Citrus Sinensis ID: 003502

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-----

MELRSRKTIGQSSGSGDAQGKQGNSGEGDSKGKEREEVGPSNLVYCREQPAQAKGKKNESNKKKKTRGKKRQRTGSSLLWEIWEEEHERWIDMHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEGYPGKKNGKKSSVGGVQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

ccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccHHHHHHHHccccccccccccHHHHHHHHHHHHccccccccccHHHHccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccEEEEccHHHHHHHHHHHccccccccEEEEEEcccccccHHHHccccEEEcccHHHHHHcccccccccccccccccccEEcEEEEEEEEEcccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccEEEEEEEcccccccccccHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccccccEEEEEEccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccccHHccccccccccccHHHHHHHHHHcccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccEEEEEccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHccccccEEEEEEccccHHcccHHcccEEEEEcccccHHHHHHHHHHHHHccccccEEEEEEEEcccHHHHHHHHHHHHHHHHHHHcccccHHHccccHHHHHHHHcc

cccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHcccHHHHHcHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHcccccccEEccccccHHHHHHHHHHHHcccccccccccccccccccccccccccEEEccHHHHHHHHHHHHHHcccccEEEEEEEcccccccHHHHHcccEEEEEHHHHHHHHHHHcccccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccccEEEcccccccccccHHHHEHEEEEEEHHHHHcccccHHHHHHHHccccccEEEEcccHHHccHHHHHHHHHHHccccccHcccccccccccccccccccccccccHHHHHHHHHHHHcHHHccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccHHEEcccccccccccHHHHcccccccccccccccccEEcccccHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHHcccccccHHcccccccccccHHHHHHHHHHHHHHccccccEEEEEHHHHHHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHHHcccccEEEEEEEcccccEEEEHHccEEEEEcccccHHHHHHHHHHHHHHcccccEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHcccHHHHHcccHHHHHHHHcc

melrsrktigqssgsgdaqgkqgnsgegdskgkereevgpsnlvycreqpaqakgkknesnkkkktrgkkrqrtgSSLLWEIWEEEHERWIDmhekddvdldQQNAfmtetaedppdlitPLLRYQKEWLAWALKQEESAIRggilademgmGKTIQAIALVLAKREIRgtigeldassssstgllgikatlVICPVAAVTQWVSEINRFTSVGSTKVLIYhgsnrersakqfsefdFVITTYSIIEadyrkhvmppkqkcqycgksfyqKKLVVHLKYfcgpsavrteKQSKQEKKKMKSSvyegypgkkngkkssvggvqkpsggksplhslkWERIILDEAHFIKDRRSNTAKAVLALESSYkwalsgtplqnrVGELYSLVRFlqitpysyyfckdcdckvldyssaecpncphnsvrhfcwwnryvatpiqthgnsyggRRAMILLKHKVLRSVILRRTkkgraadlalpprivslrrdsldireaDYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLrqavdhpylVVYSktaslrgeteaDAEHVQQVCGLcndladdpvvtncghafckaclfdssaskfvakcptcsipltvdftanegagnrtskttikgfksssilnriqldefqssTKIEALREEIRFMVErdgsakgivFSQFTSFLDLINYSLHKSGVNCVQLVgsmsipardaainrftedpdckIFLMSLKAGGVALNLTVASHVflmdpwwnpavEQQAQDRIhrigqykpiRIVRFLIENTIEERILKLQEKKKLVFegtvggsadafgKLTEADMRFLFVT

melrsrktigqssgsgdaqgkqgnsgegdskgkereevgpsnlvycreqpaqakgkknesnkkkktrgkkrqrtgssllWEIWEEEHERWIDMHEKDDVDLDQQNAFMtetaedppdlITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIgeldassssstglLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGsnrersakqfsefdFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGpsavrtekqskqekkkmkssvyegypgkkngkkssvggvqkpsggksplhslKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILrrtkkgraadlalpprivslrrdslDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTvdftanegagnrtskttikgfksssilnriqldefqsstKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVggsadafgklteADMRFLFVT

MELRSRKTIGQSSGSGDAQGKQGNSGEGDSKGKEREEVGPSNLVYCREQPAQAkgkknesnkkkktrgkkrqrtgsSLLweiweeeherwiDMHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTekqskqekkkmkssVYEGYpgkkngkkssvggvqkpsggkspLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

*****************************************************************************LLWEIWEEEHERWIDMHE*********************DLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELD******TGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGP*************************************************SLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEG*********IKGFK*SSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLF**

************************************************************************************EEHERWIDMHEKDDV*****************DLITPLLRYQKEWLAWALKQEESA*******DEMGMGKTIQAIALVLAKRE************************LVICPVAAVTQ************STKVLIYHGSNR****KQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEGYPG*********GGVQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQ**********AMILLKHKVLRSVILRRTKKGR***LALPPRIVSLRRDSLDIREADYYESLYSESQAQFN************************************************EHVQQVCGLCNDLADDPVVTNCGHAFCKACLF***************IPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKL********************MRFLFVT

**************************************GPSNLVYCREQ*************************GSSLLWEIWEEEHERWIDMHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAV*****************YEGYPGKKN*****************PLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTA************VQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

***************************************************************************SSLLWEIWEEEHERWIDMHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKR*********************IKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVM**K*KCQYCGKSFYQKKLVVHLKYFCGPSA***************************GKKSSVGGVQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSK*******T*******QQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANE***************SSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		815	2.2.26 [Sep-21-2011]
P79051		861	ATP-dependent helicase rh	yes	no	0.781	0.739	0.405	1e-149
P31244		790	DNA repair protein RAD16	yes	no	0.595	0.613	0.443	1e-123
O60177		1040	Uncharacterized ATP-depen	no	no	0.747	0.585	0.302	3e-82
Q9FNI6		1029	Putative SWI/SNF-related	no	no	0.699	0.553	0.311	3e-82
Q10332		830	Uncharacterized ATP-depen	no	no	0.714	0.701	0.313	5e-82
Q9FIY7		1277	Putative SWI/SNF-related	no	no	0.541	0.345	0.340	9e-79
Q5NC05		1138	Transcription termination	yes	no	0.720	0.515	0.292	1e-71
Q6PCN7		1003	Helicase-like transcripti	no	no	0.514	0.417	0.358	3e-71
Q14527		1009	Helicase-like transcripti	yes	no	0.514	0.415	0.349	8e-71
Q4IJ84		1154	DNA repair protein RAD5 O	no	no	0.525	0.370	0.325	1e-70

>sp\|P79051\|RHP16_SCHPO ATP-dependent helicase rhp16 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rhp16 PE=3 SV=2	Back alignment and function desciption

 Score =  528 bits (1360), Expect = e-149,   Method: Compositional matrix adjust.
 Identities = 300/739 (40%), Positives = 428/739 (57%), Gaps = 102/739 (13%)

Query: 84  EEEHERWIDMH-EKDDV--DLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESA 140
           E  H R I  H E + V   L+++     +  E P +L+  LL +Q+E + W  +QE+S+
Sbjct: 214 ERTHYRLIRQHPELEHVWEKLEEEAPREVKQIEQPKELVLNLLPFQREGVYWLKRQEDSS 273

Query: 141 IRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAV 200
             GGILADEMGMGKTIQ IAL+L+  E RG                  K TLV+ PV A+
Sbjct: 274 FGGGILADEMGMGKTIQTIALLLS--EPRG------------------KPTLVVAPVVAI 313

Query: 201 TQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQK 260
            QW  EI+  T+   +  L Y+G  R+ S ++ S       +Y ++   Y          
Sbjct: 314 MQWKEEIDTHTNKALSTYL-YYGQARDISGEELS-------SYDVVLTSYN--------- 356

Query: 261 CQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEGYPGKKNGKKSSVGG 320
                +S Y+K+                                      ++G +   G 
Sbjct: 357 ---VIESVYRKE--------------------------------------RSGFRRKNGV 375

Query: 321 VQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGE 380
           V++    KS LH +++ RIILDEAH IK R  NTA+AV  L ++ K  LSGTPLQNR+GE
Sbjct: 376 VKE----KSLLHQMEFYRIILDEAHGIKSRTCNTARAVCGLRTTRKICLSGTPLQNRIGE 431

Query: 381 LYSLVRFLQITPYSYYFCKDCDCKVLDY---SSAECPNCPHNSVRHFCWWNRYVATPIQT 437
           L+SL+RFL+  P++YY+C  C+CK L +     + C  C H  + H C++N  +  PIQ 
Sbjct: 432 LFSLLRFLRADPFAYYYCLQCECKSLHWRFSDRSNCDECGHKPMSHTCYFNAEMLKPIQK 491

Query: 438 HGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESL 497
            G    G+ A   + H +L+ ++LRRTK  RA DL LPPR+V +R+D  +  E D Y+SL
Sbjct: 492 FGYEGPGKLAFKKV-HSLLKHIMLRRTKLERADDLGLPPRVVEVRKDLFNEEEEDVYQSL 550

Query: 498 YSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHV 557
           Y +S+ +FNTY+  G V+NNYA+IF L+TR+RQ  DHP LV+ SK  ++  E + +    
Sbjct: 551 YMDSKRKFNTYLAEGVVLNNYANIFQLITRMRQMADHPDLVLASKRKTVDIENQENI--- 607

Query: 558 QQVCGLCNDLADDPVVTNCGHAFCKACL---FDSSASKFVAKCPTCSIPLTVDFTANEGA 614
             VC +C+++A D + + C H FC+ C+    +++       CP+C IPL++D +A    
Sbjct: 608 --VCKICDEVAQDAIESRCHHTFCRLCVTEYINAAGDGENVNCPSCFIPLSIDLSAPALE 665

Query: 615 GNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSF 674
                K     FK++SILNRI ++ ++SSTKIEAL EE+  + ++D + K IVFSQFTS 
Sbjct: 666 DFSEEK-----FKNASILNRIDMNSWRSSTKIEALVEELYLLRKKDRTLKSIVFSQFTSM 720

Query: 675 LDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVAS 734
           LDLI++ L K+G NCV+L G M+  AR A I  F+ D +  IFL+SLKAGGVALNLT AS
Sbjct: 721 LDLIHWRLRKAGFNCVKLDGGMTPKARAATIEAFSNDINITIFLVSLKAGGVALNLTEAS 780

Query: 735 HVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTV 794
            VF+MDPWWN AV+ QA DRIHRIGQ +PI+++   IEN+IE +I++LQEKK  +   T+
Sbjct: 781 QVFMMDPWWNGAVQWQAMDRIHRIGQKRPIKVITLCIENSIESKIIELQEKKAQMIHATI 840

Query: 795 GGSADAFGKLTEADMRFLF 813
                A  +L+  DM+FLF
Sbjct: 841 DQDEKALNQLSVEDMQFLF 859

Involved in global genome repair (GGR) via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: -

>sp\|P31244\|RAD16_YEAST DNA repair protein RAD16 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD16 PE=1 SV=1	Back alignment and function description

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

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

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

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

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

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

>sp\|Q14527\|HLTF_HUMAN Helicase-like transcription factor OS=Homo sapiens GN=HLTF PE=1 SV=2	Back alignment and function description

>sp\|Q4IJ84\|RAD5_GIBZE DNA repair protein RAD5 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=RAD5 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		815
255567695		874	DNA repair helicase rad5,16, putative [R	0.923	0.861	0.709	0.0
297739163		964	unnamed protein product [Vitis vinifera]	0.883	0.746	0.734	0.0
359485610		989	PREDICTED: ATP-dependent helicase rhp16-	0.885	0.730	0.714	0.0
356547089		924	PREDICTED: ATP-dependent helicase rhp16-	0.932	0.822	0.699	0.0
356542082		926	PREDICTED: ATP-dependent helicase rhp16-	0.979	0.861	0.671	0.0
15220993		833	Helicase protein with RING/U-box domain	0.899	0.879	0.662	0.0
297848774		843	SNF2 domain-containing protein [Arabidop	0.903	0.873	0.661	0.0
357471341		935	DNA repair protein RAD5 [Medicago trunca	0.895	0.780	0.716	0.0
449490335		875	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.976	0.909	0.627	0.0
449468370		867	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.976	0.918	0.622	0.0

>gi\|255567695\|ref\|XP_002524826.1\| DNA repair helicase rad5,16, putative [Ricinus communis] gi\|223535886\|gb\|EEF37546.1\| DNA repair helicase rad5,16, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1152 bits (2981), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 551/777 (70%), Positives = 639/777 (82%), Gaps = 24/777 (3%)

Query: 62  KKKKTRGKKRQRTGSSLLWEIWEEEHERWIDMHEKDDVDLDQQNAFMTETAEDPPDLITP 121
           +KK+    KR+R    LLW+IWEEE+ERWID H  +DVD+D Q+  +TETAE P +LI P
Sbjct: 99  RKKRRYSSKRKRNKVILLWKIWEEENERWIDDHLTEDVDIDHQHGIVTETAEPPAELIMP 158

Query: 122 LLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASS-- 179
           LLRYQKEWLAWALKQEES+ +GGILADEMGMGKTIQAIALVLAKREI     E + ++  
Sbjct: 159 LLRYQKEWLAWALKQEESSTKGGILADEMGMGKTIQAIALVLAKREILRQNRESNGATLL 218

Query: 180 -SSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDF 238
             SS    GIK TLV+CPV AVTQWV EI+RFT+ GSTKVL+YHG+NRE+S+K F  FDF
Sbjct: 219 PGSSIDPSGIKPTLVVCPVVAVTQWVKEIDRFTTEGSTKVLVYHGANREKSSKHFLGFDF 278

Query: 239 VITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKK 298
           VITTYS +EA++RK++MPPK KC YCGKSFY+ KL  HLKYFCGP A RT KQSKQ++KK
Sbjct: 279 VITTYSTVEAEFRKYMMPPKDKCAYCGKSFYENKLATHLKYFCGPDAFRTAKQSKQDRKK 338

Query: 299 MKSS------------------VYEGYPGKKNGKKSSVGGVQKP-SGGKSPLHSLKWERI 339
           +K+S                  V  G   +K      +  V+      KS LHS+KW+RI
Sbjct: 339 LKTSPTEKARSDESPKIQDDVDVISGRTYRKRHAAMEISEVELALRKEKSVLHSMKWDRI 398

Query: 340 ILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCK 399
           ILDEAH++KD+R NTAKA+ ALESSYKWALSGTPLQNRVGELYSLVRFLQI PYS+Y CK
Sbjct: 399 ILDEAHYVKDKRCNTAKAIFALESSYKWALSGTPLQNRVGELYSLVRFLQIVPYSFYLCK 458

Query: 400 DCDCKVLDY-SSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRS 458
           DCDC++LDY  S +C +CPH+SVRHFCWWN+YVA PIQ +G    G+RAM+LL HKVLR+
Sbjct: 459 DCDCRILDYRPSTQCSSCPHSSVRHFCWWNKYVAKPIQGYGTKDIGKRAMLLLTHKVLRN 518

Query: 459 VILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNY 518
           ++LRRTKKGRAADLALPPR+V LRRD+LD++E DYY+SLY+ESQAQFNTYVQAGT+MNNY
Sbjct: 519 IVLRRTKKGRAADLALPPRMVMLRRDTLDVKEEDYYQSLYNESQAQFNTYVQAGTLMNNY 578

Query: 519 AHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGH 578
           AHIFDLLTRLRQAVDHPYLVVYSKT   RG    D ++ +QVC +C+D A+DPVVT+C H
Sbjct: 579 AHIFDLLTRLRQAVDHPYLVVYSKTPPQRGGNLFDTDN-EQVCDICHDPAEDPVVTSCSH 637

Query: 579 AFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLD 638
            FCKACL D SAS     CPTC   LTVD T    AG++T+KTTI GFKSSSILNRIQL+
Sbjct: 638 VFCKACLLDFSASLGRVSCPTCYSLLTVDLTTKTDAGDQTAKTTIMGFKSSSILNRIQLN 697

Query: 639 EFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSI 698
           +FQ+STKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLI+YSLHKSG+NCVQLVGSMS+
Sbjct: 698 DFQTSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLISYSLHKSGINCVQLVGSMSL 757

Query: 699 PARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRI 758
           PARD AI RF+EDP+CKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVE+QAQDRIHRI
Sbjct: 758 PARDNAIKRFSEDPNCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVERQAQDRIHRI 817

Query: 759 GQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT 815
           GQYKPIRIVRF+IENTIEERIL+LQEKK+LVFEGT+GGS++A GKLT  DM+FLF+T
Sbjct: 818 GQYKPIRIVRFVIENTIEERILQLQEKKELVFEGTLGGSSEALGKLTAEDMQFLFIT 874

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297739163\|emb\|CBI28814.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359485610\|ref\|XP_002269303.2\| PREDICTED: ATP-dependent helicase rhp16-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356547089\|ref\|XP_003541950.1\| PREDICTED: ATP-dependent helicase rhp16-like [Glycine max]	Back alignment and taxonomy information

>gi\|356542082\|ref\|XP_003539500.1\| PREDICTED: ATP-dependent helicase rhp16-like [Glycine max]	Back alignment and taxonomy information

>gi\|15220993\|ref\|NP_172004.1\| Helicase protein with RING/U-box domain [Arabidopsis thaliana] gi\|332189671\|gb\|AEE27792.1\| Helicase protein with RING/U-box domain [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297848774\|ref\|XP_002892268.1\| SNF2 domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297338110\|gb\|EFH68527.1\| SNF2 domain-containing protein [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|357471341\|ref\|XP_003605955.1\| DNA repair protein RAD5 [Medicago truncatula] gi\|355507010\|gb\|AES88152.1\| DNA repair protein RAD5 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449490335\|ref\|XP_004158575.1\| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent helicase rhp16-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449468370\|ref\|XP_004151894.1\| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent helicase rhp16-like [Cucumis sativus]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		815
TAIR\|locus:2207175		833	AT1G05120 [Arabidopsis thalian	0.592	0.579	0.749	4.4e-268
TAIR\|locus:2196115		678	AT1G02670 [Arabidopsis thalian	0.242	0.292	0.708	4.8e-161
GENEDB_PFALCIPARUM\|PFL2440w		1647	PFL2440w "DNA repair protein r	0.312	0.154	0.457	1.1e-149
UNIPROTKB\|Q8I4S6		1647	PFL2440w "DNA repair protein r	0.312	0.154	0.457	1.1e-149
POMBASE\|SPCC330.01c		861	rhp16 "Rad16 homolog Rhp16" [S	0.579	0.548	0.474	3.9e-144
CGD\|CAL0006085		852	RAD16 [Candida albicans (taxid	0.580	0.555	0.456	1.5e-138
SGD\|S000000318		790	RAD16 "Protein that binds dama	0.575	0.593	0.455	5e-138
UNIPROTKB\|G4MPA7		986	MGG_07014 "DNA repair protein	0.571	0.472	0.429	5.7e-123
TAIR\|locus:2162504		1029	RAD5 [Arabidopsis thaliana (ta	0.530	0.419	0.343	2.4e-87
DICTYBASE\|DDB_G0272082		1838	DDB_G0272082 "CHR group protei	0.213	0.094	0.463	7.2e-87

TAIR\|locus:2207175 AT1G05120 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1968 (697.8 bits), Expect = 4.4e-268, Sum P(2) = 4.4e-268
 Identities = 365/487 (74%), Positives = 426/487 (87%)

Query:   331 LHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQI 390
             LHS+KW RIILDEAH+IK+RRSNTA+AV ALE++Y+WALSGTPLQNRVGELYSL+RFLQI
Sbjct:   349 LHSVKWNRIILDEAHYIKERRSNTARAVFALEATYRWALSGTPLQNRVGELYSLIRFLQI 408

Query:   391 TPYSYYFCKDCDCKVLDYSSAE-CPNCPHNSVRHFCWWNRYVATPIQTHGNSYG-GRRAM 448
              PYSYYFCKDCDC++LDY + + CP+CPHN+VRHFCWWN+YVA PI  +G S+G G+RAM
Sbjct:   409 RPYSYYFCKDCDCRILDYVAHQSCPHCPHNAVRHFCWWNKYVAKPITVYG-SFGLGKRAM 467

Query:   449 ILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTY 508
             ILLKHKVL+ ++LRRTK GRAADLALPPRI++LRRD+LD++E DYYESLY  SQA+FNTY
Sbjct:   468 ILLKHKVLKDILLRRTKLGRAADLALPPRIITLRRDTLDVKEFDYYESLYKNSQAEFNTY 527

Query:   509 VQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLA 568
             ++AGT+MNNYAHIFDLLTRLRQAVDHPYLVVYS ++        D    +Q CGLC+D A
Sbjct:   528 IEAGTLMNNYAHIFDLLTRLRQAVDHPYLVVYSNSSGANANL-VDENKSEQECGLCHDPA 586

Query:   569 DDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKS 628
             +D VVT+C H FCKACL   SAS     CPTCS  LTVD+T      ++ SKTT+KGF++
Sbjct:   587 EDYVVTSCAHVFCKACLIGFSASLGKVTCPTCSKLLTVDWTTKADTEHKASKTTLKGFRA 646

Query:   629 SSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVN 688
             SSILNRI+LD+FQ+STKIEALREEIRFMVERDGSAK IVFSQFTSFLDLINY+L K GV+
Sbjct:   647 SSILNRIKLDDFQTSTKIEALREEIRFMVERDGSAKAIVFSQFTSFLDLINYTLGKCGVS 706

Query:   689 CVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVE 748
             CVQLVGSM++ ARD AIN+F EDPDC++FLMSLKAGGVALNLTVASHVF+MDPWWNPAVE
Sbjct:   707 CVQLVGSMTMAARDTAINKFKEDPDCRVFLMSLKAGGVALNLTVASHVFMMDPWWNPAVE 766

Query:   749 QQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEAD 808
             +QAQDRIHRIGQYKPIR+VRF+IENT+EERIL+LQ+KK+LVFEGTVGGS +A GKLTE D
Sbjct:   767 RQAQDRIHRIGQYKPIRVVRFIIENTVEERILRLQKKKELVFEGTVGGSQEAIGKLTEED 826

Query:   809 MRFLFVT 815
             MRFLF T
Sbjct:   827 MRFLFTT 833

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR\|locus:2196115 AT1G02670 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

GENEDB_PFALCIPARUM\|PFL2440w PFL2440w "DNA repair protein rhp16, putative" [Plasmodium falciparum (taxid:5833)]	Back alignment and assigned GO terms

UNIPROTKB\|Q8I4S6 PFL2440w "DNA repair protein rhp16, putative" [Plasmodium falciparum 3D7 (taxid:36329)]	Back alignment and assigned GO terms

POMBASE\|SPCC330.01c rhp16 "Rad16 homolog Rhp16" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

CGD\|CAL0006085 RAD16 [Candida albicans (taxid:5476)]	Back alignment and assigned GO terms

SGD\|S000000318 RAD16 "Protein that binds damaged DNA during NER" [Saccharomyces cerevisiae (taxid:4932)]	Back alignment and assigned GO terms

UNIPROTKB\|G4MPA7 MGG_07014 "DNA repair protein RAD16" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

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

DICTYBASE\|DDB_G0272082 DDB_G0272082 "CHR group protein" [Dictyostelium discoideum (taxid:44689)]	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:
	AT1G05120	SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein; SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein; FUNCTIONS IN- in 6 functions; EXPRESSED IN- 24 plant structures; EXPRESSED DURING- 15 growth stages; CONTAINS InterPro DOMAIN/s- Zinc finger, RING-type, conserved site (InterPro-IPR017907), Zinc finger, RING-type (InterPro-IPR001841), Zinc finger, RING/FYVE/PHD-type (InterPro-IPR013083), DEAD-like helicase, N-terminal (InterPro-IPR014001), DNA/RNA helicase, C-terminal (In [...] (833 aa)
		(Arabidopsis thaliana)
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		815
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	7e-61
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	3e-34
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	1e-22
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	9e-22
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-19
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	2e-16
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-15
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	9e-15
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	1e-14
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	7e-13
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	2e-11
smart00184		40	smart00184, RING, Ring finger	9e-08
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	1e-07
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-07
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-06
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	4e-06
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-05
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	1e-04
COG5152		259	COG5152, COG5152, Uncharacterized conserved protei	3e-04
TIGR00599		397	TIGR00599, rad18, DNA repair protein rad18	4e-04
pfam13445		55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	7e-04
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	0.003

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

 Score =  221 bits (563), Expect = 7e-61
 Identities = 142/497 (28%), Positives = 209/497 (42%), Gaps = 95/497 (19%)

Query: 321 VQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGE 380
           +++       L  ++W+R++LDEAH IK+ +S+  KA+  L++  +  L+GTPL+NR+GE
Sbjct: 458 LRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQFLKALNRLDLTGTPLENRLGE 517

Query: 381 LYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGN 440
           L+SL++   + P                           S   F    R    PIQ   +
Sbjct: 518 LWSLLQEF-LNPGLL----------------------GTSFAIF---TRLFEKPIQAEED 551

Query: 441 SYGG--RRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLY 498
                 R   I L  K+L   ILRRTK+       LPP+I  +    L   + + YE+L 
Sbjct: 552 IGPLEARELGIELLRKLLSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALL 611

Query: 499 SESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQ 558
             ++                     LL  L +A      +  S+   L          + 
Sbjct: 612 EGAE-----------------KNQQLLEDLEKADSDENRIGDSELNILA--------LLT 646

Query: 559 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRT 618
           ++  +CN  A                L D              +  T D        ++ 
Sbjct: 647 RLRQICNHPA----------------LVDEG------------LEATFDRIVLLLREDKD 678

Query: 619 SKTTIKGFKSSSILNRIQLDEFQ-SSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDL 677
                K     S      LDE        E    ++            ++FSQFT  LDL
Sbjct: 679 FDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKV------------LIFSQFTPVLDL 726

Query: 678 INYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVF 737
           +   L   G+  V+L GS     R   I+RF  D + K+FL+SLKAGG+ LNLT A  V 
Sbjct: 727 LEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVI 786

Query: 738 LMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGS 797
           L DPWWNPAVE QA DR HRIGQ +P+++ R +   TIEE+IL+LQEKK+ + +  +   
Sbjct: 787 LFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEEKILELQEKKQELLDSLIDAE 846

Query: 798 A-DAFGKLTEADMRFLF 813
                 KL+  D+  LF
Sbjct: 847 GEKELSKLSIEDLLDLF 863

Length = 866

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

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

>gnl\|CDD\|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase chain; Provisional	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\|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

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

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

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

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

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

>gnl\|CDD\|214546 smart00184, RING, Ring finger	Back alignment and domain information

>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

Back alignment and domain information

>gnl\|CDD\|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

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

>gnl\|CDD\|222279 pfam13639, zf-RING_2, Ring finger domain	Back alignment and domain information

>gnl\|CDD\|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger)	Back alignment and domain information

>gnl\|CDD\|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>gnl\|CDD\|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|233043 TIGR00599, rad18, DNA repair protein rad18	Back alignment and domain information

>gnl\|CDD\|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif	Back alignment and domain information

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		815
KOG1002		791	consensus Nucleotide excision repair protein RAD16	100.0
KOG0387		923	consensus Transcription-coupled repair protein CSB	100.0
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	100.0
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	100.0
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	100.0
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	100.0
KOG4439		901	consensus RNA polymerase II transcription terminat	100.0
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	100.0
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	100.0
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	100.0
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	100.0
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	100.0
KOG1001		674	consensus Helicase-like transcription factor HLTF/	100.0
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	100.0
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	100.0
PRK04914		956	ATP-dependent helicase HepA; Validated	100.0
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	100.0
KOG0298		1394	consensus DEAD box-containing helicase-like transc	100.0
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	100.0
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	100.0
KOG0383		696	consensus Predicted helicase [General function pre	100.0
PRK13766		773	Hef nuclease; Provisional	100.0
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	100.0
KOG1123		776	consensus RNA polymerase II transcription initiati	99.98
PHA02558		501	uvsW UvsW helicase; Provisional	99.98
KOG0354		746	consensus DEAD-box like helicase [General function	99.96
PTZ00110		545	helicase; Provisional	99.95
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	99.95
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	99.94
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	99.94
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	99.94
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.94
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	99.94
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	99.94
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	99.93
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	99.93
PTZ00424		401	helicase 45; Provisional	99.92
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	99.92
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.92
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.92
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	99.91
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	99.91
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.9
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	99.9
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	99.9
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	99.89
PRK10689		1147	transcription-repair coupling factor; Provisional	99.88
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.88
PRK13767		876	ATP-dependent helicase; Provisional	99.87
PRK02362		737	ski2-like helicase; Provisional	99.86
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.85
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	99.85
PRK01172		674	ski2-like helicase; Provisional	99.84
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	99.83
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	99.83
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	99.83
PRK00254		720	ski2-like helicase; Provisional	99.83
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	99.82
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	99.82
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.82
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	99.81
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	99.81
COG4096		875	HsdR Type I site-specific restriction-modification	99.81
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.8
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	99.8
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	99.79
PRK09200		790	preprotein translocase subunit SecA; Reviewed	99.79
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	99.77
KOG4284		980	consensus DEAD box protein [Transcription]	99.77
KOG0343		758	consensus RNA Helicase [RNA processing and modific	99.77
PRK09401		1176	reverse gyrase; Reviewed	99.76
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.76
COG1201		814	Lhr Lhr-like helicases [General function predictio	99.76
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	99.76
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	99.75
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	99.75
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	99.75
PHA02653		675	RNA helicase NPH-II; Provisional	99.74
PRK05580		679	primosome assembly protein PriA; Validated	99.74
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	99.73
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	99.72
COG1204		766	Superfamily II helicase [General function predicti	99.72
KOG0347		731	consensus RNA helicase [RNA processing and modific	99.7
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	99.7
TIGR00595		505	priA primosomal protein N'. All proteins in this f	99.69
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	99.69
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.69
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	99.69
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	99.68
COG1205		851	Distinct helicase family with a unique C-terminal	99.68
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	99.67
KOG0341		610	consensus DEAD-box protein abstrakt [RNA processin	99.66
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.66
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	99.64
COG4889		1518	Predicted helicase [General function prediction on	99.64
COG1202		830	Superfamily II helicase, archaea-specific [General	99.63
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	99.62
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.6
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	99.6
PRK14701		1638	reverse gyrase; Provisional	99.6
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	99.59
KOG0334		997	consensus RNA helicase [RNA processing and modific	99.58
PRK12904		830	preprotein translocase subunit SecA; Reviewed	99.58
KOG0346		569	consensus RNA helicase [RNA processing and modific	99.57
PRK09694		878	helicase Cas3; Provisional	99.57
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.52
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.52
KOG0327		397	consensus Translation initiation factor 4F, helica	99.51
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	99.51
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	99.5
PRK13107		908	preprotein translocase subunit SecA; Reviewed	99.49
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.49
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.47
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	99.47
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	99.46
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.44
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	99.43
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	99.41
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	99.41
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	99.37
PRK05298		652	excinuclease ABC subunit B; Provisional	99.36
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	99.33
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.32
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	99.31
PRK12326		764	preprotein translocase subunit SecA; Reviewed	99.31
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	99.24
KOG0353		695	consensus ATP-dependent DNA helicase [General func	99.22
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.22
COG1198		730	PriA Primosomal protein N' (replication factor Y)	99.18
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	99.13
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	99.12
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.07
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	99.02
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	99.0
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	98.98
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	98.97
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	98.91
PF11496		297	HDA2-3: Class II histone deacetylase complex subun	98.91
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	98.85
CHL00122		870	secA preprotein translocase subunit SecA; Validate	98.83
COG0610		962	Type I site-specific restriction-modification syst	98.82
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	98.75
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	98.74
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	98.67
KOG0950		1008	consensus DNA polymerase theta/eta, DEAD-box super	98.67
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	98.61
PF13871		278	Helicase_C_4: Helicase_C-like	98.57
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.56
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	98.51
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.48
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	98.45
KOG0349		725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	98.45
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	98.3
PRK15483		986	type III restriction-modification system StyLTI en	98.22
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	98.09
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	98.06
KOG0924		1042	consensus mRNA splicing factor ATP-dependent RNA h	97.98
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	97.86
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	97.86
COG3587		985	Restriction endonuclease [Defense mechanisms]	97.81
KOG0923		902	consensus mRNA splicing factor ATP-dependent RNA h	97.8
KOG0953		700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	97.77
KOG0925		699	consensus mRNA splicing factor ATP-dependent RNA h	97.66
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	97.61
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.61
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.58
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	97.5
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.45
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.44
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	97.22
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	97.1
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	97.09
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.0
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	96.93
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	96.83
PRK10536		262	hypothetical protein; Provisional	96.82
KOG1803		649	consensus DNA helicase [Replication, recombination	96.71
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	96.68
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.67
PRK14873		665	primosome assembly protein PriA; Provisional	96.65
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	96.62
KOG4150		1034	consensus Predicted ATP-dependent RNA helicase [RN	96.59
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	96.51
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	96.44
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	96.34
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	96.3
PF13401		131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.29
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.22
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	96.11
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	96.03
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	96.01
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	95.92
TIGR00376		637	DNA helicase, putative. The gene product may repre	95.91
KOG1805		1100	consensus DNA replication helicase [Replication, r	95.84
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	95.78
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	95.7
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	95.6
PHA02929		238	N1R/p28-like protein; Provisional	95.58
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	95.58
PHA02926		242	zinc finger-like protein; Provisional	95.54
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	95.53
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	95.52
PF14634		44	zf-RING_5: zinc-RING finger domain	95.51
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	95.43
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	95.42
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	95.34
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	95.3
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	95.29
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	95.28
PRK10875		615	recD exonuclease V subunit alpha; Provisional	95.27
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	95.15
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.13
PF06862		442	DUF1253: Protein of unknown function (DUF1253); In	95.04
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	94.93
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	94.71
KOG1785		563	consensus Tyrosine kinase negative regulator CBL [	94.68
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	94.66
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	94.4
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	94.39
PF05876		557	Terminase_GpA: Phage terminase large subunit (GpA)	94.25
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	94.1
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	94.07
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	93.99
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	93.97
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	93.87
PRK04296		190	thymidine kinase; Provisional	93.83
KOG2660		331	consensus Locus-specific chromosome binding protei	93.43
TIGR02881		261	spore_V_K stage V sporulation protein K. Members o	93.32
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	93.14
PRK06526		254	transposase; Provisional	92.42
PHA02533		534	17 large terminase protein; Provisional	91.93
TIGR03420		226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	91.67
TIGR02880		284	cbbX_cfxQ probable Rubsico expression protein CbbX	91.29
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	91.22
PRK12723		388	flagellar biosynthesis regulator FlhF; Provisional	90.98
PLN03025		319	replication factor C subunit; Provisional	90.81
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	90.54
KOG4172		62	consensus Predicted E3 ubiquitin ligase [Posttrans	90.51
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	90.37
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	90.35
CHL00181		287	cbbX CbbX; Provisional	90.21
PRK08084		235	DNA replication initiation factor; Provisional	90.13
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	89.72
PF13245		76	AAA_19: Part of AAA domain	89.7
COG5152		259	Uncharacterized conserved protein, contains RING a	89.46
PRK08116		268	hypothetical protein; Validated	89.31
PRK07003		830	DNA polymerase III subunits gamma and tau; Validat	89.3
COG3421		812	Uncharacterized protein conserved in bacteria [Fun	89.27
KOG2177		386	consensus Predicted E3 ubiquitin ligase [Posttrans	89.15
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	88.58
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	88.12
TIGR03015		269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	87.99
smart00382		148	AAA ATPases associated with a variety of cellular	87.88
PRK14949		944	DNA polymerase III subunits gamma and tau; Provisi	87.63
PRK14956		484	DNA polymerase III subunits gamma and tau; Provisi	87.57
PRK08727		233	hypothetical protein; Validated	87.52
PRK05703		424	flhF flagellar biosynthesis regulator FlhF; Valida	86.96
PRK05707		328	DNA polymerase III subunit delta'; Validated	86.78
PRK14087		450	dnaA chromosomal replication initiation protein; P	86.74
PRK14960		702	DNA polymerase III subunits gamma and tau; Provisi	85.98
KOG4265		349	consensus Predicted E3 ubiquitin ligase [Posttrans	85.76
PRK00149		450	dnaA chromosomal replication initiation protein; R	85.61
PF05621		302	TniB: Bacterial TniB protein; InterPro: IPR008868	85.55
PRK08181		269	transposase; Validated	85.36
PF14447		55	Prok-RING_4: Prokaryotic RING finger family 4	85.35
PRK06835		329	DNA replication protein DnaC; Validated	85.2
PRK00440		319	rfc replication factor C small subunit; Reviewed	85.12
KOG1813		313	consensus Predicted E3 ubiquitin ligase [Posttrans	84.86
PRK14974		336	cell division protein FtsY; Provisional	84.68
PRK06893		229	DNA replication initiation factor; Validated	84.33
PRK12402		337	replication factor C small subunit 2; Reviewed	84.13
TIGR00362		405	DnaA chromosomal replication initiator protein Dna	84.12
TIGR02768		744	TraA_Ti Ti-type conjugative transfer relaxase TraA	84.09
PTZ00112		1164	origin recognition complex 1 protein; Provisional	83.77
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	83.76
PRK04195		482	replication factor C large subunit; Provisional	83.42
PRK05642		234	DNA replication initiation factor; Validated	83.4
COG5236		493	Uncharacterized conserved protein, contains RING Z	83.38
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	83.37
PHA03368		738	DNA packaging terminase subunit 1; Provisional	83.28
PRK14961		363	DNA polymerase III subunits gamma and tau; Provisi	82.59
PF12678		73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	82.57
PF11789		57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	82.51
PRK14088		440	dnaA chromosomal replication initiation protein; P	82.15
PRK07764		824	DNA polymerase III subunits gamma and tau; Validat	82.08
PRK09112		351	DNA polymerase III subunit delta'; Validated	81.95
PRK12323		700	DNA polymerase III subunits gamma and tau; Provisi	81.89
PRK14086		617	dnaA chromosomal replication initiation protein; P	81.73
PRK14958		509	DNA polymerase III subunits gamma and tau; Provisi	81.5
PF13177		162	DNA_pol3_delta2: DNA polymerase III, delta subunit	81.14
PHA02544		316	44 clamp loader, small subunit; Provisional	81.01
PRK07994		647	DNA polymerase III subunits gamma and tau; Validat	80.36
PRK06921		266	hypothetical protein; Provisional	80.33
COG0464		494	SpoVK ATPases of the AAA+ class [Posttranslational	80.25
PRK05580		679	primosome assembly protein PriA; Validated	80.2
PRK11889		436	flhF flagellar biosynthesis regulator FlhF; Provis	80.08
KOG4159		398	consensus Predicted E3 ubiquitin ligase [Posttrans	80.05

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

Probab=100.00  E-value=5.8e-119  Score=902.33  Aligned_cols=623  Identities=57%  Similarity=0.963  Sum_probs=575.1

Q ss_pred             cccccccccccCCCCCCcccccchHHHHHHHHHHHHHhhccCCCCeeeccCCCchHHHHHHHHHhccccccccCCCCCCC
Q 003502          100 DLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASS  179 (815)
Q Consensus       100 ~~~~~~~~~~~~~~~p~~~~~~L~~yQ~~~~~~~~~~~~~~~~g~ILade~GlGKTi~ai~li~~~~~~~~~~~~~~~~~  179 (815)
                      +.+..++......++|.++..+|.|||++++.|+..++.+.+.|||||||||+|||+|+|++++...             
T Consensus       163 dlde~~p~i~e~aeqP~dlii~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~-------------  229 (791)
T KOG1002|consen  163 DLDEANPVIAERAEQPDDLIIPLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEV-------------  229 (791)
T ss_pred             hhhhcCchhhhcccCcccceecchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhcc-------------
Confidence            5667788888899999999999999999999999999999999999999999999999999998732             


Q ss_pred             CCCCCccCCccEEEEcChHHHHHHHHHHHHhcCCCCcEEEEEeCCCCcCCcccccCCCEEEechhhhHHHhhhccCCCcc
Q 003502          180 SSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQ  259 (815)
Q Consensus       180 ~~~~~~~~~~~~LIV~P~~ll~qW~~Ei~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~vvi~ty~~l~~~~~~~~~~~~~  259 (815)
                             ...|+|||||.-.+.||.+||..++. +.+++++|||.++....+.+..||+|+|||..+.+.|++.-..   
T Consensus       230 -------~ra~tLVvaP~VAlmQW~nEI~~~T~-gslkv~~YhG~~R~~nikel~~YDvVLTty~vvEs~yRk~~~G---  298 (791)
T KOG1002|consen  230 -------DRAPTLVVAPTVALMQWKNEIERHTS-GSLKVYIYHGAKRDKNIKELMNYDVVLTTYAVVESVYRKQDYG---  298 (791)
T ss_pred             -------ccCCeeEEccHHHHHHHHHHHHHhcc-CceEEEEEecccccCCHHHhhcCcEEEEecHHHHHHHHhcccc---
Confidence                   23589999999999999999999998 7999999999999999999999999999999999987652100   


Q ss_pred             cccccCcccchhhhhhhhhhccCCcchhhhhhhHHHHhhhccccccCCCCCCCCCCCCCCCCCCCCCCCCCCccceeeEE
Q 003502          260 KCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEGYPGKKNGKKSSVGGVQKPSGGKSPLHSLKWERI  339 (815)
Q Consensus       260 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~v  339 (815)
                              +                           ++|                       -......+.|+++.|.+|
T Consensus       299 --------f---------------------------rrK-----------------------ngv~ke~SlLHsi~~~Ri  320 (791)
T KOG1002|consen  299 --------F---------------------------RRK-----------------------NGVDKEKSLLHSIKFYRI  320 (791)
T ss_pred             --------c---------------------------ccc-----------------------CCcccccchhhhceeeee
Confidence                    0                           000                       012233678999999999


Q ss_pred             EeecceeccCCCchHHHHHHhhhcCcEEEeeCCCCCCchhhHHHHHHHhccCCCCccccccccccccccC---CCCCCCC
Q 003502          340 ILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYS---SAECPNC  416 (815)
Q Consensus       340 IvDEaH~~kn~~s~~~~~~~~l~~~~r~~LTgTPi~n~~~el~~ll~~L~~~~~~~~~~~~~~~~~~~~~---~~~~~~~  416 (815)
                      |+||||.||+..|+.++++..|.+.+||+|||||+||+..|||+|++||++.||++|+|..|++..+++.   ...|+.|
T Consensus       321 IlDEAH~IK~R~snTArAV~~L~tt~rw~LSGTPLQNrigElySLiRFL~i~Pfsyyfc~~cdc~~~~~~ftdr~~c~~c  400 (791)
T KOG1002|consen  321 ILDEAHNIKDRQSNTARAVFALETTYRWCLSGTPLQNRIGELYSLIRFLNINPFSYYFCTKCDCASLDWKFTDRMHCDHC  400 (791)
T ss_pred             ehhhhcccccccccHHHHHHhhHhhhhhhccCCcchhhHHHHHHHHHHHccCcchhhhhhhccccccceeecccccCCcc
Confidence            9999999999999999999999999999999999999999999999999999999999999999998875   5789999


Q ss_pred             CCCCcchhhhHhhhhcccccccCCCcchhHHHHHHHHHHhhHhhhhhccCCcccccCCCCeEEEEeecCCCHHHHHHHHH
Q 003502          417 PHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYES  496 (815)
Q Consensus       417 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~~~lrr~k~~v~~~~~lp~~~~~~~~~~l~~~~~~~y~~  496 (815)
                      .++..+|+.+|+.++..||+.++....|..+.. ..+.++..+|+||++-..+.++.|||+++.+....++.++.++|+.
T Consensus       401 ~h~~m~h~~~~n~~mlk~IqkfG~eGpGk~af~-~~h~llk~ImlrrTkl~RAdDLgLPPRiv~vRrD~fn~eE~D~YeS  479 (791)
T KOG1002|consen  401 SHNIMQHTCFFNHFMLKPIQKFGVEGPGKEAFN-NIHTLLKNIMLRRTKLERADDLGLPPRIVTVRRDFFNEEEKDLYES  479 (791)
T ss_pred             cchhhhhhhhhcccccccchhhcccCchHHHHH-HHHHHHHHHHHHHhhcccccccCCCccceeeehhhhhhHHHHHHHH
Confidence            999999999999999999999999888888777 5578999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHhcCcccccccccccccCCChhhhhhhhhhcCcccccCCCCccccC
Q 003502          497 LYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNC  576 (815)
Q Consensus       497 l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  576 (815)
                      ++......|+.+.+.|.+.++++++|.+|.++||+++||+|+.++....+.     +......+|.+|++++++++.++|
T Consensus       480 LY~dSkrkfntyieeGvvlNNYAnIF~LitRmRQ~aDHP~LVl~S~~~n~~-----~enk~~~~C~lc~d~aed~i~s~C  554 (791)
T KOG1002|consen  480 LYKDSKRKFNTYIEEGVVLNNYANIFTLITRMRQAADHPDLVLYSANANLP-----DENKGEVECGLCHDPAEDYIESSC  554 (791)
T ss_pred             HHHhhHHhhhhHHhhhhhhhhHHHHHHHHHHHHHhccCcceeeehhhcCCC-----ccccCceeecccCChhhhhHhhhh
Confidence            999999999999999999999999999999999999999999887544433     333445789999999999999999


Q ss_pred             CchhhhhhHhhhcccc---CCCCCCCCCCCcccccccCCCCCCCCccccccCccccchhhhhhccccCcchHHHHHHHHH
Q 003502          577 GHAFCKACLFDSSASK---FVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEI  653 (815)
Q Consensus       577 ~~~~c~~c~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~Kl~~l~~~l  653 (815)
                      .|.||+.|+..++.++   ....||.|.+++++|.     +.....+..++++..++|++++.+++|..|+|+++|++.|
T Consensus       555 hH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDl-----se~alek~~l~~Fk~sSIlnRinm~~~qsSTKIEAL~EEl  629 (791)
T KOG1002|consen  555 HHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDL-----SEPALEKTDLKGFKASSILNRINMDDWQSSTKIEALVEEL  629 (791)
T ss_pred             hHHHHHHHHHHHHHhhhcccCCCCccccccccccc-----cchhhhhcchhhhhhHHHhhhcchhhhcchhHHHHHHHHH
Confidence            9999999998876543   3699999999999884     3344566788999999999999999999999999999999


Q ss_pred             HHHHhcCCCceEEEEccChhHHHHHHHHHHhCCCcEEEEecCCCHHHHHHHHHhhcCCCCceEEEEecCCCccccccccc
Q 003502          654 RFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVA  733 (815)
Q Consensus       654 ~~~~~~~~~~KvIIFs~~~~~~~~l~~~L~~~g~~~~~i~G~~~~~~R~~~i~~F~~~~~~~vlL~st~~g~~GlNL~~a  733 (815)
                      ..+++++..-|.||||||+.|+++|...|.+.|+.++.+.|+|++..|...|+.|.++++++|||+|.++||..|||+.|
T Consensus       630 ~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteA  709 (791)
T KOG1002|consen  630 YFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEA  709 (791)
T ss_pred             HHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CEEEEeCCCCCcchHHHHhHhhhcCCCCCcEEEEEEEeCCcHHHHHHHHHHHHHHHhhhhcCCCcccccCCCHHHHHhhh
Q 003502          734 SHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLF  813 (815)
Q Consensus       734 ~~vI~~d~~wnp~~~~QaigR~~R~GQ~~~V~vy~l~~~~TiEe~i~~~~~~K~~~~~~~~~~~~~~~~~~~~~~~~~l~  813 (815)
                      ++|+++||||||+++.||.+|+|||||.++|.|.+|+.++|||++|+++|++|..+|++++|++++++++++++||++||
T Consensus       710 SqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE~kIieLQeKKa~mihaTi~qde~Ai~kLt~eDmqfLF  789 (791)
T KOG1002|consen  710 SQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIEEKIIELQEKKANMIHATIGQDEEAISKLTEEDMQFLF  789 (791)
T ss_pred             ceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhccHHHHHHHHHHHHhhhhhhhcCCcHHHHHhcCHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 003502          814 VT  815 (815)
Q Consensus       814 ~~  815 (815)
                      .+
T Consensus       790 ~n  791 (791)
T KOG1002|consen  790 NN  791 (791)
T ss_pred             cC
Confidence            75

>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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>TIGR00603 rad25 DNA repair helicase rad25	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

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

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

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

>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

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

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

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

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

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional	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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0335 consensus ATP-dependent RNA helicase [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

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

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

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

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

>KOG0348 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

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

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

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

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

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

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

>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

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

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

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

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

>KOG0341 consensus DEAD-box protein abstrakt [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

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

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

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

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

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

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

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

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

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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

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

>smart00487 DEXDc DEAD-like helicases superfamily	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

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

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

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

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

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

>TIGR00631 uvrb excinuclease ABC, B subunit	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

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

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

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

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

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

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

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

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

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

>KOG0951 consensus RNA helicase BRR2, 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

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

>PRK12903 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional	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

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

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

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

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

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

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

>KOG0953 consensus Mitochondrial RNA helicase SUV3, DEAD-box superfamily [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

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

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

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

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

>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A	Back alignment and domain information

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional	Back alignment and domain information

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

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

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A	Back alignment and domain information

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

>KOG1803 consensus DNA helicase [Replication, recombination and repair]	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

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

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

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

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

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA 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

>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>smart00504 Ubox Modified RING finger domain	Back alignment and domain information

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

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

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A	Back alignment and domain information

>TIGR00599 rad18 DNA repair protein rad18	Back alignment and domain information

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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

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

>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]	Back alignment and domain information

>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>PHA02929 N1R/p28-like protein; Provisional	Back alignment and domain information

>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PHA02926 zinc finger-like protein; Provisional	Back alignment and domain information

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B	Back alignment and domain information

>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]	Back alignment and domain information

>PF14634 zf-RING_5: zinc-RING finger domain	Back alignment and domain information

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

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

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

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

>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A	Back alignment and domain information

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family	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

>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

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

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

>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]	Back alignment and domain information

>smart00184 RING Ring finger	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

>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)

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

>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis	Back alignment and domain information

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

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A	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

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1	Back alignment and domain information

>PRK04296 thymidine kinase; Provisional	Back alignment and domain information

>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]	Back alignment and domain information

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

>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK06526 transposase; Provisional	Back alignment and domain information

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

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

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX	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

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

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

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

>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>CHL00181 cbbX CbbX; Provisional	Back alignment and domain information

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

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

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

>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]	Back alignment and domain information

>PRK08116 hypothetical protein; Validated	Back alignment and domain information

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

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

>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

>PRK08727 hypothetical protein; Validated	Back alignment and domain information

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

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

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

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

>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed	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

>PRK08181 transposase; Validated	Back alignment and domain information

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4	Back alignment and domain information

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

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

>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]	Back alignment and domain information

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

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

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

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C	Back alignment and domain information

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

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

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

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

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

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional	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

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

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

>PRK06921 hypothetical protein; Provisional	Back alignment and domain information

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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		815
3mwy_W		800	Crystal Structure Of The Chromodomain-atpase Portio		4e-27
1z6a_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN		9e-20
1z5z_A		271	Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal		1e-19
1z63_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COM		1e-19
1z3i_X		644	Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMA		2e-18

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