment and domain information

>TIGR00963 secA preprotein translocase, SecA subunit	Back alignment and domain information

>TIGR00631 uvrb excinuclease ABC, B subunit	Back alignment and domain information

>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Back alignment and domain information

>PRK05298 excinuclease ABC subunit B; Provisional	Back alignment and domain information

>PRK12906 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]	Back alignment and domain information

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional	Back alignment and domain information

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]	Back alignment and domain information

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins	Back alignment and domain information

>PRK12900 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	Back alignment and domain information

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>smart00490 HELICc helicase superfamily c-terminal domain	Back alignment and domain information

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK13104 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3	Back alignment and domain information

>PRK12904 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK13107 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional	Back alignment and domain information

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]	Back alignment and domain information

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	Back alignment and domain information

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12903 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK12326 preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family	Back alignment and domain information

>PRK12899 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PRK12901 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]	Back alignment and domain information

>PRK13103 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases	Back alignment and domain information

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>CHL00122 secA preprotein translocase subunit SecA; Validated	Back alignment and domain information

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]	Back alignment and domain information

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain	Back alignment and domain information

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]	Back alignment and domain information

>cd00268 DEADc DEAD-box helicases	Back alignment and domain information

>PRK12902 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]	Back alignment and domain information

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]	Back alignment and domain information

>PRK14873 primosome assembly protein PriA; Provisional	Back alignment and domain information

>smart00487 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	Back alignment and domain information

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]	Back alignment and domain information

>cd00046 DEXDc DEAD-like helicases superfamily	Back alignment and domain information

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]	Back alignment and domain information

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional	Back alignment and domain information

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]	Back alignment and domain information

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein	Back alignment and domain information

>TIGR00604 rad3 DNA repair helicase (rad3)	Back alignment and domain information

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]	Back alignment and domain information

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]	Back alignment and domain information

>PF13307 Helicase_C_2: Helicase C-terminal domain; PDB: 4A15_A 2VSF_A 3CRV_A 3CRW_1 2VL7_A	Back alignment and domain information

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]	Back alignment and domain information

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3	Back alignment and domain information

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4	Back alignment and domain information

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]	Back alignment and domain information

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>COG4889 Predicted helicase [General function prediction only]	Back alignment and domain information

>TIGR00596 rad1 DNA repair protein (rad1)	Back alignment and domain information

>PRK05580 primosome assembly protein PriA; Validated	Back alignment and domain information

>PRK14873 primosome assembly protein PriA; Provisional	Back alignment and domain information

>PRK10917 ATP-dependent DNA helicase RecG; Provisional	Back alignment and domain information

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]	Back alignment and domain information

>TIGR00595 priA primosomal protein N'	Back alignment and domain information

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1	Back alignment and domain information

>TIGR00596 rad1 DNA repair protein (rad1)	Back alignment and domain information

>KOG0347 consensus RNA helicase [RNA processing and modification]	Back alignment and domain information

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>TIGR00580 mfd transcription-repair coupling factor (mfd)	Back alignment and domain information

>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	Back alignment and domain information

>PRK13104 secA preprotein translocase subunit SecA; Reviewed	Back alignment and domain information

>PF13871 Helicase_C_4: Helicase_C-like	Back alignment and domain information

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin	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
Query		574
3kx2_B		767	Crystal Structure Of Prp43p In Complex With Adp Len		0.0
2xau_A		773	Crystal Structure Of The Prp43p Deah-Box Rna Helica		0.0
3i4u_A		270	Crystal Structure Analysis Of A Helicase Associated		2e-56
3llm_A		235	Crystal Structure Analysis Of A Rna Helicase Length		2e-07

>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp Length = 767

Back alignment and structure

Iteration: 1

Score = 727 bits (1877), Expect = 0.0, Method: Compositional matrix adjust. Identities = 357/550 (64%), Positives = 437/550 (79%), Gaps = 19/550 (3%) Query: 12 RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71 +Y+TDGMLLREAM D L RY I+LDEAHERTLATD+L GLLK+V+K RPDLK+++MSA Sbjct: 189 KYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSA 248 Query: 72 TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131 TL+AEKFQ YF APL+ VPGR +PVE++YT E +RDYL++AIRTV+QIH E +GDIL+ Sbjct: 249 TLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILL 308 Query: 132 FLTGEEEIEDACRKITKEITNMGDQV------GPVKVVPLYSTLPPAMQQKIFEXXXXXX 185 FLTGE+EIEDA RKI+ E GDQ+ GP+ V PLY +LPP QQ+IFE Sbjct: 309 FLTGEDEIEDAVRKISLE----GDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESH 364 Query: 186 XXXXXXXRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAH 245 RK+V+STNIAETSLTIDGIVYV+DPGF+KQKVYNPR+RVESLLVSPISKASA Sbjct: 365 NGRPG--RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQ 422 Query: 246 QRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDF 305 QR+GRAGRT+PGKCFRLYTE++F +L Q+YPEILRSNL++TVL LKKLGIDDLVHFDF Sbjct: 423 QRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDF 482 Query: 306 MDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEI 365 MDPPAPET+MRALE LNYL LDD+GNLT +G S+FPLDP ++ ML+ S ++ CS EI Sbjct: 483 MDPPAPETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEI 542 Query: 366 LSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDP----SW 421 L+I AMLSVPN F+RP + +K AD+AK F H DGDH+TLLNVYHA+K + W Sbjct: 543 LTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKW 602 Query: 422 CYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAH 481 C D+++N+R+L +ADN+R QL R+M R+NL+L + D+ S Y+ NIRKA+ +G+FMQVA Sbjct: 603 CRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAK 662 Query: 482 LERTGQ--YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDI 539 +R+G Y+TVKDNQ V +HPS L H EWVIYNE+VLTS+N+IRTVT VR EWLI+I Sbjct: 663 -KRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEI 721 Query: 540 APHYYDLSNF 549 AP YYDLSNF Sbjct: 722 APAYYDLSNF 731

PyMOL of 3kx2

>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In Complex With Adp Length = 773

Back alignment and structure

>pdb|3I4U|A Chain A, Crystal Structure Analysis Of A Helicase Associated Domain Length = 270

Back alignment and structure

>pdb|3LLM|A Chain A, Crystal Structure Analysis Of A Rna Helicase Length = 235

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
Query		574
2xau_A		773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	0.0
3i4u_A		270	ATP-dependent RNA helicase DHX8; splicing, ATP-bin	1e-151
2v6i_A		431	RNA helicase; membrane, hydrolase, transmembrane,	8e-85
2z83_A		459	Helicase/nucleoside triphosphatase; hydrolase, mem	1e-81
2jlq_A		451	Serine protease subunit NS3; ribonucleoprotein, nu	2e-78
2wv9_A		673	Flavivirin protease NS2B regulatory subunit, FLAV	3e-77
2whx_A		618	Serine protease/ntpase/helicase NS3; transcription	2e-73
1yks_A		440	Genome polyprotein [contains: flavivirin protease	3e-68
3o8b_A		666	HCV NS3 protease/helicase; ntpase, RNA, translocat	2e-65
3llm_A		235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	2e-37
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-06

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B* Length = 773	Back alignment and structure

 Score = 1019 bits (2637), Expect = 0.0
 Identities = 364/570 (63%), Positives = 450/570 (78%), Gaps = 9/570 (1%)

Query: 12  RYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSA 71
           +Y+TDGMLLREAM D  L RY  I+LDEAHERTLATD+L GLLK+V+K RPDLK+++MSA
Sbjct: 189 KYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSA 248

Query: 72  TLEAEKFQGYFYGAPLMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILV 131
           TL+AEKFQ YF  APL+ VPGR +PVE++YT E +RDYL++AIRTV+QIH  E +GDIL+
Sbjct: 249 TLDAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILL 308

Query: 132 FLTGEEEIEDACRKITKEITNMGDQ--VGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGG 189
           FLTGE+EIEDA RKI+ E   +  +   GP+ V PLY +LPP  QQ+IFEPAP      G
Sbjct: 309 FLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPES--HNG 366

Query: 190 PPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPISKASAHQRSG 249
            PGRK+V+STNIAETSLTIDGIVYV+DPGF+KQKVYNPR+RVESLLVSPISKASA QR+G
Sbjct: 367 RPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAG 426

Query: 250 RAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPP 309
           RAGRT+PGKCFRLYTE++F  +L  Q+YPEILRSNL++TVL LKKLGIDDLVHFDFMDPP
Sbjct: 427 RAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPP 486

Query: 310 APETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSIS 369
           APET+MRALE LNYL  LDD+GNLT +G   S+FPLDP ++ ML+ S ++ CS EIL+I 
Sbjct: 487 APETMMRALEELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIV 546

Query: 370 AMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNED----PSWCYDN 425
           AMLSVPN F+RP + +K AD+AK  F H DGDH+TLLNVYHA+K +         WC D+
Sbjct: 547 AMLSVPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKWCRDH 606

Query: 426 FVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGYFMQVAHLERT 485
           ++N+R+L +ADN+R QL R+M R+NL+L + D+ S  Y+ NIRKA+ +G+FMQVA     
Sbjct: 607 YLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGFFMQVAKKRSG 666

Query: 486 GQ-YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYY 544
            + Y+TVKDNQ V +HPS  L H  EWVIYNE+VLTS+N+IRTVT VR EWLI+IAP YY
Sbjct: 667 AKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEIAPAYY 726

Query: 545 DLSNFPQCEAKRVLERLYRKREKERENNRK 574
           DLSNF + + K  LER+  K ++  E  + 
Sbjct: 727 DLSNFQKGDVKLSLERIKEKVDRLNELKQG 756

PyMOL of 2xau

>3i4u_A ATP-dependent RNA helicase DHX8; splicing, ATP-binding, hydrolase, mRNA processing, splicing, nucleotide-binding, nucleus, phosphoprotein, SPLI; 2.10A {Homo sapiens} Length = 270	Back alignment and structure

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431	Back alignment and structure

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459	Back alignment and structure

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451	Back alignment and structure

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673	Back alignment and structure

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A Length = 618	Back alignment and structure

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440	Back alignment and structure

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666	Back alignment and structure

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens} Length = 235	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
Query		574
2xau_A		773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
3i4u_A		270	ATP-dependent RNA helicase DHX8; splicing, ATP-bin	100.0
2p6r_A		702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
2va8_A		715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
2zj8_A		720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.97
2z83_A		459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.96
2jlq_A		451	Serine protease subunit NS3; ribonucleoprotein, nu	99.96
3eiq_A		414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.95
3l9o_A		1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.95
4a4z_A		997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.95
2whx_A		618	Serine protease/ntpase/helicase NS3; transcription	99.95
2db3_A		434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.95
3o8b_A		666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.95
3pey_A		395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.95
3fht_A		412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.95
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.95
2i4i_A		417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.94
1s2m_A		400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.94
2v1x_A		591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.94
1yks_A		440	Genome polyprotein [contains: flavivirin protease	99.94
2j0s_A		410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.94
2v6i_A		431	RNA helicase; membrane, hydrolase, transmembrane,	99.94
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.94
3rc3_A		677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.94
3i5x_A		563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.94
3fmp_B		479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.93
2xgj_A		1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.93
1oyw_A		523	RECQ helicase, ATP-dependent DNA helicase; winged	99.93
3eaq_A		212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.93
2wv9_A		673	Flavivirin protease NS2B regulatory subunit, FLAV	99.93
3sqw_A		579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.93
2ykg_A		696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.93
1fuu_A		394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.93
3i32_A		300	Heat resistant RNA dependent ATPase; RNA helicase,	99.92
3fho_A		508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.92
2z0m_A		337	337AA long hypothetical ATP-dependent RNA helicase	99.92
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.91
4a2p_A		556	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
3tbk_A		555	RIG-I helicase domain; DECH helicase, ATP binding,	99.9
3oiy_A		414	Reverse gyrase helicase domain; topoisomerase, DNA	99.9
4gl2_A		699	Interferon-induced helicase C domain-containing P;	99.88
4a2q_A		797	RIG-I, retinoic acid inducible protein I; hydrolas	99.88
1gm5_A		780	RECG; helicase, replication restart; HET: DNA ADP;	99.87
4a2w_A		936	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
2eyq_A		1151	TRCF, transcription-repair coupling factor; MFD, S	99.86
4ddu_A		1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.83
1gku_B		1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.82
1tf5_A		844	Preprotein translocase SECA subunit; ATPase, helic	99.81
2rb4_A		175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.8
2hjv_A		163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.8
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.8
1fuk_A		165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.79
2d7d_A		661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.79
2oca_A		510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.78
1t5i_A		172	C_terminal domain of A probable ATP-dependent RNA	99.78
1c4o_A		664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.77
2p6n_A		191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.77
2jgn_A		185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.77
3h1t_A		590	Type I site-specific restriction-modification syst	99.77
2fsf_A		853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.76
1nkt_A		922	Preprotein translocase SECA 1 subunit; preprotein	99.73
2yjt_D		170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.56
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.65
3jux_A		822	Protein translocase subunit SECA; protein transloc	99.61
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.58
2w00_A		1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.53
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	99.51
3llm_A		235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.47
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.43
1z5z_A		271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.25
1qde_A		224	EIF4A, translation initiation factor 4A; DEAD box	98.53
3iuy_A		228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	98.52
3ber_A		249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	98.49
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.47
3ly5_A		262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	98.45
3fe2_A		242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	98.45
2pl3_A		236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	98.44
3dkp_A		245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	98.42
1q0u_A		219	Bstdead; DEAD protein, RNA binding protein; 1.85A	98.39
2gxq_A		207	Heat resistant RNA dependent ATPase; RNA helicase,	98.39
1vec_A		206	ATP-dependent RNA helicase P54; DEAD-box protein,	98.38
3bor_A		237	Human initiation factor 4A-II; translation initiat	98.38
2oxc_A		230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	98.35
3fmo_B		300	ATP-dependent RNA helicase DDX19B; nuclear porin,	98.34
1t6n_A		220	Probable ATP-dependent RNA helicase; RECA-like fol	98.32
1wrb_A		253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	98.15
3b6e_A		216	Interferon-induced helicase C domain-containing P;	98.07
2ipc_A		997	Preprotein translocase SECA subunit; nucleotide bi	97.87
1rif_A		282	DAR protein, DNA helicase UVSW; bacteriophage, REC	97.25
2fz4_A		237	DNA repair protein RAD25; RECA-like domain, DNA da	96.67
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	96.18
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	96.07
3hgt_A		328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	92.46
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	82.64
2ipc_A		997	Preprotein translocase SECA subunit; nucleotide bi	81.89
3im1_A		328	Protein SNU246, PRE-mRNA-splicing helicase BRR2; A	81.54

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*	Back alignment and structure

Probab=100.00  E-value=1.9e-101  Score=877.13  Aligned_cols=557  Identities=65%  Similarity=1.055  Sum_probs=516.8

Q ss_pred             cCCCeEEEchHHHHHHHhcCCCCCCccEEEEecCCCCCcchHHHHHHHHHHHhhCCCccEEEEccCCCHHHHHhhhCCCC
Q 008209            7 VLLGGRYLTDGMLLREAMTDPLLERYKVIVLDEAHERTLATDVLFGLLKEVLKNRPDLKLVVMSATLEAEKFQGYFYGAP   86 (574)
Q Consensus         7 ~~~~I~~~T~g~Ll~~l~~~~~L~~~~~vIiDE~HeR~~~~d~ll~~lk~~~~~~~~~klvlmSATl~~~~~~~~f~~~~   86 (574)
                      ..++|+|+|+|+|++.+..++.+.++++|||||+|+|+++.|.++++++.+...+++.|+|+||||++.+.+++||++++
T Consensus       184 ~~~~I~v~T~G~l~r~l~~~~~l~~~~~lIlDEah~R~ld~d~~~~~l~~l~~~~~~~~iIl~SAT~~~~~l~~~~~~~~  263 (773)
T 2xau_A          184 NKTILKYMTDGMLLREAMEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDAEKFQRYFNDAP  263 (773)
T ss_dssp             TTCSEEEEEHHHHHHHHHHSTTCTTEEEEEECSGGGCCHHHHHHHHHHHHHHHHCTTCEEEEEESCSCCHHHHHHTTSCC
T ss_pred             CCCCEEEECHHHHHHHHhhCccccCCCEEEecCccccccchHHHHHHHHHHHHhCCCceEEEEeccccHHHHHHHhcCCC
Confidence            45889999999999999999999999999999999999999999999999998889999999999999999999999999


Q ss_pred             eEEeCCeeeceeEEeecCCchhHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHHHHHHHHHHHhhc--CCCCCCeEEEE
Q 008209           87 LMKVPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKEITNM--GDQVGPVKVVP  164 (574)
Q Consensus        87 ~i~~~gr~~~v~~~y~~~~~~~~~~~~~~~~~~i~~~~~~g~iLVFl~~~~ei~~~~~~L~~~~~~~--~~~~~~~~v~~  164 (574)
                      ++.++|+.+||+++|.+.+..++....+..+.+++...++|++||||||+++|+.+++.|.+.+..+  .....++.+.+
T Consensus       264 vi~v~gr~~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~  343 (773)
T 2xau_A          264 LLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYP  343 (773)
T ss_dssp             EEECCCCCCCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_pred             cccccCcccceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEE
Confidence            9999999999999999998889998888899998887789999999999999999999998643322  11235788999


Q ss_pred             cCCCCCHHHHhhhcCCCC-----CCCCCCCCCCcEEEEecccccccccCCCeEEEEcCCcccceeecCCCCcceeeeeec
Q 008209          165 LYSTLPPAMQQKIFEPAP-----PPSKEGGPPGRKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRVRVESLLVSPI  239 (574)
Q Consensus       165 lhs~l~~~~q~~v~~~~~-----~g~~~~~~~~~kvivaT~iae~gitip~v~~VID~g~~k~~~y~~~~~~~~l~~~~i  239 (574)
                      +||+|++++|.++++.++     +|.       ++||||||+||+|||||+|++|||+|+.|++.||+.+|++.|.+.|+
T Consensus       344 lhg~l~~~eR~~v~~~f~~~~~~~g~-------~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~  416 (773)
T 2xau_A          344 LYGSLPPHQQQRIFEPAPESHNGRPG-------RKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPI  416 (773)
T ss_dssp             ECTTCCHHHHGGGGSCCCCCSSSSCC-------EEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEEC
T ss_pred             eCCCCCHHHHHHHHhhcccccCCCCc-------eEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccC
Confidence            999999999999999998     777       99999999999999999999999999999999999999999999999


Q ss_pred             cHhhHHHhcccCCCCCCCeEEeeccccccccccCCCCcchhccCCchhhHHHHhhcCCCCccccCCCCCCcHHHHHHHHH
Q 008209          240 SKASAHQRSGRAGRTQPGKCFRLYTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALE  319 (574)
Q Consensus       240 s~~~~~QR~GRaGR~~~G~~~rl~t~~~~~~~l~~~~~pei~~~~l~~~~L~l~~~~~~~~~~~~~l~~P~~~~l~~al~  319 (574)
                      |+++|.||+|||||.++|.||+||++.++...+.++..|||++.+|.+++|+++.+|+.++..|+|++||+.+++..|++
T Consensus       417 S~~s~~QR~GRaGR~~~G~~~~l~~~~~~~~~l~~~~~pEi~r~~L~~~~L~l~~~gi~~~~~f~~~~~p~~~~i~~a~~  496 (773)
T 2xau_A          417 SKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALE  496 (773)
T ss_dssp             CHHHHHHHHHGGGSSSSEEEEESSCHHHHHHTSCSSCCCGGGGSCCHHHHHHHHHTTCCCGGGCCCSSCCCHHHHHHHHH
T ss_pred             CHHHHHhhccccCCCCCCEEEEEecHHHhcccccccCCCccccCcHHHHHHHHHHcCCCChhhccccCCCcHHHHHHHHH
Confidence            99999999999999999999999999999667999999999999999999999999999999999999999999999999


Q ss_pred             HHHHcCCccCCCCcChhhhhhccCCCCHHHHHHHHhccCCCCchhhHhHHhhccCCCcccCChhHHHHHHHHHHhhCCCC
Q 008209          320 VLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREAQKAADEAKARFGHID  399 (574)
Q Consensus       320 ~L~~lgald~~~~lT~lG~~~~~lpl~p~~~~~ll~~~~~~c~~~~~~i~a~ls~~~~f~~~~~~~~~~~~~~~~~~~~~  399 (574)
                      .|..+||||++|++|++|+.|+.||++|++|+||+.|..++|++++++|+|+|+++++|+.|.+.+++++.++..|.+..
T Consensus       497 ~L~~lgald~~~~lT~lG~~~a~~pl~p~~~~~l~~~~~~~c~~~~l~i~a~ls~~~~f~~~~~~~~~~~~~~~~f~~~~  576 (773)
T 2xau_A          497 ELNYLACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVPNVFIRPTKDKKRADDAKNIFAHPD  576 (773)
T ss_dssp             HHHHTTSBCTTSCBCHHHHHHTTSSSCHHHHHHHHHGGGGTCHHHHHHHHHHHTSCCCBCCCTTCHHHHHHHHHTTCCTT
T ss_pred             HHHHcCCcccCCCcChhhhhhccccCCHHHHHHHHhhcccCchhHHHHHHHhcccCCcccCChHHHHHHHHHHHhccCCC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcHHHHHHHHHHHHhCC---CC-chhHhhhcCCHHHHHHHHHHHHHHHHHHHHcCCcccCCCCCCchhHHHHHHHHHhcc
Q 008209          400 GDHLTLLNVYHAYKQNN---ED-PSWCYDNFVNHRALKSADNVRQQLVRIMARFNLKLCSNDFNSRDYYVNIRKAMLAGY  475 (574)
Q Consensus       400 sD~l~~l~~~~~~~~~~---~~-~~~c~~~~l~~~~l~~~~~ir~qL~~~l~~~~~~~~~~~~~~~~~~~~i~~~l~~g~  475 (574)
                      |||++++++|++|....   .. ..||++||||+++|+++.++++||.+++++.+++..+...+...++..|++||++||
T Consensus       577 ~D~~~~l~~~~~~~~~~~~~~~~~~~c~~~~l~~~~l~~~~~~~~ql~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~g~  656 (773)
T 2xau_A          577 GDHITLLNVYHAFKSDEAYEYGIHKWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKALASGF  656 (773)
T ss_dssp             BHHHHHHHHHHHHTSHHHHHHCHHHHHHHTTBCHHHHHHHHHHHHHHHHHHHHTTCCCCCCCTTSTTHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHhccccchHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcCCCcCCCCCCchhhHHHHHHHHHHhC
Confidence            99999999999997543   34 689999999999999999999999999999988765543333456688999999999


Q ss_pred             ccceeeecCCCc-EEEeecCeEEEEcCCCCCCCCCcEEEEEEecccchhhcccccccCHHHHHhHcCcccccccCCchhH
Q 008209          476 FMQVAHLERTGQ-YLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTSRNFIRTVTDVRGEWLIDIAPHYYDLSNFPQCEA  554 (574)
Q Consensus       476 ~~niA~~~~~~~-y~~~~~~~~~~ihpsS~l~~~~~~ivy~e~~~t~k~~i~~vt~I~~~wl~~~~~~~~~~~~~~~~~~  554 (574)
                      |+|||++.+.|. |.++.+|+.++|||+|+|...|+||||+|++.|++.||+.||+|+|+||.+++|++|...+++.++.
T Consensus       657 ~~~~a~~~~~~~~y~~~~~~~~~~ihp~s~l~~~~~~~v~~e~~~t~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~  736 (773)
T 2xau_A          657 FMQVAKKRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDV  736 (773)
T ss_dssp             TTSEEEECCC--CEEETTTCCEEEECTTCCCCTTCSEEEEEEEEESSSEEEEEEEECCHHHHHHHCTTTSCGGGCCSSHH
T ss_pred             hHhheeeccCCCcceEeeCCCEEEECCCcccCCCCCEEEEEEeeccchhheeecccCCHHHHHHHHHHheeeccCCchhH
Confidence            999999998775 9989999999999999998679999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhh
Q 008209          555 KRVLERLYRKREKERE  570 (574)
Q Consensus       555 ~~~~~~~~~~~~~~~~  570 (574)
                      |+.++.+.++...+.+
T Consensus       737 ~~~~~~~~~~~~~~~~  752 (773)
T 2xau_A          737 KLSLERIKEKVDRLNE  752 (773)
T ss_dssp             HHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHHhhhhhh
Confidence            9999988888765543

PyMOL of 2xau

>3i4u_A ATP-dependent RNA helicase DHX8; splicing, ATP-binding, hydrolase, mRNA processing, splicing, nucleotide-binding, nucleus, phosphoprotein, SPLI; 2.10A {Homo sapiens}	Back alignment and structure

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A	Back alignment and structure

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}	Back alignment and structure

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*	Back alignment and structure

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B	Back alignment and structure

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B	Back alignment and structure

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A	Back alignment and structure

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A	Back alignment and structure

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}	Back alignment and structure

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}	Back alignment and structure

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A	Back alignment and structure

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A	Back alignment and structure

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}	Back alignment and structure

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...	Back alignment and structure

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*	Back alignment and structure

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B	Back alignment and structure

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}	Back alignment and structure

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A	Back alignment and structure

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*	Back alignment and structure

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*	Back alignment and structure

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A	Back alignment and structure

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A	Back alignment and structure

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A	Back alignment and structure

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A	Back alignment and structure

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A	Back alignment and structure

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}	Back alignment and structure

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}	Back alignment and structure

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*	Back alignment and structure

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A	Back alignment and structure

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}	Back alignment and structure

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}	Back alignment and structure

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*	Back alignment and structure

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*	Back alignment and structure

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}	Back alignment and structure

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}	Back alignment and structure

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*	Back alignment and structure

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}	Back alignment and structure

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*	Back alignment and structure

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}	Back alignment and structure

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}	Back alignment and structure

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19	Back alignment and structure

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}	Back alignment and structure

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1	Back alignment and structure

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A	Back alignment and structure

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*	Back alignment and structure

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A	Back alignment and structure

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}	Back alignment and structure

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}	Back alignment and structure

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*	Back alignment and structure

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19	Back alignment and structure

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*	Back alignment and structure

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}	Back alignment and structure

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*	Back alignment and structure

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}	Back alignment and structure

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}	Back alignment and structure

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}	Back alignment and structure

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*	Back alignment and structure

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A	Back alignment and structure

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}	Back alignment and structure

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}	Back alignment and structure

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*	Back alignment and structure

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A	Back alignment and structure

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*	Back alignment and structure

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}	Back alignment and structure

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}	Back alignment and structure

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19	Back alignment and structure

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A	Back alignment and structure

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}	Back alignment and structure

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}	Back alignment and structure

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}	Back alignment and structure

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A	Back alignment and structure

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}	Back alignment and structure

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}	Back alignment and structure

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19	Back alignment and structure

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A	Back alignment and structure

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*	Back alignment and structure

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*	Back alignment and structure

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}	Back alignment and structure

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19	Back alignment and structure

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19	Back alignment and structure

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}	Back alignment and structure

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}	Back alignment and structure

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23	Back alignment and structure

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19	Back alignment and structure

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*	Back alignment and structure

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A	Back alignment and structure

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*	Back alignment and structure

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}	Back alignment and structure

>3im1_A Protein SNU246, PRE-mRNA-splicing helicase BRR2; ATPase, RNA helicase, rnpase, RNA unwindase, molecular model mRNA splicing; 1.65A {Saccharomyces cerevisiae} PDB: 3im2_A* 3hib_A	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		574
d1yksa2		299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	6e-63
d2bmfa2		305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-31
d1a1va1		136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	5e-12
d1yksa1		140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	7e-06

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299	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: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score =  207 bits (527), Expect = 6e-63
 Identities = 47/350 (13%), Positives = 85/350 (24%), Gaps = 63/350 (18%)

Query: 90  VPGRLHPVEIFYTQEPERDYLEAAIRTVVQIHMCEPSGDILVFLTGEEEIEDACRKITKE 149
            P     +E   T  P   +            +         FL            + K 
Sbjct: 6   FPHSNGEIEDVQTDIPSEPWNTGHDW------ILADKRPTAWFLPSIRAANVMAASLRKA 59

Query: 150 ITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAETSLTID 209
                       VV L           I +                +++T+IAE    + 
Sbjct: 60  GK---------SVVVLNRKTFEREYPTIKQK-----------KPDFILATDIAEMGANLC 99

Query: 210 GIVYVIDPGFA-KQKVYNPRVRVESLLVSPISKASAHQRSGRAGRTQPGKCFRLYTEKSF 268
            +  V+D   A K  + +   +V       IS +SA QR GR GR  P +    Y    +
Sbjct: 100 -VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRN-PNRDGDSYY---Y 154

Query: 269 NNDLQPQTYPEILRSN----LANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYL 324
           +          +        L N  +    +     V          E  +R  +   + 
Sbjct: 155 SEPTSENNAHHVCWLEASMLLDNMEVRGGMVAPLYGVEGTKTPVSPGEMRLRDDQRKVFR 214

Query: 325 GALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYNCSNEILSISAMLSVPNCFVRPREA 384
             + +      +  ++++  L     K                         CF  P E 
Sbjct: 215 ELVRNCDLPVWLSWQVAKAGLKTNDRKW------------------------CFEGPEEH 250

Query: 385 QKAADEA-KARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALK 433
           +   D     +     G    L   +    +           F+     +
Sbjct: 251 EILNDSGETVKCRAPGGAKKPLRPRWC--DERVSSDQSALSEFIKFAEGR 298

PyMOL of d1yksa2

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305	Back information, alignment and structure

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136	Back information, alignment and structure

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140	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
Query		574
d1yksa2		299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.97
d2bmfa2		305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.93
d1fuka_		162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.82
d2j0sa2		168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.81
d1s2ma2		171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.81
d1hv8a2		155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.81
d1oywa3		200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.81
d2rb4a1		168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.8
d1t5ia_		168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.8
d1c4oa2		174	Nucleotide excision repair enzyme UvrB {Thermus th	99.79
d1t5la2		181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.78
d1jr6a_		138	HCV helicase domain {Human hepatitis C virus (HCV)	99.74
d2p6ra4		201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.71
d1wp9a2		286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.64
d1a1va2		299	HCV helicase domain {Human hepatitis C virus (HCV)	99.58
d2eyqa5		211	Transcription-repair coupling factor, TRCF {Escher	99.53
d1gm5a4		206	RecG helicase domain {Thermotoga maritima [TaxId:	99.51
d2fwra1		200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.32
d1gkub2		248	Helicase-like "domain" of reverse gyrase {Archaeon	99.24
d1tf5a4		175	Translocation ATPase SecA, nucleotide-binding doma	98.64
d1z3ix1		346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.63
d1hv8a1		208	Putative DEAD box RNA helicase {Archaeon Methanoco	98.57
d1veca_		206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.53
d1z5za1		244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.5
d1s2ma1		206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.49
d2p6ra3		202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	98.47
d2j0sa1		222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.45
d1qdea_		212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.45
d1t6na_		207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.44
d1a1va1		136	HCV helicase domain {Human hepatitis C virus (HCV)	98.43
d1yksa1		140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.42
d2g9na1		218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.4
d1q0ua_		209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.35
d1wrba1		238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.08
d1wp9a1		200	putative ATP-dependent RNA helicase PF2015 {Pyroco	97.81
d1nkta4		219	Translocation ATPase SecA, nucleotide-binding doma	97.73
d1oywa2		206	RecQ helicase domain {Escherichia coli [TaxId: 562	97.71
d1gkub1		237	Helicase-like "domain" of reverse gyrase {Archaeon	97.49
d1gm5a3		264	RecG helicase domain {Thermotoga maritima [TaxId:	96.15
d2fz4a1		206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	95.81
d2eyqa3		233	Transcription-repair coupling factor, TRCF {Escher	95.7
d1rifa_		282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	94.65
d2eyqa3		233	Transcription-repair coupling factor, TRCF {Escher	92.01
d2p6ra1		85	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	91.43
d1z3ix2		298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	90.6
d1gm5a3		264	RecG helicase domain {Thermotoga maritima [TaxId:	89.3
d1hv8a1		208	Putative DEAD box RNA helicase {Archaeon Methanoco	82.69
d2j0sa1		222	Probable ATP-dependent RNA helicase DDX48 {Human (	82.03

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}	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: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.97  E-value=7.6e-34  Score=282.38  Aligned_cols=260  Identities=17%  Similarity=0.075  Sum_probs=191.6

Q ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHHHhhcCCCCCCeEEEEcCCCCCHHHHhhhcCCCCCCCCCCCCCCcEEEEecccccc
Q 008209          125 PSGDILVFLTGEEEIEDACRKITKEITNMGDQVGPVKVVPLYSTLPPAMQQKIFEPAPPPSKEGGPPGRKIVVSTNIAET  204 (574)
Q Consensus       125 ~~g~iLVFl~~~~ei~~~~~~L~~~~~~~~~~~~~~~v~~lhs~l~~~~q~~v~~~~~~g~~~~~~~~~kvivaT~iae~  204 (574)
                      .+|++||||||..+++.+++.|.+         .+..|+++||.++.+++.++    +++.       ++|||||||+|+
T Consensus        35 ~~g~~~~F~~s~~~~~~~a~~L~~---------~g~~V~~l~~~~~~~e~~~~----~~~~-------~~~~~~t~~~~~   94 (299)
T d1yksa2          35 DKRPTAWFLPSIRAANVMAASLRK---------AGKSVVVLNRKTFEREYPTI----KQKK-------PDFILATDIAEM   94 (299)
T ss_dssp             CCSCEEEECSCHHHHHHHHHHHHH---------TTCCEEECCSSSCC------------CC-------CSEEEESSSTTC
T ss_pred             cCCCEEEEeCCHHHHHHHHHHHHh---------cCCeEEEEcCcCcHhHHhhh----hcCC-------cCEEEEechhhh
Confidence            489999999999999999999987         35679999999998887764    3455       899999999999


Q ss_pred             cccCCCeEEEEcCCcc-cceeecCCCCcceeeeeeccHhhHHHhcccCCCCCCC-eEEeecccccccccc--CCCCcchh
Q 008209          205 SLTIDGIVYVIDPGFA-KQKVYNPRVRVESLLVSPISKASAHQRSGRAGRTQPG-KCFRLYTEKSFNNDL--QPQTYPEI  280 (574)
Q Consensus       205 gitip~v~~VID~g~~-k~~~y~~~~~~~~l~~~~is~~~~~QR~GRaGR~~~G-~~~rl~t~~~~~~~l--~~~~~pei  280 (574)
                      |+|| +|.+|||+|+. |...||+.+++..+...|+|++++.||+||+||.+++ .||.+|+....++..  .....+++
T Consensus        95 ~~~~-~~~~vid~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~~~~~~~~~~y~~~~~~d~~~~~~~te~~i  173 (299)
T d1yksa2          95 GANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTSENNAHHVCWLEASM  173 (299)
T ss_dssp             CTTC-CCSEEEECCEEEEEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCCTTCCCEEEEECSCCCCCCTTBHHHHHHHH
T ss_pred             ceec-CceEEEecCceeceeeecCCCCeeEEeeeecCHHHHHHhcccccccCCCceEEEEeCCCCCCcccchhhhhhHHH
Confidence            9999 59999999995 8889999999999999999999999999999998653 466677654332111  11122333


Q ss_pred             ccCCchhhHHHHhhcCCCCccccCCCCCCcHHHHHHHHHHHHHcCCccCCCCcChhhhhhccCCCCHHHHHHHHhccCCC
Q 008209          281 LRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDDGNLTEMGEKMSEFPLDPQMSKMLVESPKYN  360 (574)
Q Consensus       281 ~~~~l~~~~L~l~~~~~~~~~~~~~l~~P~~~~l~~al~~L~~lgald~~~~lT~lG~~~~~lpl~p~~~~~ll~~~~~~  360 (574)
                      .   ++++.+.++.+|..+...++|+++|+.+....+++.|..+|+|+..+-+|++|+.++..++.+...++++.+....
T Consensus       174 ~---l~~i~l~~~~~g~~~~~e~~~~~~p~g~~~L~~~~~l~~l~aL~~~d~p~~La~~va~~~~~~~~~~~~f~~P~e~  250 (299)
T d1yksa2         174 L---LDNMEVRGGMVAPLYGVEGTKTPVSPGEMRLRDDQRKVFRELVRNCDLPVWLSWQVAKAGLKTNDRKWCFEGPEEH  250 (299)
T ss_dssp             H---HTTSCCGGGCCCCCSTTHHHHSSSCTTTTCCCHHHHHHHHHHHHTTCCCHHHHHHHHHTTCCTTCCGGGSCSCGGG
T ss_pred             H---hhCcccccccccccchhhhccccCCCchhhhhHhHHHHHHHHHhhcCCCcchHHHHHhcccccccccceeECchhc
Confidence            3   3444456777888888888999999888777889999999999988888899999999988887776654442211


Q ss_pred             CchhhHhHHhhccCCCcccCChhHHHHHHHHHHhhCCCCCcHHHHHHHHHHHHhCCCCchhHhhhcCCHHHHH
Q 008209          361 CSNEILSISAMLSVPNCFVRPREAQKAADEAKARFGHIDGDHLTLLNVYHAYKQNNEDPSWCYDNFVNHRALK  433 (574)
Q Consensus       361 c~~~~~~i~a~ls~~~~f~~~~~~~~~~~~~~~~~~~~~sD~l~~l~~~~~~~~~~~~~~~c~~~~l~~~~l~  433 (574)
                      .      +.+-..                 ....|....|||+++++.|.  .....+..||.++||.+..|+
T Consensus       251 ~------i~~~~~-----------------~~~~f~~~~Gd~~~L~~r~~--D~R~~sd~~~l~nFiq~a~~r  298 (299)
T d1yksa2         251 E------ILNDSG-----------------ETVKCRAPGGAKKPLRPRWC--DERVSSDQSALSEFIKFAEGR  298 (299)
T ss_dssp             C------CBCTTS-----------------CBCEEECTTSCEEECCCSSE--EGGGSSSHHHHHHHHHHHTTT
T ss_pred             h------hhhhhc-----------------cccceeCCCcceeeeeeeEe--cccccCcHHHHHHHHHHHhcC
Confidence            1      001000                 11234467899999887662  222345579999999887765

PyMOL of d1yksa2

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}	Back information, alignment and structure

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}	Back information, alignment and structure

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}	Back information, alignment and structure

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}	Back information, alignment and structure

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1tf5a4 c.37.1.19 (A:396-570) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}	Back information, alignment and structure

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}	Back information, alignment and structure

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}	Back information, alignment and structure

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}	Back information, alignment and structure

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}	Back information, alignment and structure

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}	Back information, alignment and structure

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}	Back information, alignment and structure

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2p6ra1 a.4.5.43 (A:404-488) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}	Back information, alignment and structure

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure