Citrus Sinensis ID: 007505

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-------580-------590-------600-

MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR

cEEEEccEEEEcccccccHHHHHHHHHHHHHHHHcccEEEEcccccccHHHHHHHHHHHHHcccccccccEEEccccHHHHHHHHHHHHHHHHccccccccccEEEEcccccccccccHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHcccccccccHHHHHHHHHHcccccHHHHHHHcccccEEEEcccccccHHHHHHHHHHcccccEEEEcccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHccEEEcccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccEEEEEccccccccccccccEEEEcccHHHHHHHHHHcccEEEEEcccccccccHHHHHcccccEEEEEcccccccccccEEEEcccccccEEEEEcccccHHHHHHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHHccHHHHHHccccEEEEcccccHHHHHHHHHHHHccccccEEEEEEEc

cEEEEccEEEEcccccccHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHccccccEEEEEcccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEcccccccccHcHHHcccccEHHHHHHHHHHHHHHHHHHcccccccccHHHcHHHcccccccccccccHHHHHHHHHcccccHHHHHHHHHHHccEEEEEHHHHccHHHHHHHHHHcccccEEEEEccccHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHcHHHHccccccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHcHHccccHHHHHHHHHHccccccccHHcHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccccEEEEEccccccccccccEEEEEEccHHHHHHHHHHHccEEEEEccccccHHHHHHHcccccEEEEccccEccccccEEEEEEccccccEEEEcEcccccHHHHHHHHHHHHHHHHHccccEEEEcccHHHHHHHHHHHHHccHHHHHHHcccEEEccccHHHHHHHHHHHHHHccccccEEEEEEcc

mifkledvtvyfpydniypeQYSYMLELKRALDAkghcllemptgtgKTIALLSLITSYvlskpenpvkliYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVDAACRKRTASWVRALAaenpnietceFFENYEKAAsaavlppgvytlQDLRAfgkqqgwcpyFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLAlrgnlpiadawlsnpalpsdilkeavpgnirRAEHFLHVLRRLVQYLRGrletenvekegpvSFVASITAHAGIDQKTLRFCYERLHSLMLTleitdtdeflHIQTICDFAtlvgtytrgfsiiiepfdermphipdpvlqlschdaslavkpvfdRFQSvvitsgtlspidlyprllnfhpvvsrsfkmsltrdcicpmvltrgsdqlpvstkfdmrsdpgvarNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYrkacdcgrgavffsvar

mifkledvtvyfpydNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSyvlskpenpVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVlaaenrdsvdaACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEgatrnlsrinqeierfkatdagrlRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLetenvekegpvSFVASitahagidqKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITsgtlspidlyPRLLNFHPVVSRSFKMSLTRDCICPMVltrgsdqlpvstkfdmrsdpGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR

**FKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSV**

MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDA*************KTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVDAACRKRTA*************ETCEFFENYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASI************FCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTxxxxxxxxxxxxxxxxxxxxxDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR

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		601	2.2.26 [Sep-21-2011]
Q8W4M7		758	DNA repair helicase UVH6	yes	no	1.0	0.792	0.875	0.0
A6QLJ0		760	TFIIH basal transcription	yes	no	1.0	0.790	0.534	0.0
Q55G81		776	TFIIH basal transcription	yes	no	0.986	0.764	0.533	0.0
P18074		760	TFIIH basal transcription	yes	no	1.0	0.790	0.534	0.0
Q60452		760	TFIIH basal transcription	yes	no	1.0	0.790	0.532	0.0
O08811		760	TFIIH basal transcription	yes	no	1.0	0.790	0.534	0.0
P26659		772	DNA repair helicase rad15	yes	no	0.998	0.777	0.505	0.0
P06839		778	DNA repair helicase RAD3	yes	no	0.998	0.771	0.461	1e-171
P0C928		1177	Regulator of telomere elo	no	no	0.913	0.466	0.252	1e-40
Q7QEI1		991	Regulator of telomere elo	no	no	0.898	0.544	0.234	3e-36

>sp\|Q8W4M7\|ERCC2_ARATH DNA repair helicase UVH6 OS=Arabidopsis thaliana GN=UVH6 PE=1 SV=1	Back alignment and function desciption

 Score = 1123 bits (2905), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 526/601 (87%), Positives = 569/601 (94%)

Query: 1   MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYV 60
           MIFK+EDVTVYFPYDNIYPEQY YM+ELKRALDAKGHCLLEMPTGTGKTIALLSLITSY 
Sbjct: 1   MIFKIEDVTVYFPYDNIYPEQYEYMVELKRALDAKGHCLLEMPTGTGKTIALLSLITSYR 60

Query: 61  LSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSR 120
           LS+P++P+KL+YCTRTVHEMEKTL ELKLLH+YQ RHLG  AKILA+GLSSRKNLCVN++
Sbjct: 61  LSRPDSPIKLVYCTRTVHEMEKTLGELKLLHDYQVRHLGTQAKILALGLSSRKNLCVNTK 120

Query: 121 VLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDL 180
           VLAAENRDSVDAACRKRTASWVRAL+ ENPN+E C+FFENYEKAA  A+LPPGVYTL+DL
Sbjct: 121 VLAAENRDSVDAACRKRTASWVRALSTENPNVELCDFFENYEKAAENALLPPGVYTLEDL 180

Query: 181 RAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNID 240
           RAFGK +GWCPYFLARHM+QFANV+VYSYQYLLDPKVAG ISKE+QKESVVVFDEAHNID
Sbjct: 181 RAFGKNRGWCPYFLARHMIQFANVIVYSYQYLLDPKVAGFISKELQKESVVVFDEAHNID 240

Query: 241 NVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPI 300
           NVCIEALSVSVRR TLEGA RNL++I QEI+RFKATDAGRLRAEYNRLVEGLALRG+L  
Sbjct: 241 NVCIEALSVSVRRVTLEGANRNLNKIRQEIDRFKATDAGRLRAEYNRLVEGLALRGDLSG 300

Query: 301 ADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVAS 360
            D WL+NPALP DILKEAVPGNIRRAEHF+HVLRRL+QYL  RL+TENVEKE PVSFV+S
Sbjct: 301 GDQWLANPALPHDILKEAVPGNIRRAEHFVHVLRRLLQYLGVRLDTENVEKESPVSFVSS 360

Query: 361 ITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEP 420
           + + AGI+QKTL+FCY+RL SLMLTLEITDTDEFL IQT+CDFATLVGTY RGFSIIIEP
Sbjct: 361 LNSQAGIEQKTLKFCYDRLQSLMLTLEITDTDEFLPIQTVCDFATLVGTYARGFSIIIEP 420

Query: 421 FDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS 480
           +DERMPHIPDP+LQLSCHDASLA+KPVFDRFQSVVITSGTLSPIDLYPRLLNF PVVSRS
Sbjct: 421 YDERMPHIPDPILQLSCHDASLAIKPVFDRFQSVVITSGTLSPIDLYPRLLNFTPVVSRS 480

Query: 481 FKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFV 540
           FKMS+TRDCICPMVLTRGSDQLPVSTKFDMRSDPGV RNYGKLLVEMVSIVPDG+VCFFV
Sbjct: 481 FKMSMTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVVRNYGKLLVEMVSIVPDGVVCFFV 540

Query: 541 SYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVA 600
           SYSYMD IIATWN++GILKEIMQ KLVFIETQDVVETTLALDNYR+ACDCGRGAVFFSVA
Sbjct: 541 SYSYMDGIIATWNETGILKEIMQQKLVFIETQDVVETTLALDNYRRACDCGRGAVFFSVA 600

Query: 601 R 601
           R
Sbjct: 601 R 601

Putative ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair (NER) of UV-damaged DNA. May open DNA around the damage. Essential during plant growth. May negatively regulate a common response program mediated by UV damage and heat stress, that leads to tissue death and reduced chloroplast function.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 2

>sp\|A6QLJ0\|ERCC2_BOVIN TFIIH basal transcription factor complex helicase XPD subunit OS=Bos taurus GN=ERCC2 PE=2 SV=1	Back alignment and function description

>sp\|Q55G81\|ERCC2_DICDI TFIIH basal transcription factor complex helicase repD subunit OS=Dictyostelium discoideum GN=repD PE=2 SV=1	Back alignment and function description

>sp\|P18074\|ERCC2_HUMAN TFIIH basal transcription factor complex helicase XPD subunit OS=Homo sapiens GN=ERCC2 PE=1 SV=1	Back alignment and function description

>sp\|Q60452\|ERCC2_CRIGR TFIIH basal transcription factor complex helicase XPD subunit OS=Cricetulus griseus GN=ERCC2 PE=1 SV=1	Back alignment and function description

>sp\|O08811\|ERCC2_MOUSE TFIIH basal transcription factor complex helicase XPD subunit OS=Mus musculus GN=Ercc2 PE=2 SV=2	Back alignment and function description

>sp\|P26659\|RAD15_SCHPO DNA repair helicase rad15 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rad15 PE=1 SV=2	Back alignment and function description

>sp\|P06839\|RAD3_YEAST DNA repair helicase RAD3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD3 PE=1 SV=1	Back alignment and function description

>sp\|P0C928\|RTEL1_DANRE Regulator of telomere elongation helicase 1 OS=Danio rerio GN=rtel1 PE=3 SV=1	Back alignment and function description

>sp\|Q7QEI1\|RTEL1_ANOGA Regulator of telomere elongation helicase 1 homolog OS=Anopheles gambiae GN=AGAP000634 PE=3 SV=5	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		601
255559474		758	DNA repair helicase rad3/xp-d, putative	1.0	0.792	0.918	0.0
224062561		758	predicted protein [Populus trichocarpa]	1.0	0.792	0.901	0.0
225437002		758	PREDICTED: DNA repair helicase UVH6 [Vit	1.0	0.792	0.898	0.0
356559661		758	PREDICTED: DNA repair helicase UVH6-like	1.0	0.792	0.883	0.0
356499550		758	PREDICTED: DNA repair helicase UVH6-like	1.0	0.792	0.881	0.0
15218736		758	DNA repair helicase UVH6 [Arabidopsis th	1.0	0.792	0.875	0.0
6503086		758	nucleotide excision repair protein XP-D	1.0	0.792	0.873	0.0
297843126		758	hypothetical protein ARALYDRAFT_470299 [	1.0	0.792	0.875	0.0
3850576		735	Strong similarity to gb\|U04968 nucleotid	1.0	0.817	0.856	0.0
449491590		598	PREDICTED: LOW QUALITY PROTEIN: DNA repa	0.993	0.998	0.879	0.0

>gi\|255559474\|ref\|XP_002520757.1\| DNA repair helicase rad3/xp-d, putative [Ricinus communis] gi\|223540142\|gb\|EEF41719.1\| DNA repair helicase rad3/xp-d, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1174 bits (3037), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 552/601 (91%), Positives = 582/601 (96%)

Query: 1   MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYV 60
           M F++EDVTVYFPYDNIYPEQYSYM+ELKRALDAKGHCLLEMPTGTGKTIALLSLITSY 
Sbjct: 1   MKFQIEDVTVYFPYDNIYPEQYSYMIELKRALDAKGHCLLEMPTGTGKTIALLSLITSYS 60

Query: 61  LSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSR 120
           LSKP++PVKLIYCTRTVHEMEKTLAELKLLHNYQ +HLGPAA+ILAIGLSSRKNLCVN R
Sbjct: 61  LSKPQSPVKLIYCTRTVHEMEKTLAELKLLHNYQIKHLGPAARILAIGLSSRKNLCVNPR 120

Query: 121 VLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDL 180
           VLAAENRDSVDA CRK TASW+RA+AAENPNI TCEFFENYE+AASAAVLPPGVYTLQDL
Sbjct: 121 VLAAENRDSVDAGCRKLTASWMRAMAAENPNIPTCEFFENYERAASAAVLPPGVYTLQDL 180

Query: 181 RAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNID 240
           R +GK++GWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNID
Sbjct: 181 RTYGKEKGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNID 240

Query: 241 NVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPI 300
           NVCIEALSVSVR+QTLEGA+RNLSRINQEIERFKATDAGRLRAEYNRLVEGLA RGNL +
Sbjct: 241 NVCIEALSVSVRKQTLEGASRNLSRINQEIERFKATDAGRLRAEYNRLVEGLAQRGNLAV 300

Query: 301 ADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVAS 360
            D WLSNPALP DILKEAVPGNIRRAEHFLHVLRRLVQYL+GRL+TENVEKE PVSFVAS
Sbjct: 301 TDTWLSNPALPDDILKEAVPGNIRRAEHFLHVLRRLVQYLKGRLDTENVEKESPVSFVAS 360

Query: 361 ITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEP 420
           + + AGIDQKTL+FCY+RLHSLMLTLEITDTDEFLH+QTICDFATLVGTY+RGFSIIIEP
Sbjct: 361 LNSQAGIDQKTLKFCYDRLHSLMLTLEITDTDEFLHVQTICDFATLVGTYSRGFSIIIEP 420

Query: 421 FDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS 480
           FDERMPHIPDPVLQLSCHDASLA+KPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS
Sbjct: 421 FDERMPHIPDPVLQLSCHDASLAIKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS 480

Query: 481 FKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFV 540
           F MSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVS+VPDGIVCFFV
Sbjct: 481 FTMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSVVPDGIVCFFV 540

Query: 541 SYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVA 600
           SYSYMD II +WN++GILKEIMQHKLVFIETQDVVETTLALDNYR+ACDCGRGAVFFSVA
Sbjct: 541 SYSYMDGIINSWNETGILKEIMQHKLVFIETQDVVETTLALDNYRRACDCGRGAVFFSVA 600

Query: 601 R 601
           R
Sbjct: 601 R 601

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224062561\|ref\|XP_002300852.1\| predicted protein [Populus trichocarpa] gi\|222842578\|gb\|EEE80125.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|225437002\|ref\|XP_002277634.1\| PREDICTED: DNA repair helicase UVH6 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356559661\|ref\|XP_003548117.1\| PREDICTED: DNA repair helicase UVH6-like [Glycine max]	Back alignment and taxonomy information

>gi\|356499550\|ref\|XP_003518602.1\| PREDICTED: DNA repair helicase UVH6-like [Glycine max]	Back alignment and taxonomy information

>gi|15218736|ref|NP_171818.1| DNA repair helicase UVH6 [Arabidopsis thaliana] gi|30678494|ref|NP_849584.1| DNA repair helicase UVH6 [Arabidopsis thaliana] gi|57013122|sp|Q8W4M7.1|ERCC2_ARATH RecName: Full=DNA repair helicase UVH6; AltName: Full=ERCC2 homolog; AltName: Full=RAD3 homolog; Short=AtUVH6; Short=AtXPD; AltName: Full=UV hypersensitive protein 6; AltName: Full=XPD homolog gi|17064790|gb|AAL32549.1| Strong similarity to nucleotide excision repair protein [Arabidopsis thaliana] gi|20258776|gb|AAM13910.1| putative DNA repair protein [Arabidopsis thaliana] gi|22651570|gb|AAM10793.1| DNA repair/transcription factor protein [Arabidopsis thaliana] gi|34098809|gb|AAQ56787.1| At1g03190 [Arabidopsis thaliana] gi|332189421|gb|AEE27542.1| DNA repair helicase UVH6 [Arabidopsis thaliana] gi|332189422|gb|AEE27543.1| DNA repair helicase UVH6 [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|6503086\|gb\|AAF14582.1\|AF188623_1 nucleotide excision repair protein XP-D homolog [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297843126\|ref\|XP_002889444.1\| hypothetical protein ARALYDRAFT_470299 [Arabidopsis lyrata subsp. lyrata] gi\|297335286\|gb\|EFH65703.1\| hypothetical protein ARALYDRAFT_470299 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|3850576\|gb\|AAC72116.1\| Strong similarity to gb\|U04968 nucleotide excision repair protein (ERCC2) from Cricetulus grisseus [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|449491590\|ref\|XP_004158946.1\| PREDICTED: LOW QUALITY PROTEIN: DNA repair helicase UVH6-like [Cucumis sativus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		601
TAIR\|locus:2014525		758	UVH6 "ULTRAVIOLET HYPERSENSITI	1.0	0.792	0.875	7.9e-291
UNIPROTKB\|F1PMH9		771	ERCC2 "Uncharacterized protein	0.993	0.774	0.536	3.1e-179
ZFIN\|ZDB-GENE-040426-997		760	ercc2 "excision repair cross-c	1.0	0.790	0.539	1e-178
UNIPROTKB\|Q91941		760	ERCC2/XPD "ERCC2/XPD protein"	1.0	0.790	0.535	7.3e-178
UNIPROTKB\|J9NWT1		707	ERCC2 "Uncharacterized protein	1.0	0.850	0.534	2.5e-177
UNIPROTKB\|A6QLJ0		760	ERCC2 "TFIIH basal transcripti	1.0	0.790	0.534	4e-177
UNIPROTKB\|F1N2P3		759	ERCC2 "TFIIH basal transcripti	0.993	0.786	0.536	6.5e-177
UNIPROTKB\|P18074		760	ERCC2 "TFIIH basal transcripti	1.0	0.790	0.534	1.1e-176
RGD\|1309109		760	Ercc2 "excision repair cross-c	1.0	0.790	0.532	1.7e-176
UNIPROTKB\|Q60452		760	ERCC2 "TFIIH basal transcripti	1.0	0.790	0.532	2.2e-176

TAIR\|locus:2014525 UVH6 "ULTRAVIOLET HYPERSENSITIVE 6" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2793 (988.2 bits), Expect = 7.9e-291, P = 7.9e-291
 Identities = 526/601 (87%), Positives = 569/601 (94%)

Query:     1 MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYV 60
             MIFK+EDVTVYFPYDNIYPEQY YM+ELKRALDAKGHCLLEMPTGTGKTIALLSLITSY 
Sbjct:     1 MIFKIEDVTVYFPYDNIYPEQYEYMVELKRALDAKGHCLLEMPTGTGKTIALLSLITSYR 60

Query:    61 LSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSR 120
             LS+P++P+KL+YCTRTVHEMEKTL ELKLLH+YQ RHLG  AKILA+GLSSRKNLCVN++
Sbjct:    61 LSRPDSPIKLVYCTRTVHEMEKTLGELKLLHDYQVRHLGTQAKILALGLSSRKNLCVNTK 120

Query:   121 VLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQDL 180
             VLAAENRDSVDAACRKRTASWVRAL+ ENPN+E C+FFENYEKAA  A+LPPGVYTL+DL
Sbjct:   121 VLAAENRDSVDAACRKRTASWVRALSTENPNVELCDFFENYEKAAENALLPPGVYTLEDL 180

Query:   181 RAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNID 240
             RAFGK +GWCPYFLARHM+QFANV+VYSYQYLLDPKVAG ISKE+QKESVVVFDEAHNID
Sbjct:   181 RAFGKNRGWCPYFLARHMIQFANVIVYSYQYLLDPKVAGFISKELQKESVVVFDEAHNID 240

Query:   241 NVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPI 300
             NVCIEALSVSVRR TLEGA RNL++I QEI+RFKATDAGRLRAEYNRLVEGLALRG+L  
Sbjct:   241 NVCIEALSVSVRRVTLEGANRNLNKIRQEIDRFKATDAGRLRAEYNRLVEGLALRGDLSG 300

Query:   301 ADAWLSNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVAS 360
              D WL+NPALP DILKEAVPGNIRRAEHF+HVLRRL+QYL  RL+TENVEKE PVSFV+S
Sbjct:   301 GDQWLANPALPHDILKEAVPGNIRRAEHFVHVLRRLLQYLGVRLDTENVEKESPVSFVSS 360

Query:   361 ITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEP 420
             + + AGI+QKTL+FCY+RL SLMLTLEITDTDEFL IQT+CDFATLVGTY RGFSIIIEP
Sbjct:   361 LNSQAGIEQKTLKFCYDRLQSLMLTLEITDTDEFLPIQTVCDFATLVGTYARGFSIIIEP 420

Query:   421 FDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS 480
             +DERMPHIPDP+LQLSCHDASLA+KPVFDRFQSVVITSGTLSPIDLYPRLLNF PVVSRS
Sbjct:   421 YDERMPHIPDPILQLSCHDASLAIKPVFDRFQSVVITSGTLSPIDLYPRLLNFTPVVSRS 480

Query:   481 FKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFV 540
             FKMS+TRDCICPMVLTRGSDQLPVSTKFDMRSDPGV RNYGKLLVEMVSIVPDG+VCFFV
Sbjct:   481 FKMSMTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVVRNYGKLLVEMVSIVPDGVVCFFV 540

Query:   541 SYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVA 600
             SYSYMD IIATWN++GILKEIMQ KLVFIETQDVVETTLALDNYR+ACDCGRGAVFFSVA
Sbjct:   541 SYSYMDGIIATWNETGILKEIMQQKLVFIETQDVVETTLALDNYRRACDCGRGAVFFSVA 600

Query:   601 R 601
             R
Sbjct:   601 R 601

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006139 "nucleobase-containing compound metabolic process" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

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

GO:0016817 "hydrolase activity, acting on acid anhydrides" evidence=IEA

GO:0016818 "hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides" evidence=IEA

GO:0006281 "DNA repair" evidence=IMP

GO:0009408 "response to heat" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0000724 "double-strand break repair via homologous recombination" evidence=RCA

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

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

GO:0006457 "protein folding" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0010212 "response to ionizing radiation" evidence=RCA

GO:0010286 "heat acclimation" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

GO:0009411 "response to UV" evidence=IMP

UNIPROTKB\|F1PMH9 ERCC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-040426-997 ercc2 "excision repair cross-complementing rodent repair deficiency, complementation group 2" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|Q91941 ERCC2/XPD "ERCC2/XPD protein" [Xiphophorus maculatus (taxid:8083)]	Back alignment and assigned GO terms

UNIPROTKB\|J9NWT1 ERCC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|A6QLJ0 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N2P3 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|P18074 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

RGD\|1309109 Ercc2 "excision repair cross-complementing rodent repair deficiency, complementation group 2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q60452 ERCC2 "TFIIH basal transcription factor complex helicase XPD subunit" [Cricetulus griseus (taxid:10029)]	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)
P18074	ERCC2_HUMAN	3, ., 6, ., 4, ., 1, 2	0.5341	1.0	0.7907	yes	no
O08811	ERCC2_MOUSE	3, ., 6, ., 4, ., 1, 2	0.5341	1.0	0.7907	yes	no
Q8W4M7	ERCC2_ARATH	3, ., 6, ., 4, ., 1, 2	0.8752	1.0	0.7928	yes	no
A6QLJ0	ERCC2_BOVIN	3, ., 6, ., 4, ., 1, 2	0.5341	1.0	0.7907	yes	no
P26659	RAD15_SCHPO	3, ., 6, ., 4, ., 1, 2	0.5058	0.9983	0.7772	yes	no
Q55G81	ERCC2_DICDI	3, ., 6, ., 4, ., 1, 2	0.5332	0.9866	0.7641	yes	no
Q60452	ERCC2_CRIGR	3, ., 6, ., 4, ., 1, 2	0.5324	1.0	0.7907	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	3.6.4.12	0.991
3rd Layer	3.6.4	0.976

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	eugene3.00020503	hypothetical protein (758 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_I000900	hypothetical protein (803 aa)		•	•	•	0.959
	estExt_fgenesh4_pm.C_1650003	hypothetical protein (413 aa)	•	•	•	•	0.953
	gw1.V.5266.1	hypothetical protein (289 aa)	•	•	•	•	0.853
	estExt_fgenesh4_pg.C_LG_IV0538	hypothetical protein (449 aa)	•	•	•	•	0.836
	estExt_Genewise1_v1.C_1330021	hypothetical protein (334 aa)		•	•	•	0.799
	gw1.V.2541.1	hypothetical protein (1081 aa)	•	•		•	0.686
	gw1.70.559.1	hypothetical protein (329 aa)	•		•	•	0.639
	eugene3.00290111	hypothetical protein (982 aa)			•	•	0.619
	fgenesh4_pg.C_LG_I002797	hypothetical protein (1088 aa)	•		•	•	0.607
	estExt_Genewise1_v1.C_LG_IV2251	hypothetical protein (909 aa)			•	•	0.568

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		601
TIGR00604		705	TIGR00604, rad3, DNA repair helicase (rad3)	0.0
smart00488		289	smart00488, DEXDc2, DEAD-like helicases superfamil	1e-114
COG1199		654	COG1199, DinG, Rad3-related DNA helicases [Transcr	5e-62
pfam06733		168	pfam06733, DEAD_2, DEAD_2	2e-57
pfam06777		146	pfam06777, DUF1227, Protein of unknown function (D	1e-56
smart00491		142	smart00491, HELICc2, helicase superfamily c-termin	4e-11
pfam13307		165	pfam13307, Helicase_C_2, Helicase C-terminal domai	1e-07
PRK11747		697	PRK11747, dinG, ATP-dependent DNA helicase DinG; P	0.002

>gnl\|CDD\|233047 TIGR00604, rad3, DNA repair helicase (rad3)	Back alignment and domain information

 Score =  626 bits (1617), Expect = 0.0
 Identities = 269/596 (45%), Positives = 391/596 (65%), Gaps = 6/596 (1%)

Query: 7   DVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPEN 66
           ++ VYFPY+ IYPEQ SYM +LKR+LD     +LEMP+GTGKTI+LLSLI +Y   KPE 
Sbjct: 1   ELLVYFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPE- 59

Query: 67  PVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAEN 126
             K+IY +RT  ++E+   EL+ L +Y+T  +G  + +  + L+SRKNLC++  V     
Sbjct: 60  VRKIIYASRTHSQLEQATEELRKLMSYRTPRIGEESPVSGLSLASRKNLCLHPEVSKERQ 119

Query: 127 RDSVDAACRKRTASWVRALAAENPNIETCEFFEN-YEKAASAAVLPPGVYTLQDLRAFGK 185
              V+  C K T S ++    E PN+E+CEF+EN  E      +L   +  ++DL  +G+
Sbjct: 120 GKVVNGKCIKLTVSKIKEQRTEKPNVESCEFYENFDELREVEDLLLSEIMDIEDLVEYGE 179

Query: 186 QQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNIDNVCIE 245
             G CPYF  R M+ FAN+V+  YQYLLDPK+   +S E+ K+S+V+FDEAHN+DNVCI 
Sbjct: 180 LLGLCPYFATRKMLPFANIVLLPYQYLLDPKIRSAVSIEL-KDSIVIFDEAHNLDNVCIS 238

Query: 246 ALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWL 305
           +LS ++  ++L+  ++ ++   ++IE  K  DA +L  E  +LVEGL     L   D +L
Sbjct: 239 SLSSNLSVRSLKRCSKEIAEYFEKIEERKEVDARKLLDELQKLVEGLKQEDLLTDEDIFL 298

Query: 306 SNPALPSDILKEAVPGNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHA 365
           +NP LP ++L EAVPGNIR AE FLH L R ++YL+  L+   V  E P +F+  +    
Sbjct: 299 ANPVLPKEVLPEAVPGNIRIAEIFLHKLSRYLEYLKDALKVLGVVSELPDAFLEHLK-EK 357

Query: 366 GIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERM 425
               + LRFC ERL +L+  LEIT  ++F  +  +  FATLV TYT GF   IEP++   
Sbjct: 358 TFIDRPLRFCSERLSNLLRELEITHPEDFSALVLLFTFATLVLTYTNGFLEGIEPYEN-- 415

Query: 426 PHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSL 485
             +P+P+L+  C D S+A+KP+F+R +SV++ SGTLSP+D +PR L F+PV   S    L
Sbjct: 416 KTVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHIL 475

Query: 486 TRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYM 545
            R+ +  +++TRGSDQ+P+S+ F++R+DP + RN G+LLVE   I+PDGIV FF SYSY+
Sbjct: 476 KRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSKIIPDGIVVFFPSYSYL 535

Query: 546 DEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR 601
           + I++TW + GIL+ I + KL+F+ET+D  ET+ AL+ Y++A   GRGAV  SVA 
Sbjct: 536 ENIVSTWKEMGILENIEKKKLIFVETKDAQETSDALERYKQAVSEGRGAVLLSVAG 591

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 705

>gnl\|CDD\|214693 smart00488, DEXDc2, DEAD-like helicases superfamily	Back alignment and domain information

>gnl\|CDD\|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|219153 pfam06733, DEAD_2, DEAD_2	Back alignment and domain information

>gnl\|CDD\|191608 pfam06777, DUF1227, Protein of unknown function (DUF1227)	Back alignment and domain information

>gnl\|CDD\|214694 smart00491, HELICc2, helicase superfamily c-terminal domain	Back alignment and domain information

>gnl\|CDD\|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain	Back alignment and domain information

>gnl\|CDD\|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		601
KOG1131		755	consensus RNA polymerase II transcription initiati	100.0
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	100.0
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	100.0
KOG1133		821	consensus Helicase of the DEAD superfamily [Replic	100.0
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	100.0
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	100.0
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	100.0
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	100.0
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	100.0
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	100.0
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	100.0
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	100.0
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	100.0
PF06777		146	DUF1227: Protein of unknown function (DUF1227); In	99.74
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	99.4
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.32
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.31
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	99.28
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	99.26
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	99.25
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	99.24
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	99.24
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	99.23
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	99.21
PTZ00110		545	helicase; Provisional	99.2
PTZ00424		401	helicase 45; Provisional	99.19
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	99.16
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	99.14
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	99.11
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.1
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	99.06
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.06
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	99.03
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	99.0
PRK13767		876	ATP-dependent helicase; Provisional	98.98
smart00487		201	DEXDc DEAD-like helicases superfamily.	98.96
PRK02362		737	ski2-like helicase; Provisional	98.91
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	98.89
PRK01172		674	ski2-like helicase; Provisional	98.88
PRK00254		720	ski2-like helicase; Provisional	98.85
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.84
PRK09694		878	helicase Cas3; Provisional	98.81
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	98.79
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	98.77
PRK09401		1176	reverse gyrase; Reviewed	98.77
PRK10689		1147	transcription-repair coupling factor; Provisional	98.76
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	98.75
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	98.73
COG1204		766	Superfamily II helicase [General function predicti	98.7
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	98.68
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	98.66
PRK13766		773	Hef nuclease; Provisional	98.65
KOG0354		746	consensus DEAD-box like helicase [General function	98.63
PRK09200		790	preprotein translocase subunit SecA; Reviewed	98.61
PHA02653		675	RNA helicase NPH-II; Provisional	98.61
PHA02558		501	uvsW UvsW helicase; Provisional	98.6
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.6
PRK14701		1638	reverse gyrase; Provisional	98.57
PRK05580		679	primosome assembly protein PriA; Validated	98.57
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.56
COG1205		851	Distinct helicase family with a unique C-terminal	98.55
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	98.54
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	98.52
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	98.51
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	98.5
COG1201		814	Lhr Lhr-like helicases [General function predictio	98.48
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	98.47
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	98.43
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.42
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	98.38
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	98.3
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	98.3
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	98.28
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	98.23
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	98.23
COG4889		1518	Predicted helicase [General function prediction on	98.21
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	98.21
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	98.17
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	98.17
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	98.17
TIGR00595		505	priA primosomal protein N'. All proteins in this f	98.13
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	98.13
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	98.09
COG1202		830	Superfamily II helicase, archaea-specific [General	98.08
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	98.01
KOG0343		758	consensus RNA Helicase [RNA processing and modific	97.99
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	97.95
KOG0346		569	consensus RNA helicase [RNA processing and modific	97.94
PF13245		76	AAA_19: Part of AAA domain	97.9
PRK04914		956	ATP-dependent helicase HepA; Validated	97.82
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.81
PRK12904		830	preprotein translocase subunit SecA; Reviewed	97.78
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	97.77
PRK13107		908	preprotein translocase subunit SecA; Reviewed	97.74
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	97.68
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	97.65
KOG0334		997	consensus RNA helicase [RNA processing and modific	97.63
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	97.59
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	97.58
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	97.56
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	97.54
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	97.49
KOG1803		649	consensus DNA helicase [Replication, recombination	97.46
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	97.37
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	97.21
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.21
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.21
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	97.17
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	97.05
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	97.04
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.95
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	96.87
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	96.86
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	96.85
COG4096		875	HsdR Type I site-specific restriction-modification	96.8
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	96.76
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	96.74
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	96.74
TIGR00376		637	DNA helicase, putative. The gene product may repre	96.7
KOG4284		980	consensus DEAD box protein [Transcription]	96.62
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	96.58
KOG1805		1100	consensus DNA replication helicase [Replication, r	96.49
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	96.45
PRK15483		986	type III restriction-modification system StyLTI en	96.39
PRK10536		262	hypothetical protein; Provisional	96.18
PF00580		315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.17
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	96.15
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	96.05
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	95.96
CHL00122		870	secA preprotein translocase subunit SecA; Validate	95.88
KOG0353		695	consensus ATP-dependent DNA helicase [General func	95.85
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	95.74
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	95.64
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	95.62
PRK12326		764	preprotein translocase subunit SecA; Reviewed	95.54
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	95.46
KOG0327		397	consensus Translation initiation factor 4F, helica	95.43
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	95.39
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	95.38
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	95.31
PF01695		178	IstB_IS21: IstB-like ATP binding protein; InterPro	95.27
KOG0347		731	consensus RNA helicase [RNA processing and modific	95.17
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	95.16
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	95.16
TIGR02640		262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	95.15
COG1198		730	PriA Primosomal protein N' (replication factor Y)	95.08
PHA02244		383	ATPase-like protein	95.05
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	94.87
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	94.85
PRK08181		269	transposase; Validated	94.77
COG1484		254	DnaC DNA replication protein [DNA replication, rec	94.68
PRK06835		329	DNA replication protein DnaC; Validated	94.5
KOG0387		923	consensus Transcription-coupled repair protein CSB	94.42
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	94.21
COG0714		329	MoxR-like ATPases [General function prediction onl	94.15
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	93.87
PRK13531		498	regulatory ATPase RavA; Provisional	93.71
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	93.61
PRK05298		652	excinuclease ABC subunit B; Provisional	93.54
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	93.31
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309		127	Torsin: Torsin; InterPro: IPR010448 This family co	93.22
PF01078		206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	92.91
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	92.79
PRK06526		254	transposase; Provisional	92.74
PF00308		219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	92.7
KOG1123		776	consensus RNA polymerase II transcription initiati	92.69
PRK06921		266	hypothetical protein; Provisional	92.68
PRK12377		248	putative replication protein; Provisional	92.62
PRK13894		319	conjugal transfer ATPase TrbB; Provisional	92.61
PRK08939		306	primosomal protein DnaI; Reviewed	92.42
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	92.35
COG1474		366	CDC6 Cdc6-related protein, AAA superfamily ATPase	92.34
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	92.08
PRK07952		244	DNA replication protein DnaC; Validated	92.01
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	91.99
PRK13407		334	bchI magnesium chelatase subunit I; Provisional	91.97
TIGR02030		337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	91.85
PRK09183		259	transposase/IS protein; Provisional	91.84
PF05970		364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	91.71
PRK14873		665	primosome assembly protein PriA; Provisional	91.67
KOG0989		346	consensus Replication factor C, subunit RFC4 [Repl	91.51
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	91.48
PF06745		226	KaiC: KaiC; InterPro: IPR014774 This entry represe	91.31
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	90.7
KOG1002		791	consensus Nucleotide excision repair protein RAD16	90.66
PRK13900		332	type IV secretion system ATPase VirB11; Provisiona	90.05
cd01124		187	KaiC KaiC is a circadian clock protein primarily f	89.95
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	89.69
TIGR02768		744	TraA_Ti Ti-type conjugative transfer relaxase TraA	89.69
PRK08116		268	hypothetical protein; Validated	89.68
PRK05973		237	replicative DNA helicase; Provisional	89.61
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	89.55
PRK05642		234	DNA replication initiation factor; Validated	89.54
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	89.51
PF02367		123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	89.48
PRK13889		988	conjugal transfer relaxase TraA; Provisional	89.4
PRK10919		672	ATP-dependent DNA helicase Rep; Provisional	89.36
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	89.3
PRK14952		584	DNA polymerase III subunits gamma and tau; Provisi	89.05
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	88.89
PF00158		168	Sigma54_activat: Sigma-54 interaction domain; Inte	88.84
TIGR00764		608	lon_rel lon-related putative ATP-dependent proteas	88.79
PRK14955		397	DNA polymerase III subunits gamma and tau; Provisi	88.73
PRK05201		443	hslU ATP-dependent protease ATP-binding subunit Hs	88.73
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	88.65
PRK13833		323	conjugal transfer protein TrbB; Provisional	88.61
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	88.6
cd00984		242	DnaB_C DnaB helicase C terminal domain. The hexame	88.6
PHA00729		226	NTP-binding motif containing protein	88.56
smart00382		148	AAA ATPases associated with a variety of cellular	88.49
COG0606		490	Predicted ATPase with chaperone activity [Posttran	88.46
PRK08533		230	flagellar accessory protein FlaH; Reviewed	88.36
TIGR03420		226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	88.3
PRK11773		721	uvrD DNA-dependent helicase II; Provisional	88.26
TIGR01650		327	PD_CobS cobaltochelatase, CobS subunit. This model	88.26
PRK10875		615	recD exonuclease V subunit alpha; Provisional	88.24
PRK08727		233	hypothetical protein; Validated	88.18
TIGR02782		299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	88.07
TIGR00150		133	HI0065_YjeE ATPase, YjeE family. Members of this f	88.04
PRK12402		337	replication factor C small subunit 2; Reviewed	87.99
TIGR03877		237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	87.96
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	87.85
CHL00081		350	chlI Mg-protoporyphyrin IX chelatase	87.75
PRK11331		459	5-methylcytosine-specific restriction enzyme subun	87.51
TIGR00390		441	hslU ATP-dependent protease HslVU, ATPase subunit.	87.49
TIGR01074		664	rep ATP-dependent DNA helicase Rep. Designed to id	87.42
TIGR01075		715	uvrD DNA helicase II. Designed to identify uvrD me	87.4
PLN03025		319	replication factor C subunit; Provisional	87.35
PRK14962		472	DNA polymerase III subunits gamma and tau; Provisi	87.34
COG1219		408	ClpX ATP-dependent protease Clp, ATPase subunit [P	87.32
COG3973		747	Superfamily I DNA and RNA helicases [General funct	87.3
COG4962		355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	87.08
TIGR02880		284	cbbX_cfxQ probable Rubsico expression protein CbbX	87.06
TIGR02785		1232	addA_Gpos recombination helicase AddA, Firmicutes	87.02
KOG0991		333	consensus Replication factor C, subunit RFC2 [Repl	86.85
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	86.65
COG3587		985	Restriction endonuclease [Defense mechanisms]	86.62
PRK13851		344	type IV secretion system protein VirB11; Provision	86.47
PRK14956		484	DNA polymerase III subunits gamma and tau; Provisi	86.42
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	86.36
TIGR00382		413	clpX endopeptidase Clp ATP-binding regulatory subu	86.07
PRK14087		450	dnaA chromosomal replication initiation protein; P	85.92
PRK14961		363	DNA polymerase III subunits gamma and tau; Provisi	85.91
PF05673		249	DUF815: Protein of unknown function (DUF815); Inte	85.83
PF07728		139	AAA_5: AAA domain (dynein-related subfamily); Inte	85.65
PF13191		185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	85.61
PHA02653		675	RNA helicase NPH-II; Provisional	85.54
PRK00411		394	cdc6 cell division control protein 6; Reviewed	85.37
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	85.32
PRK08084		235	DNA replication initiation factor; Provisional	85.29
PRK00440		319	rfc replication factor C small subunit; Reviewed	85.01
KOG0745		564	consensus Putative ATP-dependent Clp-type protease	84.79
TIGR02928		365	orc1/cdc6 family replication initiation protein. M	84.73
PRK08903		227	DnaA regulatory inactivator Hda; Validated	84.73
PF14532		138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	84.7
PRK05342		412	clpX ATP-dependent protease ATP-binding subunit Cl	84.69
PF07726		131	AAA_3: ATPase family associated with various cellu	84.68
PF12775		272	AAA_7: P-loop containing dynein motor region D3; P	84.58
cd01130		186	VirB11-like_ATPase Type IV secretory pathway compo	84.55
PRK14960		702	DNA polymerase III subunits gamma and tau; Provisi	84.46
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	84.26
TIGR03015		269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	84.26
PRK11608		326	pspF phage shock protein operon transcriptional ac	83.94
KOG1807		1025	consensus Helicases [Replication, recombination an	83.58
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	83.57
cd01122		271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	83.45
KOG0744		423	consensus AAA+-type ATPase [Posttranslational modi	83.43
COG2804		500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	83.4
PF01580		205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	83.39
PF13401		131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	83.18
COG0593		408	DnaA ATPase involved in DNA replication initiation	83.06
TIGR03880		224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	82.94
PTZ00112		1164	origin recognition complex 1 protein; Provisional	82.88
PRK06067		234	flagellar accessory protein FlaH; Validated	82.84
PRK11054		684	helD DNA helicase IV; Provisional	82.83
PRK04328		249	hypothetical protein; Provisional	82.72
PRK06645		507	DNA polymerase III subunits gamma and tau; Validat	82.55
KOG4439		901	consensus RNA polymerase II transcription terminat	82.49
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	82.31
PF00437		270	T2SE: Type II/IV secretion system protein; InterPr	82.28
PHA02544		316	44 clamp loader, small subunit; Provisional	82.27
TIGR01073		726	pcrA ATP-dependent DNA helicase PcrA. Designed to	82.26
PRK13765		637	ATP-dependent protease Lon; Provisional	82.14
PRK13826		1102	Dtr system oriT relaxase; Provisional	82.1
TIGR03878		259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	82.09
PRK10646		153	ADP-binding protein; Provisional	82.06
PF02456		369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	81.97
TIGR00635		305	ruvB Holliday junction DNA helicase, RuvB subunit.	81.93
PF05496		233	RuvB_N: Holliday junction DNA helicase ruvB N-term	81.88
PRK14950		585	DNA polymerase III subunits gamma and tau; Provisi	81.88
TIGR02442		633	Cob-chelat-sub cobaltochelatase subunit. A number	81.65
PF13481		193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	81.55
PRK12422		445	chromosomal replication initiation protein; Provis	81.55
PF02534		469	T4SS-DNA_transf: Type IV secretory system Conjugat	81.53
COG0467		260	RAD55 RecA-superfamily ATPases implicated in signa	81.52
PHA02533		534	17 large terminase protein; Provisional	81.49
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	81.43
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	81.13
PRK05896		605	DNA polymerase III subunits gamma and tau; Validat	80.93
COG0610		962	Type I site-specific restriction-modification syst	80.89
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	80.25
PRK00080		328	ruvB Holliday junction DNA helicase RuvB; Reviewed	80.15
TIGR02902		531	spore_lonB ATP-dependent protease LonB. Members of	80.12
TIGR02524		358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	80.06
PRK14958		509	DNA polymerase III subunits gamma and tau; Provisi	80.01

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]	Back alignment and domain information

Probab=100.00  E-value=6.7e-108  Score=808.78  Aligned_cols=599  Identities=62%  Similarity=1.068  Sum_probs=571.8

Q ss_pred             CeEEEcCeeeeCCCCCCCHHHHHHHHHHHHHHhhcCcEEEEccCCChhHHHHHHHHHHHHHhCCCCCcEEEEEcccchhH
Q 007505            1 MIFKLEDVTVYFPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEM   80 (601)
Q Consensus         1 ~~~~i~~~~~~fp~~~~r~~Q~~~~~~v~~~l~~~~~~~~EapTGtGKTla~L~~~l~~~~~~~~~~~kvv~~t~T~~~~   80 (601)
                      |+|.|+++.|+|||..+||+|.++|.++.++|+.++|.++|.|+|||||.++|.-.++|....|+...|+|||+||.+.+
T Consensus         1 Mk~~id~l~v~FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p~~~~KliYCSRTvpEi   80 (755)
T KOG1131|consen    1 MKFYIDDLLVYFPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYPDEHRKLIYCSRTVPEI   80 (755)
T ss_pred             CeeeecCeeEecCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCCcccceEEEecCcchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999985444999999999999


Q ss_pred             HHHHHHHHhhhhhhcccCCCccceEEEeecCccccccchhhhhccChhhHHHHhHHhhhHHHHhhhhcCCCCCCCccccc
Q 007505           81 EKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVDAACRKRTASWVRALAAENPNIETCEFFEN  160 (601)
Q Consensus        81 ~q~~~el~~l~~~~~~~~~~~~~~~~~~l~~r~~lC~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~c~~~~~  160 (601)
                      +..++||+++..|..+.+|.+.++..+.|.||+|+|+|+.+....++..++..|+.+..+|.+++...+.+...|.|++|
T Consensus        81 eK~l~El~~l~~y~~k~~g~~~~flglglssRKNlCi~~~v~~~r~g~~VD~~Cr~ltas~vr~~~~ed~~~~~C~f~en  160 (755)
T KOG1131|consen   81 EKALEELKRLMDYREKHLGYPEPFLGLGLSSRKNLCIHPEVLKERNGNVVDAACRKLTASYVRAKLAEDPNVELCDFFEN  160 (755)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCceeeeeeccccccccCHHHHHHhcCCchhHHHHHHhHHHHHHHHhcCCCcchhhHHhh
Confidence            99999999999999888888889999999999999999999988888889999999999999999888777889999999


Q ss_pred             hHHhhhccCCCCCCCCHHHHHHhccccCcchhHHHHHhhccCcEEEecCccccCHHhhhHhhhccCCCcEEEEeCCCChH
Q 007505          161 YEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEAHNID  240 (601)
Q Consensus       161 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~Cpy~~~r~~~~~adivv~n~~~ll~~~~~~~~~~~l~~~~ilIiDEAHnl~  240 (601)
                      +..  ....+|.++|+.+++.+.|...+.||||.+|..+..|+|||-+||||+||.+.+.+..++.+.++|||||||||.
T Consensus       161 ~~~--~~~~lp~gvy~~~dL~~~g~~k~~CPYflaR~~I~~~nvivYsYhYllDPkIa~~VSkels~~svVvFDEAHNID  238 (755)
T KOG1131|consen  161 LED--KESLLPVGVYTLEDLKEYGEKKGWCPYFLARRMIPFANVIVYSYHYLLDPKIAELVSKELSKESVVVFDEAHNID  238 (755)
T ss_pred             hhc--ccccCCcccccHHHHHHhhhcCCcChHHHHHHhhhcccEEEEehhhhcChHHHHHHHHhhCcCcEEEeccccccc
Confidence            876  234689999999999999999999999999999999999999999999999988887788899999999999999


Q ss_pred             HHHHHhcccccCHHHHHHHHHHHHHHHHHHHHhhhhchhHHHHHHHHHHHHHhhcCCCccccccccCCCCChhhhhhhcC
Q 007505          241 NVCIEALSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVP  320 (601)
Q Consensus       241 ~~~~~~~s~~is~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (601)
                      ++|.+.+|+.|+...++.+.+.+..+.+.+.+++..+.++|+++|+++.++|........++.+++||++|++++.+..|
T Consensus       239 nvCIeslSv~i~r~~l~ra~~~l~~l~~~v~r~k~~d~~kl~~eY~klvegL~~~~~~~~~d~~lanPvLP~dvl~EavP  318 (755)
T KOG1131|consen  239 NVCIESLSVDITRRTLERASRNLNSLEQLVNRVKETDSQKLQDEYEKLVEGLKDASAERDEDQFLANPVLPDDVLKEAVP  318 (755)
T ss_pred             chhhhhhhhhhhHHHHHHHHHHHHHHHHHHHhhhhcchhHHHHHHHHHHHHhhccccccCccchhcCCCCchhhhhhhCC
Confidence            99999999999999999999999999888888888899999999999999998765555567899999999999999999


Q ss_pred             CchhchhhHHHHHHHHHHHHHhhhhcccccccChhhHHHHHHhhhccCcchhhhhHHHHHHHHHHhhccCCCccchhHHH
Q 007505          321 GNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTI  400 (601)
Q Consensus       321 ~~i~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~~l~~~  400 (601)
                      |||+++++|+.++++++++++.+++..++..++|.+|++.+.+...+++++++||.+||+.++.+|++.+.++|.+++.+
T Consensus       319 GniR~aeHFv~fLkR~~ey~ktrl~~~hv~~Esp~sFl~~i~~~~~IerKplrFCaeRL~~L~~tLeitd~~df~~l~~v  398 (755)
T KOG1131|consen  319 GNIRRAEHFVSFLKRLLEYLKTRLKVHHVIQESPASFLKSIKSLTFIERKPLRFCAERLSSLVRTLEITDVEDFGALKTV  398 (755)
T ss_pred             cchhhHHHHHHHHHHHHHHHHHhhhheeeeccCcHHHHHHHHHhhhhhccchHHHHHHHHHHHHHhccCchhhhhHHHHH
Confidence            99999999999999999999999998888899999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHhhcccCCceEEEEecCCCCCCCCCCCeEEEEecCccccchHHhhccCEEEEecCCCCCccchhhhcCCCCccccc
Q 007505          401 CDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS  480 (601)
Q Consensus       401 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ldps~~l~~l~~~~~svIltSgTLsp~~~f~~~Lg~~~~~~~~  480 (601)
                      .+|.+++.+|.+||.+++++.+.+.++..++++++.|+|+|.+.+++|++++|||.|||||+|++.|.++|+|.++...+
T Consensus       399 ~~faTlVstY~kGF~iIiEPfd~~~~tv~npil~~sClDaSiAikPVf~RFqsViITSGTlspldmyPk~lnf~pv~~~s  478 (755)
T KOG1131|consen  399 ADFATLVSTYSKGFSIIIEPFDDRNPTVPNPILRFSCLDASIAIKPVFERFQSVIITSGTLSPLDMYPKILNFGPVVGAS  478 (755)
T ss_pred             HHHHHHHHHHhcCcEEEEcccccCCCCCCCCeeEEeecccchhhhHHHHhhheEEEecCcccccccCchhhccCcccchh
Confidence            99999999999999999999998888888999999999999999999999999999999999999999999999988899


Q ss_pred             ceeeecCCceeeeeeecCCCCCcceeeeccCCChHHHHHHHHHHHHhhcccCCeEEEEecCHHHHHHHHHHHHhcchHHH
Q 007505          481 FKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKE  560 (601)
Q Consensus       481 ~~~~~~~~~~~~~~i~~g~~~~~l~s~f~~r~~~~~~~~l~~~i~~~~~~~~gg~LVfFpSy~~l~~v~~~~~~~~~~~~  560 (601)
                      +++.+.++++.|.++++|.++..++|.|+-|+++....++|+.+.+..+.+|||+++|||||-+|+.+...|...||.++
T Consensus       479 ~~mtLaR~c~~PmiitrG~Dqv~iss~fe~r~d~~VvrnyG~llve~sk~vpdG~v~ff~sylYmesiv~~w~~~gil~e  558 (755)
T KOG1131|consen  479 FTMTLARNCLLPLIITRGNDQVAISSKFEARGDPSVVRNYGNLLVEMSKIVPDGIVCFFPSYLYMESIVSRWYEQGILDE  558 (755)
T ss_pred             hheecccccccceeeecCCcchhhhhhhhhccChHHHhhcCcceeeecccCCCceEEEEehHHHHHHHHHHHHHHhHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCCeeEEecCCchhHHHHHHHHHHhcCCCCCeEEEEEcC
Q 007505          561 IMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR  601 (601)
Q Consensus       561 l~~~k~if~E~~~~~~~~~~l~~fk~~~~~~~gaiLfaV~R  601 (601)
                      +.+.|.+|+|.++..+++.++++|+++|+.|+|||||+|+|
T Consensus       559 i~k~KL~fIetpD~~ETs~al~ny~~aC~~gRGavl~sVar  599 (755)
T KOG1131|consen  559 IMKYKLLFIETPDFRETSLALANYRYACDNGRGAVLLSVAR  599 (755)
T ss_pred             HhhCceEEEeCCchhhhHHHHHHHHHHhcCCCCceEEEEec
Confidence            99999999999999999999999999999999999999998

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

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

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

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

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

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

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

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

>smart00489 DEXDc3 DEAD-like helicases superfamily	Back alignment and domain information

>smart00488 DEXDc2 DEAD-like helicases superfamily	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

>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases	Back alignment and domain information

>cd00268 DEADc DEAD-box helicases	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

>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

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

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

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

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

>PRK11776 ATP-dependent RNA helicase DbpA; 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

>PTZ00110 helicase; Provisional	Back alignment and domain information

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

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

>PRK00254 ski2-like helicase; Provisional	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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]	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

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

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

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

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

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

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

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

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

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

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

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

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

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

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

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

>COG1111 MPH1 ERCC4-like helicases [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

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

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

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

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

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

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

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional	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

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

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

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

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

>smart00492 HELICc3 helicase superfamily c-terminal domain	Back alignment and domain information

>smart00491 HELICc2 helicase superfamily c-terminal domain	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

>KOG0343 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

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

>PF13245 AAA_19: Part of AAA domain	Back alignment and domain information

>PRK04914 ATP-dependent helicase HepA; Validated	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

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

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

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

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

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

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

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

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

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

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]	Back alignment and domain information

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

>KOG1803 consensus DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]	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

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []	Back alignment and domain information

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A	Back alignment and domain information

>KOG0336 consensus 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

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

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A	Back alignment and domain information

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

>KOG0340 consensus ATP-dependent RNA helicase [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

>KOG0337 consensus ATP-dependent RNA helicase [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

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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

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

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

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]	Back alignment and domain information

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

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional	Back alignment and domain information

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA	Back alignment and domain information

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

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

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

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

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]	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

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

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

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

>KOG0951 consensus RNA helicase BRR2, DEAD-box superfamily [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

>PRK12906 secA 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

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

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif	Back alignment and domain information

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

>PF07517 SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011115 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane	Back alignment and domain information

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

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN	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

>PHA02244 ATPase-like protein	Back alignment and domain information

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length	Back alignment and domain information

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

>PRK08181 transposase; Validated	Back alignment and domain information

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK06835 DNA replication protein DnaC; 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

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

>COG0714 MoxR-like ATPases [General function prediction only]	Back alignment and domain information

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

>PRK13531 regulatory ATPase RavA; Provisional	Back alignment and domain information

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

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

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold	Back alignment and domain information

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins	Back alignment and domain information

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX	Back alignment and domain information

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

>PRK06526 transposase; Provisional	Back alignment and domain information

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication	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

>PRK06921 hypothetical protein; Provisional	Back alignment and domain information

>PRK12377 putative replication protein; Provisional	Back alignment and domain information

>PRK13894 conjugal transfer ATPase TrbB; Provisional	Back alignment and domain information

>PRK08939 primosomal protein DnaI; Reviewed	Back alignment and domain information

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function	Back alignment and domain information

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>PRK07952 DNA replication protein DnaC; Validated	Back alignment and domain information

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

>PRK13407 bchI magnesium chelatase subunit I; Provisional	Back alignment and domain information

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I	Back alignment and domain information

>PRK09183 transposase/IS protein; Provisional	Back alignment and domain information

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins	Back alignment and domain information

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

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]	Back alignment and domain information

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

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical	Back alignment and domain information

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

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]	Back alignment and domain information

>PRK13900 type IV secretion system ATPase VirB11; Provisional	Back alignment and domain information

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs	Back alignment and domain information

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

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA	Back alignment and domain information

>PRK08116 hypothetical protein; Validated	Back alignment and domain information

>PRK05973 replicative DNA helicase; Provisional	Back alignment and domain information

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

>PRK05642 DNA replication initiation factor; Validated	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

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop	Back alignment and domain information

>PRK13889 conjugal transfer relaxase TraA; Provisional	Back alignment and domain information

>PRK10919 ATP-dependent DNA helicase Rep; Provisional	Back alignment and domain information

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

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor	Back alignment and domain information

>TIGR00764 lon_rel lon-related putative ATP-dependent protease	Back alignment and domain information

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional	Back alignment and domain information

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

>PRK13833 conjugal transfer protein TrbB; Provisional	Back alignment and domain information

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit	Back alignment and domain information

>cd00984 DnaB_C DnaB helicase C terminal domain	Back alignment and domain information

>PHA00729 NTP-binding motif containing protein	Back alignment and domain information

>smart00382 AAA ATPases associated with a variety of cellular activities	Back alignment and domain information

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK08533 flagellar accessory protein FlaH; Reviewed	Back alignment and domain information

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda	Back alignment and domain information

>PRK11773 uvrD DNA-dependent helicase II; Provisional	Back alignment and domain information

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit	Back alignment and domain information

>PRK10875 recD exonuclease V subunit alpha; Provisional	Back alignment and domain information

>PRK08727 hypothetical protein; Validated	Back alignment and domain information

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB	Back alignment and domain information

>TIGR00150 HI0065_YjeE ATPase, YjeE family	Back alignment and domain information

>PRK12402 replication factor C small subunit 2; Reviewed	Back alignment and domain information

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family	Back alignment and domain information

>TIGR01448 recD_rel helicase, putative, RecD/TraA family	Back alignment and domain information

>CHL00081 chlI Mg-protoporyphyrin IX chelatase	Back alignment and domain information

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional	Back alignment and domain information

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit	Back alignment and domain information

>TIGR01074 rep ATP-dependent DNA helicase Rep	Back alignment and domain information

>TIGR01075 uvrD DNA helicase II	Back alignment and domain information

>PLN03025 replication factor C subunit; Provisional	Back alignment and domain information

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]	Back alignment and domain information

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]	Back alignment and domain information

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX	Back alignment and domain information

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type	Back alignment and domain information

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]	Back alignment and domain information

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

>COG3587 Restriction endonuclease [Defense mechanisms]	Back alignment and domain information

>PRK13851 type IV secretion system protein VirB11; Provisional	Back alignment and domain information

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]	Back alignment and domain information

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)	Back alignment and domain information

>PRK14087 dnaA chromosomal replication initiation protein; Provisional	Back alignment and domain information

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function	Back alignment and domain information

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []	Back alignment and domain information

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A	Back alignment and domain information

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

>PRK00411 cdc6 cell division control protein 6; Reviewed	Back alignment and domain information

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]	Back alignment and domain information

>PRK08084 DNA replication initiation factor; Provisional	Back alignment and domain information

>PRK00440 rfc replication factor C small subunit; Reviewed	Back alignment and domain information

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>TIGR02928 orc1/cdc6 family replication initiation protein	Back alignment and domain information

>PRK08903 DnaA regulatory inactivator Hda; Validated	Back alignment and domain information

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H	Back alignment and domain information

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional	Back alignment and domain information

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model	Back alignment and domain information

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A	Back alignment and domain information

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases	Back alignment and domain information

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily	Back alignment and domain information

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional	Back alignment and domain information

>KOG1807 consensus Helicases [Replication, recombination and repair]	Back alignment and domain information

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

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases	Back alignment and domain information

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies	Back alignment and domain information

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B	Back alignment and domain information

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]	Back alignment and domain information

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family	Back alignment and domain information

>PTZ00112 origin recognition complex 1 protein; Provisional	Back alignment and domain information

>PRK06067 flagellar accessory protein FlaH; Validated	Back alignment and domain information

>PRK11054 helD DNA helicase IV; Provisional	Back alignment and domain information

>PRK04328 hypothetical protein; Provisional	Back alignment and domain information

>PRK06645 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

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

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]	Back alignment and domain information

>PHA02544 44 clamp loader, small subunit; Provisional	Back alignment and domain information

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA	Back alignment and domain information

>PRK13765 ATP-dependent protease Lon; Provisional	Back alignment and domain information

>PRK13826 Dtr system oriT relaxase; Provisional	Back alignment and domain information

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family	Back alignment and domain information

>PRK10646 ADP-binding protein; Provisional	Back alignment and domain information

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []	Back alignment and domain information

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit	Back alignment and domain information

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair	Back alignment and domain information

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit	Back alignment and domain information

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C	Back alignment and domain information

>PRK12422 chromosomal replication initiation protein; Provisional	Back alignment and domain information

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues	Back alignment and domain information

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]	Back alignment and domain information

>PHA02533 17 large terminase protein; Provisional	Back alignment and domain information

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

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

>PRK05896 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]	Back alignment and domain information

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

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed	Back alignment and domain information

>TIGR02902 spore_lonB ATP-dependent protease LonB	Back alignment and domain information

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB	Back alignment and domain information

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		601
4a15_A		620	Crystal Structure Of An Xpd Dna Complex Length = 62		1e-11
2vsf_A		602	Structure Of Xpd From Thermoplasma Acidophilum Leng		2e-11

>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex Length = 620

Back alignment and structure

Iteration: 1

Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 65/246 (26%), Positives = 109/246 (44%), Gaps = 34/246 (13%) Query: 28 LKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAEL 87 L+ +L LE PTG+GKTI L Y E +K++Y RT + E+ + EL Sbjct: 15 LRSSLQKSYGVALESPTGSGKTIMALKSALQY---SSERKLKVLYLVRTNSQEEQVIKEL 71 Query: 88 KLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRV---LAAENRDSVDAACRKRTASWVRA 144 R L KI AI + R N+C+ R+ L N +S+ C + R Sbjct: 72 --------RSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKK----RE 119 Query: 145 LAAENPNIETCEFFENYE--KAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFA 202 + A N C +F N++ + L + T ++ +G++ CPY + + A Sbjct: 120 VMAGNE--AACPYF-NFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDA 176 Query: 203 NVVVYSYQYLLDPKVA-------GIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQT 255 ++V+ Y Y L+ VA G+ ++ V++ DEAHN+ ++ S + ++ Sbjct: 177 DIVIAPYAYFLNRSVAEKFLSHWGVSRNQI----VIILDEAHNLPDIGRSIGSFRISVES 232 Query: 256 LEGATR 261 L A R Sbjct: 233 LNRADR 238

PyMOL of 4a15

>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum Length = 602

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		601
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	1e-115
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	6e-80
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	5e-73
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-06

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620	Back alignment and structure

 Score =  356 bits (915), Expect = e-115
 Identities = 105/595 (17%), Positives = 209/595 (35%), Gaps = 98/595 (16%)

Query: 12  FPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLI 71
           +        Q   +  L+ +L       LE PTG+GKTI  L     Y     E  +K++
Sbjct: 2   YEN---RQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYS---SERKLKVL 55

Query: 72  YCTRTVHEMEKTLAELKLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRVLAAENRDSVD 131
           Y  RT  + E+ + EL+ L +          KI AI +  R N+C+  R++   +  + +
Sbjct: 56  YLVRTNSQEEQVIKELRSLSSTM--------KIRAIPMQGRVNMCILYRMVDDLHEINAE 107

Query: 132 AACRKRTASWVRALAAENPNIETCEFFENYEK-AASAAVLPPGVYTLQDLRAFGKQQGWC 190
           +   K      R + A N     C +F    +   +   L   + T ++   +G++   C
Sbjct: 108 S-LAKFCNMKKREVMAGNE--AACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVC 164

Query: 191 PYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEM---QKESVVVFDEAHNIDNVCIEAL 247
           PY   +  +  A++V+  Y Y L+  VA          + + V++ DEAHN+ ++     
Sbjct: 165 PYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIG 224

Query: 248 SVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSN 307
           S  +  ++L  A R                    +   + L+E +               
Sbjct: 225 SFRISVESLNRADREAQAYGDPEL--------SQKIHVSDLIEMI--------------R 262

Query: 308 PALPSDILKEAVPGNIR-RAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHAG 366
            AL S + +    G++R R + F+  +R + +     + +          +V +      
Sbjct: 263 SALQSMVSERCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVEN--EKEK 320

Query: 367 IDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMP 426
           + +    +C      ++   +                          ++ I+ P D    
Sbjct: 321 VGKVPFSYCSSVASRIIAFSD---------------------QDEEKYAAILSPED---- 355

Query: 427 HIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLT 486
                 +Q +C D S  ++ + +     +  SGTL P D Y  +  F     +  ++   
Sbjct: 356 ---GGYMQAACLDPSGILEVLKES--KTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPP 410

Query: 487 RDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMD 546
            +               VS+K+D   +  + R    ++ +++  V    + +F SYS MD
Sbjct: 411 ENRYIAYY-------DGVSSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSYSLMD 462

Query: 547 EIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVAR 601
            +    +            +      D  E    L  +R+          F+V+ 
Sbjct: 463 RVENRVSF---------EHMKEYRGIDQKELYSMLKKFRR-----DHGTIFAVSG 503

PyMOL of 4a15

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1* Length = 551	Back alignment and structure

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii} Length = 540	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		601
4a15_A		620	XPD helicase, ATP-dependent DNA helicase TA0057; h	100.0
3crv_A		551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	100.0
2vl7_A		540	XPD; helicase, unknown function; 2.25A {Sulfolobus	100.0
1qde_A		224	EIF4A, translation initiation factor 4A; DEAD box	99.49
3fe2_A		242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.47
1vec_A		206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.47
3iuy_A		228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.47
3ber_A		249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.47
3dkp_A		245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.46
2oxc_A		230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.44
1q0u_A		219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.44
1wrb_A		253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.44
1t6n_A		220	Probable ATP-dependent RNA helicase; RECA-like fol	99.43
2pl3_A		236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.43
2gxq_A		207	Heat resistant RNA dependent ATPase; RNA helicase,	99.42
3bor_A		237	Human initiation factor 4A-II; translation initiat	99.39
3ly5_A		262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.38
1fuu_A		394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.34
1s2m_A		400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.32
2db3_A		434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.32
3pey_A		395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.32
2z0m_A		337	337AA long hypothetical ATP-dependent RNA helicase	99.31
2i4i_A		417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.31
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.31
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.3
3fmo_B		300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.29
2j0s_A		410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.28
3eiq_A		414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.27
3b6e_A		216	Interferon-induced helicase C domain-containing P;	99.26
3sqw_A		579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.25
3fht_A		412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.23
3i5x_A		563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.22
3tbk_A		555	RIG-I helicase domain; DECH helicase, ATP binding,	99.22
3oiy_A		414	Reverse gyrase helicase domain; topoisomerase, DNA	99.19
4a2p_A		556	RIG-I, retinoic acid inducible protein I; hydrolas	99.19
2ykg_A		696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.18
1gm5_A		780	RECG; helicase, replication restart; HET: DNA ADP;	99.16
4a2q_A		797	RIG-I, retinoic acid inducible protein I; hydrolas	99.14
3fmp_B		479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.14
2v1x_A		591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.12
1oyw_A		523	RECQ helicase, ATP-dependent DNA helicase; winged	99.11
1wp9_A		494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.08
4a2w_A		936	RIG-I, retinoic acid inducible protein I; hydrolas	99.08
3fho_A		508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.06
4gl2_A		699	Interferon-induced helicase C domain-containing P;	99.05
2eyq_A		1151	TRCF, transcription-repair coupling factor; MFD, S	99.04
1rif_A		282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.01
2fz4_A		237	DNA repair protein RAD25; RECA-like domain, DNA da	98.97
2xgj_A		1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	98.95
4a4z_A		997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	98.95
2oca_A		510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	98.94
2zj8_A		720	DNA helicase, putative SKI2-type helicase; RECA fo	98.93
4ddu_A		1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	98.92
3l9o_A		1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	98.92
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	98.9
2va8_A		715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	98.9
2p6r_A		702	Afuhel308 helicase; protein-DNA complex, SF2 helic	98.86
1gku_B		1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	98.84
3h1t_A		590	Type I site-specific restriction-modification syst	98.83
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.78
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.74
2w00_A		1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	98.7
4f92_B		1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	98.67
1tf5_A		844	Preprotein translocase SECA subunit; ATPase, helic	98.56
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.52
2fsf_A		853	Preprotein translocase SECA subunit; ATPase, DNA-R	98.52
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.51
2ipc_A		997	Preprotein translocase SECA subunit; nucleotide bi	98.48
1nkt_A		922	Preprotein translocase SECA 1 subunit; preprotein	98.45
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	98.36
4b3f_X		646	DNA-binding protein smubp-2; hydrolase, helicase;	98.13
2z83_A		459	Helicase/nucleoside triphosphatase; hydrolase, mem	97.95
2jlq_A		451	Serine protease subunit NS3; ribonucleoprotein, nu	97.86
1yks_A		440	Genome polyprotein [contains: flavivirin protease	97.85
2wv9_A		673	Flavivirin protease NS2B regulatory subunit, FLAV	97.82
2gk6_A		624	Regulator of nonsense transcripts 1; UPF1, helicas	97.81
2v6i_A		431	RNA helicase; membrane, hydrolase, transmembrane,	97.75
2whx_A		618	Serine protease/ntpase/helicase NS3; transcription	97.63
3llm_A		235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	97.6
2wjy_A		800	Regulator of nonsense transcripts 1; nonsense medi	97.52
3jux_A		822	Protein translocase subunit SECA; protein transloc	97.35
3upu_A		459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.94
3rc3_A		677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	96.71
3o8b_A		666	HCV NS3 protease/helicase; ntpase, RNA, translocat	96.7
2xau_A		773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	96.55
1w36_D		608	RECD, exodeoxyribonuclease V alpha chain; recombin	96.4
2xzl_A		802	ATP-dependent helicase NAM7; hydrolase-RNA complex	95.78
1c4o_A		664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.59
2d7d_A		661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.74
3lfu_A		647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	94.72
3e1s_A		574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.2
2w58_A		202	DNAI, primosome component (helicase loader); ATP-b	93.89
3ec2_A		180	DNA replication protein DNAC; helicase loader, rep	93.18
3n70_A		145	Transport activator; sigma-54, ntpase, PSI, MCSG,	92.78
3co5_A		143	Putative two-component system transcriptional RES	92.73
2o0j_A		385	Terminase, DNA packaging protein GP17; nucleotide-	92.7
2qgz_A		308	Helicase loader, putative primosome component; str	92.55
3cpe_A		592	Terminase, DNA packaging protein GP17; large termi	92.39
1uaa_A		673	REP helicase, protein (ATP-dependent DNA helicase	92.36
2r44_A		331	Uncharacterized protein; putative ATPase, structur	92.27
3nbx_X		500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	92.13
1pjr_A		724	PCRA; DNA repair, DNA replication, SOS response, h	91.67
3hws_A		363	ATP-dependent CLP protease ATP-binding subunit CL;	89.81
1ofh_A		310	ATP-dependent HSL protease ATP-binding subunit HSL	89.69
1a5t_A		334	Delta prime, HOLB; zinc finger, DNA replication; 2	89.29
2bjv_A		265	PSP operon transcriptional activator; AAA, transcr	89.13
3u4q_A		1232	ATP-dependent helicase/nuclease subunit A; helicas	89.01
1jbk_A		195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	88.95
1njg_A		250	DNA polymerase III subunit gamma; rossman-like fol	88.44
3te6_A		318	Regulatory protein SIR3; heterochromatin, gene sil	88.41
2chg_A		226	Replication factor C small subunit; DNA-binding pr	88.19
4fcw_A		311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	88.03
1iqp_A		327	RFCS; clamp loader, extended AAA-ATPase domain, co	87.84
2p65_A		187	Hypothetical protein PF08_0063; CLPB, malaria, str	87.84
2b8t_A		223	Thymidine kinase; deoxyribonucleoside kinase, zinc	87.82
3sqw_A		579	ATP-dependent RNA helicase MSS116, mitochondrial;	86.92
3bos_A		242	Putative DNA replication factor; P-loop containing	86.23
3pfi_A		338	Holliday junction ATP-dependent DNA helicase RUVB;	86.14
1xti_A		391	Probable ATP-dependent RNA helicase P47; alpha-bet	86.03
1sxj_C		340	Activator 1 40 kDa subunit; clamp loader, processi	85.97
1g8p_A		350	Magnesium-chelatase 38 kDa subunit; parallel beta	85.63
1ojl_A		304	Transcriptional regulatory protein ZRAR; response	85.41
1hv8_A		367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	85.08
1sxj_D		353	Activator 1 41 kDa subunit; clamp loader, processi	84.82
3h4m_A		285	Proteasome-activating nucleotidase; ATPase, PAN, A	84.47
3pey_A		395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	84.03
3syl_A		309	Protein CBBX; photosynthesis, rubisco activase, AA	83.92
3b9p_A		297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	83.88
3uk6_A		368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	83.61
2v1x_A		591	ATP-dependent DNA helicase Q1; DNA strand annealin	83.39
1l8q_A		324	Chromosomal replication initiator protein DNAA; AA	83.21
2zts_A		251	Putative uncharacterized protein PH0186; KAIC like	82.99
3pvs_A		447	Replication-associated recombination protein A; ma	82.66
1um8_A		376	ATP-dependent CLP protease ATP-binding subunit CL;	82.34
3i5x_A		563	ATP-dependent RNA helicase MSS116; protein-RNA com	82.15
3vfd_A		389	Spastin; ATPase, microtubule severing, hydrolase;	82.15
3pxi_A		758	Negative regulator of genetic competence CLPC/MEC;	82.14
1jr3_A		373	DNA polymerase III subunit gamma; processivity, pr	82.04
2i4i_A		417	ATP-dependent RNA helicase DDX3X; DEAD, structural	81.84
1hqc_A		324	RUVB; extended AAA-ATPase domain, complex with nuc	81.83
3pxg_A		468	Negative regulator of genetic competence CLPC/MEC;	81.58
2qz4_A		262	Paraplegin; AAA+, SPG7, protease, ADP, structural	81.45
2chq_A		319	Replication factor C small subunit; DNA-binding pr	81.45
3t15_A		293	Ribulose bisphosphate carboxylase/oxygenase activ	81.09
1oyw_A		523	RECQ helicase, ATP-dependent DNA helicase; winged	81.03
3u61_B		324	DNA polymerase accessory protein 44; AAA+, ATP hyd	80.56
3cf0_A		301	Transitional endoplasmic reticulum ATPase; AAA, P9	80.37
1lv7_A		257	FTSH; alpha/beta domain, four helix bundle, hydrol	80.14
2va8_A		715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	80.05

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

Probab=100.00  E-value=1.9e-66  Score=571.59  Aligned_cols=486  Identities=21%  Similarity=0.292  Sum_probs=331.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhcCcEEEEccCCChhHHHHHHHHHHHHHhCCCCCcEEEEEcccchhHHHHHHHHHhhhhh
Q 007505           14 YDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNY   93 (601)
Q Consensus        14 ~~~~r~~Q~~~~~~v~~~l~~~~~~~~EapTGtGKTla~L~~~l~~~~~~~~~~~kvv~~t~T~~~~~q~~~el~~l~~~   93 (601)
                      |++ ||+|++||.+|++++.+++++++|||||||||+|||+|++.++...  ++ ||+|+|||++|++|+++|++++...
T Consensus         2 ~~~-R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--~~-kvli~t~T~~l~~Qi~~el~~l~~~   77 (620)
T 4a15_A            2 YEN-RQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--KL-KVLYLVRTNSQEEQVIKELRSLSST   77 (620)
T ss_dssp             ----CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--TC-EEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCC-CHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--CC-eEEEECCCHHHHHHHHHHHHHHhhc
Confidence            665 9999999999999999999999999999999999999999998754  56 9999999999999999999998642


Q ss_pred             hcccCCCccceEEEeecCcccccc-chhhhhccChhhHHH---HhHHhhhHHHHhhhhcCCCCCCCccccchHHhhhc-c
Q 007505           94 QTRHLGPAAKILAIGLSSRKNLCV-NSRVLAAENRDSVDA---ACRKRTASWVRALAAENPNIETCEFFENYEKAASA-A  168 (601)
Q Consensus        94 ~~~~~~~~~~~~~~~l~~r~~lC~-~~~~~~~~~~~~~~~---~c~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~-~  168 (601)
                              .+++++.++||.++|+ ++.+..... ...++   .|..+...|..      .+...|+||.+.....+. .
T Consensus        78 --------~~~~~~~l~gr~~lC~~~~~~~~~~~-~~~~~~~~~C~~l~~~~~~------~~~~~C~~~~~~~~~gd~~~  142 (620)
T 4a15_A           78 --------MKIRAIPMQGRVNMCILYRMVDDLHE-INAESLAKFCNMKKREVMA------GNEAACPYFNFKIRSDETKR  142 (620)
T ss_dssp             --------SCCCEEECCCHHHHCSSHHHHCCCSS-CCHHHHHHHHHHHHHHHHT------TCTTSSTTCSGGGGCHHHHH
T ss_pred             --------cCeEEEEEECCCcccccChhhhhccc-chhhhHHHHHHHHHhcccc------CCCCCCCcccccCcccchhH
Confidence                    2678999999999999 988765433 23343   78877654421      123689999875321110 0


Q ss_pred             CCCCCCCCHHHHHHhccccCcchhHHHHHhhccCcEEEecCccccCHHhhhHhhh---ccCCCcEEEEeCCCChHHHHHH
Q 007505          169 VLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISK---EMQKESVVVFDEAHNIDNVCIE  245 (601)
Q Consensus       169 ~~~~~~~~~~~l~~~~~~~~~Cpy~~~r~~~~~adivv~n~~~ll~~~~~~~~~~---~l~~~~ilIiDEAHnl~~~~~~  245 (601)
                      .+...+++++++.+.|+.++.||||.+|+.+.+|||||+|||||||+.+++.+..   ..++++++||||||||+|+|++
T Consensus       143 ~l~~~~~die~l~~~~~~~~~CPy~~aR~~~~~ADvVV~ny~ylld~~~r~~~~~~~~i~p~~~ivI~DEAHNL~d~a~~  222 (620)
T 4a15_A          143 FLFDELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRS  222 (620)
T ss_dssp             HHHHHCCCHHHHHHHHHHTTCCHHHHHHHHGGGCSEEEEEHHHHTCHHHHHHHHHHHTCCGGGEEEEETTGGGHHHHHHH
T ss_pred             HhccCCCCHHHHHHHhhhcCCCccHHHHHHhhcCCEEEeCchhhcCHHHHHHHHHhhccCcCCeEEEEECCCchHHHHHH
Confidence            1133578999999999999999999999999999999999999999998865322   2468999999999999999999


Q ss_pred             hcccccCHHHHHHHHHHHHHHHHHHHHhhh-hchhHHHHH----HHHHHHHHhhcCCCccccccccCCCCChhhhhhhcC
Q 007505          246 ALSVSVRRQTLEGATRNLSRINQEIERFKA-TDAGRLRAE----YNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVP  320 (601)
Q Consensus       246 ~~s~~is~~~l~~~~~~l~~~~~~~~~~~~-~~~~~l~~~----~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  320 (601)
                      ++|.++|..+|..+.+++..+....  +.. .....+...    +..+...+..             . ..         
T Consensus       223 ~~S~~ls~~~l~~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~~~~~-------------~-~~---------  277 (620)
T 4a15_A          223 IGSFRISVESLNRADREAQAYGDPE--LSQKIHVSDLIEMIRSALQSMVSERCG-------------K-GD---------  277 (620)
T ss_dssp             HHCEEEEHHHHHHHHHHHHHTTCCE--EETTEEHHHHHHHHHHHHHHHHHHHCS-------------S-SC---------
T ss_pred             hhcceeCHHHHHHHHHHHHHHHhhh--hhhhHHHHHHHHHHHHHHHHHHHHhhc-------------c-cc---------
Confidence            9999999999999988776542100  000 001111111    1111111100             0 00         


Q ss_pred             CchhchhhHHHHHHHHHHHHHhhhhcccccccChhhHHHHHHhhhccCcchhhhhHHHHHHHHHHhhccCCCccchhHHH
Q 007505          321 GNIRRAEHFLHVLRRLVQYLRGRLETENVEKEGPVSFVASITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTI  400 (601)
Q Consensus       321 ~~i~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~~l~~~  400 (601)
                      ..+ ....+...+..+.....+.          ...++..+..           +.+.+..   ............+..+
T Consensus       278 ~~~-~~~~l~~~~~~~~~~~~~~----------l~~~~~~l~~-----------~~~~~~~---~~~~~~~~~~~~~~~~  332 (620)
T 4a15_A          278 VRI-RFQEFMEYMRIMNKRSERE----------IRSLLNYLYL-----------FGEYVEN---EKEKVGKVPFSYCSSV  332 (620)
T ss_dssp             EEE-CTHHHHHHHHHHHTCCHHH----------HHHHHHHHHH-----------HHHHHHH---HHHHTTSCCCCHHHHH
T ss_pred             cCC-ChHHHHHHHHHhhcccHHH----------HHHHHHHHHH-----------HHHHHHh---hccccccccccHHHHH
Confidence            000 0111111111110000000          0000111100           0000000   0000001112234455


Q ss_pred             HhHHHhhcccC-CceEEEEecCCCCCCCCCCCeEEEEecCccccchHHhhccCEEEEecCCCCCccchhhhcCCCCcccc
Q 007505          401 CDFATLVGTYT-RGFSIIIEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSR  479 (601)
Q Consensus       401 ~~f~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~ldps~~l~~l~~~~~svIltSgTLsp~~~f~~~Lg~~~~~~~  479 (601)
                      .+|+......+ .++..|++..+       +..|+++|+||+..|+ +| ++++||||||||+|+++|.+.||++ ....
T Consensus       333 ~~fl~~~~~~~~~~~~~~~~~~~-------~~~l~~~~l~~~~~l~-~~-~~~~~il~SaTL~p~~~~~~~lGl~-~~~~  402 (620)
T 4a15_A          333 ASRIIAFSDQDEEKYAAILSPED-------GGYMQAACLDPSGILE-VL-KESKTIHMSGTLDPFDFYSDITGFE-IPFK  402 (620)
T ss_dssp             HHHHHHHHTSCTTTEEEEEECGG-------GCEEEEEECCTHHHHG-GG-GGSEEEEEESSCCSHHHHHHHHCCC-CCEE
T ss_pred             HHHHHHHhhcCCCCEEEEEEeCC-------CcEEEEEECCHHHHHH-HH-hCCeEEEEccCCCcHHHHHHHhCCC-ceee
Confidence            56665553333 37888887542       4689999999999999 99 9999999999999999999999998 6667


Q ss_pred             cceeeecCCceeeeeeecCCCCCcceeeeccCCChHHHHHHHHHHHHhhcccCCeEEEEecCHHHHHHHHHHHHhcchHH
Q 007505          480 SFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILK  559 (601)
Q Consensus       480 ~~~~~~~~~~~~~~~i~~g~~~~~l~s~f~~r~~~~~~~~l~~~i~~~~~~~~gg~LVfFpSy~~l~~v~~~~~~~~~~~  559 (601)
                      +++++++..+....+ +.     .++++|+.|+ +.+++++++.|.++++.+|||+|||||||.+|+++++.|+.     
T Consensus       403 ~~~spf~~~~~~~~~-~~-----~~~~~~~~r~-~~~~~~~~~~i~~l~~~~~g~~lvlF~Sy~~l~~v~~~l~~-----  470 (620)
T 4a15_A          403 KIGEIFPPENRYIAY-YD-----GVSSKYDTLD-EKELDRMATVIEDIILKVKKNTIVYFPSYSLMDRVENRVSF-----  470 (620)
T ss_dssp             ECCCCSCGGGEEEEE-EC-----CC-------C-HHHHHHHHHHHHHHHHHHCSCEEEEESCHHHHHHHTSSCCS-----
T ss_pred             ecCCCCCHHHeEEEE-eC-----CCCCcCCCCC-HHHHHHHHHHHHHHHHhCCCCEEEEeCCHHHHHHHHHHHHh-----
Confidence            788888877765443 22     3677887775 45678999999999999999999999999999999999962     


Q ss_pred             HHhcCCeeEEecCC--chhHHHHHHHHHHhcCCCCCeEEEEEcC
Q 007505          560 EIMQHKLVFIETQD--VVETTLALDNYRKACDCGRGAVFFSVAR  601 (601)
Q Consensus       560 ~l~~~k~if~E~~~--~~~~~~~l~~fk~~~~~~~gaiLfaV~R  601 (601)
                       +.  ..   |+++  ..++..++++|+     ++|||||||+|
T Consensus       471 -~~--~~---~~q~~~~~~~~~ll~~f~-----~~~~vL~~v~~  503 (620)
T 4a15_A          471 -EH--MK---EYRGIDQKELYSMLKKFR-----RDHGTIFAVSG  503 (620)
T ss_dssp             -CC--EE---CCTTCCSHHHHHHHHHHT-----TSCCEEEEETT
T ss_pred             -cc--hh---ccCCCChhHHHHHHHHhc-----cCCcEEEEEec
Confidence             21  22   7776  346788999999     47899999975

PyMOL of 4a15

>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

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}	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

>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

>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

>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

>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

>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

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} 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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

>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

>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

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

>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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

>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

>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

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

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

>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

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A	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

>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

>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

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A	Back alignment and structure

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_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

>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

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A	Back alignment and structure

>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

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}	Back alignment and structure

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

>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

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*	Back alignment and structure

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}	Back alignment and structure

>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

>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

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*	Back alignment and structure

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*	Back alignment and structure

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}	Back alignment and structure

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*	Back alignment and structure

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}	Back alignment and structure

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}	Back alignment and structure

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*	Back alignment and structure

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}	Back alignment and structure

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*	Back alignment and structure

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19	Back alignment and structure

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}	Back alignment and structure

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}	Back alignment and structure

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*	Back alignment and structure

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A	Back alignment and structure

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*	Back alignment and structure

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*	Back alignment and structure

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*	Back alignment and structure

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*	Back alignment and structure

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20	Back alignment and structure

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*	Back alignment and structure

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}	Back alignment and structure

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}	Back alignment and structure

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*	Back alignment and structure

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20	Back alignment and structure

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}	Back alignment and structure

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*	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

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A	Back alignment and structure

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}	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

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20	Back alignment and structure

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G	Back alignment and structure

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}	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

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20	Back alignment and structure

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}	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

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*	Back alignment and structure

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}	Back alignment and structure

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*	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

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*	Back alignment and structure

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}	Back alignment and structure

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}	Back alignment and structure

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20	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

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}	Back alignment and structure

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}	Back alignment and structure

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*	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

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*	Back alignment and structure

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}	Back alignment and structure

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}	Back alignment and structure

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A	Back alignment and structure

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A	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

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*	Back alignment and structure

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}	Back alignment and structure

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20	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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		601
d2j0sa1		222	Probable ATP-dependent RNA helicase DDX48 {Human (	99.34
d1t6na_		207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.32
d2g9na1		218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.31
d1veca_		206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.3
d1wp9a1		200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.29
d1qdea_		212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.29
d1gkub1		237	Helicase-like "domain" of reverse gyrase {Archaeon	99.29
d1wrba1		238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.27
d1hv8a1		208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.25
d1oywa2		206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.2
d1s2ma1		206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.13
d1q0ua_		209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.12
d2p6ra3		202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.11
d2eyqa3		233	Transcription-repair coupling factor, TRCF {Escher	99.01
d1gm5a3		264	RecG helicase domain {Thermotoga maritima [TaxId:	98.95
d2bmfa2		305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.91
d1yksa1		140	YFV helicase domain {Yellow fever virus [TaxId: 11	98.82
d2fz4a1		206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.19
d1z63a1		230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.17
d1rifa_		282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	98.13
d1z3ix2		298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.56
d1a1va1		136	HCV helicase domain {Human hepatitis C virus (HCV)	97.53
d1uaaa1		306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	96.36
d1t5la1		413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.08
d1pjra1		318	DEXX box DNA helicase {Bacillus stearothermophilus	95.9
d1w36d1		359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.8
d1fnna2		276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	94.35
d1g8pa_		333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.99
d1c4oa1		408	Nucleotide excision repair enzyme UvrB {Thermus th	93.74
g1qhh.1		623	DEXX box DNA helicase {Bacillus stearothermophilus	92.78
d1in4a2		238	Holliday junction helicase RuvB {Thermotoga mariti	92.78
d1ofha_		309	HslU {Haemophilus influenzae [TaxId: 727]}	92.17
d1a5ta2		207	delta prime subunit of DNA polymerase III, N-domai	92.08
d1iqpa2		231	Replication factor C {Archaeon Pyrococcus furiosus	91.96
d1ixsb2		239	Holliday junction helicase RuvB {Thermus thermophi	91.42
d1w5sa2		287	CDC6-like protein APE0152, N-terminal domain {Aero	91.11
d1g6oa_		323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	91.08
d1sxjc2		227	Replication factor C3 {Baker's yeast (Saccharomyce	90.47
d1sxjb2		224	Replication factor C4 {Baker's yeast (Saccharomyce	90.41
d1lv7a_		256	AAA domain of cell division protein FtsH {Escheric	89.81
d1g41a_		443	HslU {Haemophilus influenzae [TaxId: 727]}	89.8
d1tf5a3		273	Translocation ATPase SecA, nucleotide-binding doma	89.68
d1nkta3		288	Translocation ATPase SecA, nucleotide-binding doma	89.44
d1cr2a_		277	Gene 4 protein (g4p, DNA primase), helicase domain	88.41
d1ixza_		247	AAA domain of cell division protein FtsH {Thermus	88.2
d1gvnb_		273	Plasmid maintenance system epsilon/zeta, toxin zet	88.07
d1l8qa2		213	Chromosomal replication initiation factor DnaA {Aq	87.97
d1um8a_		364	ClpX {Helicobacter pylori [TaxId: 210]}	87.83
d1ny5a2		247	Transcriptional activator sigm54 (NtrC1), C-termin	87.26
d1sxjd2		237	Replication factor C2 {Baker's yeast (Saccharomyce	87.12
d2i3ba1		189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	86.7
d1svma_		362	Papillomavirus large T antigen helicase domain {Si	86.26
d1njfa_		239	delta prime subunit of DNA polymerase III, N-domai	85.89
d1sxje2		252	Replication factor C5 {Baker's yeast (Saccharomyce	85.84
d1d2na_		246	Hexamerization domain of N-ethylmalemide-sensitive	85.26
d1sxja2		253	Replication factor C1 {Baker's yeast (Saccharomyce	84.36
d1okkd2		207	GTPase domain of the signal recognition particle r	83.89
d1hv8a2		155	Putative DEAD box RNA helicase {Archaeon Methanoco	83.78
d1a1va1		136	HCV helicase domain {Human hepatitis C virus (HCV)	82.79
d1e32a2		258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	82.61
d2fz4a1		206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	81.74
d1tf7a1		242	Circadian clock protein KaiC {Synechococcus sp. st	81.25
d1qvra3		315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	81.17
d1r6bx3		315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	81.05
d1lw7a2		192	Transcriptional regulator NadR, ribosylnicotinamid	80.75

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=1.7e-12  Score=121.30  Aligned_cols=76  Identities=12%  Similarity=0.104  Sum_probs=64.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhhcCcEEEEccCCChhHHHHHHHHHHHHHhCCCCCcEEEEEcccchhHHHHHHHHHhhh
Q 007505           12 FPYDNIYPEQYSYMLELKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLH   91 (601)
Q Consensus        12 fp~~~~r~~Q~~~~~~v~~~l~~~~~~~~EapTGtGKTla~L~~~l~~~~~~~~~~~kvv~~t~T~~~~~q~~~el~~l~   91 (601)
                      .+|..|+|.|.+.+..+.    +|+++++.||||+|||+||++|.+........+. +.+|.++|..+..|+.++++++.
T Consensus        35 ~g~~~pt~IQ~~aIp~il----~g~dvi~~a~TGSGKTlayllPil~~l~~~~~~~-~~lil~PtreLa~Qi~~~~~~l~  109 (222)
T d2j0sa1          35 YGFEKPSAIQQRAIKQII----KGRDVIAQSQSGTGKTATFSISVLQCLDIQVRET-QALILAPTRELAVQIQKGLLALG  109 (222)
T ss_dssp             HTCCSCCHHHHHHHHHHH----TTCCEEEECCTTSSHHHHHHHHHHHTCCTTSCSC-CEEEECSSHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHH----CCCCeEEEcCcchhhhhhhcccccccccccccCc-eeEEecchHHHHHHHHHHHHHHh
Confidence            368888999988776654    6899999999999999999999998765554444 89999999999999999888874


Q ss_pred             h
Q 007505           92 N   92 (601)
Q Consensus        92 ~   92 (601)
                      +
T Consensus       110 ~  110 (222)
T d2j0sa1         110 D  110 (222)
T ss_dssp             T
T ss_pred             C
Confidence            3

PyMOL of d2j0sa1

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}	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

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

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

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

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}	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

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

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {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

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

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}	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

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

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	Back information, alignment and structure

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}	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

>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

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}	Back information, alignment and structure

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}	Back information, alignment and structure

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}	Back information, alignment and structure

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}	Back information, alignment and structure

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}	Back information, alignment and structure

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}	Back information, alignment and structure

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}	Back information, alignment and structure

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}	Back information, alignment and structure

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}	Back information, alignment and structure

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}	Back information, alignment and structure

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}	Back information, alignment and structure

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}	Back information, alignment and structure

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}	Back information, alignment and structure

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}	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

>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

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}	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

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}	Back information, alignment and structure

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}	Back information, alignment and structure