Citrus Sinensis ID: 004925

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---

MHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEGYPGKKNGKKSSVGGVQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

ccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccccccccccccEEcccccccccccccccccccccccccccccccEEEEcccHHHHHHHHHHHHcccccccEEEEEEccccccccHHcccccEEEccccHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccEEEcccccccccccccccccccccccccccEEEEEEEEEEccccccccccHHHHHHHHHHcccEEEEEcccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHccccccccccccccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEEEEEcccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHccccccEEEEEEccccHHHHcHHHccEEEEEcccccHHHHHHHHHHHHHccccccEEEEEEEEcccHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHcc

ccccccccHHccccccccccccccccccccHHHHHHHHHHHHHHHcccccccEEccccccHHHHHHHHHHHHcccccccccccccccccccccccccccEEEccHHHHHHHHHHHHHHcccccEEEEEEccccccccHHHHHcccEEEEEHHHHHHHHHHHccccccccccccccccccccccEEEEccccHHcccccccccHHcccccccccccccccccccEEcccccHccccccHHHHEHEEEEEEHHHHHcccccHHHHHHHHccccccEEEEcccHHHccHHHHHHHHHHHccccccHcccccccccccccccccccccccccHHHHHHHHHHHHcHHHccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHccccHHEEccccccccccccHHHcccccEcccccccccccEEcccccHHHHHHHHHHccccccccccccccccccccccccccccccccccHccccccccHcccccccccccHHHHHHHHHHHHHHccccccEEEEEHHHHHHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHHHcccccEEEEEEEcccccEEEEHHccEEEEEcccccHHHHHHHHHHHHHHcccccEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHcccHHHHHcccHHHHHHHHcc

mhekddvdLDQQNAfmtetaedppdlitPLLRYQKEWLAWALKQEESAIRggilademgmGKTIQAIALVLAKREIRgtigeldassssstgllgikatlVICPVAAVTQWVSEINRFTSVGSTKVLIYhgsnrersakqfsefdFVITTYSIIEadyrkhvmppkqkcqycgksfyqKKLVVHLKYfcgpsavrteKQSKQEKKKMKSSvyegypgkkngkkssvggvqkpsggksplhslkWERIILDEAHFIKDRRSNTAKAVLALESSYkwalsgtplqnrVGELYSLVRFlqitpysyyfckdcdckvldyssaecpncphnsvrhfcwwnryvatpiqthgnsyggRRAMILLKHKVLRSVILRRTkkgraadlalpprivslrrdsldireaDYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLrqavdhpylVVYSktaslrgeteaDAEHVQQVCGLcndladdpvvtncghafckaclfdssaskfvakcptcsipltvdftanegagnrtskttikgfksssilnriqldefqssTKIEALREEIRFMVErdgsakgivFSQFTSFLDLINYSLHKSGVNCVQLVgsmsipardaainrftedpdckIFLMSLKAGGVALNLTVASHVflmdpwwnpavEQQAQDRIhrigqykpiRIVRFLIENTIEERILKLQEKKKLVFegtvggsadafgKLTEADMRFLFVT

mhekddvdlDQQNAFmtetaedppdlITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIgeldassssstglLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGsnrersakqfsefdFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGpsavrtekqskqekkkmkssvyegypgkkngkkssvggvqkpsggksplhslKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILrrtkkgraadlalpprivslrrdslDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTvdftanegagnrtskttikgfksssilnriqldefqsstKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVggsadafgklteADMRFLFVT

MHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTekqskqekkkmkssVYEGYpgkkngkkssvggvqkpsggkspLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

*************************LITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELD******TGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGP*************************************************SLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEG*********IKGFK*SSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLF**

**EKDDV*******************ITPLLRYQKEWLAWALKQEE***********MGMGKTIQAIALVLAKREI***********************LVICPVAAVTQWVSEIN**TSVGSTKVLIYHGSNRE**AKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEG***************QKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQ**********AMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFN******************************LVVYSKT*******EADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLF**************SIPLTVDFTANEGAG*RTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVE*DGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKL********************MRFLFVT

MHEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAV*****************YEGYPGKKN*****************PLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTA************VQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

****************TETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKR*********************IKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVM****KCQYCGKSFYQKKLVVHLKYFCGP******************************KKSSVGGVQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSK**************VQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFT******************SSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLFVT

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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		723	2.2.26 [Sep-21-2011]
P79051		861	ATP-dependent helicase rh	no	no	0.840	0.706	0.413	1e-148
P31244		790	DNA repair protein RAD16	yes	no	0.670	0.613	0.443	1e-123
O60177		1040	Uncharacterized ATP-depen	no	no	0.842	0.585	0.302	3e-82
Q9FNI6		1029	Putative SWI/SNF-related	no	no	0.788	0.553	0.311	4e-82
Q10332		830	Uncharacterized ATP-depen	no	no	0.804	0.701	0.313	7e-82
Q9FIY7		1277	Putative SWI/SNF-related	no	no	0.609	0.345	0.340	6e-79
Q6PCN7		1003	Helicase-like transcripti	yes	no	0.579	0.417	0.358	4e-71
Q5NC05		1138	Transcription termination	no	no	0.811	0.515	0.292	7e-71
Q14527		1009	Helicase-like transcripti	yes	no	0.579	0.415	0.349	8e-71
Q4IJ84		1154	DNA repair protein RAD5 O	no	no	0.591	0.370	0.325	3e-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 =  526 bits (1354), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 292/707 (41%), Positives = 415/707 (58%), Gaps = 99/707 (14%)

Query: 21  EDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTI 80
           E P +L+  LL +Q+E + W  +QE+S+  GGILADEMGMGKTIQ IAL+L+  E RG  
Sbjct: 246 EQPKELVLNLLPFQREGVYWLKRQEDSSFGGGILADEMGMGKTIQTIALLLS--EPRG-- 301

Query: 81  GELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQ 140
                           K TLV+ PV A+ QW  EI+  T+   +  L Y+G  R+ S ++
Sbjct: 302 ----------------KPTLVVAPVVAIMQWKEEIDTHTNKALSTYL-YYGQARDISGEE 344

Query: 141 FSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQS 200
            S       +Y ++   Y               +S Y+K+                    
Sbjct: 345 LS-------SYDVVLTSYN------------VIESVYRKE-------------------- 365

Query: 201 KQEKKKMKSSVYEGYPGKKNGKKSSVGGVQKPSGGKSPLHSLKWERIILDEAHFIKDRRS 260
                             ++G +   G V++    KS LH +++ RIILDEAH IK R  
Sbjct: 366 ------------------RSGFRRKNGVVKE----KSLLHQMEFYRIILDEAHGIKSRTC 403

Query: 261 NTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDY---S 317
           NTA+AV  L ++ K  LSGTPLQNR+GEL+SL+RFL+  P++YY+C  C+CK L +    
Sbjct: 404 NTARAVCGLRTTRKICLSGTPLQNRIGELFSLLRFLRADPFAYYYCLQCECKSLHWRFSD 463

Query: 318 SAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRA 377
            + C  C H  + H C++N  +  PIQ  G    G+ A   + H +L+ ++LRRTK  RA
Sbjct: 464 RSNCDECGHKPMSHTCYFNAEMLKPIQKFGYEGPGKLAFKKV-HSLLKHIMLRRTKLERA 522

Query: 378 ADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLR 437
            DL LPPR+V +R+D  +  E D Y+SLY +S+ +FNTY+  G V+NNYA+IF L+TR+R
Sbjct: 523 DDLGLPPRVVEVRKDLFNEEEEDVYQSLYMDSKRKFNTYLAEGVVLNNYANIFQLITRMR 582

Query: 438 QAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACL---F 494
           Q  DHP LV+ SK  ++  E + +      VC +C+++A D + + C H FC+ C+    
Sbjct: 583 QMADHPDLVLASKRKTVDIENQENI-----VCKICDEVAQDAIESRCHHTFCRLCVTEYI 637

Query: 495 DSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKI 554
           +++       CP+C IPL++D +A         K     FK++SILNRI ++ ++SSTKI
Sbjct: 638 NAAGDGENVNCPSCFIPLSIDLSAPALEDFSEEK-----FKNASILNRIDMNSWRSSTKI 692

Query: 555 EALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAIN 614
           EAL EE+  + ++D + K IVFSQFTS LDLI++ L K+G NCV+L G M+  AR A I 
Sbjct: 693 EALVEELYLLRKKDRTLKSIVFSQFTSMLDLIHWRLRKAGFNCVKLDGGMTPKARAATIE 752

Query: 615 RFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRI 674
            F+ D +  IFL+SLKAGGVALNLT AS VF+MDPWWN AV+ QA DRIHRIGQ +PI++
Sbjct: 753 AFSNDINITIFLVSLKAGGVALNLTEASQVFMMDPWWNGAVQWQAMDRIHRIGQKRPIKV 812

Query: 675 VRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLF 721
           +   IEN+IE +I++LQEKK  +   T+     A  +L+  DM+FLF
Sbjct: 813 ITLCIENSIESKIIELQEKKAQMIHATIDQDEKALNQLSVEDMQFLF 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\|Q6PCN7\|HLTF_MOUSE Helicase-like transcription factor OS=Mus musculus GN=Hltf PE=1 SV=1	Back alignment and function description

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

>sp\|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		723
255567695		874	DNA repair helicase rad5,16, putative [R	0.997	0.824	0.715	0.0
297739163		964	unnamed protein product [Vitis vinifera]	0.973	0.730	0.735	0.0
359485610		989	PREDICTED: ATP-dependent helicase rhp16-	0.976	0.713	0.713	0.0
356542082		926	PREDICTED: ATP-dependent helicase rhp16-	0.995	0.777	0.720	0.0
356547089		924	PREDICTED: ATP-dependent helicase rhp16-	0.995	0.779	0.716	0.0
15220993		833	Helicase protein with RING/U-box domain	0.970	0.842	0.672	0.0
357471341		935	DNA repair protein RAD5 [Medicago trunca	0.983	0.760	0.721	0.0
297848774		843	SNF2 domain-containing protein [Arabidop	0.970	0.832	0.672	0.0
449490335		875	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.990	0.818	0.669	0.0
449468370		867	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.990	0.825	0.664	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 = 1112 bits (2877), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 533/745 (71%), Positives = 616/745 (82%), Gaps = 24/745 (3%)

Query: 2   HEKDDVDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMG 61
           H  +DVD+D Q+  +TETAE P +LI PLLRYQKEWLAWALKQEES+ +GGILADEMGMG
Sbjct: 131 HLTEDVDIDHQHGIVTETAEPPAELIMPLLRYQKEWLAWALKQEESSTKGGILADEMGMG 190

Query: 62  KTIQAIALVLAKREIRGTIGELDASS---SSSTGLLGIKATLVICPVAAVTQWVSEINRF 118
           KTIQAIALVLAKREI     E + ++    SS    GIK TLV+CPV AVTQWV EI+RF
Sbjct: 191 KTIQAIALVLAKREILRQNRESNGATLLPGSSIDPSGIKPTLVVCPVVAVTQWVKEIDRF 250

Query: 119 TSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPKQKCQYCGKSFYQ 178
           T+ GSTKVL+YHG+NRE+S+K F  FDFVITTYS +EA++RK++MPPK KC YCGKSFY+
Sbjct: 251 TTEGSTKVLVYHGANREKSSKHFLGFDFVITTYSTVEAEFRKYMMPPKDKCAYCGKSFYE 310

Query: 179 KKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSS------------------VYEGYPGKKN 220
            KL  HLKYFCGP A RT KQSKQ++KK+K+S                  V  G   +K 
Sbjct: 311 NKLATHLKYFCGPDAFRTAKQSKQDRKKLKTSPTEKARSDESPKIQDDVDVISGRTYRKR 370

Query: 221 GKKSSVGGVQKP-SGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSG 279
                +  V+      KS LHS+KW+RIILDEAH++KD+R NTAKA+ ALESSYKWALSG
Sbjct: 371 HAAMEISEVELALRKEKSVLHSMKWDRIILDEAHYVKDKRCNTAKAIFALESSYKWALSG 430

Query: 280 TPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDY-SSAECPNCPHNSVRHFCWWNRY 338
           TPLQNRVGELYSLVRFLQI PYS+Y CKDCDC++LDY  S +C +CPH+SVRHFCWWN+Y
Sbjct: 431 TPLQNRVGELYSLVRFLQIVPYSFYLCKDCDCRILDYRPSTQCSSCPHSSVRHFCWWNKY 490

Query: 339 VATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIRE 398
           VA PIQ +G    G+RAM+LL HKVLR+++LRRTKKGRAADLALPPR+V LRRD+LD++E
Sbjct: 491 VAKPIQGYGTKDIGKRAMLLLTHKVLRNIVLRRTKKGRAADLALPPRMVMLRRDTLDVKE 550

Query: 399 ADYYESLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGET 458
            DYY+SLY+ESQAQFNTYVQAGT+MNNYAHIFDLLTRLRQAVDHPYLVVYSKT   RG  
Sbjct: 551 EDYYQSLYNESQAQFNTYVQAGTLMNNYAHIFDLLTRLRQAVDHPYLVVYSKTPPQRGGN 610

Query: 459 EADAEHVQQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTA 518
             D ++ +QVC +C+D A+DPVVT+C H FCKACL D SAS     CPTC   LTVD T 
Sbjct: 611 LFDTDN-EQVCDICHDPAEDPVVTSCSHVFCKACLLDFSASLGRVSCPTCYSLLTVDLTT 669

Query: 519 NEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQ 578
              AG++T+KTTI GFKSSSILNRIQL++FQ+STKIEALREEIRFMVERDGSAKGIVFSQ
Sbjct: 670 KTDAGDQTAKTTIMGFKSSSILNRIQLNDFQTSTKIEALREEIRFMVERDGSAKGIVFSQ 729

Query: 579 FTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNL 638
           FTSFLDLI+YSLHKSG+NCVQLVGSMS+PARD AI RF+EDP+CKIFLMSLKAGGVALNL
Sbjct: 730 FTSFLDLISYSLHKSGINCVQLVGSMSLPARDNAIKRFSEDPNCKIFLMSLKAGGVALNL 789

Query: 639 TVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVF 698
           TVASHVFLMDPWWNPAVE+QAQDRIHRIGQYKPIRIVRF+IENTIEERIL+LQEKK+LVF
Sbjct: 790 TVASHVFLMDPWWNPAVERQAQDRIHRIGQYKPIRIVRFVIENTIEERILQLQEKKELVF 849

Query: 699 EGTVGGSADAFGKLTEADMRFLFVT 723
           EGT+GGS++A GKLT  DM+FLF+T
Sbjct: 850 EGTLGGSSEALGKLTAEDMQFLFIT 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\|356542082\|ref\|XP_003539500.1\| PREDICTED: ATP-dependent helicase rhp16-like [Glycine max]	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\|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\|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\|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\|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		723
TAIR\|locus:2207175		833	AT1G05120 [Arabidopsis thalian	0.668	0.579	0.749	1.2e-267
TAIR\|locus:2196115		678	AT1G02670 [Arabidopsis thalian	0.273	0.292	0.708	4.8e-161
GENEDB_PFALCIPARUM\|PFL2440w		1647	PFL2440w "DNA repair protein r	0.352	0.154	0.457	1.1e-149
UNIPROTKB\|Q8I4S6		1647	PFL2440w "DNA repair protein r	0.352	0.154	0.457	1.1e-149
POMBASE\|SPCC330.01c		861	rhp16 "Rad16 homolog Rhp16" [S	0.652	0.548	0.474	3.9e-144
CGD\|CAL0006085		852	RAD16 [Candida albicans (taxid	0.654	0.555	0.456	1.5e-138
SGD\|S000000318		790	RAD16 "Protein that binds dama	0.648	0.593	0.455	5e-138
UNIPROTKB\|G4MPA7		986	MGG_07014 "DNA repair protein	0.644	0.472	0.429	5.7e-123
DICTYBASE\|DDB_G0272082		1838	DDB_G0272082 "CHR group protei	0.240	0.094	0.463	7.3e-88
TAIR\|locus:2162504		1029	RAD5 [Arabidopsis thaliana (ta	0.597	0.419	0.343	2.4e-87

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

 Score = 1968 (697.8 bits), Expect = 1.2e-267, Sum P(2) = 1.2e-267
 Identities = 365/487 (74%), Positives = 426/487 (87%)

Query:   239 LHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQI 298
             LHS+KW RIILDEAH+IK+RRSNTA+AV ALE++Y+WALSGTPLQNRVGELYSL+RFLQI
Sbjct:   349 LHSVKWNRIILDEAHYIKERRSNTARAVFALEATYRWALSGTPLQNRVGELYSLIRFLQI 408

Query:   299 TPYSYYFCKDCDCKVLDYSSAE-CPNCPHNSVRHFCWWNRYVATPIQTHGNSYG-GRRAM 356
              PYSYYFCKDCDC++LDY + + CP+CPHN+VRHFCWWN+YVA PI  +G S+G G+RAM
Sbjct:   409 RPYSYYFCKDCDCRILDYVAHQSCPHCPHNAVRHFCWWNKYVAKPITVYG-SFGLGKRAM 467

Query:   357 ILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTY 416
             ILLKHKVL+ ++LRRTK GRAADLALPPRI++LRRD+LD++E DYYESLY  SQA+FNTY
Sbjct:   468 ILLKHKVLKDILLRRTKLGRAADLALPPRIITLRRDTLDVKEFDYYESLYKNSQAEFNTY 527

Query:   417 VQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLA 476
             ++AGT+MNNYAHIFDLLTRLRQAVDHPYLVVYS ++        D    +Q CGLC+D A
Sbjct:   528 IEAGTLMNNYAHIFDLLTRLRQAVDHPYLVVYSNSSGANANL-VDENKSEQECGLCHDPA 586

Query:   477 DDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKS 536
             +D VVT+C H FCKACL   SAS     CPTCS  LTVD+T      ++ SKTT+KGF++
Sbjct:   587 EDYVVTSCAHVFCKACLIGFSASLGKVTCPTCSKLLTVDWTTKADTEHKASKTTLKGFRA 646

Query:   537 SSILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVN 596
             SSILNRI+LD+FQ+STKIEALREEIRFMVERDGSAK IVFSQFTSFLDLINY+L K GV+
Sbjct:   647 SSILNRIKLDDFQTSTKIEALREEIRFMVERDGSAKAIVFSQFTSFLDLINYTLGKCGVS 706

Query:   597 CVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVE 656
             CVQLVGSM++ ARD AIN+F EDPDC++FLMSLKAGGVALNLTVASHVF+MDPWWNPAVE
Sbjct:   707 CVQLVGSMTMAARDTAINKFKEDPDCRVFLMSLKAGGVALNLTVASHVFMMDPWWNPAVE 766

Query:   657 QQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEAD 716
             +QAQDRIHRIGQYKPIR+VRF+IENT+EERIL+LQ+KK+LVFEGTVGGS +A GKLTE D
Sbjct:   767 RQAQDRIHRIGQYKPIRVVRFIIENTVEERILRLQKKKELVFEGTVGGSQEAIGKLTEED 826

Query:   717 MRFLFVT 723
             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

DICTYBASE\|DDB_G0272082 DDB_G0272082 "CHR group protein" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

TAIR\|locus:2162504 RAD5 [Arabidopsis thaliana (taxid:3702)]	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		723
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	2e-62
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	2e-34
pfam00176		301	pfam00176, SNF2_N, SNF2 family N-terminal domain	1e-22
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	2e-22
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-19
COG0553		866	COG0553, HepA, Superfamily II DNA/RNA helicases, S	3e-16
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	1e-15
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	9e-15
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-12
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	6e-12
PLN03142		1033	PLN03142, PLN03142, Probable chromatin-remodeling	2e-11
smart00184		40	smart00184, RING, Ring finger	2e-07
cd00162		45	cd00162, RING, RING-finger (Really Interesting New	3e-07
pfam13923		45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	6e-07
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	5e-06
pfam13639		46	pfam13639, zf-RING_2, Ring finger domain	6e-06
pfam00097		40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	2e-05
COG5574		271	COG5574, PEX10, RING-finger-containing E3 ubiquiti	1e-04
COG5152		259	COG5152, COG5152, Uncharacterized conserved protei	1e-04
TIGR00599		397	TIGR00599, rad18, DNA repair protein rad18	3e-04
pfam13445		55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	8e-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 =  223 bits (570), Expect = 2e-62
 Identities = 142/497 (28%), Positives = 209/497 (42%), Gaps = 95/497 (19%)

Query: 229 VQKPSGGKSPLHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGE 288
           +++       L  ++W+R++LDEAH IK+ +S+  KA+  L++  +  L+GTPL+NR+GE
Sbjct: 458 LRRFLVDHGGLKKIEWDRVVLDEAHRIKNDQSSEGKALQFLKALNRLDLTGTPLENRLGE 517

Query: 289 LYSLVRFLQITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGN 348
           L+SL++   + P                           S   F    R    PIQ   +
Sbjct: 518 LWSLLQEF-LNPGLL----------------------GTSFAIF---TRLFEKPIQAEED 551

Query: 349 SYGG--RRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLY 406
                 R   I L  K+L   ILRRTK+       LPP+I  +    L   + + YE+L 
Sbjct: 552 IGPLEARELGIELLRKLLSPFILRRTKEDVEVLKELPPKIEKVLECELSEEQRELYEALL 611

Query: 407 SESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQ 466
             ++                     LL  L +A      +  S+   L          + 
Sbjct: 612 EGAE-----------------KNQQLLEDLEKADSDENRIGDSELNILA--------LLT 646

Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRT 526
           ++  +CN  A                L D              +  T D        ++ 
Sbjct: 647 RLRQICNHPA----------------LVDEG------------LEATFDRIVLLLREDKD 678

Query: 527 SKTTIKGFKSSSILNRIQLDEFQ-SSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDL 585
                K     S      LDE        E    ++            ++FSQFT  LDL
Sbjct: 679 FDYLKKPLIQLSKGKLQALDELLLDKLLEEGHYHKV------------LIFSQFTPVLDL 726

Query: 586 INYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVF 645
           +   L   G+  V+L GS     R   I+RF  D + K+FL+SLKAGG+ LNLT A  V 
Sbjct: 727 LEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVI 786

Query: 646 LMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGS 705
           L DPWWNPAVE QA DR HRIGQ +P+++ R +   TIEE+IL+LQEKK+ + +  +   
Sbjct: 787 LFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEEKILELQEKKQELLDSLIDAE 846

Query: 706 A-DAFGKLTEADMRFLF 721
                 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\|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\|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		723
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
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	100.0
KOG4439		901	consensus RNA polymerase II transcription terminat	100.0
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	100.0
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	100.0
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	100.0
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	100.0
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	100.0
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	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
PRK04914		956	ATP-dependent helicase HepA; Validated	100.0
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	100.0
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	100.0
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	100.0
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	100.0
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	100.0
KOG0298		1394	consensus DEAD box-containing helicase-like transc	100.0
PRK13766		773	Hef nuclease; Provisional	100.0
KOG0383		696	consensus Predicted helicase [General function pre	100.0
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.98
PHA02558		501	uvsW UvsW helicase; Provisional	99.98
KOG0354		746	consensus DEAD-box like helicase [General function	99.97
KOG1123		776	consensus RNA polymerase II transcription initiati	99.95
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	99.94
PTZ00110		545	helicase; Provisional	99.94
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	99.93
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.93
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	99.93
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	99.93
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	99.93
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.93
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	99.93
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	99.93
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	99.92
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	99.92
PTZ00424		401	helicase 45; Provisional	99.92
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.91
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	99.9
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.9
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	99.89
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	99.89
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	99.89
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	99.88
PRK10689		1147	transcription-repair coupling factor; Provisional	99.87
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	99.87
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	99.87
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	99.86
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	99.86
PRK02362		737	ski2-like helicase; Provisional	99.85
PRK13767		876	ATP-dependent helicase; Provisional	99.85
COG4096		875	HsdR Type I site-specific restriction-modification	99.84
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	99.83
PRK01172		674	ski2-like helicase; Provisional	99.83
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	99.82
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	99.81
PRK00254		720	ski2-like helicase; Provisional	99.81
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	99.8
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.79
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.79
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.79
PRK09200		790	preprotein translocase subunit SecA; Reviewed	99.76
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	99.76
PHA02653		675	RNA helicase NPH-II; Provisional	99.75
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	99.75
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	99.75
PRK09401		1176	reverse gyrase; Reviewed	99.75
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.74
COG1201		814	Lhr Lhr-like helicases [General function predictio	99.72
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	99.72
COG4889		1518	Predicted helicase [General function prediction on	99.71
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	99.7
KOG0343		758	consensus RNA Helicase [RNA processing and modific	99.7
KOG4284		980	consensus DEAD box protein [Transcription]	99.69
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	99.69
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	99.69
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	99.69
COG1204		766	Superfamily II helicase [General function predicti	99.69
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	99.69
PRK05580		679	primosome assembly protein PriA; Validated	99.68
COG1202		830	Superfamily II helicase, archaea-specific [General	99.67
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	99.67
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	99.67
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	99.66
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	99.65
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	99.65
TIGR00595		505	priA primosomal protein N'. All proteins in this f	99.65
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	99.64
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	99.64
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.63
COG1205		851	Distinct helicase family with a unique C-terminal	99.62
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.61
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	99.6
PRK14701		1638	reverse gyrase; Provisional	99.59
KOG0341		610	consensus DEAD-box protein abstrakt [RNA processin	99.59
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	99.59
PRK09694		878	helicase Cas3; Provisional	99.58
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	99.56
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.54
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	99.54
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	99.54
KOG0346		569	consensus RNA helicase [RNA processing and modific	99.51
PRK12904		830	preprotein translocase subunit SecA; Reviewed	99.5
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.48
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.48
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.48
KOG0347		731	consensus RNA helicase [RNA processing and modific	99.47
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	99.46
KOG0327		397	consensus Translation initiation factor 4F, helica	99.46
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.46
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	99.45
PRK13107		908	preprotein translocase subunit SecA; Reviewed	99.42
KOG0334		997	consensus RNA helicase [RNA processing and modific	99.42
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	99.42
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.42
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	99.4
PRK05298		652	excinuclease ABC subunit B; Provisional	99.38
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	99.35
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	99.33
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.32
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	99.32
KOG0353		695	consensus ATP-dependent DNA helicase [General func	99.31
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	99.26
KOG1513		1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	99.26
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	99.25
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	99.22
PRK12326		764	preprotein translocase subunit SecA; Reviewed	99.2
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	99.18
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.18
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	99.17
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	99.12
COG1198		730	PriA Primosomal protein N' (replication factor Y)	99.11
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.07
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	99.04
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	99.03
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	98.95
COG0610		962	Type I site-specific restriction-modification syst	98.9
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	98.89
KOG0950		1008	consensus DNA polymerase theta/eta, DEAD-box super	98.77
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.64
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	98.62
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.58
PF11496		297	HDA2-3: Class II histone deacetylase complex subun	98.58
CHL00122		870	secA preprotein translocase subunit SecA; Validate	98.54
PF13871		278	Helicase_C_4: Helicase_C-like	98.51
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	98.48
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	98.46
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	98.46
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	98.45
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	98.45
PRK15483		986	type III restriction-modification system StyLTI en	98.41
KOG0349		725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	98.34
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	98.3
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	98.25
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	98.23
KOG0953		700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	98.07
KOG0924		1042	consensus mRNA splicing factor ATP-dependent RNA h	97.91
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	97.9
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	97.85
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	97.73
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.63
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.61
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	97.54
COG3587		985	Restriction endonuclease [Defense mechanisms]	97.53
KOG0923		902	consensus mRNA splicing factor ATP-dependent RNA h	97.48
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	97.15
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.14
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.1
PF06862		442	DUF1253: Protein of unknown function (DUF1253); In	97.06
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.02
PRK10536		262	hypothetical protein; Provisional	96.99
PRK14873		665	primosome assembly protein PriA; Provisional	96.77
KOG1803		649	consensus DNA helicase [Replication, recombination	96.67
TIGR00376		637	DNA helicase, putative. The gene product may repre	96.63
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	96.62
KOG0925		699	consensus mRNA splicing factor ATP-dependent RNA h	96.61
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	96.49
PF15227		42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	96.45
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	96.44
KOG4150		1034	consensus Predicted ATP-dependent RNA helicase [RN	96.38
PF13401		131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.36
KOG1805		1100	consensus DNA replication helicase [Replication, r	96.29
PF05876		557	Terminase_GpA: Phage terminase large subunit (GpA)	96.28
PLN03208		193	E3 ubiquitin-protein ligase RMA2; Provisional	96.24
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	95.98
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	95.97
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	95.97
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	95.96
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	95.93
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	95.73
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	95.68
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.65
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	95.43
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	95.36
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	95.2
PRK10875		615	recD exonuclease V subunit alpha; Provisional	95.2
KOG2164		513	consensus Predicted E3 ubiquitin ligase [Posttrans	95.14
PF13923		39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	95.14
PF13920		50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	95.01
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	94.97
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	94.91
PF00097		41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	94.5
PRK07003		830	DNA polymerase III subunits gamma and tau; Validat	94.48
smart00504		63	Ubox Modified RING finger domain. Modified RING fi	94.29
KOG0317		293	consensus Predicted E3 ubiquitin ligase, integral	94.26
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	94.25
PRK06526		254	transposase; Provisional	94.08
KOG0320		187	consensus Predicted E3 ubiquitin ligase [Posttrans	94.03
TIGR00599		397	rad18 DNA repair protein rad18. This family is bas	94.02
TIGR02881		261	spore_V_K stage V sporulation protein K. Members o	93.99
COG3421		812	Uncharacterized protein conserved in bacteria [Fun	93.94
PF14634		44	zf-RING_5: zinc-RING finger domain	93.68
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	93.66
KOG0823		230	consensus Predicted E3 ubiquitin ligase [Posttrans	93.6
PRK12723		388	flagellar biosynthesis regulator FlhF; Provisional	93.51
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	93.42
TIGR03420		226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	93.4
PRK08084		235	DNA replication initiation factor; Provisional	93.34
KOG0978		698	consensus E3 ubiquitin ligase involved in syntaxin	93.2
PLN03025		319	replication factor C subunit; Provisional	93.2
PRK04296		190	thymidine kinase; Provisional	93.04
PF13445		43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	92.92
TIGR02880		284	cbbX_cfxQ probable Rubsico expression protein CbbX	92.77
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	92.7
PF13245		76	AAA_19: Part of AAA domain	92.6
PRK12323		700	DNA polymerase III subunits gamma and tau; Provisi	92.47
PRK14956		484	DNA polymerase III subunits gamma and tau; Provisi	92.35
PHA02929		238	N1R/p28-like protein; Provisional	92.35
COG5574		271	PEX10 RING-finger-containing E3 ubiquitin ligase [	92.35
PRK14949		944	DNA polymerase III subunits gamma and tau; Provisi	92.32
PRK14960		702	DNA polymerase III subunits gamma and tau; Provisi	92.19
PHA02533		534	17 large terminase protein; Provisional	92.07
PRK00149		450	dnaA chromosomal replication initiation protein; R	91.9
PRK05707		328	DNA polymerase III subunit delta'; Validated	91.88
smart00382		148	AAA ATPases associated with a variety of cellular	91.87
PRK08181		269	transposase; Validated	91.81
CHL00181		287	cbbX CbbX; Provisional	91.5
PRK14087		450	dnaA chromosomal replication initiation protein; P	91.44
PRK05703		424	flhF flagellar biosynthesis regulator FlhF; Valida	91.31
PRK14964		491	DNA polymerase III subunits gamma and tau; Provisi	91.24
PRK14958		509	DNA polymerase III subunits gamma and tau; Provisi	91.11
KOG2879		298	consensus Predicted E3 ubiquitin ligase [Posttrans	90.98
TIGR00362		405	DnaA chromosomal replication initiator protein Dna	90.82
TIGR03015		269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	90.82
PF14835		65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	90.74
smart00184		39	RING Ring finger. E3 ubiquitin-protein ligase acti	90.53
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	90.42
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	90.26
PRK14086		617	dnaA chromosomal replication initiation protein; P	90.22
PRK06645		507	DNA polymerase III subunits gamma and tau; Validat	90.18
PRK07994		647	DNA polymerase III subunits gamma and tau; Validat	90.13
PRK06893		229	DNA replication initiation factor; Validated	89.97
cd00162		45	RING RING-finger (Really Interesting New Gene) dom	89.82
PHA02926		242	zinc finger-like protein; Provisional	89.8
PRK14088		440	dnaA chromosomal replication initiation protein; P	89.73
TIGR00570		309	cdk7 CDK-activating kinase assembly factor MAT1. A	89.69
PRK08727		233	hypothetical protein; Validated	89.58
PRK14952		584	DNA polymerase III subunits gamma and tau; Provisi	89.56
PRK07764		824	DNA polymerase III subunits gamma and tau; Validat	89.49
PRK14974		336	cell division protein FtsY; Provisional	89.47
KOG0991		333	consensus Replication factor C, subunit RFC2 [Repl	89.22
PRK07940		394	DNA polymerase III subunit delta'; Validated	89.13
PRK09112		351	DNA polymerase III subunit delta'; Validated	89.12
PRK14961		363	DNA polymerase III subunits gamma and tau; Provisi	89.11
PRK08769		319	DNA polymerase III subunit delta'; Validated	89.1
PRK14955		397	DNA polymerase III subunits gamma and tau; Provisi	88.96
PRK09111		598	DNA polymerase III subunits gamma and tau; Validat	88.84
PF05621		302	TniB: Bacterial TniB protein; InterPro: IPR008868	88.83
PRK14962		472	DNA polymerase III subunits gamma and tau; Provisi	88.79
PRK08116		268	hypothetical protein; Validated	88.73
PRK00440		319	rfc replication factor C small subunit; Reviewed	88.64
TIGR02768		744	TraA_Ti Ti-type conjugative transfer relaxase TraA	88.6
PRK06835		329	DNA replication protein DnaC; Validated	88.52
PRK12402		337	replication factor C small subunit 2; Reviewed	88.26
PRK08691		709	DNA polymerase III subunits gamma and tau; Validat	87.9
PRK12422		445	chromosomal replication initiation protein; Provis	87.67
PRK05642		234	DNA replication initiation factor; Validated	87.64
PF02456		369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	87.12
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	86.84
PRK14969		527	DNA polymerase III subunits gamma and tau; Provisi	86.51
KOG0740		428	consensus AAA+-type ATPase [Posttranslational modi	86.49
PRK11889		436	flhF flagellar biosynthesis regulator FlhF; Provis	86.3
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	86.11
PF00448		196	SRP54: SRP54-type protein, GTPase domain; InterPro	86.04
PHA02544		316	44 clamp loader, small subunit; Provisional	85.97
cd01121		372	Sms Sms (bacterial radA) DNA repair protein. This	85.79
PRK06964		342	DNA polymerase III subunit delta'; Validated	85.79
PRK14954		620	DNA polymerase III subunits gamma and tau; Provisi	85.77
PRK05986		191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	85.72
PRK14959		624	DNA polymerase III subunits gamma and tau; Provisi	85.68
PRK14948		620	DNA polymerase III subunits gamma and tau; Provisi	85.57
PRK08451		535	DNA polymerase III subunits gamma and tau; Validat	85.52
PRK04195		482	replication factor C large subunit; Provisional	85.18
PRK14951		618	DNA polymerase III subunits gamma and tau; Provisi	85.1
PRK14963		504	DNA polymerase III subunits gamma and tau; Provisi	84.9
COG4626		546	Phage terminase-like protein, large subunit [Gener	84.86
PF04564		73	U-box: U-box domain; InterPro: IPR003613 Quality c	84.83
PRK14965		576	DNA polymerase III subunits gamma and tau; Provisi	84.72
COG5432		391	RAD18 RING-finger-containing E3 ubiquitin ligase [	84.7
PRK07471		365	DNA polymerase III subunit delta'; Validated	84.68
PRK05896		605	DNA polymerase III subunits gamma and tau; Validat	84.54
PRK11054		684	helD DNA helicase IV; Provisional	84.29
COG3973		747	Superfamily I DNA and RNA helicases [General funct	84.24
TIGR02688		449	conserved hypothetical protein TIGR02688. Members	84.17
PRK14950		585	DNA polymerase III subunits gamma and tau; Provisi	84.16
PRK06871		325	DNA polymerase III subunit delta'; Validated	83.99
PF00580		315	UvrD-helicase: UvrD/REP helicase N-terminal domain	83.79
cd01120		165	RecA-like_NTPases RecA-like NTPases. This family i	83.76
PRK06647		563	DNA polymerase III subunits gamma and tau; Validat	83.69
KOG0287		442	consensus Postreplication repair protein RAD18 [Re	83.68
COG1484		254	DnaC DNA replication protein [DNA replication, rec	83.61
PRK09183		259	transposase/IS protein; Provisional	83.38
PF13639		44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	83.34
KOG0824		324	consensus Predicted E3 ubiquitin ligase [Posttrans	83.24
PF13177		162	DNA_pol3_delta2: DNA polymerase III, delta subunit	82.77
KOG0739		439	consensus AAA+-type ATPase [Posttranslational modi	82.73
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	82.52
PRK05563		559	DNA polymerase III subunits gamma and tau; Validat	82.44
PRK13889		988	conjugal transfer relaxase TraA; Provisional	82.41
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	82.22
COG2256		436	MGS1 ATPase related to the helicase subunit of the	82.18
PF00004		132	AAA: ATPase family associated with various cellula	82.13
TIGR00595		505	priA primosomal protein N'. All proteins in this f	82.12
PRK05580		679	primosome assembly protein PriA; Validated	81.86
PF03354		477	Terminase_1: Phage Terminase ; InterPro: IPR005021	81.63
PRK08699		325	DNA polymerase III subunit delta'; Validated	81.47
PRK06090		319	DNA polymerase III subunit delta'; Validated	81.12
CHL00095		821	clpC Clp protease ATP binding subunit	81.08
KOG1131		755	consensus RNA polymerase II transcription initiati	80.96
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	80.9
PRK14722		374	flhF flagellar biosynthesis regulator FlhF; Provis	80.83
COG0464		494	SpoVK ATPases of the AAA+ class [Posttranslational	80.07
PHA03368		738	DNA packaging terminase subunit 1; Provisional	80.07

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

Probab=100.00  E-value=1.3e-97  Score=744.02  Aligned_cols=624  Identities=57%  Similarity=0.962  Sum_probs=574.9

Q ss_pred             CCccccccccccCCCCCCCCccCChHHHHHHHHHHHHhccCCCCCCcccCCCCCcHHHHHHHHHhcCccccCCCCccCCC
Q 004925            7 VDLDQQNAFMTETAEDPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVLAKREIRGTIGELDAS   86 (723)
Q Consensus         7 ~~~~~~~~~~~~~~~~p~~~~~~L~p~Q~~~~~~~~~~~~~~~~g~iLad~~GlGKT~~al~~i~~~~~~~~~~~~~~~~   86 (723)
                      +|++..++..++..++|.++..+|.|||++++.|+..++.+.++||||||+||+|||+++|++++....           
T Consensus       162 ~dlde~~p~i~e~aeqP~dlii~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~~-----------  230 (791)
T KOG1002|consen  162 TDLDEANPVIAERAEQPDDLIIPLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEVD-----------  230 (791)
T ss_pred             hhhhhcCchhhhcccCcccceecchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhccc-----------
Confidence            488999999999999999999999999999999999999999999999999999999999999987322           


Q ss_pred             CCCCCCCCCCCceEEEechhhHHHHHHHHHhhcCCCCcEEEEEeCCCCCCCccccCCCCEEEechhhhHHhhhhccCCCc
Q 004925           87 SSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQFSEFDFVITTYSIIEADYRKHVMPPK  166 (723)
Q Consensus        87 ~~~~~~~~~~~~~LIv~P~~l~~qW~~ei~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~ivi~t~~~l~~~~~~~~~~~~  166 (723)
                               ..|+|||||...+.||.+||..++. +..++++|+|.+.....+.+..||+|+|||..+.+.+++...   
T Consensus       231 ---------ra~tLVvaP~VAlmQW~nEI~~~T~-gslkv~~YhG~~R~~nikel~~YDvVLTty~vvEs~yRk~~~---  297 (791)
T KOG1002|consen  231 ---------RAPTLVVAPTVALMQWKNEIERHTS-GSLKVYIYHGAKRDKNIKELMNYDVVLTTYAVVESVYRKQDY---  297 (791)
T ss_pred             ---------cCCeeEEccHHHHHHHHHHHHHhcc-CceEEEEEecccccCCHHHhhcCcEEEEecHHHHHHHHhccc---
Confidence                     2689999999999999999999998 699999999999999999999999999999999999875210   


Q ss_pred             ccccccCccchhhhhhhhhhhccCCcchhhhhhhHHHHhhhccccccCCCCCCCCCCcCCCCCCCCCCCCCCccceeeEE
Q 004925          167 QKCQYCGKSFYQKKLVVHLKYFCGPSAVRTEKQSKQEKKKMKSSVYEGYPGKKNGKKSSVGGVQKPSGGKSPLHSLKWER  246 (723)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  246 (723)
                                                                     +.     .++      -......+.|+.+.|-+
T Consensus       298 -----------------------------------------------Gf-----rrK------ngv~ke~SlLHsi~~~R  319 (791)
T KOG1002|consen  298 -----------------------------------------------GF-----RRK------NGVDKEKSLLHSIKFYR  319 (791)
T ss_pred             -----------------------------------------------cc-----ccc------CCcccccchhhhceeee
Confidence                                                           00     000      01223356799999999


Q ss_pred             EEeeccccccCCCcHHHHHHHhhhcCceEEEeCcCCCCchhhHHHHHHHhccCcCCcccccCCcccccCCC---CCCCCC
Q 004925          247 IILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQITPYSYYFCKDCDCKVLDYS---SAECPN  323 (723)
Q Consensus       247 vIiDEaH~~kn~~s~~~~~l~~l~~~~~l~LTaTP~~n~~~dl~~~l~lL~~~~~~~~~~~~~~~~~~~~~---~~~~~~  323 (723)
                      ||+||||.+|+..|.+.+++..+.+.+||.|||||++|+++++|+++++|+..||.+++|..+++...++.   ...|+.
T Consensus       320 iIlDEAH~IK~R~snTArAV~~L~tt~rw~LSGTPLQNrigElySLiRFL~i~Pfsyyfc~~cdc~~~~~~ftdr~~c~~  399 (791)
T KOG1002|consen  320 IILDEAHNIKDRQSNTARAVFALETTYRWCLSGTPLQNRIGELYSLIRFLNINPFSYYFCTKCDCASLDWKFTDRMHCDH  399 (791)
T ss_pred             eehhhhcccccccccHHHHHHhhHhhhhhhccCCcchhhHHHHHHHHHHHccCcchhhhhhhccccccceeecccccCCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999998776   467889


Q ss_pred             CCCCCccchhhhhhhccccccccCCCcchhHHHHHHHHHHhHhHhhhhccCCcccccCCCCceEEEEEecCCHHHHHHHH
Q 004925          324 CPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYE  403 (723)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~rr~~~~~~~~~~lp~~~~~~~~~~l~~~~~~~y~  403 (723)
                      |++..+.|+.+|+.++.++++..+....+.++.. ..+.++..+|+||++-+...++.|||+++.+-..-++.++.++|+
T Consensus       400 c~h~~m~h~~~~n~~mlk~IqkfG~eGpGk~af~-~~h~llk~ImlrrTkl~RAdDLgLPPRiv~vRrD~fn~eE~D~Ye  478 (791)
T KOG1002|consen  400 CSHNIMQHTCFFNHFMLKPIQKFGVEGPGKEAFN-NIHTLLKNIMLRRTKLERADDLGLPPRIVTVRRDFFNEEEKDLYE  478 (791)
T ss_pred             ccchhhhhhhhhcccccccchhhcccCchHHHHH-HHHHHHHHHHHHHhhcccccccCCCccceeeehhhhhhHHHHHHH
Confidence            9999999999999999999999988888877776 558999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHhhccCcccccccccccccCCCccccccccccccccccCCCCCcccc
Q 004925          404 SLYSESQAQFNTYVQAGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTN  483 (723)
Q Consensus       404 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  483 (723)
                      .++......++.+.+.+...++++++|.+++++||+++||+++..+.......     ......+|..|.+..+++...+
T Consensus       479 SLY~dSkrkfntyieeGvvlNNYAnIF~LitRmRQ~aDHP~LVl~S~~~n~~~-----enk~~~~C~lc~d~aed~i~s~  553 (791)
T KOG1002|consen  479 SLYKDSKRKFNTYIEEGVVLNNYANIFTLITRMRQAADHPDLVLYSANANLPD-----ENKGEVECGLCHDPAEDYIESS  553 (791)
T ss_pred             HHHHhhHHhhhhHHhhhhhhhhHHHHHHHHHHHHHhccCcceeeehhhcCCCc-----cccCceeecccCChhhhhHhhh
Confidence            99999999999999999999999999999999999999999998875544433     3345678999999999999999


Q ss_pred             cCCccchhhhhhhhcCc---CCCCCCCCCCCcccccccccCCCCCCccccccCCccccchhhccccccCcchHHHHHHHH
Q 004925          484 CGHAFCKACLFDSSASK---FVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSSILNRIQLDEFQSSTKIEALREE  560 (723)
Q Consensus       484 ~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~Kl~~l~~~  560 (723)
                      |.|.||.-|+.+.....   .+..||.|...+.+++...     ...+..+.++..++|+..++++.+..|+|+++|++.
T Consensus       554 ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~-----alek~~l~~Fk~sSIlnRinm~~~qsSTKIEAL~EE  628 (791)
T KOG1002|consen  554 CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEP-----ALEKTDLKGFKASSILNRINMDDWQSSTKIEALVEE  628 (791)
T ss_pred             hhHHHHHHHHHHHHHhhhcccCCCCccccccccccccch-----hhhhcchhhhhhHHHhhhcchhhhcchhHHHHHHHH
Confidence            99999999998776554   5699999999999984443     344567889999999999999999999999999999


Q ss_pred             HHHHHhhcCCceEEEEcccHhHHHHHHHHHHhCCCeEEEeecCCCHHHHHHHHHhhcCCCCceEEEEecCCCcccccccc
Q 004925          561 IRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGGVALNLTV  640 (723)
Q Consensus       561 l~~~~~~~~~~KvIIF~~~~~~~~~l~~~L~~~g~~~~~i~g~~~~~~r~~~i~~F~~~~~~~vll~s~~~~~eGlnL~~  640 (723)
                      |..+.++...-|.|||+||...++.|...|.+.|+.++.+.|+|++..|...|+.|.++.+|+|+|+|.++||+.+||..
T Consensus       629 l~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLte  708 (791)
T KOG1002|consen  629 LYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTE  708 (791)
T ss_pred             HHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeech
Confidence            99999888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCEEEEECCCCChhhHHHHHHhhhhcCCcccEEEEEEEeCCCHHHHHHHHHHHHHHHhhcccCCCccccCCCCHHHHHhh
Q 004925          641 ASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFL  720 (723)
Q Consensus       641 a~~vI~~d~~wn~~~~~Q~iGRi~R~Gq~~~V~v~~l~~~~t~ee~~~~~~~~K~~~~~~~~~~~~~~~~~~~~~~~~~l  720 (723)
                      |++|+++||.|||...-|+..||+|+||.++|.|++|..++|+|+++...+.+|.+++++.+|++....+.++++||.||
T Consensus       709 ASqVFmmDPWWNpaVe~Qa~DRiHRIGQ~rPvkvvrf~iEnsiE~kIieLQeKKa~mihaTi~qde~Ai~kLt~eDmqfL  788 (791)
T KOG1002|consen  709 ASQVFMMDPWWNPAVEWQAQDRIHRIGQYRPVKVVRFCIENSIEEKIIELQEKKANMIHATIGQDEEAISKLTEEDMQFL  788 (791)
T ss_pred             hceeEeecccccHHHHhhhhhhHHhhcCccceeEEEeehhccHHHHHHHHHHHHhhhhhhhcCCcHHHHHhcCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcC
Q 004925          721 FVT  723 (723)
Q Consensus       721 ~~~  723 (723)
                      |.+
T Consensus       789 F~n  791 (791)
T KOG1002|consen  789 FNN  791 (791)
T ss_pred             hcC
Confidence            974

>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

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

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

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

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

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

>KOG0390 consensus DNA repair protein, SNF2 family [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

>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

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

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

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

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

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

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

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e	Back alignment and domain information

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

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

>KOG0383 consensus Predicted helicase [General function prediction only]	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

>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

>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

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

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

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

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

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

>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

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

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

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

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

>PTZ00424 helicase 45; 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

>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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0335 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

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

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

>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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]	Back alignment and domain information

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

>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

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

>KOG0339 consensus ATP-dependent 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

>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

>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

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB	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

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

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

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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]	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

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

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

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

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

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

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

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

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

>TIGR00631 uvrb excinuclease ABC, B subunit	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

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

>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]	Back alignment and domain information

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

>KOG0334 consensus 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

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

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

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

>cd00268 DEADc DEAD-box helicases	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

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

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

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

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

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

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

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

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

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

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

>TIGR00596 rad1 DNA repair protein (rad1)	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

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

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

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

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

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

>PRK12903 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

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

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

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

>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

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

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

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

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

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

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

>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]	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

>KOG0920 consensus ATP-dependent RNA helicase A [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

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

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

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

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

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

>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

>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

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated	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

>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

>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

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

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

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

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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

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

>KOG0925 consensus mRNA splicing factor 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

>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

>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

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

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

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]	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

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

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	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

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional	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

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

>TIGR01448 recD_rel helicase, putative, RecD/TraA family	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

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

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

>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>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

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

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

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

>smart00504 Ubox Modified RING finger domain	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

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

>PRK06526 transposase; Provisional	Back alignment and domain information

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

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

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

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

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

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

>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

>PRK08084 DNA replication initiation factor; 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

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

>PRK04296 thymidine kinase; Provisional	Back alignment and domain information

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

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

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

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

>PRK12323 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

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

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

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

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

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

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

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

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

>PRK08181 transposase; Validated	Back alignment and domain information

>CHL00181 cbbX CbbX; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

>smart00184 RING Ring finger	Back alignment and domain information

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

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

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

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

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

>PRK06893 DNA replication initiation factor; Validated	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

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

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

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

>PRK08727 hypothetical protein; Validated	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>PRK09111 DNA polymerase III subunits gamma and tau; Validated	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

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

>PRK08116 hypothetical protein; Validated	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional	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

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

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

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

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

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

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated	Back alignment and domain information

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

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

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

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

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

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

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]	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

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

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

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

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

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

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

>TIGR02688 conserved hypothetical protein TIGR02688	Back alignment and domain information

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

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

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

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

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

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

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

>PRK09183 transposase/IS protein; Provisional	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

>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	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

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

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

>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin	Back alignment and domain information

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

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

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

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

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)	Back alignment and domain information

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

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

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

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

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

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

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

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		723
3mwy_W		800	Crystal Structure Of The Chromodomain-atpase Portio		3e-27
1z6a_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN		8e-20
1z63_A		500	Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COM		1e-19
1z5z_A		271	Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal		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