Citrus Sinensis ID: 004604

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---

MAAISPIDISSSDSDLDIGESDTSETRQSGNVRILPPWATKAAVNARTGYGGQSQKVPSFERSYASNGSSSNANSYSQEKLQMLPGFSDDHQMSNGQADDSHYLSGNKNVGQLQTVNPRIANVASADYEKISSQQALKRTLPAFPQPHSLNTKSKSSVENMNSSQIRDTFGNAYHLAGPSTVNSKGYIRDYYVKKNDDDIMMYEGNRILPSSLMHGKSVSMTQFGGPSDLAYRSGSADERAVGGDERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDDNGNAGLDKVKETGESDDIKPVPEVSTSTRSFSRRRPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKISNVSKRGKKGKKGNVNSSIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILFLSGIF

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccHHccHHHHHHHHHHHHHHHccccccccccHHHcccccccHHHHHHHHHHHHHcccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHcccccccEEEEEEcccccccHHHHccccEEEEccHHHHccccccccccHHHHHHHcccccccccHHHHHHHHcccccccccccccccccccccccccccccccEEEEEEEEEcccccccHHHHHHHHHHHcccccEEEEccccccccHHHHHHHHHHccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHccHHHcccccccccccccHHHHccccHHHHHHHHHHHHHcccccccccccccccccEEEccccccc

ccccccEEEcccccccEEccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccHHccccccccccccccHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccEEcccccccHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHccccccEEEcccccccccHHHHHHHHHHHHcccccccEEEEEcHHHHHHHHHHHHHHccccccEEEEEEEcccccccHHHHccccEEEEEEEEEcccccccccccccHHHccccccccccccccccccccccccccccccccEEEEcHHHHHcccccHHcccEEEEEEHHHHHccccHHHHHHHHHHHHHccEEEEcccHHHHHHHHHHHHHHHccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEccccEEEEEEEcccHHHHHHHHHHHHHcHHHHHHHHccccccccHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHccHHHHHHHHHHHHHHcccEEEEHHHHHHHHHHHHHHHHcccc

maaispidisssdsdldigesdtsetrqsgnvrilppwatKAAVnartgyggqsqkvpsfersyasngsssnansysqeklqmlpgfsddhqmsngqaddshylsgnknvgqlqtvnprianvasadyekiSSQQALKrtlpafpqphslntkskssvenmnssqirdtfgnayhlagpstvnskgyirdyyvkkndddimmyegnrilpsslmhgksvsmtqfggpsdlayrsgsaderavggdeRLIYQAALEdlnqpkveatlpdgllSVNLLKHQKIALAWMLQKETRSLhclggiladdqglgkTISIIALIQMQRSlqsksktevlgnqktealnldddddngnagldkvketgesddikpvpevststrsfsrrrpaagtlvvcpASVLRQWARELEDKVPDKAALSVLIYhggsrtkdpvelaKYDVVLTTYSIVtnevpkqpsvdeeeadekngetyglssefsvnkkrKKISNvskrgkkgkkgnvnssidygcgplakvgwFRVVLDEAQTIKNHRTQVARACCSLRAkrrwclsgtpiqnsIDDLYSYFrflkydpyavYKSFYstikipisrnslhGYKKLQAVLRAIMLRRtkgtfidgqpiinlppktisltkvdfskEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQAcdhpllvkeydfdsvgkISGEMAKRLPRDMLIDLLSRLetssaiccvcsvsfyfkrntSILFLSGIF

maaispidisssdsdldigesdtsetrqsgnvrilppwATKAAVNARTGYGGQSQKVPSFERSYASNGSSSNANSYSQEKLQMLPGFSDDHQMSNGQADDSHYLSGNKNVGQLQTVNPRIANVASADYEKISSQQALKRTlpafpqphslntkskssvENMNSSQIRDTFGNAYHlagpstvnskgyIRDYYVKKNDDDIMMYEGNRILPSSLMHGKSVSMTQFGGPSDLAYRSGSADERAVGGDERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTealnldddddngNAGLDkvketgesddikpvpevststrsfsrrrpaagtlvvcpaSVLRQWARELEDKVPDKAALSVLIyhggsrtkdpveLAKYDVVLTTYSIvtnevpkqpsvdeeeadekngetyglssefsvnkkrkkisnvskrgkkgkkgnvnssidygcGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLrakrrwclsgtpiqnsIDDLYSYFRFLKYDPYAVYKSFYSTIKipisrnslhgyKKLQAVLRAIMLRRTKgtfidgqpiinlppktisltKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILFLSGIF

MAAispidisssdsdldigesdTSETRQSGNVRILPPWATKAAVNARTGYGGQSQKVPSFERsyasngsssnansysQEKLQMLPGFSDDHQMSNGQADDSHYLSGNKNVGQLQTVNPRIANVASADYEKISSQQALKRTLPAFPQPHSLNTKSKSSVENMNSSQIRDTFGNAYHLAGPSTVNSKGYIRDYYVKKNDDDIMMYEGNRILPSSLMHGKSVSMTQFGGPSDLAYRSGSADERAVGGDERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEalnldddddngnagldKVKETGESDDIKPVPEVststrsfsrrrPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKIsnvskrgkkgkkgnvnssIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILFLSGIF

*********************************ILPPWATKAA*****************************************************************************************************************************TFGNAYHLAGPSTVNSKGYIRDYYVKKNDDDIMMYEGNRIL************************************ERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQM*****************************************************************AGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTN*****************************************************SIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILFLSG**

****SPI*************************************************************************************************************************************************************************************************************************************************************************VNLLKHQKIALAWMLQKETR**********DDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDDNGNAGLDKVKETGESDDIKPVPEVSTSTRSFSRRRPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPS*************************************************YGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKF***********NYANILLMLLRLRQACDHPLLVKE***********************DLLSRLETSSAICCVCSVSFYFKRNTSILFLSGIF

MAAISPIDIS******************SGNVRILPPWATKAAVNAR*****************************SQEKLQMLPGFSDDHQMSNGQADDSHYLSGNKNVGQLQTVNPRIANVASADYEKISSQQALKRTLPAFPQPHSLN***********SSQIRDTFGNAYHLAGPSTVNSKGYIRDYYVKKNDDDIMMYEGNRILPSSLMHGKSVSMTQFGGPSDLAY*********VGGDERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDDNGNAGLDKVKE***********************RPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEV**********************************************GNVNSSIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILFLSGIF

************DSDL*I************NVRILPPWATKAA******Y*GQSQKVPSFERS**************************************************************************************************************************GYIRDYYVKKNDDDIMMYEGNRILP**************************************IYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDDNGNAGLDKVKETGESDDIKPVPEVSTSTRSFSRRRPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEV****************************************GKKGKKGNVNSSIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILFLSGIF

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		743	2.2.26 [Sep-21-2011]
Q9FNI6		1029	Putative SWI/SNF-related	no	no	0.427	0.309	0.350	3e-56
O60177		1040	Uncharacterized ATP-depen	yes	no	0.444	0.317	0.334	2e-53
Q9FIY7		1277	Putative SWI/SNF-related	no	no	0.423	0.246	0.340	2e-51
Q9FF61		881	Putative SWI/SNF-related	no	no	0.524	0.442	0.3	5e-51
O13762		897	Uncharacterized ATP-depen	no	no	0.454	0.376	0.333	1e-50
Q10332		830	Uncharacterized ATP-depen	no	no	0.484	0.433	0.299	2e-49
Q5NC05		1138	Transcription termination	yes	no	0.448	0.292	0.3	1e-47
Q08562		1619	ATP-dependent helicase UL	yes	no	0.469	0.215	0.32	3e-47
P34739		1061	Transcription termination	yes	no	0.469	0.328	0.312	5e-46
Q4WVM1		1245	DNA repair protein rad5 O	no	no	0.415	0.248	0.298	5e-46

>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 desciption

 Score =  220 bits (561), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 138/394 (35%), Positives = 197/394 (50%), Gaps = 76/394 (19%)

Query: 298 GGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDDNGNAGLDKVK 357
           GGILAD  GLGKT+  I+L+ +  S ++ S   +  N +                 DKV 
Sbjct: 414 GGILADAMGLGKTVMTISLL-LAHSWKAASTGFLCPNYEG----------------DKVI 456

Query: 358 ETGESDDIKPVPEVSTSTRSFSRRR-------PAAGTLVVCPASVLRQWARELEDKVPDK 410
            +   DD+   P  +T    F +R           G L+VCP ++L QW  E+E      
Sbjct: 457 SSS-VDDLTSPPVKATKFLGFDKRLLEQKSVLQNGGNLIVCPMTLLGQWKTEIEMHA-KP 514

Query: 411 AALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEKNGETYGLSS 470
            +LSV +++G SR KD   L++ DVV+TTY ++T+E  ++ S D E              
Sbjct: 515 GSLSVYVHYGQSRPKDAKLLSQSDVVITTYGVLTSEFSQENSADHE-------------- 560

Query: 471 EFSVNKKRKKISNVSKRGKKGKKGNVNSSIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQV 530
                                               +  V WFR+VLDEA TIKN ++Q+
Sbjct: 561 -----------------------------------GIYAVRWFRIVLDEAHTIKNSKSQI 585

Query: 531 ARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRNSLHG 590
           + A  +L A RRWCL+GTPIQN+++DLYS  RFL+ +P+  +  +   ++ P       G
Sbjct: 586 SLAAAALVADRRWCLTGTPIQNNLEDLYSLLRFLRIEPWGTWAWWNKLVQKPFEEGDERG 645

Query: 591 YKKLQAVLRAIMLRRTK-GTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKK 649
            K +Q++L+ IMLRRTK  T  +G+PI+ LPP    +   + S+ E  FY  L   S  K
Sbjct: 646 LKLVQSILKPIMLRRTKSSTDREGRPILVLPPADARVIYCELSESERDFYDALFKRSKVK 705

Query: 650 FKAFADAGTVNQNYANILLMLLRLRQACDHPLLV 683
           F  F + G V  NYA+IL +LLRLRQ CDHP LV
Sbjct: 706 FDQFVEQGKVLHNYASILELLLRLRQCCDHPFLV 739

Possesses intrinsic ATP-dependent nucleosome-remodeling activity. This activity may be required for DNA repair.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>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\|Q9FIY7\|SM3L3_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 3 OS=Arabidopsis thaliana GN=At5g43530 PE=3 SV=1	Back alignment and function description

>sp\|Q9FF61\|SM3L1_ARATH Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 1 OS=Arabidopsis thaliana GN=At5g05130 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\|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\|Q5NC05\|TTF2_MOUSE Transcription termination factor 2 OS=Mus musculus GN=Ttf2 PE=1 SV=2	Back alignment and function description

>sp\|Q08562\|ULS1_YEAST ATP-dependent helicase ULS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ULS1 PE=1 SV=1	Back alignment and function description

>sp\|P34739\|TTF2_DROME Transcription termination factor 2 OS=Drosophila melanogaster GN=lds PE=1 SV=2	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

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		743
359484139		1013	PREDICTED: uncharacterized ATP-dependent	0.966	0.708	0.680	0.0
255544141		993	DNA repair helicase rad5,16, putative [R	0.948	0.709	0.673	0.0
224095220		923	chromatin remodeling complex subunit [Po	0.842	0.678	0.730	0.0
356574101		1027	PREDICTED: ATP-dependent helicase ULS1-l	0.946	0.684	0.645	0.0
356534462		975	PREDICTED: putative SWI/SNF-related matr	0.899	0.685	0.659	0.0
449464954		1015	PREDICTED: uncharacterized ATP-dependent	0.932	0.682	0.615	0.0
18403061		981	SNF2 and helicase domain-containing prot	0.885	0.670	0.572	0.0
297742732		907	unnamed protein product [Vitis vinifera]	0.849	0.695	0.570	0.0
297847386		980	SNF2 domain-containing protein [Arabidop	0.876	0.664	0.574	0.0
15231009		1047	SNF2 and helicase domain-containing prot	0.827	0.587	0.546	0.0

>gi\|359484139\|ref\|XP_002267403.2\| PREDICTED: uncharacterized ATP-dependent helicase C23E6.02-like [Vitis vinifera]	Back alignment and taxonomy information

 Score =  938 bits (2424), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 503/739 (68%), Positives = 590/739 (79%), Gaps = 21/739 (2%)

Query: 4   ISPIDISSSDSDLDIG----ESDTSETRQS---GNVRILPPWATKAAVNARTGYGGQSQK 56
           + PIDI+SS           E+DTS   +S    N RILPPW + +  N+++   G  QK
Sbjct: 1   MDPIDITSSSDSDFDFEDDRETDTSPVGESVAFANSRILPPWPSTSGTNSKSTSHGHFQK 60

Query: 57  VPSFERSYASNGSSSNANSYSQEKLQMLPGFSDDHQMSNG---QADDSHYLSGNKNV--- 110
           VPS +R+ ASNGSSSN   Y   K+QM P F DD + SN    +  D +Y + N ++   
Sbjct: 61  VPSPKRASASNGSSSNFYHYP-PKIQMHPSFDDDIRASNRHNFREADFNYSTENGDMLDV 119

Query: 111 -GQLQTVNPRIANVASADYEKISSQQALKRTLPAFPQPHSLNTKSKSSVENMNSSQIRDT 169
               Q +N   A++  ADYEK+S Q A++RTLP+  QP + +    ++V N+ SS I D+
Sbjct: 120 ENHQQLINLNKADIFGADYEKLS-QPAMRRTLPSTLQPSAPSAGMNNTVGNIGSSHIHDS 178

Query: 170 FGNAYHLAGPSTVNSKGYIRDYYVKKNDDDIMMYE--GNRILPSSLMHGKSVSMTQFGGP 227
            G ++H  GP  +N+  Y+++++ + NDD+++MYE  G+RILP SLMHGKSV  TQ+GG 
Sbjct: 179 QGKSFHPVGP-ILNNMNYMKEHFGRGNDDEVIMYENSGSRILPPSLMHGKSVPSTQYGGV 237

Query: 228 SDLAYRSGSADERAVGGDERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWML 287
           S+ AYR G A+E A   DERL+YQAAL+DLNQPKVEATLPDGLL+V+LL+HQKIALAWM 
Sbjct: 238 SESAYRPGVAEEMAANTDERLVYQAALQDLNQPKVEATLPDGLLTVSLLRHQKIALAWMH 297

Query: 288 QKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDD 347
           QKETRSLHCLGGILADDQGLGKT+S+IALIQMQ+SLQSKSK+E L N  TEALNLDDDDD
Sbjct: 298 QKETRSLHCLGGILADDQGLGKTVSMIALIQMQKSLQSKSKSEELHNHSTEALNLDDDDD 357

Query: 348 NGNA-GLDKVKETGESDDIKPVPEVSTSTRSFSRRRPAAGTLVVCPASVLRQWARELEDK 406
           N NA G DK K+T E+ D KP+ EVS S   F RRRPAAGTLVVCPASVLRQWAREL++K
Sbjct: 358 NANAAGSDKGKQTEETSDSKPISEVSASLPEFRRRRPAAGTLVVCPASVLRQWARELDEK 417

Query: 407 VPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEKNGETY 466
           V ++A LSV +YHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQP VD++E DE+NGE Y
Sbjct: 418 VSEEAKLSVCLYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPLVDDDEGDERNGEKY 477

Query: 467 GLSSEFSVNKKRKKISNVSKRGKKGKKGNVNSSIDYGCGPLAKVGWFRVVLDEAQTIKNH 526
           GLSSEFSVNKKRKK SNVSKRGKKG+KG  +SSIDY CGPLA+VGWFRV+LDEAQTIKNH
Sbjct: 478 GLSSEFSVNKKRKKPSNVSKRGKKGRKGIDSSSIDYDCGPLARVGWFRVILDEAQTIKNH 537

Query: 527 RTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPISRN 586
           RTQVARACCSLRAKRRWCLSGTPIQN+IDDLYSYFRFLKYDPYAVYKSFY+TIK+PISRN
Sbjct: 538 RTQVARACCSLRAKRRWCLSGTPIQNAIDDLYSYFRFLKYDPYAVYKSFYNTIKVPISRN 597

Query: 587 SLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDS 646
           S+HGYKKLQAVLRAIMLRRTKGT IDG PIINLPPKTI L+KVDFS EE AFY KLE+DS
Sbjct: 598 SVHGYKKLQAVLRAIMLRRTKGTLIDGTPIINLPPKTICLSKVDFSSEERAFYSKLEADS 657

Query: 647 LKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDM 706
             +FK +A AGTVNQNYANILLMLLRLRQACDHPLLVK Y+ DS+ K+S EMAK+LP D+
Sbjct: 658 RSQFKEYAAAGTVNQNYANILLMLLRLRQACDHPLLVKGYNTDSIRKVSSEMAKKLPSDI 717

Query: 707 LIDLLSRLETSSAICCVCS 725
           LI+LL  LET SAIC VC+
Sbjct: 718 LINLLDILET-SAICRVCN 735

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255544141\|ref\|XP_002513133.1\| DNA repair helicase rad5,16, putative [Ricinus communis] gi\|223548144\|gb\|EEF49636.1\| DNA repair helicase rad5,16, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|224095220\|ref\|XP_002310362.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222853265\|gb\|EEE90812.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356574101\|ref\|XP_003555190.1\| PREDICTED: ATP-dependent helicase ULS1-like [Glycine max]	Back alignment and taxonomy information

>gi\|356534462\|ref\|XP_003535773.1\| PREDICTED: putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 3-like [Glycine max]	Back alignment and taxonomy information

>gi\|449464954\|ref\|XP_004150194.1\| PREDICTED: uncharacterized ATP-dependent helicase C23E6.02-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|18403061\|ref\|NP_564568.1\| SNF2 and helicase domain-containing protein [Arabidopsis thaliana] gi\|14532630\|gb\|AAK64043.1\| putative DNA-binding protein [Arabidopsis thaliana] gi\|23296945\|gb\|AAN13207.1\| putative DNA-binding protein [Arabidopsis thaliana] gi\|332194424\|gb\|AEE32545.1\| SNF2 and helicase domain-containing protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297742732\|emb\|CBI35366.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297847386\|ref\|XP_002891574.1\| SNF2 domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297337416\|gb\|EFH67833.1\| SNF2 domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|15231009\|ref\|NP_188635.1\| SNF2 and helicase domain-containing protein [Arabidopsis thaliana] gi\|11994776\|dbj\|BAB03166.1\| transcription factor-like protein [Arabidopsis thaliana] gi\|332642797\|gb\|AEE76318.1\| SNF2 and helicase domain-containing protein [Arabidopsis thaliana]	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		743
TAIR\|locus:2008096		981	AT1G50410 [Arabidopsis thalian	0.791	0.599	0.604	7e-180
TAIR\|locus:2095360		1047	AT3G20010 [Arabidopsis thalian	0.461	0.327	0.688	2e-171
TAIR\|locus:2008470		1280	EDA16 "embryo sac development	0.702	0.407	0.510	6.2e-129
TAIR\|locus:2089318		638	AT3G16600 [Arabidopsis thalian	0.138	0.161	0.718	2.3e-102
POMBASE\|SPBC23E6.02		1040	rrp2 "ATP-dependent DNA helica	0.293	0.209	0.392	2.2e-58
ASPGD\|ASPL0000030172		1184	AN5483 [Emericella nidulans (t	0.242	0.152	0.446	4.9e-57
POMBASE\|SPAC17A2.12		897	rrp1 "ATP-dependent DNA helica	0.293	0.243	0.383	1.6e-50
TAIR\|locus:2162504		1029	RAD5 [Arabidopsis thaliana (ta	0.234	0.169	0.474	3.4e-50
SGD\|S000005717		1619	ULS1 "Protein involved in prot	0.230	0.105	0.419	3e-48
UNIPROTKB\|E1C366		1150	TTF2 "Uncharacterized protein"	0.196	0.126	0.390	3.1e-48

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

 Score = 1746 (619.7 bits), Expect = 7.0e-180, P = 7.0e-180
 Identities = 377/624 (60%), Positives = 431/624 (69%)

Query:   111 GQLQTVNPRIANVASADYEKISSQQALKRTLP-AFPQPHSLNTKSKSSVENMNSSQIRDT 169
             G    V  RI N++  DYEK SSQQA KRT P  F +P     +      N N+S  R  
Sbjct:    85 GNGSIVTSRIPNISVGDYEKFSSQQAFKRTHPPTFSRP-PFPPRPDIGTSNGNASHFR-- 141

Query:   170 FGNAYHLAGPSTVNSKGYIRDYYVKKNDDDIMMYEGNRILPSSLMHGKSVSMTQFGGPSD 229
              G A+   G   V +                    G RILP S+ HG S S + F G SD
Sbjct:   142 -GGAHDDLGMGRVTN--------------------GTRILPPSVAHGTSASPSHFNGLSD 180

Query:   230 LAYRSGSADERAVGGDERLIYQAALEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQK 289
               +R+G  +ER    DERLIYQAAL++LNQPK E  LP GLLSV L+KHQKIALAWM QK
Sbjct:   181 PMHRNGIGEERNSENDERLIYQAALQELNQPKSEVDLPAGLLSVPLMKHQKIALAWMFQK 240

Query:   290 ETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEXXXXXXXXXXX 349
             ET SLHC+GGILADDQGLGKT+S IALI  Q   ++K K++  GNQ+ E           
Sbjct:   241 ETNSLHCMGGILADDQGLGKTVSTIALILKQMH-EAKLKSKNSGNQEAEALDLDADDESE 299

Query:   350 XXXX---XKVKE-TGESDD--IKPVP--EVXXXXXXXXXXXPAAGTLVVCPASVLRQWAR 401
                     K    +G + D  IK     E            PAAGTL+VCPASV+RQWAR
Sbjct:   300 NAFEKPESKASNGSGVNGDSGIKKAKGEEASTSTRKFNRKRPAAGTLIVCPASVVRQWAR 359

Query:   402 ELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEK 461
             EL++KV D+A LSVLIYHGG+RTKDP+ELAKYDVV+TTY+IV+NEVPKQP VD++E DEK
Sbjct:   360 ELDEKVTDEAKLSVLIYHGGNRTKDPIELAKYDVVMTTYAIVSNEVPKQPLVDDDENDEK 419

Query:   462 NGETYGLSSEFSVNKKRKKIXXXXXXXXXXXXXXXXX-XIDYGCGPLAKVGWFRVVLDEA 520
             N E YGL+S FS+NKKRK +                    D   G LAKVGWFRVVLDEA
Sbjct:   420 NSEKYGLASGFSINKKRKNVVGTTKKSKKKKGNNNAGDSSDPDSGTLAKVGWFRVVLDEA 479

Query:   521 QTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIK 580
             QTIKNHRTQVARACC LRAKRRWCLSGTPIQN+IDDLYSYFRFLKYDPYAVYKSF   IK
Sbjct:   480 QTIKNHRTQVARACCGLRAKRRWCLSGTPIQNTIDDLYSYFRFLKYDPYAVYKSFCHQIK 539

Query:   581 IPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYK 640
              PISRNSL GYKKLQAVLRAIMLRRTKGT +DGQPIINLPPKTI+L++VDFS EE +FY 
Sbjct:   540 GPISRNSLQGYKKLQAVLRAIMLRRTKGTLLDGQPIINLPPKTINLSQVDFSVEERSFYV 599

Query:   641 KLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAK 700
             KLESDS  +FKA+A AGT+NQNYANILLMLLRLRQACDHP LVK Y+ DSVGK+S E  K
Sbjct:   600 KLESDSRSQFKAYAAAGTLNQNYANILLMLLRLRQACDHPQLVKRYNSDSVGKVSEEAVK 659

Query:   701 RLPRDMLIDLLSRLETSSAICCVC 724
             +LP++ L+ LLSRLE SS ICCVC
Sbjct:   660 KLPKEDLVSLLSRLE-SSPICCVC 682

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:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0006487 "protein N-linked glycosylation" evidence=RCA

GO:0006816 "calcium ion transport" evidence=RCA

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

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

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

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

POMBASE\|SPBC23E6.02 rrp2 "ATP-dependent DNA helicase (predicted)" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000030172 AN5483 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

POMBASE\|SPAC17A2.12 rrp1 "ATP-dependent DNA helicase (predicted)" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

TAIR\|locus:2162504 RAD5 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

SGD\|S000005717 ULS1 "Protein involved in proteolytic control of sumoylated substrates" [Saccharomyces cerevisiae (taxid:4932)]	Back alignment and assigned GO terms

UNIPROTKB\|E1C366 TTF2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	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	3.6.4.12	LOW CONFIDENCE 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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		743
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	4e-51
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	4e-35
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	5e-12
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-10
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	8e-08

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

 Score =  179 bits (457), Expect = 4e-51
 Identities = 89/313 (28%), Positives = 139/313 (44%), Gaps = 78/313 (24%)

Query: 387 TLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVE------LAKYDVVLTTY 440
           TLVVCP S L  W  E E   P   AL V++YHG  R +  +       L  YDVV+TTY
Sbjct: 51  TLVVCPLSTLHNWLNEFEKWAP---ALRVVVYHGDGRERSKLRQSMAKRLDTYDVVITTY 107

Query: 441 SIVTNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKISNVSKRGKKGKKGNVNSSI 500
            ++  +                               +K +S ++K              
Sbjct: 108 EVLRKD-------------------------------KKLLSLLNK-------------- 122

Query: 501 DYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSY 560
                    V W RVVLDEA  +KN ++++ +A   L+ + R  L+GTPIQN++++L++ 
Sbjct: 123 ---------VEWDRVVLDEAHRLKNSKSKLYKALKKLKTRNRLLLTGTPIQNNLEELWAL 173

Query: 561 FRFLKYDPYAVYKSFYSTIKIPISRNSLH----------GYKKLQAVLRAIMLRRTKGTF 610
             FL+  P+  +K F     IPI+  + +          G  +L  +L+  +LRRTK   
Sbjct: 174 LNFLRPGPFGSFKVFEEWFNIPIANTADNKNKNLEKGKEGINRLHKLLKPFLLRRTKDDV 233

Query: 611 IDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLML 670
                   LPPKT  +   + S E+   YKKL +          + G  N   A++L ++
Sbjct: 234 EKS-----LPPKTEHVLYCNLSDEQRKLYKKLLTKRRLALSFAVEGGEKNVGIASLLNLI 288

Query: 671 LRLRQACDHPLLV 683
           ++LR+ C+HP L 
Sbjct: 289 MQLRKICNHPYLF 301

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

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		743
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	100.0
KOG1002		791	consensus Nucleotide excision repair protein RAD16	100.0
KOG0387		923	consensus Transcription-coupled repair protein CSB	100.0
KOG4439		901	consensus RNA polymerase II transcription terminat	100.0
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	100.0
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	100.0
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	100.0
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	100.0
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	100.0
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	100.0
KOG1001		674	consensus Helicase-like transcription factor HLTF/	100.0
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	100.0
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	100.0
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	100.0
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	100.0
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	100.0
KOG0383		696	consensus Predicted helicase [General function pre	100.0
KOG0298		1394	consensus DEAD box-containing helicase-like transc	100.0
PRK04914		956	ATP-dependent helicase HepA; Validated	99.98
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	99.98
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	99.87
PRK13766		773	Hef nuclease; Provisional	99.6
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.53
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.51
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.5
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.44
PHA02558		501	uvsW UvsW helicase; Provisional	99.41
KOG1123		776	consensus RNA polymerase II transcription initiati	99.23
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.18
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	99.06
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	99.02
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	99.0
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	98.96
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	98.91
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	98.89
COG4096		875	HsdR Type I site-specific restriction-modification	98.89
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	98.82
PRK10689		1147	transcription-repair coupling factor; Provisional	98.79
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	98.75
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	98.73
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	98.7
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	98.67
PRK01172		674	ski2-like helicase; Provisional	98.66
PRK02362		737	ski2-like helicase; Provisional	98.65
PRK00254		720	ski2-like helicase; Provisional	98.64
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	98.63
PTZ00110		545	helicase; Provisional	98.59
PTZ00424		401	helicase 45; Provisional	98.58
KOG0354		746	consensus DEAD-box like helicase [General function	98.57
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	98.55
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	98.55
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	98.55
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	98.48
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	98.47
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	98.46
COG1204		766	Superfamily II helicase [General function predicti	98.44
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	98.42
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	98.38
PRK05580		679	primosome assembly protein PriA; Validated	98.35
COG1205		851	Distinct helicase family with a unique C-terminal	98.33
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	98.29
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	98.29
PRK09401		1176	reverse gyrase; Reviewed	98.28
PRK13767		876	ATP-dependent helicase; Provisional	98.26
COG4889		1518	Predicted helicase [General function prediction on	98.07
TIGR00595		505	priA primosomal protein N'. All proteins in this f	98.03
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	97.99
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	97.98
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	97.96
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	97.95
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	97.84
COG1201		814	Lhr Lhr-like helicases [General function predictio	97.75
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	97.73
PRK14701		1638	reverse gyrase; Provisional	97.62
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	97.51
PHA02653		675	RNA helicase NPH-II; Provisional	97.5
PRK15483		986	type III restriction-modification system StyLTI en	97.45
COG0610		962	Type I site-specific restriction-modification syst	97.4
PRK09200		790	preprotein translocase subunit SecA; Reviewed	97.36
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	97.36
PRK09694		878	helicase Cas3; Provisional	97.3
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	97.21
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.17
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	97.08
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	97.06
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	96.91
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	96.86
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	96.86
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.8
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	96.74
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	96.63
PRK12326		764	preprotein translocase subunit SecA; Reviewed	96.58
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	96.57
PF11496		297	HDA2-3: Class II histone deacetylase complex subun	96.52
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	96.52
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	96.47
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	96.27
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	96.23
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	96.22
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	96.22
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	96.19
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	96.18
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	96.16
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	96.13
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	96.06
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	96.0
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	95.95
PRK12904		830	preprotein translocase subunit SecA; Reviewed	95.95
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	95.92
PRK13107		908	preprotein translocase subunit SecA; Reviewed	95.82
COG1202		830	Superfamily II helicase, archaea-specific [General	95.61
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	95.54
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	95.54
PRK10536		262	hypothetical protein; Provisional	95.5
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	95.26
KOG0343		758	consensus RNA Helicase [RNA processing and modific	95.12
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	94.98
COG3587		985	Restriction endonuclease [Defense mechanisms]	94.89
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	94.85
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	94.84
KOG4284		980	consensus DEAD box protein [Transcription]	94.07
KOG0353		695	consensus ATP-dependent DNA helicase [General func	93.85
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	93.5
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	93.46
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	93.38
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	93.34
PRK14873		665	primosome assembly protein PriA; Provisional	93.06
CHL00122		870	secA preprotein translocase subunit SecA; Validate	92.97
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	92.13
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	91.98
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	91.81
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	91.68
TIGR00376		637	DNA helicase, putative. The gene product may repre	91.62
PHA02533		534	17 large terminase protein; Provisional	91.54
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	91.31
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	91.29
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	90.85
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	90.71
KOG1803		649	consensus DNA helicase [Replication, recombination	90.47
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	90.16
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	89.91
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	89.43
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	89.42
COG1198		730	PriA Primosomal protein N' (replication factor Y)	89.32
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	88.83
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	88.78
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	88.72
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	88.66
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	87.95
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	87.59
PRK10875		615	recD exonuclease V subunit alpha; Provisional	87.24
PRK04296		190	thymidine kinase; Provisional	86.59
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	86.15
KOG0347		731	consensus RNA helicase [RNA processing and modific	85.96
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	85.63
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	84.08
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	82.18
KOG0334		997	consensus RNA helicase [RNA processing and modific	81.74

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

Probab=100.00  E-value=2.3e-65  Score=569.58  Aligned_cols=343  Identities=26%  Similarity=0.445  Sum_probs=287.4

Q ss_pred             cCCCCccccccchhhHHHHHHHHHhhhccccccceEEEccCCCchHHHHHHHHHHHhhhcccchhhhccccccccccCCC
Q 004604          265 TLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLDD  344 (743)
Q Consensus       265 ~~P~~~~~~~L~phQ~~gl~wml~~e~~~~~~~GGILADdMGLGKTiqaIAli~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (743)
                      +.|..+....|++||.+||.||.++..   ++-+||||||||||||+|+|||+.+++..                     
T Consensus       158 ~sP~~v~~g~lr~YQveGlnWLi~l~e---ngingILaDEMGLGKTlQtIs~l~yl~~~---------------------  213 (971)
T KOG0385|consen  158 DSPSYVKGGELRDYQLEGLNWLISLYE---NGINGILADEMGLGKTLQTISLLGYLKGR---------------------  213 (971)
T ss_pred             CCchhhcCCccchhhhccHHHHHHHHh---cCcccEeehhcccchHHHHHHHHHHHHHh---------------------
Confidence            367776668999999999999999876   45579999999999999999999987753                     


Q ss_pred             CCCCCCcccccccccCCCCCCCCCCccccccccccCCCCCCcEEEEeChhhHHHHHHHHHHhCCCCCCcEEEEEeCCCCC
Q 004604          345 DDDNGNAGLDKVKETGESDDIKPVPEVSTSTRSFSRRRPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRT  424 (743)
Q Consensus       345 d~~~~~~~~~~~k~~~~~~~~~~~~~~~~s~~~~~~~~~~~~tLIV~P~Sll~qW~~Ei~k~~~~~~~l~V~iy~G~~r~  424 (743)
                                                          ++..+|+||+||.|++.||.+||.+|+|   .+++++|+|....
T Consensus       214 ------------------------------------~~~~GPfLVi~P~StL~NW~~Ef~rf~P---~l~~~~~~Gdk~e  254 (971)
T KOG0385|consen  214 ------------------------------------KGIPGPFLVIAPKSTLDNWMNEFKRFTP---SLNVVVYHGDKEE  254 (971)
T ss_pred             ------------------------------------cCCCCCeEEEeeHhhHHHHHHHHHHhCC---CcceEEEeCCHHH
Confidence                                                1445889999999999999999999999   8999999999854


Q ss_pred             CC-----hhhhccCCEEEeehhhhhccCCCCCCCchHHhhhhcccccCCcchhhhhhhhhhcccccccccCCCCCCCCCC
Q 004604          425 KD-----PVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKISNVSKRGKKGKKGNVNSS  499 (743)
Q Consensus       425 ~~-----~~~l~~~DVVITTY~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~kk~~~~~k~~~~~~  499 (743)
                      +.     ...-..+||+||||+++.++-                                                    
T Consensus       255 R~~~~r~~~~~~~fdV~iTsYEi~i~dk----------------------------------------------------  282 (971)
T KOG0385|consen  255 RAALRRDIMLPGRFDVCITSYEIAIKDK----------------------------------------------------  282 (971)
T ss_pred             HHHHHHHhhccCCCceEeehHHHHHhhH----------------------------------------------------
Confidence            32     222358999999999987641                                                    


Q ss_pred             cccCCCCccccCccEEEEcCCcccCChhhHHHHHHHhcccCcEEEEecCCCCCCHHHHHHHHHhhCCCCCCcHHHHHHHh
Q 004604          500 IDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTI  579 (743)
Q Consensus       500 ~~~~~~~L~~i~w~rVIlDEAH~IKN~~Sk~skal~~L~a~~R~lLTGTPiqN~l~EL~sLl~FL~p~~~~~~~~F~~~f  579 (743)
                           +.|..+.|.++||||||+|||.++..++.++.+.+.+|++|||||+||++.|||+||+||.|+.|.+.+.|...|
T Consensus       283 -----~~lk~~~W~ylvIDEaHRiKN~~s~L~~~lr~f~~~nrLLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF  357 (971)
T KOG0385|consen  283 -----SFLKKFNWRYLVIDEAHRIKNEKSKLSKILREFKTDNRLLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWF  357 (971)
T ss_pred             -----HHHhcCCceEEEechhhhhcchhhHHHHHHHHhcccceeEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHH
Confidence                 347889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCchhHHHHHHHhhhceEEEEecCcccCCCCccCCCCceEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhhcCCc
Q 004604          580 KIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTV  659 (743)
Q Consensus       580 ~~pi~~~~~~~~~~L~~lL~~~mLRRtK~dv~~g~pil~LPpk~e~vv~v~Ls~~Qr~lY~~l~~~~~~~~~~~~~~g~~  659 (743)
                      ......++...+.+|+.+|+||+|||.|.+|..     .||||.+.+++|.|+..|+++|.+++..-...+.   ..+. 
T Consensus       358 ~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~-----sLppKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n---~~~~-  428 (971)
T KOG0385|consen  358 DFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEK-----SLPPKKELIIYVGMSSMQKKWYKAILMKDLDALN---GEGK-  428 (971)
T ss_pred             cccccccCHHHHHHHHhhhhHHHHHHHHHhHhh-----cCCCcceeeEeccchHHHHHHHHHHHHhcchhhc---cccc-
Confidence            877666777788999999999999999999986     7999999999999999999999999776544332   2222 


Q ss_pred             cccHHHHHHHHHHHHHHcCCcccccccCCCccccchHHHHhcC-CHHHHHHHHHHhhhccccccccceeeEeecccchhh
Q 004604          660 NQNYANILLMLLRLRQACDHPLLVKEYDFDSVGKISGEMAKRL-PRDMLIDLLSRLETSSAICCVCSVSFYFKRNTSILF  738 (743)
Q Consensus       660 ~~~~~~iL~lL~rLRqiC~HP~Lv~~~~~~~~~~~~~e~~~~l-~~~~l~~Ll~~l~~~~~~c~~C~~~l~f~q~~~~L~  738 (743)
                       .....+++++|+||++||||+|+.+.+...--.....+...- ..-+++.||.+|..      .+|++|+|||+|+|||
T Consensus       429 -~~k~kL~NI~mQLRKccnHPYLF~g~ePg~pyttdehLv~nSGKm~vLDkLL~~Lk~------~GhRVLIFSQmt~mLD  501 (971)
T KOG0385|consen  429 -GEKTKLQNIMMQLRKCCNHPYLFDGAEPGPPYTTDEHLVTNSGKMLVLDKLLPKLKE------QGHRVLIFSQMTRMLD  501 (971)
T ss_pred             -chhhHHHHHHHHHHHhcCCccccCCCCCCCCCCcchHHHhcCcceehHHHHHHHHHh------CCCeEEEeHHHHHHHH
Confidence             245788999999999999999999977632111222222211 12367788888865      4589999999999999


Q ss_pred             cccCC
Q 004604          739 LSGIF  743 (743)
Q Consensus       739 ~~~~~  743 (743)
                      |++.|
T Consensus       502 ILeDy  506 (971)
T KOG0385|consen  502 ILEDY  506 (971)
T ss_pred             HHHHH
Confidence            98754

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]	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

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [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

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

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

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]	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

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

>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

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

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]	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

>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

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

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

>PRK13766 Hef nuclease; 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

>smart00487 DEXDc DEAD-like helicases superfamily	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

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

>PHA02558 uvsW UvsW helicase; 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

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

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

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

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1	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

>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]	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

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

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

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

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family	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

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

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

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

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

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

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

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

>TIGR01587 cas3_core CRISPR-associated helicase Cas3	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

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

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

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

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]	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

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

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

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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

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

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

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

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

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

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

>PRK12899 secA 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

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

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

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

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

>PF11496 HDA2-3: Class II histone deacetylase complex subunits 2 and 3; InterPro: IPR021006 This entry contains the class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi	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

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

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

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

>smart00488 DEXDc2 DEAD-like helicases superfamily	Back alignment and domain information

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

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

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

>KOG0330 consensus ATP-dependent 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

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

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

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

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

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

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

>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]	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

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

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

>KOG0348 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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [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

>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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

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

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA	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

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

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

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, 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

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

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

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

>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]	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

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

>PRK12901 secA 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

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

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

>PRK04296 thymidine kinase; Provisional	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

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

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

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

>KOG0334 consensus 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		743
1z6a_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN		1e-20
1z63_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COM		3e-20
3mwy_W		800	Crystal Structure Of The Chromodomain-atpase Portio		1e-07
1z3i_X		644	Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMA		8e-06

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

Back alignment and structure

Iteration: 1

Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust. Identities = 65/178 (36%), Positives = 97/178 (54%), Gaps = 7/178 (3%) Query: 507 LAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKY 566 L +V W +V+DEAQ IKN +T++ +A L++K R L+GTPI+N +DDL+S FL Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNP 204 Query: 567 DPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLPPKTISL 626 Y F S PI + ++L+A++ +LRRTK D I +LP K + Sbjct: 205 GLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTK---YDKAIINDLPDKIETN 261 Query: 627 TKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLVK 684 + + E+ A YK E ++L F D+ T + IL LL+L+Q DHP L+K Sbjct: 262 VYCNLTPEQAAMYKA-EVENL--FNNI-DSVTGIKRKGMILSTLLKLKQIVDHPALLK 315

PyMOL of 1z6a

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

Back alignment and structure

>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of The Yeast Chd1 Chromatin Remodeler Length = 800

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		743
1z63_A		500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	3e-63
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	1e-19
1z3i_X		644	Similar to RAD54-like; recombination ATPase helica	2e-15
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	1e-17
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	8e-07
3mwy_W		800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	8e-05
1z5z_A		271	Helicase of the SNF2/RAD54 family; hydrolase, reco	1e-13
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-08
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	3e-07
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	6e-07
3dmq_A		968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	7e-07

>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 =  218 bits (558), Expect = 3e-63
 Identities = 108/460 (23%), Positives = 166/460 (36%), Gaps = 145/460 (31%)

Query: 254 LEDLNQPKVEATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISI 313
              +     +   P  + +  L  +Q    +WM  +    L   G  LADD GLGKT+  
Sbjct: 18  GSHMASKSFQLLEPYNIKAN-LRPYQIKGFSWM--RFMNKLG-FGICLADDMGLGKTLQT 73

Query: 314 IALIQMQRSLQSKSKTEVLGNQKTEALNLDDDDDNGNAGLDKVKETGESDDIKPVPEVST 373
           IA+                                        K+               
Sbjct: 74  IAV------------------------------------FSDAKKEN------------- 84

Query: 374 STRSFSRRRPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKY 433
                    P   +LV+CP SVL+ W  EL    P    L   ++H         +L  Y
Sbjct: 85  ------ELTP---SLVICPLSVLKNWEEELSKFAPH---LRFAVFHEDRSKI---KLEDY 129

Query: 434 DVVLTTYSIVTNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKISNVSKRGKKGKK 493
           D++LT                          TY +                         
Sbjct: 130 DIILT--------------------------TYAV------------------------- 138

Query: 494 GNVNSSIDYGCGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNS 553
             +          L +V W  +V+DEAQ IKN +T++ +A   L++K R  L+GTPI+N 
Sbjct: 139 --LLRDTR-----LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENK 191

Query: 554 IDDLYSYFRFLKYDP--YAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFI 611
           +DDL+S   FL  +P     Y  F S    PI +      ++L+A++   +LRRTK    
Sbjct: 192 VDDLWSIMTFL--NPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTKY--- 246

Query: 612 DGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLL 671
           D   I +LP K  +    + + E+ A YK    +         D+ T  +    IL  LL
Sbjct: 247 DKAIINDLPDKIETNVYCNLTPEQAAMYKAEVENLFNNI----DSVTGIKRKGMILSTLL 302

Query: 672 RLRQACDHPLLVKEYDFDSVGKISGEMAKRLPRDMLIDLL 711
           +L+Q  DHP L+K     SV + SG+M         ++++
Sbjct: 303 KLKQIVDHPALLKG-GEQSVRR-SGKM------IRTMEII 334

PyMOL of 1z63

>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

>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

>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

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 Length = 271	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

>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

>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

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		743
d1z63a1		230	c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 h	3e-20
d1z63a1		230	c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 h	2e-09
d1z3ix2		298	c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fis	4e-12
d1z3ix2		298	c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fis	7e-09
d1z3ix1		346	c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fi	2e-08
d2fwra1		200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	0.001
d1z5za1		244	c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 h	0.002

>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 = 88.2 bits (217), Expect = 3e-20
 Identities = 44/117 (37%), Positives = 65/117 (55%), Gaps = 3/117 (2%)

Query: 504 CGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRF 563
              L +V W  +V+DEAQ IKN +T++ +A   L++K R  L+GTPI+N +DDL+S   F
Sbjct: 117 DTRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTF 176

Query: 564 LKYDPYAVYKSFYSTIKIPISRNSLHGYKKLQAVLRAIMLRRTKGTFIDGQPIINLP 620
           L       Y  F S    PI +      ++L+A++   +LRRTK    D   I +LP
Sbjct: 177 LNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAIISPFILRRTK---YDKAIINDLP 230

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

>d1z3ix1 c.37.1.19 (X:390-735) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]} Length = 346	Back information, alignment and structure

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} Length = 200	Back information, alignment and structure

>d1z5za1 c.37.1.19 (A:663-906) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]} Length = 244	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		743
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 [	99.87
d1rifa_		282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.86
d1wp9a1		200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.77
d2p6ra3		202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.57
d1gkub1		237	Helicase-like "domain" of reverse gyrase {Archaeon	99.37
d1gm5a3		264	RecG helicase domain {Thermotoga maritima [TaxId:	99.32
d1z3ix1		346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.31
d1a1va1		136	HCV helicase domain {Human hepatitis C virus (HCV)	99.22
d1yksa1		140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.21
d2eyqa3		233	Transcription-repair coupling factor, TRCF {Escher	99.14
d1z5za1		244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.13
d1oywa2		206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.1
d1hv8a1		208	Putative DEAD box RNA helicase {Archaeon Methanoco	98.95
d1wrba1		238	putative ATP-dependent RNA helicase VlgB {Flatworm	98.8
d1qdea_		212	Initiation factor 4a {Baker's yeast (Saccharomyces	98.76
d2g9na1		218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	98.74
d1veca_		206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	98.66
d2j0sa1		222	Probable ATP-dependent RNA helicase DDX48 {Human (	98.65
d2bmfa2		305	Dengue virus helicase {Dengue virus type 2 [TaxId:	98.63
d1t6na_		207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	98.61
d1s2ma1		206	Putative ATP-dependent RNA helicase DHH1 {Baker's	98.47
d1q0ua_		209	Probable DEAD box RNA helicase YqfR {Bacillus stea	98.29
d1tf5a3		273	Translocation ATPase SecA, nucleotide-binding doma	97.5
d1w36d1		359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.42
d1nkta3		288	Translocation ATPase SecA, nucleotide-binding doma	97.25
d1sxje2		252	Replication factor C5 {Baker's yeast (Saccharomyce	87.32

>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=353.39  Aligned_cols=226  Identities=36%  Similarity=0.610  Sum_probs=195.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCC
Q ss_conf             56898754544542159999999870203566666099816897269999999999721002210222033210125678
Q 004604          264 ATLPDGLLSVNLLKHQKIALAWMLQKETRSLHCLGGILADDQGLGKTISIIALIQMQRSLQSKSKTEVLGNQKTEALNLD  343 (743)
Q Consensus       264 ~~~P~~~~~~~L~~hQ~~gl~wml~~e~~~~~~~GGILADdMGLGKTiqaIali~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (743)
                      ..+|.++ +..|+|||++|+.||+.++..   ..|||||||||||||+++|+++......                    
T Consensus         3 ~~~P~~~-~~~L~~yQ~~~v~~~~~~~~~---~~g~iLaDe~GlGKT~~~i~~~~~~~~~--------------------   58 (230)
T d1z63a1           3 LLEPYNI-KANLRPYQIKGFSWMRFMNKL---GFGICLADDMGLGKTLQTIAVFSDAKKE--------------------   58 (230)
T ss_dssp             CCCCCSC-SSCCCHHHHHHHHHHHHHHHT---TCCEEECCCTTSCHHHHHHHHHHHHHHT--------------------
T ss_pred             CCCCHHH-HCCHHHHHHHHHHHHHHHHHC---CCCEEEEECCCCCHHHHHHHHHHHHHHC--------------------
T ss_conf             7694465-045069999999999986216---9987998589988699998735544212--------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCCEEEEEECCCC
Q ss_conf             88888876643211259889999987666543222478999857999582459999999997499999818999948998
Q 004604          344 DDDDNGNAGLDKVKETGESDDIKPVPEVSTSTRSFSRRRPAAGTLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSR  423 (743)
Q Consensus       344 ~d~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tLIVvP~Sll~qW~~Ei~k~~~~~~~L~V~iy~G~~r  423 (743)
                                                            ...+++|||||++++.||.+|+.+|++   ...+..+++...
T Consensus        59 --------------------------------------~~~~~~LIv~p~~l~~~W~~e~~~~~~---~~~~~~~~~~~~   97 (230)
T d1z63a1          59 --------------------------------------NELTPSLVICPLSVLKNWEEELSKFAP---HLRFAVFHEDRS   97 (230)
T ss_dssp             --------------------------------------TCCSSEEEEECSTTHHHHHHHHHHHCT---TSCEEECSSSTT
T ss_pred             --------------------------------------CCCCCCCEECCHHHHHHHHHHHHHHCC---CCCCEEECCCCC
T ss_conf             --------------------------------------355644110535542677777776402---544101014210


Q ss_pred             CCCHHHHCCCCEEEEEHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             88824330387899414556202899999735776421155457750233444321000000024578888877776668
Q 004604          424 TKDPVELAKYDVVLTTYSIVTNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKISNVSKRGKKGKKGNVNSSIDYG  503 (743)
Q Consensus       424 ~~~~~~l~~~DVVITTY~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~f~~~k~~k~~~~~~kk~~~~~k~~~~~~~~~~  503 (743)
                      .   ....+++|+|++|+.+.+..                                                        
T Consensus        98 ~---~~~~~~~vvi~~~~~~~~~~--------------------------------------------------------  118 (230)
T d1z63a1          98 K---IKLEDYDIILTTYAVLLRDT--------------------------------------------------------  118 (230)
T ss_dssp             S---CCGGGSSEEEEEHHHHTTCH--------------------------------------------------------
T ss_pred             H---HHCCCCCEEEEEHHHHHHHH--------------------------------------------------------
T ss_conf             0---00257688985499998688--------------------------------------------------------


Q ss_pred             CCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             88855437129998587445772229999998400692999956799899899999999618899886799998813665
Q 004604          504 CGPLAKVGWFRVVLDEAQTIKNHRTQVARACCSLRAKRRWCLSGTPIQNSIDDLYSYFRFLKYDPYAVYKSFYSTIKIPI  583 (743)
Q Consensus       504 ~~~L~~i~w~rVIlDEAH~IKN~~S~~ska~~~L~a~~RwlLTGTPIqNsl~DL~sLl~FL~p~~~~~~~~F~~~~~~pi  583 (743)
                        .+....|++||+||||.+||..++++++++.+.+++||+|||||++|++.|||++++||+|++|+++..|.+.|..++
T Consensus       119 --~l~~~~~~~vI~DEah~~k~~~s~~~~~~~~l~a~~r~~LTgTPi~n~~~dl~~ll~~l~p~~~~~~~~F~~~~~~~~  196 (230)
T d1z63a1         119 --RLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPI  196 (230)
T ss_dssp             --HHHTCCEEEEEEETGGGGSCTTSHHHHHHHTSCEEEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHH
T ss_pred             --HHHCCCCEEEEEEHHHCCCCCCHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf             --874165139999710034432205566654404655799725267767888998887628986789999999984455


Q ss_pred             CCCCHHHHHHHHHHHHCEEEEEECCC--CCCCCCCCCCC
Q ss_conf             57865678999985301578872475--45898744799
Q 004604          584 SRNSLHGYKKLQAVLRAIMLRRTKGT--FIDGQPIINLP  620 (743)
Q Consensus       584 ~~~~~~~~~~L~~lL~~~mLRRtK~d--v~~g~pii~LP  620 (743)
                      .+++....++|+.++++||+||+|+|  |..     +||
T Consensus       197 ~~~~~~~~~~L~~~l~~~~lRr~K~d~~v~~-----dLP  230 (230)
T d1z63a1         197 KKGDNMAKEELKAIISPFILRRTKYDKAIIN-----DLP  230 (230)
T ss_dssp             HTTCHHHHHHHHHHHTTTEECCCTTCHHHHT-----TSC
T ss_pred             HCCCHHHHHHHHHHHHCCEEEEECCCCCHHH-----CCC
T ss_conf             3267789999999842337997168861755-----679

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

>d1z3ix1 c.37.1.19 (X:390-735) 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

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

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

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

>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

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {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

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

>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

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {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