Citrus Sinensis ID: 001825

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-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930-------940-------950-------960-------970-------980-------990------1000------101

MLMADNAWLCGEVSAADEFADDQGLSIDMDTLLGILEEEKQPDRVKSSPGDLSLRNLSQDELVQDVGSHSNLQLQSGFKGDMRDIATYPLYGLEISGAESGGLGDSSSQLEPTEQKCSPLQTCSASFSDWFNQNSGTCCPESVGISQFETPGCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVGSHIDSRSVDASPSSITENFDERYGHYGASIGNRLGSSVPEGNLCTYVDVPYTDAEVSSHNVASTDSTICHGSEIISDDDYYSAMPCYINTGDTIFGDPSSFNFQHLLSSEETATKPKDEEGEFTTEIACSSSGLVLNAQGGPGKGSMLKVPAIDYLDAKRQCEDSKNGLPIYGNSLSNITLGDGKRSAQPCTYSHSHSSRTKQMVFAKDEGNDDLFPCWSTVSDSVEPIDEAVGRNSSYHDGCNSFPFKDSGQSFIGLSPSLLSQNQVVHAKEEHEDLILESKRARFCQEICDGSSSRSPIDGRHLSLNLNGSRQYFPYAQPSTLNKKELDGVKEDMEAEIKTRSMASHLLKLSPESIQSNSSDCKSHVDDEPDICILEDISQPARSNQSLVLGKTLSMNRSACSNHSVALGKPVVTSQHSSYSDYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLETLNLDEEDNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPKQPLGDKEDEEEKMKIEGEDLPPMYCSSSKKRKCPPSSDRKGSKQKKGPDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGEDCLLY

ccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHcccccccccccccHHHHcccccccccccccccccHHHHcccccccccccccccccccHHcccccccccccEEEcccHHHHHHHHHHHHHHccccccEEEEEEcccccccccccccccEEEcHHHHHHHHcccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEccccccccHHHHHHHHHHHccccEEEEEcccccccHHHHHHHHHHccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHccccccccccc

cccccccccccEEEcccccccccccEEEHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccccccccEEEccccccccccccccccEEEEccccccccEEEcccccccEccccccccccHcHcccccccccccccccEEEEEEEEcccccccccccccEEEccccccccccccccccEEEcccccccccccccccccccccHHHHHHHHHHcccccHHcccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccHcccccccccEEcccccEEEEEccccHHHHcccccccccccccccccccccccccccccccccccccccEccccccccccccccccHHcccccEEEcHHHcHHHHHccccccccccccccccccccccHcccccccHcHccHHHHHHHHccHHHHHHHHHcccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccHHHHHHHHHcccccccHHHHHccccHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccEEcccccccHHHHHHHHHHHccccccccccHccccccccccccccccccHHHHHHHHHHHHHcccccccccccccHHcccccccccccEEEEccHHHHHHHHHHHHHHcccccccEEEEEccccccccHHHHHHccEEEEEHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccHHHHHHHHHHEEHHHHHHHHccHHHHHHHHHHHHHHccEEEcccHHHccHHHHHHHHHHHcccccccHHHHHHHHHcHHHcccHHHHHHHHHHHHHHHHHHHHHccEEEc

mlmadnawlcgevsaadefaddqglsidMDTLLGIleeekqpdrvksspgdlslrnlsqDELVqdvgshsnlqlqsgfkgdmrdiatyplygleisgaesgglgdsssqlepteqkcsplqtcsasfsdwfnqnsgtccpesvgisqfetpgcstassfsegdgyhfldhrntldfgvlgakagirfghvgshidsrsvdaspssitenfderyghygasignrlgssvpegnlctyvdvpytdaevsshnvastdstichgseiisdddyysampcyintgdtifgdpssfnfqhllsseetatkpkdeegeftteiacsssglvlnaqggpgkgsmlkvpaidyldakrqcedsknglpiygnslsnitlgdgkrsaqpctyshshssrtKQMVFAkdegnddlfpcwstvsdsvepideavgrnssyhdgcnsfpfkdsgqsfiglspsllsqnqvvhAKEEHEDLILESKRARFCQEicdgsssrspidgrhlslnlngsrqyfpyaqpstlnkkeldgVKEDMEAEIKTRSMASHLlklspesiqsnssdckshvddepdiciledisqparsnqslvlgktlsmnrsacsnhsvalgkpvvtsqhssysdypgypgvpltglggmkskaSDERLILQVAMQgisqpnaeasapdgvlavPLLRHQRIALSWMVQketsslhcsggiladdqglgkTISTIALILkerppsfrteddnKRQLEtlnldeedngiqvngldlvkqesdycrvvpngssaksfnfveqakgrpaagtlvvcpTSVLRQWAEELRNKVTSKGSLSVLVYhgssrtkdpcelakfdVVITTYSIVSmevpkqplgdkedeeekmkiegedlppmycssskkrkcppssdrkgskqkkgpdgllldivagplakvgWFRVVLDEAQSIKNHRTQVARACWGLrakrrwclsgtpiQNAIDDLYSYFrflrydpfavYKSFCSMikvpisknpvkGYKKLQAVLKTIMLRRTKGEDCLLY

MLMADNAWLCGEVSAADEFADDQGLSIDMDTLLGILEeekqpdrvksspgdlSLRNLSQDELVQDVGshsnlqlqsgfkgdMRDIATYPLYGLEISGAESGGLGDSSSQLEPTEQKCSPLQTCSASFSDWFNQNSGTCCPESVGISQFETPGCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVgshidsrsvdaspSSITENFDERYGHYGASIGNRLGSSVPEGNLCTYVDVPYTDAEVSSHnvastdsticHGSEIISDDDYYSAMPCYINTGDTIFGDPSSFNFQHLLSSEETATKPKDEEGEFTTEIACSSSGLVLNAQGGPGKGSMLKVPAIDYLDAKRQCEDSKNGLPIYGNSLSNITLGDGKRSAQPctyshshssrtKQMVFAKDEGNDDLFPCWSTVSDSVEPIDEAVGRNSSYHDGCNSFPFKDSGQSFIGLSPSLLSQNQVVHAKEEHEDLILESKRARFCQEIcdgsssrspidgRHLSLNLNGSRQyfpyaqpstlnkkeldGVKEDMEAEIKTRSMASHLLKLSPESIQSNSSDCKSHVDDEPDICILedisqparsNQSLVLGKTLSMNRSACSNHSVALGKPVVTSQHSSYSDYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALIlkerppsfrteddNKRQLEtlnldeedngiqVNGLDLVKQESDYCRVVPngssaksfnfVEQAkgrpaagtlvvCPTSVLRQWAEELrnkvtskgslSVLVYhgssrtkdpcelAKFDVVITTYSIvsmevpkqplgdkedeeekmkiegedlppmycssskkrkcppssdrkgskqkkgpdgLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKvpisknpvkgyKKLQAVLKTIMlrrtkgedclly

MLMADNAWLCGEVSAADEFADDQGLSIDMDTLLGILEEEKQPDRVKSSPGDLSLRNLSQDELVQDVGSHSNLQLQSGFKGDMRDIATYPLYGLEISGAESGGLGDSSSQLEPTEQKCSPLQTCSASFSDWFNQNSGTCCPESVGISQFETPGCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVGSHIDSRSVDASPSSITENFDERYGHYGASIGNRLGSSVPEGNLCTYVDVPYTDAEVSSHNVASTDSTICHGSEIISDDDYYSAMPCYINTGDTIFGDPSSFNFQHLLSSEETATKPKDEEGEFTTEIACSSSGLVLNAQGGPGKGSMLKVPAIDYLDAKRQCEDSKNGLPIYGNSLSNITLGDGKRSAQPCTYSHSHSSRTKQMVFAKDEGNDDLFPCWSTVSDSVEPIDEAVGRNSSYHDGCNSFPFKDSGQSFIGLSPSLLSQNQVVHAKEEHEDLILESKRARFCQEICDGSSSRSPIDGRHLSLNLNGSRQYFPYAQPSTLNKKELDGVKEDMEAEIKTRSMASHLLKLSPESIQSNSSDCKSHVDDEPDICILEDISQPARSNQSLVLGKTLSMNRSACSNHSVALGKPVVTSQHSSYSDYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLETLNLDEEDNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPKQPLGdkedeeekmkiegedLPPMYcssskkrkcppssdrkGSKQKKGPDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGEDCLLY

*****NAWLCGEVSAADEFADDQGLSIDMDTLLGIL*******************************************GDMRDIATYPLYGLEI***************************CSASFSDWFNQNSGTCCPESVGISQFETPGCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVGSHI***************FDERYGHYGASIGNRLGSSVPEGNLCTYVDVPYTDAEVSSHNVASTDSTICHGSEIISDDDYYSAMPCYINTGDTIFGDPSSFNFQH****************************LVL***********LKVPAIDYLDAKR*C*****GLPIYGNSL**I*********************************DDLFPCWSTVSDSV***************GCNSFPF******FIGL*******************LILESKRARFCQEIC**********************************************************************************ICIL**************************************************Y**V****************LILQVA***************GVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILK***************************IQVNGLDLVKQESDYCRVVPNG**AKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSM*****************************************************GLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTK*******

*******WLCGEVSAADEFADDQGLSIDMDTLLGIL*********************************************************************************************WFNQNSGTCCP**V*****************************TLD******************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************ERLILQVA*****************LAVPLLRHQRIALSWMVQK*************DDQGLGKTISTIALILKERPPSFRTE*******************************************************PAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPKQPLGDK***************************************KGPDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKG***LLY

MLMADNAWLCGEVSAADEFADDQGLSIDMDTLLGILEEEK**********DLSLRNLSQDELVQDVGSHSNLQLQSGFKGDMRDIATYPLYGLEISGAES********************QTCSASFSDWFNQNSGTCCPESVGISQFETPGCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVGSHID**********ITENFDERYGHYGASIGNRLGSSVPEGNLCTYVDVPYTDAEVSSHNVASTDSTICHGSEIISDDDYYSAMPCYINTGDTIFGDPSSFNFQHLLSSEE***********FTTEIACSSSGLVLNAQGGPGKGSMLKVPAIDYLDAKRQCEDSKNGLPIYGNSLSNITLG*******************KQMVFAKDEGNDDLFPCWSTVSDSVEPIDEAVGRNSSYHDGCNSFPFKDSGQSFIGLSPSLLSQNQVVHAKEEHEDLILESKRARFCQEICDGSSSRSPIDGRHLSLNLNGSRQYFPYAQPSTLNKKELDGVKEDMEAEIKTRSMASHLLKLSP**************DDEPDICILEDISQPARSNQSLVLGKTLSMNRSACSNHSVALGKPVVTSQHSSYSDYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLETLNLDEEDNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPKQ************KIEGEDLPPMY**********************GPDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGEDCLLY

****DNAWLCGEVSAADEFADDQGLSIDMDTLLGILEEE*******************************************RDIA***************************************************CCPES**I*QF*T*GCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVGSHIDSRSVDASPSSITENFDERYGHYGASIGNRLGSSVPEGNLCTYVDVPYTDAEVSSHNVASTDSTICHGSEIISDDDYYSAMPCYINTGDTIFGDPSSFNFQHLLSSEETATKPKDEEGEFTTEIACSSSGLVLNAQGGPGKGSMLKVPAIDYLDAKRQCEDSKNGLPIYGNSLSNITLGDGKRSAQPCTYSHSHSSRTKQMVFAKDEGNDDLFPCWSTVSDSVEPI********SYHDGCNSFPFKDSGQSFIGLSPSLLSQNQVVHAKEEHEDLILESKRARFCQEICDGSSSRSPIDGRHLSLNLNGSRQYFPYAQPSTLNKKELDGVKEDMEAEIKT***ASHLLKLSP******************************************************************************************DERLILQVAMQ*******EASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKER***********************NGIQVNGLDLVKQESDYC********************RPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPK*******************************************QKKGPDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGEDCLLY

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		1009	2.2.26 [Sep-21-2011]
Q5NC05		1138	Transcription termination	yes	no	0.288	0.255	0.314	1e-40
Q9UNY4		1162	Transcription termination	yes	no	0.262	0.228	0.315	6e-38
O60177		1040	Uncharacterized ATP-depen	yes	no	0.252	0.245	0.292	3e-37
Q9FNI6		1029	Putative SWI/SNF-related	no	no	0.242	0.238	0.328	5e-37
O13762		897	Uncharacterized ATP-depen	no	no	0.237	0.267	0.310	2e-33
Q4WVM1		1245	DNA repair protein rad5 O	no	no	0.229	0.186	0.309	9e-32
P0CQ67		1198	DNA repair protein RAD5 O	N/A	no	0.256	0.216	0.310	6e-30
P0CQ66		1198	DNA repair protein RAD5 O	no	no	0.256	0.216	0.310	6e-30
Q10332		830	Uncharacterized ATP-depen	no	no	0.239	0.291	0.311	6e-30
Q6PCN7		1003	Helicase-like transcripti	no	no	0.173	0.174	0.305	6e-28

>sp\|Q5NC05\|TTF2_MOUSE Transcription termination factor 2 OS=Mus musculus GN=Ttf2 PE=1 SV=2	Back alignment and function desciption

 Score =  169 bits (428), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 119/378 (31%), Positives = 188/378 (49%), Gaps = 87/378 (23%)

Query: 625  LTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLRHQRIALSWMVQKETS 684
            L  +  + S+A DE   L  +++      A A  P G L VPLL HQ+ AL+W++ +E  
Sbjct: 508  LYNVWKITSEAIDE---LHRSLKSCPGETAVAEDPAG-LKVPLLLHQKQALAWLLWRE-- 561

Query: 685  SLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLETLNLDEEDNGIQVNGL 744
            S    GGILADD GLGKT++ IALIL ++  + +   + +R      L + D+ +     
Sbjct: 562  SQKPQGGILADDMGLGKTLTMIALILTKK--NQQKSKEKERSEPVTWLSKNDSSV----- 614

Query: 745  DLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKG 804
                                   F        ++GTL+VCP S++  W  E+  +VTS  
Sbjct: 615  -----------------------FT-------SSGTLIVCPASLIHHWKNEVEKRVTS-N 643

Query: 805  SLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPKQPLGDKEDEEEKMKIEGEDLPP 864
             L + +YHG +R++    L+ +D+VITTYS+++ E+P              K EGE    
Sbjct: 644  RLRIYLYHGPNRSRHAKVLSTYDIVITTYSLLAKEIPT------------TKQEGEV--- 688

Query: 865  MYCSSSKKRKCPPSSDRKGSKQKKGPDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQ 924
                        P ++            L ++  + PL +V W R++LDEA ++KN R Q
Sbjct: 689  ------------PGAN------------LSVEGTSAPLLQVVWARIILDEAHNVKNPRVQ 724

Query: 925  VARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVK 984
             + A   L+A+ RW ++GTPIQN + D+YS  +FLR  PF  +    S+ K  +    +K
Sbjct: 725  TSIAVCKLQAQARWAVTGTPIQNNLLDMYSLMKFLRCSPFDEF----SLWKSQVDNGSMK 780

Query: 985  GYKKLQAVLKTIMLRRTK 1002
            G ++L  + K+++LRRTK
Sbjct: 781  GGERLSILTKSLLLRRTK 798

DsDNA-dependent ATPase which acts as a transcription termination factor by coupling ATP hydrolysis with removal of RNA polymerase II from the DNA template. May contribute to mitotic transcription repression. May also be involved in pre-mRNA splicing.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>sp\|Q9UNY4\|TTF2_HUMAN Transcription termination factor 2 OS=Homo sapiens GN=TTF2 PE=1 SV=2	Back alignment and function description

>sp\|O60177\|YG42_SCHPO Uncharacterized ATP-dependent helicase C23E6.02 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC23E6.02 PE=3 SV=1	Back alignment and function description

>sp\|Q9FNI6\|SM3L2_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 2 OS=Arabidopsis thaliana GN=At5g22750 PE=2 SV=1	Back alignment and function description

>sp\|O13762\|YF2C_SCHPO Uncharacterized ATP-dependent helicase C17A2.12 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC17A2.12 PE=3 SV=1	Back alignment and function description

>sp\|Q4WVM1\|RAD5_ASPFU DNA repair protein rad5 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=rad5 PE=3 SV=2	Back alignment and function description

>sp\|P0CQ67\|RAD5_CRYNB DNA repair protein RAD5 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=RAD5 PE=3 SV=1	Back alignment and function description

>sp\|P0CQ66\|RAD5_CRYNJ DNA repair protein RAD5 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=RAD5 PE=3 SV=1	Back alignment and function description

>sp\|Q10332\|YBMA_SCHPO Uncharacterized ATP-dependent helicase C582.10c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC582.10c PE=1 SV=1	Back alignment and function description

>sp\|Q6PCN7\|HLTF_MOUSE Helicase-like transcription factor OS=Mus musculus GN=Hltf PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		1009
359494872		1430	PREDICTED: uncharacterized protein LOC10	0.945	0.667	0.497	0.0
147852279		1435	hypothetical protein VITISV_020421 [Viti	0.921	0.648	0.473	0.0
255560782		1109	DNA repair helicase rad5,16, putative [R	0.894	0.814	0.469	0.0
356557665		1307	PREDICTED: uncharacterized protein LOC10	0.769	0.593	0.451	1e-172
356546663		1337	PREDICTED: uncharacterized protein LOC10	0.842	0.635	0.413	1e-172
296080908		1187	unnamed protein product [Vitis vinifera]	0.770	0.654	0.415	1e-169
449434350		1286	PREDICTED: ATP-dependent helicase ULS1-l	0.698	0.548	0.482	1e-168
449479615		1239	PREDICTED: ATP-dependent helicase ULS1-l	0.698	0.569	0.480	1e-166
357446441		1314	Helicase-like transcription factor [Medi	0.855	0.656	0.404	1e-164
224116170		800	chromatin remodeling complex subunit [Po	0.371	0.468	0.723	1e-150

>gi\|359494872\|ref\|XP_002263027.2\| PREDICTED: uncharacterized protein LOC100265351 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  854 bits (2207), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 522/1050 (49%), Positives = 649/1050 (61%), Gaps = 96/1050 (9%)

Query: 3    MADNAWLCGEVSAADEFADDQGLSIDMDTLLGILEEEKQPDRVKSSPGDLSLRNLSQDEL 62
            MADN W   + S  +  ADD+ LSID+++   IL E+  PD ++SSP D   +N+SQDE 
Sbjct: 1    MADNNW---DFSFNEFSADDEELSIDLESFYSILGED--PDPMQSSPEDFPFKNVSQDES 55

Query: 63   VQDVGSHSNLQ-----------------LQSGFKGDMRDIATYPLYGLEISGAESGGLGD 105
              D G H N Q                 L+  F  +     T    GL     ES G   
Sbjct: 56   APDFGHHDNSQPHGFQELGRASSLGDEFLRHSFNSEASHSITRGSDGL----FESAGNSI 111

Query: 106  SSSQLEPTEQKCSPLQTCSASFSDWFNQNSG--TCCPESVGISQ--------------FE 149
                  P+    SP+++ S S +DW +  SG  TCC E  G+SQ              +E
Sbjct: 112  IECAKLPSAHAGSPVRSGSGSLNDWISHVSGQETCCKERSGVSQDALSYNRVDSKEIQYE 171

Query: 150  TPGCSTASSFSEGDGYHFLDHRNTLDFGVLGAKAGIRFGHVGSHIDSRSVDASPSSITEN 209
             P CSTA SF+ G+  +  D+ N LD   L      +F H+G  I S    AS S +TEN
Sbjct: 172  IPNCSTAFSFAAGNSNYASDYTNGLDLNHLNGDTEAQFKHMGVEIHSEY--ASNSMVTEN 229

Query: 210  FDERYGHYGASIGNRLGSSVPEGNL-CTYVDVPYTDAEVSSHNVASTDSTICHGSEIISD 268
             D   G Y  +I    G  V  G   CT + +   DA++SSH+V  T+S+IC   +++ +
Sbjct: 230  SDIGLGSYEPAIEKSTGDLVTGGKYSCTSMTISLRDADISSHDVNHTESSICQIPDVVYE 289

Query: 269  D-DYYSAMPCYINTGDTIFGDPSS------FNFQHLLSSEETATKPKDEEGEFTTEIACS 321
            + + YSA+   ++   ++F DPSS      F+ Q + SSEE     KDE  E + E  C 
Sbjct: 290  NSEDYSAVQYCLSADGSLFSDPSSQYMPDCFDLQFMPSSEEMLINMKDENEELSAENTCL 349

Query: 322  SSGLVLNAQGGPGKGSMLKVPAIDYLDAK---RQCEDSKNGLPIYGNSLSNITLG--DGK 376
            +S + L+        S ++    +Y D K      E S    P  GNS SN   G  D  
Sbjct: 350  NSKMNLSQDARAS--SFVQKGLNNYSDVKGLNFNHEGSNYVSPTSGNSSSNAGYGSNDDI 407

Query: 377  RSAQPCTYSHSHSSRTKQMVFAKDEGNDDLFPCWSTVSDSVEPIDEAVGRNSSYHDGCNS 436
            RS Q  T S S+ S  ++ +  KDE  D+L      +    E +DEAV    S       
Sbjct: 408  RSIQLSTCSQSYMSNKRRAICIKDERKDELVA--PGICQPNEVVDEAVNDRFSLGVDARV 465

Query: 437  FPFKDSGQSFIGLSPSLLSQNQVVHAKEEHEDLILESKRARFCQEICDGSSSRSPIDGRH 496
            F  K+S Q      P + S+  +  AK+E+EDL L SKR R CQ I D  S RS   G  
Sbjct: 466  FADKNSRQMLSCFPPFISSKKNLFDAKDENEDLYLASKRPRHCQVIGDELSGRSQSGGGP 525

Query: 497  LSLNLNGSRQYFPYAQPSTLNKKELDGVKEDMEAE-IKTRSMASHLLKLSPESIQSNSSD 555
            L      S Q  P  + ST++ K+LD +K++ E + I+ +SM S+L K+SPESIQSNS D
Sbjct: 526  LD---TVSEQLIPSVKQSTVSNKQLDYIKDEKEGKLIQPKSMGSYLSKVSPESIQSNSLD 582

Query: 556  CKSHVDDEPDICILEDISQPARSNQSLVLGKTLSMNRSACSNHSVALGKPVVTSQHSSYS 615
             +SH+DD+ DICILEDIS+P RSN SL+LGK+L                  V++Q   YS
Sbjct: 583  HRSHIDDDTDICILEDISEPVRSNSSLLLGKSL------------------VSTQR--YS 622

Query: 616  DYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLRHQRIAL 675
            D      +  TG+ GM+++ +DERLI +VA+Q +SQP +EAS PDGVL VPLLRHQRIAL
Sbjct: 623  D-----SLHNTGVVGMRNRTNDERLIFRVALQDLSQPKSEASPPDGVLTVPLLRHQRIAL 677

Query: 676  SWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRT--EDDNKRQLETLNLD 733
            SWMVQKET+SLHCSGGILADDQGLGKT+STIALILKERP S R   ED  + +LETLNLD
Sbjct: 678  SWMVQKETASLHCSGGILADDQGLGKTVSTIALILKERPTSSRACQEDMKQSELETLNLD 737

Query: 734  EEDNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWA 793
            E+D+  +V  LD  KQ +D C V+ +GSS K  N   Q KGRPAAGTLVVCPTSVLRQWA
Sbjct: 738  EDDD--KVPELDGTKQAADSCEVMSHGSSMKKENAFVQGKGRPAAGTLVVCPTSVLRQWA 795

Query: 794  EELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVVITTYSIVSMEVPKQPLGDKEDEEE 853
            EELR+KVTSK +LSVLVYHGS+RTKDPCELA++DVV+TTYSIVSMEVPKQPL DK D+EE
Sbjct: 796  EELRSKVTSKANLSVLVYHGSNRTKDPCELARYDVVLTTYSIVSMEVPKQPLVDK-DDEE 854

Query: 854  KMKIEGEDLPPMYCSSSKKRKCPPSSDRKGSKQKKGPDGLLLDIVAGPLAKVGWFRVVLD 913
            K+K E   + P   SS+KKRK PPSSD+K  K KK  DG LL+ VA PLA+VGWFRVVLD
Sbjct: 855  KVKPEAH-VSPTELSSNKKRKYPPSSDKKCLKDKKAMDGALLESVARPLARVGWFRVVLD 913

Query: 914  EAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSM 973
            EAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNA+DDLYSYFRFLRYDP+AVYKSFCS 
Sbjct: 914  EAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAVDDLYSYFRFLRYDPYAVYKSFCST 973

Query: 974  IKVPISKNPVKGYKKLQAVLKTIMLRRTKG 1003
            IKVPI++NP  GY+KLQAVLKTIMLRRTKG
Sbjct: 974  IKVPITRNPTNGYRKLQAVLKTIMLRRTKG 1003

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|147852279\|emb\|CAN82215.1\| hypothetical protein VITISV_020421 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|255560782\|ref\|XP_002521404.1\| DNA repair helicase rad5,16, putative [Ricinus communis] gi\|223539303\|gb\|EEF40894.1\| DNA repair helicase rad5,16, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|356557665\|ref\|XP_003547135.1\| PREDICTED: uncharacterized protein LOC100805307 [Glycine max]	Back alignment and taxonomy information

>gi\|356546663\|ref\|XP_003541743.1\| PREDICTED: uncharacterized protein LOC100792901 [Glycine max]	Back alignment and taxonomy information

>gi\|296080908\|emb\|CBI18752.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449434350\|ref\|XP_004134959.1\| PREDICTED: ATP-dependent helicase ULS1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449479615\|ref\|XP_004155652.1\| PREDICTED: ATP-dependent helicase ULS1-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357446441\|ref\|XP_003593498.1\| Helicase-like transcription factor [Medicago truncatula] gi\|355482546\|gb\|AES63749.1\| Helicase-like transcription factor [Medicago truncatula]	Back alignment and taxonomy information

>gi\|224116170\|ref\|XP_002317230.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222860295\|gb\|EEE97842.1\| chromatin remodeling complex subunit [Populus trichocarpa]	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		1009
TAIR\|locus:2008470		1280	EDA16 "embryo sac development	0.390	0.307	0.560	2.8e-141
TAIR\|locus:2008096		981	AT1G50410 [Arabidopsis thalian	0.385	0.396	0.541	2.5e-104
TAIR\|locus:2095360		1047	AT3G20010 [Arabidopsis thalian	0.225	0.217	0.593	2.2e-92
TAIR\|locus:2089318		638	AT3G16600 [Arabidopsis thalian	0.111	0.175	0.654	4.1e-76
UNIPROTKB\|E1C1L9		1167	TTF2 "Uncharacterized protein"	0.099	0.085	0.451	6.8e-38
UNIPROTKB\|E1C366		1150	TTF2 "Uncharacterized protein"	0.099	0.086	0.451	8e-38
ZFIN\|ZDB-GENE-110411-73		1149	si:ch1073-303l5.1 "si:ch1073-3	0.112	0.099	0.408	1.6e-37
WB\|WBGene00020742		1001	T23H2.3 [Caenorhabditis elegan	0.103	0.103	0.444	6.1e-37
UNIPROTKB\|D4A1K7		950	Ttf2 "Protein Ttf2" [Rattus no	0.107	0.113	0.392	1.1e-35
UNIPROTKB\|E2RGF7		1150	TTF2 "Uncharacterized protein"	0.104	0.091	0.385	6e-35

TAIR\|locus:2008470 EDA16 "embryo sac development arrest 16" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1098 (391.6 bits), Expect = 2.8e-141, Sum P(4) = 2.8e-141
 Identities = 232/414 (56%), Positives = 292/414 (70%)

Query:   592 RSACSNHSVALGKPVVTSQHSSYSDYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQ 651
             +SA  +  +A+  PVV+S++S+ S             GG+K +++ E +I Q A+Q ++Q
Sbjct:   488 QSAIPHRPLAMKMPVVSSEYSTVSHN-------FNQSGGLKLQSNKENMIFQAALQDLTQ 540

Query:   652 PNAEASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILK 711
             PN+EA  PDGVL VPLLRHQRIALSWM QKETS   CSGGILADDQGLGKT+STIALILK
Sbjct:   541 PNSEAILPDGVLTVPLLRHQRIALSWMAQKETSGFPCSGGILADDQGLGKTVSTIALILK 600

Query:   712 ERP-PSFRTEDDNKRQLETLNLDE-EDNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFV 769
             ER  P+   E+  K+++  L  +  E   ++ +G     +  ++ +++ N +     + V
Sbjct:   601 ERSKPAQACEESTKKEIFDLESETGECAPLKPSGRS---KHFEHSQLLSNENKVGG-DSV 656

Query:   770 EQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCELAKFDVV 829
              +  GRPAAGTLVVCPTSV+RQWA+EL  KVTS+ +LSVLVYHGSSRTKDP ELAK+DVV
Sbjct:   657 GKVTGRPAAGTLVVCPTSVMRQWADELHKKVTSEANLSVLVYHGSSRTKDPHELAKYDVV 716

Query:   830 ITTYSIVSMEVPKQPLGXXXXXXXXXXXXXXXLPPMYXXXXXXXXXXXXXXXXGSKQKKG 889
             +TT+SIVSMEVPKQPL                    +                GSK+KK 
Sbjct:   717 VTTFSIVSMEVPKQPLVDDEDEEKDGVHDGGTAATGFCSNKKRKYPPDSKKK-GSKKKK- 774

Query:   890 PDGLLLDIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAI 949
                  ++ ++GPLAKV WFRVVLDEAQSIKN++TQVARACWGLRAKRRWCLSGTPIQN+I
Sbjct:   775 -----VEFLSGPLAKVSWFRVVLDEAQSIKNYKTQVARACWGLRAKRRWCLSGTPIQNSI 829

Query:   950 DDLYSYFRFLRYDPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKG 1003
             DDLYSYFRFL+YDP++ Y  FCS IK PI++NPVKGY+KLQA+LKT+MLRRTKG
Sbjct:   830 DDLYSYFRFLKYDPYSSYVLFCSTIKNPITRNPVKGYQKLQAILKTVMLRRTKG 883

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0004386 "helicase activity" evidence=IEA;ISS

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0009553 "embryo sac development" evidence=IMP

TAIR\|locus:2008096 AT1G50410 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2095360 AT3G20010 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2089318 AT3G16600 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|E1C1L9 TTF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|E1C366 TTF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-110411-73 si:ch1073-303l5.1 "si:ch1073-303l5.1" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

WB\|WBGene00020742 T23H2.3 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

UNIPROTKB\|D4A1K7 Ttf2 "Protein Ttf2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RGF7 TTF2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4	0.691

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	CHR935	chromatin remodeling complex subunit (800 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		1009
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	8e-41
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	4e-18
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-09
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	1e-07
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	5e-05
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	2e-04
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	0.003

>gnl\|CDD\|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain	Back alignment and domain information

 Score =  152 bits (385), Expect = 8e-41
 Identities = 91/349 (26%), Positives = 130/349 (37%), Gaps = 135/349 (38%)

Query: 670  HQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLET 729
            +Q   ++W++  E++ L   GGILAD+ GLGKT+ TIAL+                    
Sbjct: 1    YQLEGVNWLISLESNGL---GGILADEMGLGKTLQTIALLATY----------------- 40

Query: 730  LNLDEEDNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVL 789
              L E  +     G  LV        V P                            S L
Sbjct: 41   --LKEGKD---RRGPTLV--------VCP---------------------------LSTL 60

Query: 790  RQWAEELRNKVTSKGSLSVLVYHGSSRTKDPCE------LAKFDVVITTYSIVSMEVPKQ 843
              W  E         +L V+VYHG  R +          L  +DVVITTY ++       
Sbjct: 61   HNWLNEFE---KWAPALRVVVYHGDGRERSKLRQSMAKRLDTYDVVITTYEVL------- 110

Query: 844  PLGDKEDEEEKMKIEGEDLPPMYCSSSKKRKCPPSSDRKGSKQKKGPDGLLLDIVAGPLA 903
               DK+                                                    L 
Sbjct: 111  -RKDKKLLSL------------------------------------------------LN 121

Query: 904  KVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDP 963
            KV W RVVLDEA  +KN ++++ +A   L+ + R  L+GTPIQN +++L++   FLR  P
Sbjct: 122  KVEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQNNLEELWALLNFLRPGP 181

Query: 964  FAVYKSFCSMIKVPI-----SKNPV-----KGYKKLQAVLKTIMLRRTK 1002
            F  +K F     +PI     +KN       +G  +L  +LK  +LRRTK
Sbjct: 182  FGSFKVFEEWFNIPIANTADNKNKNLEKGKEGINRLHKLLKPFLLRRTK 230

This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA recombination (e.g. RAD54), and chromatin unwinding (e.g. ISWI) as well as a variety of other proteins with little functional information (e.g. lodestar, ETL1). Length = 301

>gnl\|CDD\|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

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

>gnl\|CDD\|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional	Back alignment and domain information

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		1009
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	100.0
KOG4439		901	consensus RNA polymerase II transcription terminat	100.0
KOG1002		791	consensus Nucleotide excision repair protein RAD16	100.0
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	100.0
KOG0387		923	consensus Transcription-coupled repair protein CSB	100.0
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	100.0
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	100.0
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	100.0
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	100.0
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	100.0
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	100.0
KOG1001		674	consensus Helicase-like transcription factor HLTF/	100.0
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	99.97
KOG0298		1394	consensus DEAD box-containing helicase-like transc	99.97
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.96
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.96
PRK04914		956	ATP-dependent helicase HepA; Validated	99.95
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	99.95
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	99.94
KOG0383		696	consensus Predicted helicase [General function pre	99.9
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	99.78
PRK13766		773	Hef nuclease; Provisional	99.51
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.49
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.46
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.38
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.37
PHA02558		501	uvsW UvsW helicase; Provisional	99.37
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.12
KOG1123		776	consensus RNA polymerase II transcription initiati	99.06
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	98.94
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	98.93
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	98.86
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.81
COG4096		875	HsdR Type I site-specific restriction-modification	98.74
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	98.71
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	98.63
PRK10689		1147	transcription-repair coupling factor; Provisional	98.62
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.6
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	98.57
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	98.56
PRK01172		674	ski2-like helicase; Provisional	98.5
PTZ00424		401	helicase 45; Provisional	98.49
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.49
PRK02362		737	ski2-like helicase; Provisional	98.48
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	98.47
PRK00254		720	ski2-like helicase; Provisional	98.45
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	98.43
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	98.42
KOG0354		746	consensus DEAD-box like helicase [General function	98.41
PTZ00110		545	helicase; Provisional	98.4
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.4
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	98.36
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	98.34
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	98.29
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	98.27
COG1204		766	Superfamily II helicase [General function predicti	98.26
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	98.24
COG4889		1518	Predicted helicase [General function prediction on	98.21
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	98.21
PRK05580		679	primosome assembly protein PriA; Validated	98.21
COG1205		851	Distinct helicase family with a unique C-terminal	98.15
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.13
PRK13767		876	ATP-dependent helicase; Provisional	98.13
PRK09401		1176	reverse gyrase; Reviewed	98.03
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	98.02
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	97.98
TIGR00595		505	priA primosomal protein N'. All proteins in this f	97.79
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	97.79
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	97.77
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	97.73
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.6
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	97.53
PRK14701		1638	reverse gyrase; Provisional	97.43
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.36
PHA02653		675	RNA helicase NPH-II; Provisional	97.36
PRK15483		986	type III restriction-modification system StyLTI en	97.24
COG1201		814	Lhr Lhr-like helicases [General function predictio	97.2
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	97.17
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	97.04
PRK09200		790	preprotein translocase subunit SecA; Reviewed	96.95
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.93
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	96.91
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	96.88
PRK09694		878	helicase Cas3; Provisional	96.76
COG0610		962	Type I site-specific restriction-modification syst	96.76
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	96.61
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	96.59
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	96.58
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	96.56
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	96.48
PRK12326		764	preprotein translocase subunit SecA; Reviewed	96.3
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	96.02
PRK12904		830	preprotein translocase subunit SecA; Reviewed	95.98
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.92
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	95.79
PRK13107		908	preprotein translocase subunit SecA; Reviewed	95.79
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	95.69
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	95.55
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	95.41
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	95.38
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	95.34
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	95.26
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	94.97
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	94.89
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	94.84
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	94.74
COG1202		830	Superfamily II helicase, archaea-specific [General	94.72
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	94.47
KOG0343		758	consensus RNA Helicase [RNA processing and modific	94.03
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	93.94
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	93.81
COG3587		985	Restriction endonuclease [Defense mechanisms]	93.36
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	93.2
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	92.9
PRK10536		262	hypothetical protein; Provisional	92.82
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	92.73
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	92.55
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	92.11
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	91.79
CHL00122		870	secA preprotein translocase subunit SecA; Validate	91.47
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	91.28
COG1198		730	PriA Primosomal protein N' (replication factor Y)	90.68
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	90.62
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	90.37
KOG0353		695	consensus ATP-dependent DNA helicase [General func	90.27
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	90.02
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	89.93
TIGR00376		637	DNA helicase, putative. The gene product may repre	89.55
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	89.38
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	89.35
PRK10875		615	recD exonuclease V subunit alpha; Provisional	89.09
KOG4284		980	consensus DEAD box protein [Transcription]	88.77
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	88.59
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	88.46
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	88.07
PRK14873		665	primosome assembly protein PriA; Provisional	87.89
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	87.7
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	87.19
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	87.01
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	85.97
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	85.52
KOG1131		755	consensus RNA polymerase II transcription initiati	84.89
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	84.54
KOG1803		649	consensus DNA helicase [Replication, recombination	83.64
KOG0334		997	consensus RNA helicase [RNA processing and modific	83.32
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	83.29
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	81.61
PRK07003		830	DNA polymerase III subunits gamma and tau; Validat	81.57
PF05876		557	Terminase_GpA: Phage terminase large subunit (GpA)	81.1
KOG0347		731	consensus RNA helicase [RNA processing and modific	81.06
PHA02533		534	17 large terminase protein; Provisional	80.89
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	80.73
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	80.06

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

Probab=100.00  E-value=1.1e-49  Score=478.10  Aligned_cols=341  Identities=23%  Similarity=0.331  Sum_probs=281.4

Q ss_pred             cCCccccccccccccccccccccccccccccccccCcccccccccccccCCCCCCCcceeecccCCCCCCccchhcccCC
Q 001825          510 YAQPSTLNKKELDGVKEDMEAEIKTRSMASHLLKLSPESIQSNSSDCKSHVDDEPDICILEDISQPARSNQSLVLGKTLS  589 (1009)
Q Consensus       510 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~  589 (1009)
                      -...++|..++++|+||++||.++..++..|+.             ++...|..++|.|||||.....+...+||+||.+
T Consensus       242 Wet~~~L~~~~~rG~kKv~nf~kK~~e~~~~~r-------------~E~~~~~~~dy~~VdRIia~~~~~d~eYLvKW~~  308 (1373)
T KOG0384|consen  242 WETESELLEMNVRGLKKVDNFKKKVIEEDRWRR-------------QEREEDLNKDYVIVDRIIAEQTSKDPEYLVKWRG  308 (1373)
T ss_pred             ccchHHHHhhhHHHHHHHHHHHHHHHHHHHHHH-------------hhhhhhhhhhhhhhhhhhhcccCCCceeEEEecC
Confidence            356678888999999999999999888999988             3778889999999999988777777999999999


Q ss_pred             CCCccCcchhhccCCCccccccccCCCCCCCCCCCcccCCCCCCcchHHHHHHHHHHhccCCCCCCCCCCCCcccCCCch
Q 001825          590 MNRSACSNHSVALGKPVVTSQHSSYSDYPGYPGVPLTGLGGMKSKASDERLILQVAMQGISQPNAEASAPDGVLAVPLLR  669 (1009)
Q Consensus       590 ~~~~~~~~~~~~~~~p~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~er~~l~~~l~~i~~p~~e~~~P~glLkv~LrP  669 (1009)
                      |+|.+|+|+....+.+..+.+...|..+..-...+.....-.     ..|..+.++          ...|..+-...||+
T Consensus       309 LpY~e~TWE~~~~I~~~~~~~~~~~~~Re~sk~~p~~~~~~~-----~~rp~~~Kl----------e~qp~~~~g~~LRd  373 (1373)
T KOG0384|consen  309 LPYEECTWEDAEDIAKKAQEEIEEFQSRENSKTLPNKGCKYR-----PQRPRFRKL----------EKQPEYKGGNELRD  373 (1373)
T ss_pred             CCcccccccchhhhhhhHHHHHHHHhhhhccccCCCCccccC-----ccchhHHHh----------hcCccccccchhhh
Confidence            999999999999999988877777776622221222222111     122222222          23555555578999


Q ss_pred             hHHHHHHHHHhccccCCCCcccEEEcCCCchHHHHHHHHHHHcCCCCCCCcchhhhhhhhcccccccccccccccccccc
Q 001825          670 HQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLETLNLDEEDNGIQVNGLDLVKQ  749 (1009)
Q Consensus       670 HQkegV~WMlqrE~s~~~~rGGILADEMGLGKTVqaIALIl~~r~~~~~~~~~~k~~~e~l~~de~~d~~~~~~~~~~k~  749 (1009)
                      ||++||+||+..+...   ..||||||||||||||+|+++....                                    
T Consensus       374 yQLeGlNWl~~~W~~~---~n~ILADEmgLgktvqti~fl~~l~------------------------------------  414 (1373)
T KOG0384|consen  374 YQLEGLNWLLYSWYKR---NNCILADEMGLGKTVQTITFLSYLF------------------------------------  414 (1373)
T ss_pred             hhcccchhHHHHHHhc---ccceehhhcCCCcchHHHHHHHHHH------------------------------------
Confidence            9999999999988765   6799999999999999999996542                                    


Q ss_pred             ccccccccCCCCCCccchhhhhhcCCCCCcEEEEeChhhHHHHHHHHHHHhcCCCCcEEEEEcCCCCCCCc---------
Q 001825          750 ESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSSRTKDP---------  820 (1009)
Q Consensus       750 ~~~~C~~~s~~~s~~s~~~~~q~~~rpa~~TLIVcP~SLL~QW~~EI~K~~~~~~~LkVlVy~Gs~R~k~~---------  820 (1009)
                                            ......+|.|||||.+++.+|++||..|..    +++++|+|....+..         
T Consensus       415 ----------------------~~~~~~gpflvvvplst~~~W~~ef~~w~~----mn~i~y~g~~~sr~~i~~ye~~~~  468 (1373)
T KOG0384|consen  415 ----------------------HSLQIHGPFLVVVPLSTITAWEREFETWTD----MNVIVYHGNLESRQLIRQYEFYHS  468 (1373)
T ss_pred             ----------------------HhhhccCCeEEEeehhhhHHHHHHHHHHhh----hceeeeecchhHHHHHHHHHheec
Confidence                                  112245799999999999999999999975    999999998644321         


Q ss_pred             --ccccCCCEEEEehhhhhcccCCCCCCCchhHHHHhhhcCCCCCCcccccccccCCCCCCcccccccCCCCCCcchhhc
Q 001825          821 --CELAKFDVVITTYSIVSMEVPKQPLGDKEDEEEKMKIEGEDLPPMYCSSSKKRKCPPSSDRKGSKQKKGPDGLLLDIV  898 (1009)
Q Consensus       821 --~~LakyDVVITTYstLs~ev~k~~l~d~dde~ek~~~e~~~~~~~~~ssskkRK~~~~s~kk~s~~kk~~d~~~~d~~  898 (1009)
                        ....+++++||||+++..+.                                                          
T Consensus       469 ~~~~~lkf~~lltTye~~LkDk----------------------------------------------------------  490 (1373)
T KOG0384|consen  469 SNTKKLKFNALLTTYEIVLKDK----------------------------------------------------------  490 (1373)
T ss_pred             CCccccccceeehhhHHHhccH----------------------------------------------------------
Confidence              22347999999999985431                                                          


Q ss_pred             cCcccccceeEEEEcccccccchhhHHHHHHHhcccCeEEEEeccCCCCCHHHHHHHHHhhCCCCCCChHHHHhhhcccc
Q 001825          899 AGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIKVPI  978 (1009)
Q Consensus       899 ~s~L~~i~W~RVILDEAH~IKN~~Sq~skAl~~L~Ak~RW~LTGTPIQNsL~DLySLLrFLrp~pf~~~~~F~~~f~~PI  978 (1009)
                       ..|..+.|..+++||||++||..+.++..+..++..+|+++||||+||++.|||+|++||.|+.|..+..|...+    
T Consensus       491 -~~L~~i~w~~~~vDeahrLkN~~~~l~~~l~~f~~~~rllitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~----  565 (1373)
T KOG0384|consen  491 -AELSKIPWRYLLVDEAHRLKNDESKLYESLNQFKMNHRLLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEF----  565 (1373)
T ss_pred             -hhhccCCcceeeecHHhhcCchHHHHHHHHHHhcccceeeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhh----
Confidence             238899999999999999999999999999999999999999999999999999999999999999999998887    


Q ss_pred             cCCchhhHHHHHHHHhhcccccccchhh
Q 001825          979 SKNPVKGYKKLQAVLKTIMLRRTKGEDC 1006 (1009)
Q Consensus       979 e~~~~~g~~rL~~vLk~~MLRRTK~dv~ 1006 (1009)
                      .......++.||++|+|+||||.|+||.
T Consensus       566 ~~~~e~~~~~L~~~L~P~~lRr~kkdve  593 (1373)
T KOG0384|consen  566 DEETEEQVRKLQQILKPFLLRRLKKDVE  593 (1373)
T ss_pred             cchhHHHHHHHHHHhhHHHHHHHHhhhc
Confidence            3456788999999999999999999985

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

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

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]	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

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

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

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

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

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]	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

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]	Back alignment and domain information

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

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]	Back alignment and domain information

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

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]	Back alignment and domain information

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

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

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]	Back alignment and domain information

>KOG0383 consensus Predicted helicase [General function prediction only]	Back alignment and domain information

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

>PRK13766 Hef nuclease; Provisional	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

>smart00487 DEXDc DEAD-like helicases superfamily	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

>cd00046 DEXDc DEAD-like helicases superfamily	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

>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

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

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

>TIGR00643 recG ATP-dependent DNA helicase RecG	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

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

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

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

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

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

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

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

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

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>PRK05580 primosome assembly protein PriA; Validated	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

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

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

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

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

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

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

>TIGR03714 secA2 accessory Sec system translocase SecA2	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

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

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

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

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

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

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

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

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

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

>PRK09200 preprotein translocase subunit SecA; Reviewed	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

>KOG0331 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

>PRK09694 helicase Cas3; Provisional	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

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

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

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

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

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

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

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

>PRK12904 preprotein translocase subunit SecA; Reviewed	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

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative	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

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

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

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]	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

>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

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

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

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

>KOG0338 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

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

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

>PRK12906 secA preprotein translocase subunit SecA; Reviewed	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

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

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

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

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

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

>CHL00122 secA preprotein translocase subunit SecA; Validated	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

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

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

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

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

>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]	Back alignment and domain information

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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

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

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

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

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

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	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

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

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

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

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family	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

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

>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

>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

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

>KOG0334 consensus RNA helicase [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

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

>PRK07003 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA	Back alignment and domain information

>KOG0347 consensus RNA helicase [RNA processing and modification]	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

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]	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		1009
1z6a_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN		2e-15
1z63_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COM		3e-15
1z3i_X		644	Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMA		4e-05

>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN Length = 500

Back alignment and structure

Iteration: 1

Score = 81.6 bits (200), Expect = 2e-15, Method: Compositional matrix adjust. Identities = 41/107 (38%), Positives = 64/107 (59%) Query: 902 LAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRY 961 L +V W +V+DEAQ+IKN +T++ +A L++K R L+GTPI+N +DDL+S FL Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNP 204 Query: 962 DPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGEDCLL 1008 Y F S PI K ++L+A++ +LRRTK + ++ Sbjct: 205 GLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYDKAII 251

PyMOL of 1z6a

>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX With Dsdna Length = 500

Back alignment and structure

>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF EUKARYOTIC Rad54 Length = 644

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		1009
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	1e-24
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	8e-11
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	1e-09
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	4e-14
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	2e-07
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	6e-07
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	2e-11
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	3e-06
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	3e-11
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	7e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-09
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
2fwr_A		472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	7e-04
2fz4_A		237	DNA repair protein RAD25; RECA-like domain, DNA da	9e-04

>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 Length = 500	Back alignment and structure

 Score =  108 bits (272), Expect = 1e-24
 Identities = 42/105 (40%), Positives = 64/105 (60%), Gaps = 4/105 (3%)

Query: 902  LAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRY 961
            L +V W  +V+DEAQ+IKN +T++ +A   L++K R  L+GTPI+N +DDL+S   FL  
Sbjct: 145  LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFL-- 202

Query: 962  DP--FAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGE 1004
            +P     Y  F S    PI K      ++L+A++   +LRRTK +
Sbjct: 203  NPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYD 247

PyMOL of 1z63

>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 Length = 500	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 Length = 500	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 Length = 644	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 Length = 644	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 Length = 644	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} Length = 968	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} Length = 968	Back alignment and structure

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Length = 800	Back alignment and structure

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Length = 800	Back alignment and structure

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

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

>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

>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* Length = 472	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 Length = 237	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		1009
d1z63a1		230	c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 h	6e-20
d1z63a1		230	c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 h	3e-09
d1z3ix2		298	c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fis	3e-13
d1z3ix2		298	c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fis	2e-08

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]} Length = 230	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: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 87.8 bits (216), Expect = 6e-20
 Identities = 41/107 (38%), Positives = 64/107 (59%)

Query: 902  LAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRY 961
            L +V W  +V+DEAQ+IKN +T++ +A   L++K R  L+GTPI+N +DDL+S   FL  
Sbjct: 120  LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNP 179

Query: 962  DPFAVYKSFCSMIKVPISKNPVKGYKKLQAVLKTIMLRRTKGEDCLL 1008
                 Y  F S    PI K      ++L+A++   +LRRTK +  ++
Sbjct: 180  GLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKYDKAII 226

PyMOL of d1z63a1

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]} Length = 230	Back information, alignment and structure

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 298	Back information, alignment and structure

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 298	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		1009
d1z63a1		230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	100.0
d1z3ix2		298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	100.0
d2fz4a1		206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.88
d1rifa_		282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.85
d1wp9a1		200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.72
d2p6ra3		202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.58
d1gkub1		237	Helicase-like "domain" of reverse gyrase {Archaeon	99.31
d1gm5a3		264	RecG helicase domain {Thermotoga maritima [TaxId:	99.3
d1a1va1		136	HCV helicase domain {Human hepatitis C virus (HCV)	99.22
d2eyqa3		233	Transcription-repair coupling factor, TRCF {Escher	99.16
d1yksa1		140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.14
d1oywa2		206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.14
d1hv8a1		208	Putative DEAD box RNA helicase {Archaeon Methanoco	98.91
d2g9na1		218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.68
d1t6na_		207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.67
d1qdea_		212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.66
d1wrba1		238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.66
d1veca_		206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.64
d2bmfa2		305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.51
d2j0sa1		222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.49
d1q0ua_		209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.43
d1s2ma1		206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.4
d1w36d1		359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.47
d1tf5a3		273	Translocation ATPase SecA, nucleotide-binding doma	97.47
d2b2ya1		80	ATP-dependent helicase CHD1 (Chromo domain protein	97.3
d1nkta3		288	Translocation ATPase SecA, nucleotide-binding doma	97.18
d2dy8a1		69	ATP-dependent helicase CHD1 (Chromo domain protein	94.84
d1a5ta2		207	delta prime subunit of DNA polymerase III, N-domai	88.1
d1t5la1		413	Nucleotide excision repair enzyme UvrB {Bacillus c	86.91
d1guwa_		73	Heterochromatin protein 1, HP1 {Mouse (Mus musculu	85.81

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}	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: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=100.00  E-value=0  Score=350.13  Aligned_cols=222  Identities=36%  Similarity=0.578  Sum_probs=190.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCC
Q ss_conf             79999865678864589999999860105877766489838992179999999997099998876303445431156533
Q 001825          656 ASAPDGVLAVPLLRHQRIALSWMVQKETSSLHCSGGILADDQGLGKTISTIALILKERPPSFRTEDDNKRQLETLNLDEE  735 (1009)
Q Consensus       656 ~~~P~glLkv~LrPHQkeALaWMLqrE~s~~~~rGGILADEMGLGKTIqaIALIl~~r~~~~~~~~~~k~~~e~l~~de~  735 (1009)
                      ...|.+ ++..|+|||++|+.||+.++...   .|||||||||||||+++|+++...+                      
T Consensus         3 ~~~P~~-~~~~L~~yQ~~~v~~~~~~~~~~---~g~iLaDe~GlGKT~~~i~~~~~~~----------------------   56 (230)
T d1z63a1           3 LLEPYN-IKANLRPYQIKGFSWMRFMNKLG---FGICLADDMGLGKTLQTIAVFSDAK----------------------   56 (230)
T ss_dssp             CCCCCS-CSSCCCHHHHHHHHHHHHHHHTT---CCEEECCCTTSCHHHHHHHHHHHHH----------------------
T ss_pred             CCCCHH-HHCCHHHHHHHHHHHHHHHHHCC---CCEEEEECCCCCHHHHHHHHHHHHH----------------------
T ss_conf             769446-50450699999999999862169---9879985899886999987355442----------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEEECHHHHHHHHHHHHHHHCCCCCCEEEEECCCC
Q ss_conf             44321256431112354333358999875301353301799984899938253999999999881478993899982898
Q 001825          736 DNGIQVNGLDLVKQESDYCRVVPNGSSAKSFNFVEQAKGRPAAGTLVVCPTSVLRQWAEELRNKVTSKGSLSVLVYHGSS  815 (1009)
Q Consensus       736 ~d~~~~~~~~~~k~~~~~C~~~~~~~~~~~~~~~~~~~~rpa~~TLIVcP~SLL~QW~~EI~k~~~~~~~LsVlVyhGs~  815 (1009)
                                                           ...+..++|||||++++.||.+|+.+|..   ...+..++...
T Consensus        57 -------------------------------------~~~~~~~~LIv~p~~l~~~W~~e~~~~~~---~~~~~~~~~~~   96 (230)
T d1z63a1          57 -------------------------------------KENELTPSLVICPLSVLKNWEEELSKFAP---HLRFAVFHEDR   96 (230)
T ss_dssp             -------------------------------------HTTCCSSEEEEECSTTHHHHHHHHHHHCT---TSCEEECSSST
T ss_pred             -------------------------------------HCCCCCCCCEECCHHHHHHHHHHHHHHCC---CCCCEEECCCC
T ss_conf             -------------------------------------12355644110535542677777776402---54410101421


Q ss_pred             CCCCCCCCCCCCEEEEEHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             88881001688899983032302368898998046899864208999975346655468999985336656799997410
Q 001825          816 RTKDPCELAKFDVVITTYSIVSMEVPKQPLGDKEDEEEKMKIEGEDLPPMYCSSSKKRKCPPSSDRKGSKQKKGPDGLLL  895 (1009)
Q Consensus       816 Rtk~~~~LakyDVVITTYs~L~~Ev~k~~l~d~dde~ek~~~e~~~~~~~~~s~~kkRK~p~~s~kk~s~~~k~~d~~~~  895 (1009)
                      ..   ....++++||++|+.+....                                                       
T Consensus        97 ~~---~~~~~~~vvi~~~~~~~~~~-------------------------------------------------------  118 (230)
T d1z63a1          97 SK---IKLEDYDIILTTYAVLLRDT-------------------------------------------------------  118 (230)
T ss_dssp             TS---CCGGGSSEEEEEHHHHTTCH-------------------------------------------------------
T ss_pred             CH---HHCCCCCEEEEEHHHHHHHH-------------------------------------------------------
T ss_conf             00---00257688985499998688-------------------------------------------------------


Q ss_pred             HHCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC
Q ss_conf             10048654211019997562102562229999998133683999914587899999999998607899887577774332
Q 001825          896 DIVAGPLAKVGWFRVVLDEAQSIKNHRTQVARACWGLRAKRRWCLSGTPIQNAIDDLYSYFRFLRYDPFAVYKSFCSMIK  975 (1009)
Q Consensus       896 e~~~spL~~i~W~RVILDEAH~IKN~~Sq~skAl~~LrAkrRWlLTGTPIQNsL~DLySLLrFLrp~pf~~~k~F~~~i~  975 (1009)
                           .+....|++||+||||++||..+++++++..+++++||+|||||++|++.|||++++||++++|+++..|.+.|.
T Consensus       119 -----~l~~~~~~~vI~DEah~~k~~~s~~~~~~~~l~a~~r~~LTgTPi~n~~~dl~~ll~~l~p~~~~~~~~F~~~~~  193 (230)
T d1z63a1         119 -----RLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFA  193 (230)
T ss_dssp             -----HHHTCCEEEEEEETGGGGSCTTSHHHHHHHTSCEEEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTH
T ss_pred             -----HHHCCCCEEEEEEHHHCCCCCCHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf             -----874165139999710034432205566654404655799725267767888998887628986789999999984


Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             4456782565999999971001001101020
Q 001825          976 VPISKNPVKGYKKLQAVLKTIMLRRTKGEDC 1006 (1009)
Q Consensus       976 ~Pier~~~~~~krLq~vLk~iMLRRTK~dv~ 1006 (1009)
                      .|++++...+.++|+++|++||+||||.|+.
T Consensus       194 ~~~~~~~~~~~~~L~~~l~~~~lRr~K~d~~  224 (230)
T d1z63a1         194 TPIKKGDNMAKEELKAIISPFILRRTKYDKA  224 (230)
T ss_dssp             HHHHTTCHHHHHHHHHHHTTTEECCCTTCHH
T ss_pred             HHHHCCCHHHHHHHHHHHHCCEEEEECCCCC
T ss_conf             4553267789999999842337997168861

PyMOL of d1z63a1

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

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

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

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

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

>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

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

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

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

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

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

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

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

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

>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

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

>d2b2ya1 b.34.13.2 (A:108-187) ATP-dependent helicase CHD1 (Chromo domain protein 1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dy8a1 b.34.13.2 (A:279-347) ATP-dependent helicase CHD1 (Chromo domain protein 1) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

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

>d1guwa_ b.34.13.2 (A:) Heterochromatin protein 1, HP1 {Mouse (Mus musculus), HP1 beta (MOD1, M31) [TaxId: 10090]}	Back information, alignment and structure