Citrus Sinensis ID: 003311

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--

MRLVKESKNERLTTLLEETNKLLVNLGAAVQRQKDSKHVDGIEPLKDSEDDLLDLDASENGTPRDLHPEEDDIIDSDHNDDSGDLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRGTSSLGTDVPSEREINRLAARSDEEFWLFEKMDEERRQKENYRSRLMEDHEVPEWAYSAPDNKEEQKGFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVENGQDISKLSTRGKRREYLPSEGNESASNSTGAEKKNLDMKNEIFPLASEGTSEDTFGSAPKRLRFERRNSESSDIQSVEKSEHKGVQGSGLNGHILTWNTHRKKRSSYVVQTSSSDSRGQNSNGRGNGWS

cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEEcccccccHHHHHHHHHHHHHHHccccccEEEEEEcccHHHHHHHHHHccccccEEEEEccHHHHHHHHHHHHcccccccEEEcHHHHHHHHHccccccccEEEEEEccccccccccHHHHHHHccccccEEEEccccccccHHHHHHHHHcccccccccHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHcccHHHHHHHHHHcccccccEEEEEEcccHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHccccccccccccccccHHHHHHccHHHHHHHHHHHHHHcccEEEEEHHHHHHHHHHHHHHHcccccEEEccccccHHHHHHHHHHHccccccccEEEEcccccccccccccccEEEEEcccccHHHHHHHHHHHHHccccccEEEEEEEEcccHHHHHHHHHHHHHcHHHHHHHcccccccccHHHHHHHHHHHHHHcccccccccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHccccccHHHHccccccccccccccccccccHHHHHHccccccccccccccccccccccccHHHHHHHccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccc

cccHcHcHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHcccccccccccccccccccccccHHHccccccccccHHHHHHccccHHHHHHHHHHHHccccHHHcccccHHHHHHHHHHHHHHHHcccccHHHHHccccHHHHHHHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHcccEEEEEEcccHHHHHHHHHHHHHcccccEEEEEEHHHHHHccHHHHHccEEEEEEccccHccccHHHHHHHHHHcccccEEEEcccHccccHHHHHHHHHHHcHHHccccccHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEEcHHHHHHHHHHHHHHcccEEcccccccHHHHHHHHHHHHHHcccccEEccccccccHHHHHHHHcHHHHHHHHHHHHHHcccEEEEHHHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHccccccEEEEEEEEcccccccccccccEEEEEEcccccHHHHHHHHHHHHccccccEEEEEEEEcccHHHHHHHHHHHHccccHHHHEcccccccccHHHHHHHHHHHHHHccHHcccccccHHHHHHHHHccHHHHHHHHHHHHHHcccccccHHHHccccccHHHcccccHHHHHHHHHHHccccccccccccEEEEEEccccccHHHHHHHHcccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccc

MRLVKESKNERLTTLLEETNKLLVNLGAAvqrqkdskhvdgieplkdseddlldldasengtprdlhpeeddiidsdhnddsgdllegqrQYNSAIHSIEEkvteqptllqggeLRAYQLEGLQWMLSLFNNNLNgilademglgktIQTIALIAYLLenkgvtgphvivapkavlpnwinefstwaPSIAAvvydgrpdeRKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEwfnapfkdrgqvaltdEEQLLIIRRLHHVIRpfilrrkkdevekylpgksqvILKCDMSAWQKVYYQQVTDVgrvgldtgtgkskSLQNLSMQLRkccnhpylfvgeynmWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLndfkflrldgstkteeRGTLlkqfnapdspyFMFLLSTRagglglnlqtadtviifdsdwnpqmdQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRgtsslgtdvpserEINRLAARSDEEFWLFEKMDEERRQKENYRSRlmedhevpewaysapdnkeeqkgfekgfghesssitgkrkrkEVVYADTLSDLQWMKAVENgqdisklstrgkrreylpsegnesasnstgaekknldmkneifplasegtsedtfgsapkrlrferrnsessdiqsveksehkgvqgsglnghILTWNTHRKKRSSYVVqtsssdsrgqnsngrgngws

mrlvkesknerLTTLLEETNKLLVNLGaavqrqkdskhvdgieplkdseddlldldasengtprdlhpeeddiidsdHNDDSGDLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREeffsergrfnvLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRlhhvirpfilrrkkdevekylpgksqviLKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKteergtllkqfnapdSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRahrigqkkevRVFVLVSVGSIEEVILERAKQKMGIDAKViqaglfnttstaqDRREMLKEIMRrgtsslgtdvpsereinrlaarsdeefwlfekmdeerrQKENyrsrlmedhevpewaysapdnKEEQKGFEKgfghesssitgkrkrkEVVYADTLsdlqwmkavengqdisklstrgkrreylpsegnesasnstgaekknlDMKNEIFPlasegtsedtfgsapkrlrferrnsessdiqsveksehkgvqgsglngHILTWNTHRKKRSSYvvqtsssdsrgqnsngrgngws

MRLVKESKnerlttlleetnkllvnlGAAVQRQKDSKHVDGIEPLKDSEddlldldASENGTPRDLHPEEddiidsdhnddsgdLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRGTSSLGTDVPSEREINRLAARSDEEFWLFEKMDEERRQKENYRSRLMEDHEVPEWAYSAPDNKEEQKGFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVENGQDISKLSTRGKRREYLPSEGNESASNSTGAEKKNLDMKNEIFPLASEGTSEDTFGSAPKRLRFERRNSESSDIQSVEKSEHKGVQGSGLNGHILTWNTHRKKRssyvvqtsssdsrgqnsngrgngws

*******************NKLLVNLG********************************************************************************TLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGR*******REEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGK*KSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWN*************IGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNT******************************************FWLF***********************************************************VVYADTLSDLQWMKA**********************************************************************************************GHILTWN*******************************

MRLVKESKNERLTTLLEETNKLLVNLGAAVQR***********************************************************************TEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDR*******EEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGR***********SLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVI*********************MRRGTS******PSEREINRLAARSDEEFWL******************MEDHEVPEWAYSAPDNKEEQKG*****************RKEVVYADTLSDL*****************************************************************************************************************************************

********NERLTTLLEETNKLLVNLGAAVQRQKDSKHVDGIEPLKDSEDDLLDLDASENGTPRDLHPEEDDIIDSDHNDDSGDLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRGTSSLGTDVPSEREINRLAARSDEEFWLFEKMDEERRQKENYRSRLMEDHEVPEWAYSAPD**************************EVVYADTLSDLQWMKAVENGQDISKLSTRGKRRE*****************KKNLDMKNEIFPLASEGTSEDTFGSAPKRLRFE*********************GSGLNGHILTWNTHR****************************

MRLVKESKNERLTTLLEETNKLLVNLGAAVQRQ**********************************************DDSGDL*EGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVGEYNMWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRGT*****DVPSEREINRLAARSDEEFWLFEKMDEERRQKENYRSRLMEDHEVPEWAYSAPDNKEEQKGFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVEN*******************************************************************************************GHIL*WNTHR****************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		832	2.2.26 [Sep-21-2011]
Q6DIC0		1577	Probable global transcrip	yes	no	0.729	0.384	0.517	0.0
P51531		1590	Probable global transcrip	yes	no	0.729	0.381	0.517	0.0
A7Z019		1606	Transcription activator B	no	no	0.748	0.387	0.508	0.0
Q3TKT4		1613	Transcription activator B	no	no	0.748	0.386	0.508	0.0
Q8K1P7		1613	Transcription activator B	yes	no	0.748	0.386	0.508	0.0
P51532		1647	Transcription activator B	no	no	0.748	0.378	0.488	0.0
P22082		1703	Transcription regulatory	yes	no	0.925	0.452	0.427	1e-180
P25439		1638	ATP-dependent helicase br	yes	no	0.729	0.370	0.496	1e-180
Q9UTN6		1199	Chromatin structure-remod	yes	no	0.828	0.574	0.448	1e-176
P32597		1359	Nuclear protein STH1/NPS1	no	no	0.787	0.481	0.461	1e-172

>sp\|Q6DIC0\|SMCA2_MOUSE Probable global transcription activator SNF2L2 OS=Mus musculus GN=Smarca2 PE=1 SV=1	Back alignment and function desciption

 Score =  648 bits (1672), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/646 (51%), Positives = 442/646 (68%), Gaps = 39/646 (6%)

Query: 88   GQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKT 147
            G + Y +  H+I E+V +Q  LL  G L+ YQL+GL+WM+SL+NNNLNGILADEMGLGKT
Sbjct: 702  GSQSYYTVAHAISERVEKQSALLINGTLKHYQLQGLEWMVSLYNNNLNGILADEMGLGKT 761

Query: 148  IQTIALIAYLLENKGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMRE 207
            IQTIALI YL+E+K + GP++I+ P + L NW  EF  WAPS+  + Y G P  R+++  
Sbjct: 762  IQTIALITYLMEHKRLNGPYLIIVPLSTLSNWTYEFDKWAPSVVKISYKGTPAMRRSLVP 821

Query: 208  EFFSERGRFNVLITHYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTI-SGYQIQ 266
            +  S  G+FNVL+T Y+ I++D+  L K++W YMIVDEGHR+KNH C L + + + Y   
Sbjct: 822  QLRS--GKFNVLLTTYEYIIKDKHILAKIRWKYMIVDEGHRMKNHHCKLTQVLNTHYVAP 879

Query: 267  RRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQ-VALTDEEQLLI 325
            RR+LLTGTP+QN L ELW+LLNFLLPTIF S   FE+WFNAPF   G+ V L +EE +LI
Sbjct: 880  RRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFNAPFAMTGERVDLNEEETILI 939

Query: 326  IRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTG-- 383
            IRRLH V+RPF+LRR K EVE  LP K + ++KCDMSA QK+ Y+ +   G +  D    
Sbjct: 940  IRRLHKVLRPFLLRRLKKEVESQLPEKVEYVIKCDMSALQKILYRHMQAKGILLTDGSEK 999

Query: 384  ----TGKSKSLQNLSMQLRKCCNHPYLF----------VGEYN-MWRKEEIIRASGKFEL 428
                 G +K+L N  MQLRK CNHPY+F          +G  N +    E+ RASGKFEL
Sbjct: 1000 DKKGKGGAKTLMNTIMQLRKICNHPYMFQHIEESFAEHLGYSNGVINGAELYRASGKFEL 1059

Query: 429  LDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEERGTLLKQFNA 488
            LDR+LPKLR + HRVLLF QMT LM I+E Y    +F +LRLDG+TK+E+R  LLK+FN 
Sbjct: 1060 LDRILPKLRATNHRVLLFCQMTSLMTIMEDYFAFRNFLYLRLDGTTKSEDRAALLKKFNE 1119

Query: 489  PDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVL 548
            P S YF+FLLSTRAGGLGLNLQ ADTV+IFDSDWNP  D QA+DRAHRIGQ+ EVRV  L
Sbjct: 1120 PGSQYFIFLLSTRAGGLGLNLQAADTVVIFDSDWNPHQDLQAQDRAHRIGQQNEVRVLRL 1179

Query: 549  VSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRGTSSLGTDVPS 608
             +V S+EE IL  AK K+ +D KVIQAG+F+  S++ +RR  L+ I+     +   D   
Sbjct: 1180 CTVNSVEEKILAAAKYKLNVDQKVIQAGMFDQKSSSHERRAFLQAILEHEEENEEEDEVP 1239

Query: 609  ERE-INRLAARSDEEFWLFEKMDEERRQKE----NYRSRLMEDHEVPEWAYSAPDNKEEQ 663
            + E +N++ AR +EEF LF +MD +RR+++      + RLME+ E+P W     D+ E +
Sbjct: 1240 DDETLNQMIARREEEFDLFMRMDMDRRREDARNPKRKPRLMEEDELPSWIIK--DDAEVE 1297

Query: 664  K-----GFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVENG 704
            +       EK FG       G R+R++V Y+D L++ QW++A+E+G
Sbjct: 1298 RLTCEEEEEKIFGR------GSRQRRDVDYSDALTEKQWLRAIEDG 1337

Transcriptional coactivator cooperating with nuclear hormone receptors to potentiate transcriptional activation. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene (By similarity). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.
Mus musculus (taxid: 10090)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>sp\|P51531\|SMCA2_HUMAN Probable global transcription activator SNF2L2 OS=Homo sapiens GN=SMARCA2 PE=1 SV=2	Back alignment and function description

>sp\|A7Z019\|SMCA4_BOVIN Transcription activator BRG1 OS=Bos taurus GN=SMARCA4 PE=2 SV=1	Back alignment and function description

>sp\|Q3TKT4\|SMCA4_MOUSE Transcription activator BRG1 OS=Mus musculus GN=Smarca4 PE=1 SV=1	Back alignment and function description

>sp\|Q8K1P7\|SMCA4_RAT Transcription activator BRG1 OS=Rattus norvegicus GN=Smarca4 PE=1 SV=1	Back alignment and function description

>sp\|P51532\|SMCA4_HUMAN Transcription activator BRG1 OS=Homo sapiens GN=SMARCA4 PE=1 SV=2	Back alignment and function description

>sp\|P22082\|SNF2_YEAST Transcription regulatory protein SNF2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SNF2 PE=1 SV=1	Back alignment and function description

>sp\|P25439\|BRM_DROME ATP-dependent helicase brm OS=Drosophila melanogaster GN=brm PE=1 SV=2	Back alignment and function description

>sp\|Q9UTN6\|SNF21_SCHPO Chromatin structure-remodeling complex subunit snf21 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=snf21 PE=1 SV=1	Back alignment and function description

>sp\|P32597\|STH1_YEAST Nuclear protein STH1/NPS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=STH1 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		832
224099763		1131	chromatin remodeling complex subunit [Po	0.993	0.731	0.799	0.0
359477501		1114	PREDICTED: transcription regulatory prot	0.979	0.731	0.807	0.0
297737012		1110	unnamed protein product [Vitis vinifera]	0.978	0.733	0.807	0.0
224111230		1132	chromatin remodeling complex subunit [Po	0.993	0.730	0.790	0.0
356574396		1073	PREDICTED: transcription regulatory prot	0.975	0.756	0.788	0.0
356534230		1072	PREDICTED: transcription regulatory prot	0.977	0.758	0.784	0.0
356541302		1063	PREDICTED: transcription regulatory prot	0.962	0.753	0.790	0.0
449444997		1092	PREDICTED: transcription regulatory prot	0.974	0.742	0.784	0.0
357444343		1083	Chromatin remodeling complex subunit [Me	0.978	0.751	0.767	0.0
357480785		1063	Chromatin remodeling complex subunit [Me	0.966	0.756	0.769	0.0

>gi\|224099763\|ref\|XP_002311608.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222851428\|gb\|EEE88975.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1361 bits (3522), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 667/834 (79%), Positives = 748/834 (89%), Gaps = 7/834 (0%)

Query: 1    MRLVKESKNERLTTLLEETNKLLVNLGAAVQRQKDSKHVDGIEPLKDSEDDLLDLDASEN 60
            MR+VKESKNERLT LLEETNKLLVNLGAAVQRQKD+KH DGIEPLKD E D  +LDAS N
Sbjct: 303  MRMVKESKNERLTMLLEETNKLLVNLGAAVQRQKDAKHSDGIEPLKDLEADSPELDASRN 362

Query: 61   GTPRDLHPEEDDIIDSDHNDDSGDLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQL 120
             +P D  PEED+IIDSD NDDSGDLLEGQRQYNSAIHSI+EKVTEQP++L+GG+LR YQL
Sbjct: 363  ESPLDTCPEEDEIIDSDVNDDSGDLLEGQRQYNSAIHSIQEKVTEQPSILKGGQLRPYQL 422

Query: 121  EGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNWI 180
            EGLQWMLSLFNNNLNGILADEMGLGKTIQTI+LIAYL E KG+ GPH+IVAPKAVLPNW+
Sbjct: 423  EGLQWMLSLFNNNLNGILADEMGLGKTIQTISLIAYLKETKGICGPHLIVAPKAVLPNWV 482

Query: 181  NEFSTWAPS--IAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQW 238
            NEFSTW     I A +YDGR +ERKA+RE+  S  G   VLITHYDLIMRD+ +LKK+ W
Sbjct: 483  NEFSTWIEENEIKAFLYDGRLEERKAIREQL-SREGNLQVLITHYDLIMRDKAFLKKIHW 541

Query: 239  IYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSV 298
             YMIVDEGHRLKNHECALAKTI+GYQ++RRLLLTGTPIQNSLQELWSLLNFLLP IFNS 
Sbjct: 542  QYMIVDEGHRLKNHECALAKTIAGYQLKRRLLLTGTPIQNSLQELWSLLNFLLPHIFNSE 601

Query: 299  ENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILK 358
            + FEEWFNAPF DRG+V+LTDEEQLLIIRRLH+VIRPFILRRKKDEVEKYLPGKSQVILK
Sbjct: 602  DKFEEWFNAPFADRGEVSLTDEEQLLIIRRLHNVIRPFILRRKKDEVEKYLPGKSQVILK 661

Query: 359  CDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVGEYNMWRKEE 418
            CD+SAWQKVYYQQVT++GRVGL  G+GKSKSLQNL+MQLRKCCNHPYLFVG+YNMWRK+E
Sbjct: 662  CDLSAWQKVYYQQVTEMGRVGLQNGSGKSKSLQNLTMQLRKCCNHPYLFVGDYNMWRKDE 721

Query: 419  IIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTEE 478
            I+RASGKFELLDRLLPKL  + HRVLLFSQMTRLMDILEIYL+L+D+K+LRLDGSTKTEE
Sbjct: 722  IMRASGKFELLDRLLPKLHATDHRVLLFSQMTRLMDILEIYLQLHDYKYLRLDGSTKTEE 781

Query: 479  RGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIG 538
            RGTLLK+FNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIG
Sbjct: 782  RGTLLKKFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIG 841

Query: 539  QKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRG 598
            QKKEVRVFVLVSVGS+EEVILERAKQK GIDAKVIQAGLFNTTSTAQDRREML+ IMRRG
Sbjct: 842  QKKEVRVFVLVSVGSVEEVILERAKQKKGIDAKVIQAGLFNTTSTAQDRREMLQGIMRRG 901

Query: 599  TSSLGTDVPSEREINRLAARSDEEFWLFEKMDEERRQKENYRSRLMEDHEVPEWAYSAPD 658
            TSSLGTDVPSEREINRLAARS EEF +FE+MD+ERR++E+YRSRLME+HEVPEWAY APD
Sbjct: 902  TSSLGTDVPSEREINRLAARSQEEFRIFEEMDKERRKQEDYRSRLMEEHEVPEWAYQAPD 961

Query: 659  NKEEQKGFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVENGQDISKLSTRGKRRE 718
            +KE++    KGF   S+ + GKR+RKEV Y DTLSDLQWMKAVENGQDISKLS++GK++E
Sbjct: 962  SKEDKA---KGFEQNSTGVLGKRRRKEVTYGDTLSDLQWMKAVENGQDISKLSSKGKKQE 1018

Query: 719  YLPSEGNESASNSTGAEKKNLDMKNEIFPLASEGTSEDTFGSAPKRLRFERRNSESSDIQ 778
            +  SE N++A+NS G EKK L+M+N+  P+ASEGTSEDT+ SAPKR + +   +E +D Q
Sbjct: 1019 HTRSEVNDTANNSAGTEKKVLEMRNDNMPVASEGTSEDTYASAPKRPQSDEAVTEKTDYQ 1078

Query: 779  SVEKSEHKGVQGSGLNGHILTWNTHRKKRSSYVVQTSSSDSRGQNSNGRGNGWS 832
             +EK E +GV GSG N  I TWNT++KKRSSYV  +SSSDSRGQNSN +GNGW+
Sbjct: 1079 VLEKPE-QGVGGSGWNRQIFTWNTYKKKRSSYVFPSSSSDSRGQNSNVKGNGWA 1131

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359477501\|ref\|XP_002281240.2\| PREDICTED: transcription regulatory protein SNF2-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297737012\|emb\|CBI26213.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224111230\|ref\|XP_002315787.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222864827\|gb\|EEF01958.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356574396\|ref\|XP_003555334.1\| PREDICTED: transcription regulatory protein SNF2-like [Glycine max]	Back alignment and taxonomy information

>gi\|356534230\|ref\|XP_003535660.1\| PREDICTED: transcription regulatory protein SNF2-like [Glycine max]	Back alignment and taxonomy information

>gi\|356541302\|ref\|XP_003539117.1\| PREDICTED: transcription regulatory protein SNF2-like [Glycine max]	Back alignment and taxonomy information

>gi\|449444997\|ref\|XP_004140260.1\| PREDICTED: transcription regulatory protein SNF2-like [Cucumis sativus] gi\|449481192\|ref\|XP_004156109.1\| PREDICTED: transcription regulatory protein SNF2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357444343\|ref\|XP_003592449.1\| Chromatin remodeling complex subunit [Medicago truncatula] gi\|355481497\|gb\|AES62700.1\| Chromatin remodeling complex subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|357480785\|ref\|XP_003610678.1\| Chromatin remodeling complex subunit [Medicago truncatula] gi\|355512013\|gb\|AES93636.1\| Chromatin remodeling complex subunit [Medicago truncatula]	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		832
TAIR\|locus:2150270		1064	CHR23 "chromatin remodeling 23	0.868	0.679	0.710	1.8e-280
UNIPROTKB\|K7GT64		980	LOC100622433 "Uncharacterized	0.385	0.327	0.537	9e-178
UNIPROTKB\|A5PKK5		1554	SMARCA2 "SMARCA2 protein" [Bos	0.382	0.204	0.542	2.8e-177
UNIPROTKB\|E2RKP4		1556	SMARCA2 "Uncharacterized prote	0.382	0.204	0.542	2.8e-177
UNIPROTKB\|F1SJG5		1556	SMARCA2 "Uncharacterized prote	0.382	0.204	0.542	2.8e-177
UNIPROTKB\|E9PTG1		1597	Smarca2 "Protein Smarca2" [Rat	0.382	0.199	0.542	3.3e-177
UNIPROTKB\|J9P5P2		1574	SMARCA2 "Uncharacterized prote	0.382	0.202	0.542	3.4e-177
UNIPROTKB\|P51531		1590	SMARCA2 "Probable global trans	0.382	0.2	0.542	3.9e-177
MGI\|MGI:99603		1577	Smarca2 "SWI/SNF related, matr	0.382	0.201	0.542	5.6e-177
UNIPROTKB\|D4AA07		1262	Smarca4 "Transcription activat	0.385	0.254	0.537	1.3e-176

TAIR\|locus:2150270 CHR23 "chromatin remodeling 23" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2682 (949.2 bits), Expect = 1.8e-280, Sum P(2) = 1.8e-280
 Identities = 525/739 (71%), Positives = 614/739 (83%)

Query:     1 MRLVKESKXXXXXXXXXXXXXXXXXXGAAVQRQKDSKHVDGIEPLKDSEXXXXXXXASEN 60
             M+L KESK                  GAAVQRQKD+K  +  + LK SE        S+ 
Sbjct:   276 MKLAKESKNEKLTLFLEETNKIFVSLGAAVQRQKDAKLSENTKLLKGSESDL-----SDV 330

Query:    61 GTPRDLHP-EEXXXXXXXXXXXXXXLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQ 119
               P D+ P ++              LLEG+RQ+N AIHSI+EKVT+QP+LLQGGELR+YQ
Sbjct:   331 DAPEDVLPAQDIEIIDSDNNDDSNDLLEGERQFNLAIHSIQEKVTKQPSLLQGGELRSYQ 390

Query:   120 LEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENKGVTGPHVIVAPKAVLPNW 179
             LEGLQWM+SL+NN+ NGILADEMGLGKTIQTIALIAYLLE+K + GPH+I+APKAVLPNW
Sbjct:   391 LEGLQWMVSLYNNDYNGILADEMGLGKTIQTIALIAYLLESKDLHGPHLILAPKAVLPNW 450

Query:   180 INEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWI 239
              NEF+ WAPSI+A +YDG  ++R  +R       G+FNVLITHYDLIMRD+ +LKK+ W 
Sbjct:   451 ENEFALWAPSISAFLYDGSKEKRTEIRARIAG--GKFNVLITHYDLIMRDKAFLKKIDWN 508

Query:   240 YMIVDEGHRLKNHECALAKTI-SGYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSV 298
             YMIVDEGHRLKNHECALAKT+ +GY+I+RRLLLTGTPIQNSLQELWSLLNFLLP IFNS+
Sbjct:   509 YMIVDEGHRLKNHECALAKTLGTGYRIKRRLLLTGTPIQNSLQELWSLLNFLLPHIFNSI 568

Query:   299 ENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILK 358
              NFEEWFN PF + G  +LTDEE+LLII RLHHVIRPF+LRRKK EVEK+LPGK+QVILK
Sbjct:   569 HNFEEWFNTPFAECGSASLTDEEELLIINRLHHVIRPFLLRRKKSEVEKFLPGKTQVILK 628

Query:   359 CDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCCNHPYLFVG-EYNMWRKE 417
             CDMSAWQK+YY+QVTDVGRVGL +G GKSKSLQNL+MQLRKCCNHPYLFVG +YNM +K 
Sbjct:   629 CDMSAWQKLYYKQVTDVGRVGLHSGNGKSKSLQNLTMQLRKCCNHPYLFVGADYNMCKKP 688

Query:   418 EIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDGSTKTE 477
             EI+RASGKFELLDRLLPKL+K+GHR+LLFSQMTRL+D+LEIYL LND+ +LRLDGSTKT+
Sbjct:   689 EIVRASGKFELLDRLLPKLKKAGHRILLFSQMTRLIDLLEIYLSLNDYMYLRLDGSTKTD 748

Query:   478 ERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRI 537
             +RG LLKQFN PDSPYFMFLLSTRAGGLGLNLQTADT+IIFDSDWNPQMDQQAEDRAHRI
Sbjct:   749 QRGILLKQFNEPDSPYFMFLLSTRAGGLGLNLQTADTIIIFDSDWNPQMDQQAEDRAHRI 808

Query:   538 GQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRR 597
             GQKKEVRVFVLVS+GSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREML+EIM +
Sbjct:   809 GQKKEVRVFVLVSIGSIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLEEIMSK 868

Query:   598 GTSSLGTDVPSEREINRLAARSDEEFWLFEKMDEERRQKENYRSRLMEDHEVPEWAYSAP 657
             GTSSLG DVPSEREINRLAAR++EEFW+FE+MDEERR+KENY++RLME+ EVPEWAY++ 
Sbjct:   869 GTSSLGEDVPSEREINRLAARTEEEFWMFEQMDEERRKKENYKTRLMEEKEVPEWAYTS- 927

Query:   658 DNKEEQKGFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVEN-GQDISKLSTRGKR 716
             + +E++   +  FG    S+TGKRKRKE VY+D+LSDLQWMKA+E+  +D SK+S + KR
Sbjct:   928 ETQEDKTNAKNHFG----SLTGKRKRKEAVYSDSLSDLQWMKAMESEDEDASKVSQKRKR 983

Query:   717 REYLPSEGNESASNSTGAE 735
              +      N S + +  +E
Sbjct:   984 TDTKTRMSNGSKAEAVLSE 1002

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:0006259 "DNA metabolic process" evidence=RCA

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0007126 "meiosis" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0031048 "chromatin silencing by small RNA" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

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

UNIPROTKB\|K7GT64 LOC100622433 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|A5PKK5 SMARCA2 "SMARCA2 protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RKP4 SMARCA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SJG5 SMARCA2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E9PTG1 Smarca2 "Protein Smarca2" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|J9P5P2 SMARCA2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|P51531 SMARCA2 "Probable global transcription activator SNF2L2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

MGI\|MGI:99603 Smarca2 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|D4AA07 Smarca4 "Transcription activator BRG1" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Your Input:
	GSVIVG00019937001	SubName- Full=Chromosome chr5 scaffold_2, whole genome shotgun sequence; (1077 aa)
		(Vitis vinifera)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		832
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	0.0
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	1e-115
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	1e-111
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-28
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-28
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	5e-23
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-22
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	1e-20
pfam11496		279	pfam11496, HDA2-3, Class II histone deacetylase co	2e-09
COG0513		513	COG0513, SrmB, Superfamily II DNA and RNA helicase	6e-07
PTZ00110		545	PTZ00110, PTZ00110, helicase; Provisional	7e-07
PRK04914		956	PRK04914, PRK04914, ATP-dependent helicase HepA; V	0.003

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

 Score =  548 bits (1414), Expect = 0.0
 Identities = 251/529 (47%), Positives = 354/529 (66%), Gaps = 24/529 (4%)

Query: 102 KVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLENK 161
           ++  QP+ ++G ++R YQL GL W++ L+ N +NGILADEMGLGKT+QTI+L+ YL E +
Sbjct: 158 RLLVQPSCIKG-KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTISLLGYLHEYR 216

Query: 162 GVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLIT 221
           G+TGPH++VAPK+ L NW+NE   + P + AV + G P+ER   REE     G+F+V +T
Sbjct: 217 GITGPHMVVAPKSTLGNWMNEIRRFCPVLRAVKFHGNPEERAHQREELLVA-GKFDVCVT 275

Query: 222 HYDLIMRDRQYLKKVQWIYMIVDEGHRLKNHECALAKTISGYQIQRRLLLTGTPIQNSLQ 281
            +++ ++++  LK+  W Y+I+DE HR+KN    L+KT+  +    RLL+TGTP+QN+L 
Sbjct: 276 SFEMAIKEKTALKRFSWRYIIIDEAHRIKNENSLLSKTMRLFSTNYRLLITGTPLQNNLH 335

Query: 282 ELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQVALTDEEQLLIIRRLHHVIRPFILRRK 341
           ELW+LLNFLLP IF+S E F+EWF             + +Q  ++++LH V+RPF+LRR 
Sbjct: 336 ELWALLNFLLPEIFSSAETFDEWFQIS---------GENDQQEVVQQLHKVLRPFLLRRL 386

Query: 342 KDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDTGTGKSKSLQNLSMQLRKCC 401
           K +VEK LP K + ILK  MS  QK YY+ +       ++ G G+ K L N++MQLRKCC
Sbjct: 387 KSDVEKGLPPKKETILKVGMSQMQKQYYKALLQKDLDVVNAG-GERKRLLNIAMQLRKCC 445

Query: 402 NHPYLFVGEYN---MWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEI 458
           NHPYLF G          E ++  SGK  LLD+LLPKL++   RVL+FSQMTRL+DILE 
Sbjct: 446 NHPYLFQGAEPGPPYTTGEHLVENSGKMVLLDKLLPKLKERDSRVLIFSQMTRLLDILED 505

Query: 459 YLKLNDFKFLRLDGSTKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIF 518
           YL    +++ R+DG+T  E+R   +  FN P S  F+FLLSTRAGGLG+NL TAD VI++
Sbjct: 506 YLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAGGLGINLATADIVILY 565

Query: 519 DSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVGSIEEVILERAKQKMGIDAKVIQAGLF 578
           DSDWNPQ+D QA+DRAHRIGQKKEV+VF   +  +IEE ++ERA +K+ +DA VIQ G  
Sbjct: 566 DSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQQGRL 625

Query: 579 --NTTSTAQDRREMLK---EIMRRGTSSLGTDVPSEREINRLAARSDEE 622
               T    +  +M++   E++     S  TD     +I+R+ A+ +E 
Sbjct: 626 AEQKTVNKDELLQMVRYGAEMVFSSKDSTITD----EDIDRIIAKGEEA 670

Length = 1033

>gnl\|CDD\|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain	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|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

Back alignment and domain information

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

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

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

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

>gnl\|CDD\|221124 pfam11496, HDA2-3, Class II histone deacetylase complex subunits 2 and 3	Back alignment and domain information

>gnl\|CDD\|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>gnl\|CDD\|240273 PTZ00110, PTZ00110, helicase; Provisional	Back alignment and domain information

>gnl\|CDD\|235319 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		832
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	100.0
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	100.0
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	100.0
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	100.0
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	100.0
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	100.0
KOG0387		923	consensus Transcription-coupled repair protein CSB	100.0
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	100.0
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	100.0
KOG1002		791	consensus Nucleotide excision repair protein RAD16	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
KOG4439		901	consensus RNA polymerase II transcription terminat	100.0
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	100.0
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	100.0
PRK04914		956	ATP-dependent helicase HepA; Validated	100.0
KOG0383		696	consensus Predicted helicase [General function pre	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
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	100.0
PRK13766		773	Hef nuclease; Provisional	100.0
KOG0298		1394	consensus DEAD box-containing helicase-like transc	100.0
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
PHA02558		501	uvsW UvsW helicase; Provisional	99.98
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.98
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.96
PTZ00110		545	helicase; Provisional	99.96
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	99.95
KOG0354		746	consensus DEAD-box like helicase [General function	99.95
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	99.95
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	99.95
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	99.95
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	99.95
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.95
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	99.95
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	99.94
PTZ00424		401	helicase 45; Provisional	99.94
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.94
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	99.94
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	99.93
KOG1123		776	consensus RNA polymerase II transcription initiati	99.93
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	99.92
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.92
PRK13767		876	ATP-dependent helicase; Provisional	99.91
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	99.91
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	99.91
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.91
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	99.91
PRK10689		1147	transcription-repair coupling factor; Provisional	99.9
PRK02362		737	ski2-like helicase; Provisional	99.89
PRK01172		674	ski2-like helicase; Provisional	99.88
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	99.87
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	99.87
PRK00254		720	ski2-like helicase; Provisional	99.87
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	99.84
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	99.84
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	99.83
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.83
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.83
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.83
COG1201		814	Lhr Lhr-like helicases [General function predictio	99.83
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	99.83
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	99.83
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	99.82
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	99.82
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	99.82
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	99.81
COG4096		875	HsdR Type I site-specific restriction-modification	99.81
KOG0347		731	consensus RNA helicase [RNA processing and modific	99.8
PRK09401		1176	reverse gyrase; Reviewed	99.8
KOG0341		610	consensus DEAD-box protein abstrakt [RNA processin	99.79
PRK09200		790	preprotein translocase subunit SecA; Reviewed	99.79
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	99.78
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	99.78
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	99.78
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	99.78
KOG0343		758	consensus RNA Helicase [RNA processing and modific	99.78
PHA02653		675	RNA helicase NPH-II; Provisional	99.77
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	99.77
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.77
KOG4284		980	consensus DEAD box protein [Transcription]	99.75
COG1204		766	Superfamily II helicase [General function predicti	99.75
PRK05580		679	primosome assembly protein PriA; Validated	99.74
COG4889		1518	Predicted helicase [General function prediction on	99.74
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	99.74
COG1205		851	Distinct helicase family with a unique C-terminal	99.74
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	99.73
PRK14701		1638	reverse gyrase; Provisional	99.72
COG1202		830	Superfamily II helicase, archaea-specific [General	99.72
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	99.72
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.71
TIGR00595		505	priA primosomal protein N'. All proteins in this f	99.71
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	99.71
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	99.7
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	99.7
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.69
PRK09694		878	helicase Cas3; Provisional	99.68
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	99.68
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	99.67
KOG0334		997	consensus RNA helicase [RNA processing and modific	99.66
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	99.66
KOG0346		569	consensus RNA helicase [RNA processing and modific	99.65
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	99.64
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	99.62
KOG0353		695	consensus ATP-dependent DNA helicase [General func	99.6
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.6
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	99.6
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	99.59
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.58
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	99.57
PRK12904		830	preprotein translocase subunit SecA; Reviewed	99.57
PRK13107		908	preprotein translocase subunit SecA; Reviewed	99.57
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.56
KOG0327		397	consensus Translation initiation factor 4F, helica	99.56
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	99.55
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.55
PRK05298		652	excinuclease ABC subunit B; Provisional	99.54
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.49
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	99.48
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	99.48
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.46
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	99.44
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	99.43
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.42
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.42
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	99.4
PRK12326		764	preprotein translocase subunit SecA; Reviewed	99.39
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	99.38
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.27
PF11496		297	HDA2-3: Class II histone deacetylase complex subun	99.26
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.24
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	99.2
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	99.16
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	99.15
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	99.11
COG0610		962	Type I site-specific restriction-modification syst	99.1
PF14619		74	SnAC: Snf2-ATP coupling, chromatin remodelling com	99.04
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.99
COG1198		730	PriA Primosomal protein N' (replication factor Y)	98.98
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	98.97
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	98.92
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	98.86
CHL00122		870	secA preprotein translocase subunit SecA; Validate	98.85
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	98.85
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	98.83
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	98.81
KOG0950		1008	consensus DNA polymerase theta/eta, DEAD-box super	98.79
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.76
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.71
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	98.68
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	98.67
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	98.67
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	98.63
PRK15483		986	type III restriction-modification system StyLTI en	98.52
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	98.5
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	98.49
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	98.46
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	98.4
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	98.4
PF13871		278	Helicase_C_4: Helicase_C-like	98.36
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.34
KOG0349		725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	98.32
KOG0924		1042	consensus mRNA splicing factor ATP-dependent RNA h	98.28
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	98.24
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	98.24
KOG0923		902	consensus mRNA splicing factor ATP-dependent RNA h	98.09
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	98.06
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.06
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	98.05
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.99
KOG0953		700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	97.92
KOG4150		1034	consensus Predicted ATP-dependent RNA helicase [RN	97.81
COG3587		985	Restriction endonuclease [Defense mechanisms]	97.64
PRK10536		262	hypothetical protein; Provisional	97.46
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.45
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	97.44
KOG0925		699	consensus mRNA splicing factor ATP-dependent RNA h	97.31
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.21
KOG1803		649	consensus DNA helicase [Replication, recombination	97.13
PF13401		131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.06
PRK14873		665	primosome assembly protein PriA; Provisional	97.04
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	97.03
TIGR00376		637	DNA helicase, putative. The gene product may repre	96.84
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	96.83
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	96.79
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	96.78
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.74
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	96.5
KOG1131		755	consensus RNA polymerase II transcription initiati	96.36
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	96.25
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	96.1
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	96.04
PRK14956		484	DNA polymerase III subunits gamma and tau; Provisi	95.9
PRK07003		830	DNA polymerase III subunits gamma and tau; Validat	95.75
PRK04296		190	thymidine kinase; Provisional	95.74
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	95.73
TIGR02881		261	spore_V_K stage V sporulation protein K. Members o	95.69
smart00382		148	AAA ATPases associated with a variety of cellular	95.69
PRK12723		388	flagellar biosynthesis regulator FlhF; Provisional	95.55
KOG1805		1100	consensus DNA replication helicase [Replication, r	95.39
PRK09112		351	DNA polymerase III subunit delta'; Validated	95.32
PRK10875		615	recD exonuclease V subunit alpha; Provisional	95.22
COG3421		812	Uncharacterized protein conserved in bacteria [Fun	95.02
PRK14949		944	DNA polymerase III subunits gamma and tau; Provisi	95.0
PRK12323		700	DNA polymerase III subunits gamma and tau; Provisi	94.99
PLN03025		319	replication factor C subunit; Provisional	94.94
PRK11773		721	uvrD DNA-dependent helicase II; Provisional	94.84
PRK06526		254	transposase; Provisional	94.74
PRK14960		702	DNA polymerase III subunits gamma and tau; Provisi	94.56
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	94.49
PRK08181		269	transposase; Validated	94.49
PF00448		196	SRP54: SRP54-type protein, GTPase domain; InterPro	94.47
PRK07764		824	DNA polymerase III subunits gamma and tau; Validat	94.42
CHL00181		287	cbbX CbbX; Provisional	94.4
PRK12402		337	replication factor C small subunit 2; Reviewed	94.36
PF13177		162	DNA_pol3_delta2: DNA polymerase III, delta subunit	94.34
PRK07994		647	DNA polymerase III subunits gamma and tau; Validat	94.34
TIGR03015		269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.19
TIGR01073		726	pcrA ATP-dependent DNA helicase PcrA. Designed to	94.16
TIGR02880		284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.06
PRK14958		509	DNA polymerase III subunits gamma and tau; Provisi	94.01
PRK06835		329	DNA replication protein DnaC; Validated	93.93
PRK05707		328	DNA polymerase III subunit delta'; Validated	93.7
PRK05703		424	flhF flagellar biosynthesis regulator FlhF; Valida	93.64
PRK11889		436	flhF flagellar biosynthesis regulator FlhF; Provis	93.52
TIGR02928		365	orc1/cdc6 family replication initiation protein. M	93.51
PRK14961		363	DNA polymerase III subunits gamma and tau; Provisi	93.44
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	93.44
PF06862		442	DUF1253: Protein of unknown function (DUF1253); In	93.31
KOG0989		346	consensus Replication factor C, subunit RFC4 [Repl	93.2
PRK07952		244	DNA replication protein DnaC; Validated	93.06
TIGR02639		731	ClpA ATP-dependent Clp protease ATP-binding subuni	93.04
TIGR03420		226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	93.0
PF13245		76	AAA_19: Part of AAA domain	92.98
PRK14952		584	DNA polymerase III subunits gamma and tau; Provisi	92.97
PHA02544		316	44 clamp loader, small subunit; Provisional	92.71
PRK08058		329	DNA polymerase III subunit delta'; Validated	92.67
PRK07940		394	DNA polymerase III subunit delta'; Validated	92.65
PF13173		128	AAA_14: AAA domain	92.58
PRK14951		618	DNA polymerase III subunits gamma and tau; Provisi	92.58
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	92.48
PRK08116		268	hypothetical protein; Validated	92.45
PRK09111		598	DNA polymerase III subunits gamma and tau; Validat	92.41
PRK07471		365	DNA polymerase III subunit delta'; Validated	92.4
PRK14957		546	DNA polymerase III subunits gamma and tau; Provisi	92.26
PRK07993		334	DNA polymerase III subunit delta'; Validated	92.2
PRK08451		535	DNA polymerase III subunits gamma and tau; Validat	92.11
PRK14974		336	cell division protein FtsY; Provisional	92.07
PF05621		302	TniB: Bacterial TniB protein; InterPro: IPR008868	91.97
PRK14963		504	DNA polymerase III subunits gamma and tau; Provisi	91.8
PRK14962		472	DNA polymerase III subunits gamma and tau; Provisi	91.8
PRK06090		319	DNA polymerase III subunit delta'; Validated	91.76
PRK06871		325	DNA polymerase III subunit delta'; Validated	91.72
PRK06645		507	DNA polymerase III subunits gamma and tau; Validat	91.67
PRK08084		235	DNA replication initiation factor; Provisional	91.62
PRK14964		491	DNA polymerase III subunits gamma and tau; Provisi	91.48
PRK14959		624	DNA polymerase III subunits gamma and tau; Provisi	91.27
PRK05580		679	primosome assembly protein PriA; Validated	91.27
PTZ00112		1164	origin recognition complex 1 protein; Provisional	91.2
KOG0991		333	consensus Replication factor C, subunit RFC2 [Repl	91.18
PRK08769		319	DNA polymerase III subunit delta'; Validated	91.11
PRK06921		266	hypothetical protein; Provisional	90.92
PRK08691		709	DNA polymerase III subunits gamma and tau; Validat	90.92
PRK14969		527	DNA polymerase III subunits gamma and tau; Provisi	90.86
COG0470		325	HolB ATPase involved in DNA replication [DNA repli	90.66
PF00004		132	AAA: ATPase family associated with various cellula	90.6
PRK08903		227	DnaA regulatory inactivator Hda; Validated	90.32
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	90.12
PRK05563		559	DNA polymerase III subunits gamma and tau; Validat	90.02
PRK14948		620	DNA polymerase III subunits gamma and tau; Provisi	89.85
cd01124		187	KaiC KaiC is a circadian clock protein primarily f	89.83
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	89.63
PRK06647		563	DNA polymerase III subunits gamma and tau; Validat	89.46
PRK14955		397	DNA polymerase III subunits gamma and tau; Provisi	89.39
PF00580		315	UvrD-helicase: UvrD/REP helicase N-terminal domain	89.39
PRK14965		576	DNA polymerase III subunits gamma and tau; Provisi	89.37
COG3267		269	ExeA Type II secretory pathway, component ExeA (pr	89.3
PHA02533		534	17 large terminase protein; Provisional	89.29
PRK14722		374	flhF flagellar biosynthesis regulator FlhF; Provis	89.14
PRK00440		319	rfc replication factor C small subunit; Reviewed	89.06
PRK14953		486	DNA polymerase III subunits gamma and tau; Provisi	89.02
PF05876		557	Terminase_GpA: Phage terminase large subunit (GpA)	88.91
PRK05642		234	DNA replication initiation factor; Validated	88.87
PRK14950		585	DNA polymerase III subunits gamma and tau; Provisi	88.84
TIGR02768		744	TraA_Ti Ti-type conjugative transfer relaxase TraA	88.78
cd01120		165	RecA-like_NTPases RecA-like NTPases. This family i	88.77
PRK08727		233	hypothetical protein; Validated	88.69
PRK04195		482	replication factor C large subunit; Provisional	88.29
cd01121		372	Sms Sms (bacterial radA) DNA repair protein. This	88.24
PRK00411		394	cdc6 cell division control protein 6; Reviewed	88.18
PRK06964		342	DNA polymerase III subunit delta'; Validated	88.17
PRK00149		450	dnaA chromosomal replication initiation protein; R	88.14
TIGR00362		405	DnaA chromosomal replication initiator protein Dna	88.12
PRK06731		270	flhF flagellar biosynthesis regulator FlhF; Valida	88.05
PRK14954		620	DNA polymerase III subunits gamma and tau; Provisi	88.05
PRK14087		450	dnaA chromosomal replication initiation protein; P	88.04
TIGR00595		505	priA primosomal protein N'. All proteins in this f	87.86
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	87.64
TIGR00678		188	holB DNA polymerase III, delta' subunit. At positi	87.38
PRK05896		605	DNA polymerase III subunits gamma and tau; Validat	87.07
PRK14088		440	dnaA chromosomal replication initiation protein; P	86.98
PRK00080		328	ruvB Holliday junction DNA helicase RuvB; Reviewed	86.73
PRK07133		725	DNA polymerase III subunits gamma and tau; Validat	86.7
PRK06893		229	DNA replication initiation factor; Validated	86.51
PRK12724		432	flagellar biosynthesis regulator FlhF; Provisional	86.43
PRK04132		846	replication factor C small subunit; Provisional	86.37
PRK12377		248	putative replication protein; Provisional	86.27
PHA03333		752	putative ATPase subunit of terminase; Provisional	86.27
PHA03368		738	DNA packaging terminase subunit 1; Provisional	85.85
PRK00771		437	signal recognition particle protein Srp54; Provisi	85.78
PF02456		369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	85.75
TIGR03345		852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	85.37
PRK12727		559	flagellar biosynthesis regulator FlhF; Provisional	85.21
PF05496		233	RuvB_N: Holliday junction DNA helicase ruvB N-term	85.21
PRK06305		451	DNA polymerase III subunits gamma and tau; Validat	85.03
PRK09183		259	transposase/IS protein; Provisional	84.74
PF13481		193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	84.66
PRK08699		325	DNA polymerase III subunit delta'; Validated	83.88
PF00308		219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	83.75
PRK14086		617	dnaA chromosomal replication initiation protein; P	83.59
TIGR02397		355	dnaX_nterm DNA polymerase III, subunit gamma and t	83.46
PRK13342		413	recombination factor protein RarA; Reviewed	83.19
TIGR03689		512	pup_AAA proteasome ATPase. In the Actinobacteria,	82.83
cd00561		159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	82.8
COG2256		436	MGS1 ATPase related to the helicase subunit of the	82.75
KOG2543		438	consensus Origin recognition complex, subunit 5 [R	82.49
PRK13889		988	conjugal transfer relaxase TraA; Provisional	82.42
TIGR01075		715	uvrD DNA helicase II. Designed to identify uvrD me	82.19
PTZ00293		211	thymidine kinase; Provisional	81.92
PRK06904		472	replicative DNA helicase; Validated	81.91
PRK10416		318	signal recognition particle-docking protein FtsY;	81.87
PHA03372		668	DNA packaging terminase subunit 1; Provisional	81.62
PRK12422		445	chromosomal replication initiation protein; Provis	81.62
TIGR01425		429	SRP54_euk signal recognition particle protein SRP5	81.46
PF01443		234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	81.46
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	81.41
cd03115		173	SRP The signal recognition particle (SRP) mediates	81.38
COG1484		254	DnaC DNA replication protein [DNA replication, rec	81.24
TIGR02688		449	conserved hypothetical protein TIGR02688. Members	81.19
COG1198		730	PriA Primosomal protein N' (replication factor Y)	81.17
PRK13894		319	conjugal transfer ATPase TrbB; Provisional	80.86
PHA02244		383	ATPase-like protein	80.76
TIGR01074		664	rep ATP-dependent DNA helicase Rep. Designed to id	80.73
CHL00095		821	clpC Clp protease ATP binding subunit	80.72
TIGR00708		173	cobA cob(I)alamin adenosyltransferase. Alternate n	80.67
TIGR03346		852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	80.58
COG1419		407	FlhF Flagellar GTP-binding protein [Cell motility	80.25

>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

Probab=100.00  E-value=1.4e-150  Score=1289.20  Aligned_cols=787  Identities=49%  Similarity=0.787  Sum_probs=671.0

Q ss_pred             CcchhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhhhcccCCCCCCCCCcchhcccccCCCCCCCCCCCCCCccccCCCCC
Q 003311            1 MRLVKESKNERLTTLLEETNKLLVNLGAAVQRQKDSKHVDGIEPLKDSEDDLLDLDASENGTPRDLHPEEDDIIDSDHND   80 (832)
Q Consensus         1 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~   80 (832)
                      +||+|++||+||++||+|||+||.+|+++|+.|+.+-      +...++.+.                   ..++....+
T Consensus       306 ~kl~dq~Kd~Rl~~LL~qt~~yl~sL~s~Vk~qk~~~------~~~~~~~d~-------------------~~i~~~ak~  360 (1157)
T KOG0386|consen  306 RKLQDQKKDNRLSQLLSQTDSYLPSLSSVVKGQKSEN------PDANSASDI-------------------SGISGSAKA  360 (1157)
T ss_pred             HHHHhhccccHHHHhhhhhhHHHHHHHHHHHHhhccc------cccchhhhh-------------------hhhhhhhcc
Confidence            5899999999999999999999999999999997620      000011110                   011111222


Q ss_pred             CchhHHHHHHhhhhhhhccccccccCCCcCCCCCchHHHHHHHHHHHHhhccCCCeEEEcCCCCcHHHHHHHHHHHHHHh
Q 003311           81 DSGDLLEGQRQYNSAIHSIEEKVTEQPTLLQGGELRAYQLEGLQWMLSLFNNNLNGILADEMGLGKTIQTIALIAYLLEN  160 (832)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~e~~~~~P~~l~~~~Lr~yQ~egl~wml~~~~~~~~gILaDemGlGKTiqaiali~~l~~~  160 (832)
                      +.++.......||.++|.|.++++.||+.+.||+|++||+.||+||+++|+|+.|||||||||||||+|+|++|+||++.
T Consensus       361 ~~~d~~~s~~~Yys~AH~I~E~v~~Qps~l~GG~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQtIsLitYLmE~  440 (1157)
T KOG0386|consen  361 DVDDHAESNGSYYSTAHPIKENVAKQPSSLQGGELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQTISLITYLMEH  440 (1157)
T ss_pred             hhhhhhhcchhHHHhcchhhhccccCcchhcCCCCchhhhhhhHHHhhccCCCcccccchhcccchHHHHHHHHHHHHHH
Confidence            22235667789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCEEEEeCCCchHHHHHHHHhhCCCceEEEEcCChhHHHHHHHHHHhhcCCccEEecCHHHHHHhHHHHhhcCceE
Q 003311          161 KGVTGPHVIVAPKAVLPNWINEFSTWAPSIAAVVYDGRPDERKAMREEFFSERGRFNVLITHYDLIMRDRQYLKKVQWIY  240 (832)
Q Consensus       161 ~~~~~p~LIV~P~sll~qW~~E~~k~~p~~~v~~~~g~~~~r~~~~~~~~~~~~~~dVvItTye~l~~d~~~L~~~~w~~  240 (832)
                      +...||+|||||+++|.||..||.+|+|++..+.|.|+++.|..+......  ++|+|++|||++++++...|.+++|.|
T Consensus       441 K~~~GP~LvivPlstL~NW~~Ef~kWaPSv~~i~YkGtp~~R~~l~~qir~--gKFnVLlTtyEyiikdk~lLsKI~W~y  518 (1157)
T KOG0386|consen  441 KQMQGPFLIIVPLSTLVNWSSEFPKWAPSVQKIQYKGTPQQRSGLTKQQRH--GKFNVLLTTYEYIIKDKALLSKISWKY  518 (1157)
T ss_pred             cccCCCeEEeccccccCCchhhccccccceeeeeeeCCHHHHhhHHHHHhc--ccceeeeeeHHHhcCCHHHHhccCCcc
Confidence            999999999999999999999999999999999999999999999888776  899999999999999999999999999


Q ss_pred             EEEeCCcccCChhhHHHHHHH-ccccceEEEeeccCCCCCHHHHHHHHhccCCCCCCChHHHHHHhcccccccCc-ccCC
Q 003311          241 MIVDEGHRLKNHECALAKTIS-GYQIQRRLLLTGTPIQNSLQELWSLLNFLLPTIFNSVENFEEWFNAPFKDRGQ-VALT  318 (832)
Q Consensus       241 vIiDEaHriKN~~sk~~kal~-~l~~~~rllLTGTPlqN~l~EL~sLl~fL~p~~f~~~~~F~~~f~~~~~~~~~-~~~~  318 (832)
                      +||||+|||||..|+++..+. .|.+.+|++|||||+||++.|||+||||+.|.+|++...|.+||+.||...|. ++++
T Consensus       519 MIIDEGHRmKNa~~KLt~~L~t~y~~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLt  598 (1157)
T KOG0386|consen  519 MIIDEGHRMKNAICKLTDTLNTHYRAQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELT  598 (1157)
T ss_pred             eeecccccccchhhHHHHHhhccccchhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCccccc
Confidence            999999999999999999995 88999999999999999999999999999999999999999999999999885 8999


Q ss_pred             hHHHHHHHHHHHhhhhhhhhhhhHhHHhhcCCCCeEEEEEcCCCHHHHHHHHHHHHhccccccc--CCCcchhHHHHHHH
Q 003311          319 DEEQLLIIRRLHHVIRPFILRRKKDEVEKYLPGKSQVILKCDMSAWQKVYYQQVTDVGRVGLDT--GTGKSKSLQNLSMQ  396 (832)
Q Consensus       319 ~ee~~~~~~~L~~~L~pfllRR~k~dv~~~LP~k~e~~v~~~ms~~Q~~lY~~i~~~~~~~~~~--~~~~~~~l~~~~~~  396 (832)
                      +++...+++|||+||+||+|||.|++|+..||+|++.+++|.||+.|+.+|..+.+.+....+.  +.+..+.++|..|+
T Consensus       599 eEEtlLIIrRLHkVLRPFlLRRlKkeVE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imq  678 (1157)
T KOG0386|consen  599 EEETLLIIRRLHKVLRPFLLRRLKKEVEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQ  678 (1157)
T ss_pred             chHHHHHHHHHHHhhhHHHHHhhhHHHhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHH
Confidence            9999999999999999999999999999999999999999999999999999999999888776  66677899999999


Q ss_pred             HHHhhCCCccccc---ccc-chhhHHHHhhcchHHHHHHHHHhhhhcCCeEEEEecchhHHHHHHHHHHhCCCeEEEEcC
Q 003311          397 LRKCCNHPYLFVG---EYN-MWRKEEIIRASGKFELLDRLLPKLRKSGHRVLLFSQMTRLMDILEIYLKLNDFKFLRLDG  472 (832)
Q Consensus       397 LRk~cnhP~l~~~---~~~-~~~~~~l~~~S~Kl~~L~~lL~~l~~~g~kvLIFsq~~~~ldiL~~~L~~~g~~~~rldG  472 (832)
                      ||+||||||+|..   .+. .+....+++.|||+++|+++|++|++.||+||+|||||+++++|++||..++++|.|+||
T Consensus       679 LRKiCNHP~lf~~ve~~~~~~~~~~dL~R~sGKfELLDRiLPKLkatgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG  758 (1157)
T KOG0386|consen  679 LRKLCNHPYLFANVENSYTLHYDIKDLVRVSGKFELLDRILPKLKATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDG  758 (1157)
T ss_pred             HHHhcCCchhhhhhccccccccChhHHHHhccHHHHHHhhhHHHHhcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecC
Confidence            9999999999943   222 233468999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHhhcCCCCCceEEEEeccccccccCcccCCeEEEeCCCCChhhHHHHhhhccccCCcCcEEEEEEEeCC
Q 003311          473 STKTEERGTLLKQFNAPDSPYFMFLLSTRAGGLGLNLQTADTVIIFDSDWNPQMDQQAEDRAHRIGQKKEVRVFVLVSVG  552 (832)
Q Consensus       473 ~ts~~eR~~~i~~Fn~~~~~~~v~LlSt~agg~GLNL~~ad~VI~~D~~wNp~~~~QAigRahRiGQ~k~V~V~rLit~~  552 (832)
                      +|+.++|..+++.||.|+++||+||+||+|||+|+|||+||+||+||++|||+++.||.+|||||||+++|+|+||++.+
T Consensus       759 ~TK~~eRg~ll~~FN~Pds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahrigq~~evRv~rl~tv~  838 (1157)
T KOG0386|consen  759 QTKVEERGDLLEIFNAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRIGQKKEVRVLRLITVN  838 (1157)
T ss_pred             CcchhhHHHHHHHhcCCCCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHhhchhheeeeeeehhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhcCcCCCCCCHHHHHHHHHHHHHhcccCCCCCCCCHHHHHHHHhcCHHHHHHHHHhhHH
Q 003311          553 SIEEVILERAKQKMGIDAKVIQAGLFNTTSTAQDRREMLKEIMRRGTSSLGTDVPSEREINRLAARSDEEFWLFEKMDEE  632 (832)
Q Consensus       553 siEe~Il~~~~~K~~l~~~vi~~g~~~~~~~~~~~~~~l~~il~~~~~~~~~~~~~~~~~~~l~~r~~~e~~~f~~~d~~  632 (832)
                      ++||+|++++..|++++.+||++|.|++.+++.+|+++|+.|+....++.+++++++++||.|+||+|+|+++|++||++
T Consensus       839 sveE~il~~a~~Kl~~d~kviqag~fdn~st~~eR~~~Le~~l~~~~~~~~~~v~~~~~ln~~larseeE~~~f~~md~~  918 (1157)
T KOG0386|consen  839 SVEEKILAEAFYKLDVDGKVIQAGKFDNKSTAEEREMFLEQLLEMEGDEEEEEVPDDEVLNSMLARSEEEFELFHKMDEE  918 (1157)
T ss_pred             HHHHHHHHHHHHhcCchHhhhhcccccCCCcHHHHHHHHHHHHhCCCccccccCCcHHHHHHHHhcchHHHHHHHHhhHH
Confidence            99999999999999999999999999999999999999999999998888889999999999999999999999999999


Q ss_pred             HHHhhhh---cccccCcCCcccccccCCCchhhhhccccccCCCCcCCCCcccccccccCCCCCHHHHHHHhhcCCCc-h
Q 003311          633 RRQKENY---RSRLMEDHEVPEWAYSAPDNKEEQKGFEKGFGHESSSITGKRKRKEVVYADTLSDLQWMKAVENGQDI-S  708 (832)
Q Consensus       633 ~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  708 (832)
                      |.++++.   ++||++++++|+|+.......+.........+   ..++|+|+||+|+|+|.|||.||+++++++.+. .
T Consensus       919 r~~~e~~~~~k~rl~ee~e~p~~i~~~~~~~~~~~~~~~~~~---~~~rg~r~Rkev~y~d~~te~q~~k~~e~~~~~~~  995 (1157)
T KOG0386|consen  919 RRATENQQEKKPRLVEEAELPADIYKRDQGVERLSEEEEEEK---ILGRGRRARKEVVYSDRLTEMQWLKENESVNKEDS  995 (1157)
T ss_pred             HHhhhhhccccchhhhhhhcHHHHHhcchhhhhhhhhhhhhc---cccccccccceeecccccchhhhhhhccccccccc
Confidence            9987654   67999999999999877653221111111111   357999999999999999999999999996543 3


Q ss_pred             hhhhhhccccCCCCCCCCCCCCcchhhhhhhccc------cccCCCcCCCCCccccCCCcccc-ccccccccCccchhhh
Q 003311          709 KLSTRGKRREYLPSEGNESASNSTGAEKKNLDMK------NEIFPLASEGTSEDTFGSAPKRL-RFERRNSESSDIQSVE  781 (832)
Q Consensus       709 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  781 (832)
                      +...++++|.....+.......+..-..+..+..      .......++..-.+.|...|-++ .+.+..-.+.      
T Consensus       996 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~r~~~~~~~~~~s~k~~~d~~~~i~~------ 1069 (1157)
T KOG0386|consen  996 EEEERRRGRKKSSLDTRPLSQKKRKLRPRSPKQALKIASTSIKYKDSAGRELSEVFLKLPSRKEYPDYYEIIKK------ 1069 (1157)
T ss_pred             hhhhhccCCCccccccccchhhcccccCCChHHHHHHHHHHHhcccccccccchhcccCcccccccchHHHhcc------
Confidence            3344333322222222211111110000111111      11111111222445554455333 2244322211      


Q ss_pred             hhcccccccCCCCCccccccccccccccccccCCCCCCCCCCCCCCC
Q 003311          782 KSEHKGVQGSGLNGHILTWNTHRKKRSSYVVQTSSSDSRGQNSNGRG  828 (832)
Q Consensus       782 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  828 (832)
                      ..+.+     ..+++|.+|.++..|+..+.++.+.+++|.-|+.|+.
T Consensus      1070 ~~~~~-----~~~~~i~~~~~~~~~~~~~~~~~~~~na~~~~~egs~ 1111 (1157)
T KOG0386|consen 1070 PVAID-----KIKKRIENHKYNSLKELEKDFMLLFNNARTYNEEGSR 1111 (1157)
T ss_pred             hhhHH-----HHhhhccccccchHHHHHHHHHhhcchhhhhccCCce
Confidence            11111     4578999999999999999999999999998888764

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

>KOG0384 consensus Chromodomain-helicase DNA-binding 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

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

>KOG0388 consensus SNF2 family DNA-dependent ATPase [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

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

>KOG0390 consensus DNA repair protein, SNF2 family [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

>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

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

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

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

>KOG0383 consensus Predicted helicase [General function prediction only]	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

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

>PRK13766 Hef nuclease; Provisional	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

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

>PHA02558 uvsW UvsW helicase; 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

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

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

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

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

>PRK11192 ATP-dependent RNA helicase SrmB; 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

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

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional	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

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

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

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

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

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

>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

>TIGR00643 recG ATP-dependent DNA helicase RecG	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

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

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

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

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; 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

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

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

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

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

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

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

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

>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

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

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

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

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

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

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

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

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

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

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

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

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

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

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

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

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

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

>TIGR00963 secA preprotein translocase, SecA subunit	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

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

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

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

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

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

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

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

>TIGR01054 rgy reverse gyrase	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

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

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

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

>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]	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

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

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

Back alignment and domain information

>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]	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

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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]	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

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

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

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

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

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

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

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

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

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

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

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

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

>smart00490 HELICc helicase superfamily c-terminal domain	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

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

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

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

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

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

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

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

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

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

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

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]	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

>PF14619 SnAC: Snf2-ATP coupling, chromatin remodelling complex	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0920 consensus ATP-dependent RNA helicase A [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

>KOG0922 consensus DEAH-box 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

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

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

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

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

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

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

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

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

>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

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

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

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

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

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

>PRK10536 hypothetical protein; Provisional	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

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

>KOG0925 consensus mRNA splicing factor 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

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

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

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

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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

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

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

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

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

>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

>KOG1132 consensus Helicase of the DEAD superfamily [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

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

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

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

>PRK04296 thymidine kinase; Provisional	Back alignment and domain information

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

>TIGR02881 spore_V_K stage V sporulation protein K	Back alignment and domain information

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

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

>PRK09112 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

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

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

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

>PRK06526 transposase; Provisional	Back alignment and domain information

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

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

>PRK08181 transposase; Validated	Back alignment and domain information

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]	Back alignment and domain information

>PRK07764 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>CHL00181 cbbX CbbX; Provisional	Back alignment and domain information

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

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A	Back alignment and domain information

>PRK07994 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

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

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

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

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

>PRK06835 DNA replication protein DnaC; Validated	Back alignment and domain information

>PRK05707 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated	Back alignment and domain information

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

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

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

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

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

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

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA	Back alignment and domain information

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

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

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

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

>PRK08058 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK07940 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PF13173 AAA_14: AAA domain	Back alignment and domain information

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

>PRK08116 hypothetical protein; Validated	Back alignment and domain information

>PRK09111 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK07471 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK07993 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK08451 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK14974 cell division protein FtsY; Provisional	Back alignment and domain information

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins	Back alignment and domain information

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

>PRK06090 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK06871 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

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

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

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

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

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

>PRK08769 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK06921 hypothetical protein; Provisional	Back alignment and domain information

>PRK08691 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]	Back alignment and domain information

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport	Back alignment and domain information

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

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

>PRK05563 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

>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

>PRK06647 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

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

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

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	Back alignment and domain information

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

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional	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

>PRK05642 DNA replication initiation factor; Validated	Back alignment and domain information

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

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

>cd01120 RecA-like_NTPases RecA-like NTPases	Back alignment and domain information

>PRK08727 hypothetical protein; Validated	Back alignment and domain information

>PRK04195 replication factor C large subunit; Provisional	Back alignment and domain information

>cd01121 Sms Sms (bacterial radA) DNA repair protein	Back alignment and domain information

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

>PRK06964 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed	Back alignment and domain information

>TIGR00362 DnaA chromosomal replication initiator protein DnaA	Back alignment and domain information

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated	Back alignment and domain information

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

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

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

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

>TIGR00678 holB DNA polymerase III, delta' subunit	Back alignment and domain information

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

>PRK14088 dnaA chromosomal replication initiation protein; Provisional	Back alignment and domain information

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

>PRK07133 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>PRK06893 DNA replication initiation factor; Validated	Back alignment and domain information

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

>PRK04132 replication factor C small subunit; Provisional	Back alignment and domain information

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

>PHA03333 putative ATPase subunit of terminase; Provisional	Back alignment and domain information

>PHA03368 DNA packaging terminase subunit 1; Provisional	Back alignment and domain information

>PRK00771 signal recognition particle protein Srp54; Provisional	Back alignment and domain information

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

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family	Back alignment and domain information

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

>PRK06305 DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

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

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

>PRK08699 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

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

>PRK14086 dnaA chromosomal replication initiation protein; Provisional	Back alignment and domain information

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau	Back alignment and domain information

>PRK13342 recombination factor protein RarA; Reviewed	Back alignment and domain information

>TIGR03689 pup_AAA proteasome ATPase	Back alignment and domain information

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP	Back alignment and domain information

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]	Back alignment and domain information

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

>TIGR01075 uvrD DNA helicase II	Back alignment and domain information

>PTZ00293 thymidine kinase; Provisional	Back alignment and domain information

>PRK06904 replicative DNA helicase; Validated	Back alignment and domain information

>PRK10416 signal recognition particle-docking protein FtsY; Provisional	Back alignment and domain information

>PHA03372 DNA packaging terminase subunit 1; Provisional	Back alignment and domain information

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

>TIGR01425 SRP54_euk signal recognition particle protein SRP54	Back alignment and domain information

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases	Back alignment and domain information

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

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes	Back alignment and domain information

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

>TIGR02688 conserved hypothetical protein TIGR02688	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

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

>PHA02244 ATPase-like protein	Back alignment and domain information

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

>CHL00095 clpC Clp protease ATP binding subunit	Back alignment and domain information

>TIGR00708 cobA cob(I)alamin adenosyltransferase	Back alignment and domain information

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB	Back alignment and domain information

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]	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		832
3mwy_W		800	Crystal Structure Of The Chromodomain-atpase Portio		1e-122
1z3i_X		644	Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMA		3e-65
1z6a_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN		8e-59
1z63_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COM		2e-56
1z5z_A		271	Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal		2e-20
3dmq_A		968	Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT		2e-05

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