Citrus Sinensis ID: 004518

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------

MPIKLFPNLRLLNPPLSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPTRVNSQQQQQQQQLGLRKLSTRPFRPAASSEFGRRGSRAGEIRGSKNLIDDEAELSDWVSDLRTDSFHSNKRFSKDDDVSDFRKGSGRENRGSYSMKRRRKSDSDDSYDSSRRGNRNSVNSFSRNNISNNTSRFSRRSNSELEAGNVGRKTRFSNDDENDVGEERRRGMSGIRDLLSEEVSDNDDDDDDSVLRNNARSLIGLDKENGGMSVAISSPGKHDSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK

ccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHccccccccEEEccccccHHHHHHHHHHHHHHHccccccccccccccEEEEEcccHHHHHHHHHHHHHHHHccccccEEEEEcccccHHHHHHHHcccccEEEEccHHHHHHHHcccccccccccccEEEEEccHHHHccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccEEEEEccccccccccccEEEEEEccccccHHHHHHHHHHHHccccccEEEEEccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccEEEEEcccccccccccccEEEEcccccccccccccccccccccccccEEEEEcHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccccHHHHHccccccccccccc

cccccccccEEEcccccccccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHHcccccccccccccEEEEEccHHHHHHHHHHHHHHHHHHccccEEEEEEcccccHHHHHHHHHcccEEEEEcccHHHHHHHccccEEEEcccEEEEEEcHHHHHHHcccHHHHHHHHHHccHHHcEEEEEccccHHHHHHHHHHHccccEEEEEEEEccccccccEEEEEEEEccHHHHHHHHHHHHHHHccccccEEEEEEccHHHHHHHHHHHHHccccHHHHcccccHHHHHHHHHHHHcccccEEEEEEHHHcccccccccEEEEEcccccHHHHHEEcccccccccccEEEEEEcccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccccccHHHHHHHHcccccccccccc

mpiklfpnlrllnpplsatrfpsmnlkpsvnssraipaFRRIFPfklkylglptrvnSQQQQQQQQLGlrklstrpfrpaassefgrrgsrageirgsknliddeaeLSDWVsdlrtdsfhsnkrfskdddvsdfrkgsgrenrgsysmkrrrksdsddsydssrrgnrnsvnsfsrnnisnntsrfsrrsnseleagnvgrktrfsnddendvgeerrrGMSGIRDLLseevsdnddddddsvLRNNARSLigldkenggmsvaisspgkhdsfmsesrfdqcSISALSlkgikdagyekmtivqEATLPVLLKGKDVlakaktgtgktvaFLLPSIevviksppvdrdqrrppilvlVICPTRELATQAATEASTLlkyhpsigvQVVIGGTRLALEQKRmqanpcqilvatpgrlrdHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLvapldlhfPLLYVLLREhvadnpeykVLVFCTTAMVTRMVADLLGELKLNVREihsrkpqsyrtrvsdefrkskglilvtsdvsargvdypdVTLVIQVGLPSDREQYIHRLGrtgrkgkegqgilllapwEEFFLSTikdlpilkapvpsvdpdtKKKVERALSHVEMKNKEAAYQAWLGYYNsnkkvgrdkYKLVELANEYSrsmgldnppaipklvlgkmglrnipglrsk

mpiklfpnlrllnpplsatrfpsmnlkpsvnssraipAFRRIFPFKLKYLGLPTRVNSQQQQQQQQlglrklstrpfrpaassefgrrgsrageirgsknliddEAELSDWVSDlrtdsfhsnkrfskdddvsdfrkgsgrenrgsysmkrrrksdsddsydssrrgnrnsvnsfsrnnisnntsrfsrrsnseleagnvgrktrfsnddendvgeerrrgmsgirdllseevsdnddddddsvLRNNARsligldkenggmSVAISSPGKHDSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAktgtgktvafllpsievviksppvdrdqrrpPILVLVICPTRELATQAATEAstllkyhpsiGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGElklnvreihsrkpqsyrtrvsdefrkskglilvtsdvsargvdypdVTLVIqvglpsdreqYIHRLgrtgrkgkeGQGILLLAPWEEFFLSTIKDLPIlkapvpsvdpdtKKKVERALSHVEMKNKEAAYQAWLGYYnsnkkvgrdKYKLVELANEYsrsmgldnppaipklvlgkmglrnipglrsk

MPIKlfpnlrllnpplSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPTRVNSqqqqqqqqLGLRKLSTRPFRPAASSEFGRRGSRAGEIRGSKNLIDDEAELSDWVSDLRTDSFHSNKRFSKDDDVSDFRKGSGRENRGsysmkrrrksdsddsydssrrgnrnsvnsfsrnnisnntsrfsrrsnsELEAGNVGRKTRFSNDDENDVGEERRRGMSGIRdllseevsdnddddddsvlrnnARSLIGLDKENGGMSVAISSPGKHDSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK

**********************************AIPAFRRIFPFKLKYLGLP*************************************************************************************************************************************************************************************************************************************QCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVD***RRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVE********QVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIH**************FRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAP***********************KEAAYQAWLGYYNSNKKVGRDKYKLVELANEYS**********IPKLVLGK************

***KLFPNLRLLNPPLSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPTR*********************************************************************************************************************************************************************************************************************************FDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPP*****RRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQ*RMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPI**********************VEMKNKEAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPA********************

MPIKLFPNLRLLNPPLSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPTR**************RKLSTRP**************RAGEIRGSKNLIDDEAELSDWVSDLRTDSFHSNKRFSKD***************************************RNSVNSFSRNNISNNTSRFSRRSNSELEAGNVGRKTRFSNDDENDVGEERRRGMSGIRDLLSEE*********DSVLRNNARSLIGLDKENGGMSVAISSPGKHDSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVE**********RQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK

*PIKLFPNLRLLNPPLSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPT*************************************************************************************************************************************************************************************NDDDDDDSVLRNNARSLIGLDKENGGMSVAISSPGKHDSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGL***

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		747	2.2.26 [Sep-21-2011]
Q9FFQ1		716	DEAD-box ATP-dependent RN	yes	no	0.933	0.973	0.627	0.0
Q9FNM7		850	DEAD-box ATP-dependent RN	no	no	0.819	0.72	0.675	0.0
Q0DBU5		547	DEAD-box ATP-dependent RN	yes	no	0.720	0.983	0.707	0.0
Q94C75		563	DEAD-box ATP-dependent RN	no	no	0.713	0.946	0.68	0.0
Q5ZBH5		594	DEAD-box ATP-dependent RN	yes	no	0.641	0.806	0.728	0.0
Q0JL73		536	DEAD-box ATP-dependent RN	no	no	0.643	0.897	0.709	0.0
Q6K7R9		811	DEAD-box ATP-dependent RN	no	no	0.720	0.663	0.540	1e-176
Q9C8S9		798	Probable DEAD-box ATP-dep	no	no	0.633	0.592	0.578	1e-167
O80792		845	Putative DEAD-box ATP-dep	no	no	0.633	0.559	0.573	1e-165
Q0UG00		550	ATP-dependent RNA helicas	N/A	no	0.597	0.810	0.413	6e-81

>sp\|Q9FFQ1\|RH31_ARATH DEAD-box ATP-dependent RNA helicase 31 OS=Arabidopsis thaliana GN=RH31 PE=2 SV=2	Back alignment and function desciption

 Score =  904 bits (2335), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 481/766 (62%), Positives = 556/766 (72%), Gaps = 69/766 (9%)

Query: 1   MPIKLFPNLRLLNPPLSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPTRVNSQQ 60
           MP+     +R     LS T         S N+S ++P   RIF   L +    +R+N   
Sbjct: 1   MPLNFPLRIRFFAHSLSGTHL-------SYNTSSSVPLLFRIFSSGLNHFEFGSRIN--- 50

Query: 61  QQQQQQLGLRKLSTRPFRPAASSEFGRRGSRAGEIRGSKNLIDDEAELSDWVSDLRTDSF 120
                       STRP R     EF RR    GEIR SK+LI+DE ELS+WVS  RT S 
Sbjct: 51  -----------FSTRPNRD--QPEFERRIRDGGEIRASKSLIEDEEELSNWVSGFRTGSS 97

Query: 121 HSNKRFSKDDDVSDFRKGSGRENRGSYSMKRRRKSDSDDSYDSSRRGNRNSVNSFSRNNI 180
               + S D+D  D  +G  +E                      +RG RN V+SF     
Sbjct: 98  RGILK-SDDEDEEDRSRGRNQE----------------------KRGIRNQVDSFRNKRY 134

Query: 181 SNNTSRF--SRRSNSELEAGNVGRK-TRFSNDDENDVGEERRRG---------------- 221
             +  R   SR      EA   GRK T FS D E++ G  +R                  
Sbjct: 135 GGDRERGFNSRIQGKSSEASFRGRKETSFSRDREDEKGLRKREDLRLEDESSDEDVKSLV 194

Query: 222 MSGIRDLLSEEVSDNDDDDDDSVLRNNARSLIGLDKENGGMSVAISSPGKHDSFMSESRF 281
           M  I DLLSE+  + D D     L+  A S  G DKEN  +  A  +   +DS+++++RF
Sbjct: 195 MGDIGDLLSEDDEEEDQDY--DFLKKKAVSAFGFDKEN--VIEADKTRNANDSYLTKTRF 250

Query: 282 DQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVV 341
           D   +S LSLK IKDAGYE MT+VQEATLP++LKGKDVLAKAKTGTGKTVAFLLPSIEVV
Sbjct: 251 DHYPLSPLSLKAIKDAGYETMTVVQEATLPIILKGKDVLAKAKTGTGKTVAFLLPSIEVV 310

Query: 342 IKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQK 401
           +KSPP   D +RPPIL LVICPTRELA QAATEA+TLLKYHPSIGVQVVIGGTRL LEQK
Sbjct: 311 VKSPPTSPDNKRPPILALVICPTRELANQAATEANTLLKYHPSIGVQVVIGGTRLGLEQK 370

Query: 402 RMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIEKIIAA 461
           RMQ NPCQILVATPGRL+DHIENT GFATRL GVKVLVLDEADHLLDMGFRKDIE+II+A
Sbjct: 371 RMQTNPCQILVATPGRLKDHIENTPGFATRLKGVKVLVLDEADHLLDMGFRKDIERIISA 430

Query: 462 VPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAPLDLHF 521
           VPK+RQT LFSATVPEEVRQIC +AL+RDHEF+N V EG+ ETH+QVRQMH++A LD HF
Sbjct: 431 VPKERQTFLFSATVPEEVRQICLVALRRDHEFVNCVHEGTIETHQQVRQMHMIASLDRHF 490

Query: 522 PLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSD 581
            LLY LLREH+  N +YKV+VFCTTAMVT++VADLLGEL LNVREIHSRKPQSYRTRVS+
Sbjct: 491 SLLYTLLREHIMGNVDYKVIVFCTTAMVTKLVADLLGELNLNVREIHSRKPQSYRTRVSN 550

Query: 582 EFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLL 641
           EFRKSKGLILVTSDVSARGVDYPDVTLV+QVGLP DREQYIHRLGRTGRKGKEG+GILLL
Sbjct: 551 EFRKSKGLILVTSDVSARGVDYPDVTLVLQVGLPKDREQYIHRLGRTGRKGKEGEGILLL 610

Query: 642 APWEEFFLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAYQAWLGYYNSNKK 701
           APWEE+FLS++KDLPI K+P+PS+DP+T KKV++AL HVEM+NKEAAYQAWLGYYNS K 
Sbjct: 611 APWEEYFLSSLKDLPITKSPLPSIDPETVKKVQKALCHVEMRNKEAAYQAWLGYYNSQKM 670

Query: 702 VGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK 747
           +GRDK +LVELANE+SRSMGLDNPPAIPKL+LGKMGL+N+PGLR+K
Sbjct: 671 IGRDKDRLVELANEFSRSMGLDNPPAIPKLILGKMGLKNVPGLRAK 716

Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp\|Q9FNM7\|RH26_ARATH DEAD-box ATP-dependent RNA helicase 26 OS=Arabidopsis thaliana GN=RH26 PE=1 SV=2	Back alignment and function description

>sp\|Q0DBU5\|RH31_ORYSJ DEAD-box ATP-dependent RNA helicase 31 OS=Oryza sativa subsp. japonica GN=Os06g0526600 PE=3 SV=2	Back alignment and function description

>sp\|Q94C75\|RH25_ARATH DEAD-box ATP-dependent RNA helicase 25 OS=Arabidopsis thaliana GN=RH25 PE=2 SV=2	Back alignment and function description

>sp\|Q5ZBH5\|RH25_ORYSJ DEAD-box ATP-dependent RNA helicase 25 OS=Oryza sativa subsp. japonica GN=Os01g0618400 PE=2 SV=1	Back alignment and function description

>sp\|Q0JL73\|RH26_ORYSJ DEAD-box ATP-dependent RNA helicase 26 OS=Oryza sativa subsp. japonica GN=Os01g0618500 PE=2 SV=1	Back alignment and function description

>sp\|Q6K7R9\|RH48_ORYSJ DEAD-box ATP-dependent RNA helicase 48 OS=Oryza sativa subsp. japonica GN=Os02g0826100 PE=2 SV=1	Back alignment and function description

>sp\|Q9C8S9\|RH48_ARATH Probable DEAD-box ATP-dependent RNA helicase 48 OS=Arabidopsis thaliana GN=RH48 PE=3 SV=1	Back alignment and function description

>sp\|O80792\|RH33_ARATH Putative DEAD-box ATP-dependent RNA helicase 33 OS=Arabidopsis thaliana GN=RH33 PE=3 SV=1	Back alignment and function description

>sp\|Q0UG00\|MS116_PHANO ATP-dependent RNA helicase MSS116, mitochondrial OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=MSS116 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		747
255564739		751	dead box ATP-dependent RNA helicase, put	0.973	0.968	0.700	0.0
297745425		732	unnamed protein product [Vitis vinifera]	0.963	0.983	0.699	0.0
359489723		751	PREDICTED: DEAD-box ATP-dependent RNA he	0.973	0.968	0.700	0.0
224067972		758	predicted protein [Populus trichocarpa]	0.969	0.955	0.665	0.0
449443947		841	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.973	0.864	0.643	0.0
449475575		842	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.973	0.863	0.642	0.0
339716204		783	putative DEAD-box ATP-dependent RNA heli	0.958	0.914	0.613	0.0
356522518		703	PREDICTED: DEAD-box ATP-dependent RNA he	0.902	0.958	0.686	0.0
356560282		806	PREDICTED: DEAD-box ATP-dependent RNA he	0.990	0.918	0.639	0.0
334188604		788	DEAD-box ATP-dependent RNA helicase 31 [	0.933	0.884	0.627	0.0

>gi\|255564739\|ref\|XP_002523364.1\| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi\|223537452\|gb\|EEF39080.1\| dead box ATP-dependent RNA helicase, putative [Ricinus communis]	Back alignment and taxonomy information

 Score = 1052 bits (2721), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 540/771 (70%), Positives = 620/771 (80%), Gaps = 44/771 (5%)

Query: 1   MPIKLFPNLRLLNPPLSATRFPSMNLKPSVNSSRAIPAFRRIFPFKLKYLGLPTRVNSQQ 60
           MP+KL P LR L P L  T  P M     +N +R +P F +IFPF+LKYLGL    NSQ 
Sbjct: 1   MPVKLLPQLRFLTPSLPVTSLPPMKSFSLINWNRPVPIFSQIFPFRLKYLGLSPYFNSQ- 59

Query: 61  QQQQQQLGLRKLSTRPFRPAASSEFGRRGSRAGEIRGSKNLIDDEAELSDWVSDLRTDSF 120
                 L +R+ STR FRP  ++        + E R SK+LI+DEAELSDWVS+L+T S 
Sbjct: 60  ------LSVRRFSTRSFRPRTTAR------SSSEFRQSKSLIEDEAELSDWVSELKTSSL 107

Query: 121 HSNKRFSKDDDVSDFRKGSGRENRGS---YSMKRRRKSDSDD-SYDSSRRGNRNSVNSFS 176
              K  S+D+  SD  +   +  RG     S KRRR+ ++D+ S  ++RRG ++ V+SFS
Sbjct: 108 R-GKLTSEDESDSDMTRNKSKRERGREGFSSSKRRRERETDEFSELNNRRGIKDKVDSFS 166

Query: 177 RNNIS------------NNTSRFSRR----SNSELEAGNVGRKTRFSNDDENDVGEERRR 220
           RN+ +            N   RF+ R     N++L      R +   NDD  D  +ER+ 
Sbjct: 167 RNSRASKPFDRKFIGSDNEKERFNSRRKKIGNADLGFRREKRVSVDENDDYFDKEDERKD 226

Query: 221 GMSGIRDLLSEEVSDNDDD----DDDSVLRNNARSLIGLDKENGGMSVAISSPGKHDSFM 276
            +  I DL+ EE +D+ +D    DD+ +LR N  S +G +K+        +SPG  DS++
Sbjct: 227 LIGRITDLVREEETDDANDEGCHDDEGILRKNVSSSLGFEKDRP------NSPGTSDSYL 280

Query: 277 SESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLP 336
           S+SRFDQC +S LSLKGIKDAGYEKMT+VQEATLPV+LKGKDVLAKA+TGTGKTVAFLLP
Sbjct: 281 SDSRFDQCPVSPLSLKGIKDAGYEKMTVVQEATLPVILKGKDVLAKARTGTGKTVAFLLP 340

Query: 337 SIEVVIKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRL 396
           +IEVV+KSPP  RDQ+RPPILV+VICPTRELA+QAA EA+TLLKYHPS+GVQVVIGGTRL
Sbjct: 341 AIEVVVKSPPTGRDQKRPPILVVVICPTRELASQAAAEANTLLKYHPSVGVQVVIGGTRL 400

Query: 397 ALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDIE 456
           ALEQK+MQANPCQILVATPGRL+DHIENTAGFATRLMGVKVL+LDEADHLLDMGFRKDIE
Sbjct: 401 ALEQKKMQANPCQILVATPGRLQDHIENTAGFATRLMGVKVLILDEADHLLDMGFRKDIE 460

Query: 457 KIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMHLVAP 516
           +IIAAVPKQRQTLLFSATVPEEVRQICHIAL+RDHEFINTV EG++ETH QVRQMHLVAP
Sbjct: 461 RIIAAVPKQRQTLLFSATVPEEVRQICHIALRRDHEFINTVPEGTDETHTQVRQMHLVAP 520

Query: 517 LDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYR 576
           LD HFPLLYVLL++H+ADN +YKVL+FCTTAMVTRMVA+LLGELKLNVREIHSRKPQSYR
Sbjct: 521 LDKHFPLLYVLLKDHIADNIDYKVLLFCTTAMVTRMVANLLGELKLNVREIHSRKPQSYR 580

Query: 577 TRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQ 636
           TRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLP+DREQYIHRLGRTGRKGKEG 
Sbjct: 581 TRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPADREQYIHRLGRTGRKGKEGV 640

Query: 637 GILLLAPWEEFFLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAYQAWLGYY 696
           GILLLAPWEE FLSTIKDLPI KAPVPSVDPDTKKKVER+LSHVEMKNKEAAYQAWLGYY
Sbjct: 641 GILLLAPWEESFLSTIKDLPISKAPVPSVDPDTKKKVERSLSHVEMKNKEAAYQAWLGYY 700

Query: 697 NSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK 747
           NS+K VGRDKY+LVELAN++SRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK
Sbjct: 701 NSSKLVGRDKYRLVELANDFSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK 751

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297745425\|emb\|CBI40505.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|359489723\|ref\|XP_002277120.2\| PREDICTED: DEAD-box ATP-dependent RNA helicase 31-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224067972\|ref\|XP_002302625.1\| predicted protein [Populus trichocarpa] gi\|222844351\|gb\|EEE81898.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|449443947\|ref\|XP_004139737.1\| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 26-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449475575\|ref\|XP_004154493.1\| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 31-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|339716204\|gb\|AEJ88341.1\| putative DEAD-box ATP-dependent RNA helicase [Tamarix hispida]	Back alignment and taxonomy information

>gi\|356522518\|ref\|XP_003529893.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 31-like [Glycine max]	Back alignment and taxonomy information

>gi\|356560282\|ref\|XP_003548422.1\| PREDICTED: DEAD-box ATP-dependent RNA helicase 31-like [Glycine max]	Back alignment and taxonomy information

>gi\|334188604\|ref\|NP_201168.2\| DEAD-box ATP-dependent RNA helicase 31 [Arabidopsis thaliana] gi\|332010396\|gb\|AED97779.1\| DEAD-box ATP-dependent RNA helicase 31 [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		747
TAIR\|locus:2159517		850	PDE340 "PIGMENT DEFECTIVE 340"	0.659	0.58	0.767	2.2e-231
TAIR\|locus:2159527		563	STRS2 "STRESS RESPONSE SUPPRES	0.633	0.840	0.756	1.6e-198
TAIR\|locus:2038431		798	AT1G63250 [Arabidopsis thalian	0.633	0.592	0.578	3.8e-149
TAIR\|locus:2054688		845	AT2G07750 [Arabidopsis thalian	0.655	0.579	0.560	1.5e-147
UNIPROTKB\|Q2KEF1		568	MGCH7_ch7g1085 "Putative uncha	0.617	0.811	0.417	1e-82
ASPGD\|ASPL0000028276		567	AN5623 [Emericella nidulans (t	0.597	0.786	0.378	3.2e-72
DICTYBASE\|DDB_G0282741		602	ddx18 "DEAD/DEAH box helicase"	0.580	0.720	0.362	3.1e-67
ASPGD\|ASPL0000044206		609	AN1949 [Emericella nidulans (t	0.580	0.712	0.362	4.1e-65
TAIR\|locus:2152099		633	AT5G65900 [Arabidopsis thalian	0.603	0.712	0.355	1.4e-64
ZFIN\|ZDB-GENE-030131-9685		653	ddx18 "DEAD (Asp-Glu-Ala-Asp)	0.586	0.670	0.339	2.9e-64

TAIR\|locus:2159517 PDE340 "PIGMENT DEFECTIVE 340" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2026 (718.2 bits), Expect = 2.2e-231, Sum P(2) = 2.2e-231
 Identities = 382/498 (76%), Positives = 446/498 (89%)

Query:   255 LDKENGGMSVAISSP-GKH----DSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEAT 309
             + K     +V    P G+H    DS++S++RFDQ  +S LSLK IKDAG+E MT+VQEAT
Sbjct:   353 IKKAASAKAVQTDKPTGEHVKTSDSYLSKTRFDQFPLSPLSLKAIKDAGFETMTVVQEAT 412

Query:   310 LPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVDRDQRRPPILVLVICPTRELAT 369
             LP++L+GKDVLAKAKTGTGKTVAFLLP+IE VIKSPP  RD R+PPI+VLV+CPTRELA+
Sbjct:   413 LPIILQGKDVLAKAKTGTGKTVAFLLPAIEAVIKSPPASRDSRQPPIIVLVVCPTRELAS 472

Query:   370 QAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFA 429
             QAA EA+TLLKYHPSIGVQVVIGGT+L  EQ+RMQ NPCQILVATPGRL+DHIENT+GFA
Sbjct:   473 QAAAEANTLLKYHPSIGVQVVIGGTKLPTEQRRMQTNPCQILVATPGRLKDHIENTSGFA 532

Query:   430 TRLMGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKR 489
             TRLMGVKVLVLDEADHLLDMGFR+DIE+IIAAVPKQRQT LFSATVPEEVRQICH+ALKR
Sbjct:   533 TRLMGVKVLVLDEADHLLDMGFRRDIERIIAAVPKQRQTFLFSATVPEEVRQICHVALKR 592

Query:   490 DHEFINTVEEGSEETHEQVRQMHLVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMV 549
             DHEFIN V+EGS ETH++V QM+++A LD HF LL+VLL+EH+ADN +YKV++FCTTAMV
Sbjct:   593 DHEFINCVQEGSGETHQKVTQMYMIASLDRHFSLLHVLLKEHIADNVDYKVIIFCTTAMV 652

Query:   550 TRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLV 609
             TR+VADLL +L LNVREIHSRKPQSYRTRVSDEFRKSK +ILVTSDVSARGVDYPDV+LV
Sbjct:   653 TRLVADLLSQLSLNVREIHSRKPQSYRTRVSDEFRKSKAIILVTSDVSARGVDYPDVSLV 712

Query:   610 IQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAPVPSVDPDT 669
             +Q+GLPSDREQYIHRLGRTGRKGKEG+G+LLLAPWEE+F+S++KDLPI K+P+P +DP+ 
Sbjct:   713 VQMGLPSDREQYIHRLGRTGRKGKEGEGVLLLAPWEEYFMSSVKDLPITKSPLPPIDPEA 772

Query:   670 KKKVERALSHVEMKNKEAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIP 729
              K+V++ LS VEMKNKEAAYQAWLGYY S K + RD  +LVELANE+SRSMGLD+PPAIP
Sbjct:   773 VKRVQKGLSQVEMKNKEAAYQAWLGYYKSQKMIARDTTRLVELANEFSRSMGLDSPPAIP 832

Query:   730 KLVLGKMGLRNIPGLRSK 747
             K VLGKMGL+N+PGLR+K
Sbjct:   833 KNVLGKMGLKNVPGLRTK 850

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=IDA

GO:0009220 "pyrimidine ribonucleotide biosynthetic process" evidence=RCA

TAIR\|locus:2159527 STRS2 "STRESS RESPONSE SUPPRESSOR 2" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2038431 AT1G63250 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2054688 AT2G07750 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2KEF1 MGCH7_ch7g1085 "Putative uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000028276 AN5623 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0282741 ddx18 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000044206 AN1949 [Emericella nidulans (taxid:162425)]	Back alignment and assigned GO terms

TAIR\|locus:2152099 AT5G65900 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-9685 ddx18 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 18" [Danio rerio (taxid:7955)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5ZBH5	RH25_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.7286	0.6412	0.8063	yes	no
Q0DBU5	RH31_ORYSJ	3, ., 6, ., 4, ., 1, 3	0.7071	0.7202	0.9835	yes	no
Q9FFQ1	RH31_ARATH	3, ., 6, ., 4, ., 1, 3	0.6279	0.9330	0.9734	yes	no

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	3.6.4.13	0.991
3rd Layer	3.6.4	0.976

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00027015001	SubName- Full=Chromosome chr15 scaffold_40, whole genome shotgun sequence; (732 aa)
		(Vitis vinifera)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		747
COG0513		513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-108
PRK11776		460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-80
cd00268		203	cd00268, DEADc, DEAD-box helicases	2e-74
PRK11192		434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	6e-61
PRK01297		475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-60
PTZ00110		545	PTZ00110, PTZ00110, helicase; Provisional	1e-58
PRK10590		456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	1e-57
PRK11634		629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-52
pfam00270		169	pfam00270, DEAD, DEAD/DEAH box helicase	6e-52
PRK04837		423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-51
PRK04537		572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-45
smart00487		201	smart00487, DEXDc, DEAD-like helicases superfamily	6e-43
PLN00206		518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	5e-42
PTZ00424		401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-41
cd00046		144	cd00046, DEXDc, DEAD-like helicases superfamily	7e-34
cd00079		131	cd00079, HELICc, Helicase superfamily c-terminal d	3e-26
smart00490		82	smart00490, HELICc, helicase superfamily c-termina	8e-22
pfam00271		78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-21
COG1201		814	COG1201, Lhr, Lhr-like helicases [General function	1e-13
COG1061		442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-13
COG1205		851	COG1205, COG1205, Distinct helicase family with a	4e-13
COG0514		590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	1e-12
COG1204		766	COG1204, COG1204, Superfamily II helicase [General	1e-12
TIGR00614		470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	9e-11
TIGR01389		591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	2e-08
TIGR01587		358	TIGR01587, cas3_core, CRISPR-associated helicase C	3e-07
COG1111		542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	5e-07
COG1203		733	COG1203, COG1203, CRISPR-associated helicase Cas3	8e-07
cd09639		353	cd09639, Cas3_I, CRISPR/Cas system-associated prot	2e-05
COG1202		830	COG1202, COG1202, Superfamily II helicase, archaea	0.001
PRK13766		773	PRK13766, PRK13766, Hef nuclease; Provisional	0.002
pfam13307		165	pfam13307, Helicase_C_2, Helicase C-terminal domai	0.002
TIGR04121		803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	0.003

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

 Score =  339 bits (871), Expect = e-108
 Identities = 152/479 (31%), Positives = 239/479 (49%), Gaps = 22/479 (4%)

Query: 276 MSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLL 335
            +   F    +S   L+ +KD G+E+ T +Q A +P++L G+DVL +A+TGTGKT AFLL
Sbjct: 26  KTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLL 85

Query: 336 PSIEVVIKSPPVDRDQRRPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTR 395
           P ++       + +   R  +  L++ PTRELA Q A E   L K    + V VV GG  
Sbjct: 86  PLLQ------KILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVS 139

Query: 396 LALEQKRMQANPCQILVATPGRLRDHIENTAGFATRLMGVKVLVLDEADHLLDMGFRKDI 455
           +  + + ++     I+VATPGRL D I+        L GV+ LVLDEAD +LDMGF  DI
Sbjct: 140 IRKQIEALKRGV-DIVVATPGRLLDLIKRGKL---DLSGVETLVLDEADRMLDMGFIDDI 195

Query: 456 EKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQ-MHLV 514
           EKI+ A+P  RQTLLFSAT+P+++R++       D   I    E  E T ++++Q    V
Sbjct: 196 EKILKALPPDRQTLLFSATMPDDIRELAR-RYLNDPVEIEVSVEKLERTLKKIKQFYLEV 254

Query: 515 APLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQS 574
              +    LL  LL++      E +V+VF  T  +   +A+ L +    V  +H   PQ 
Sbjct: 255 ESEEEKLELLLKLLKDE----DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQE 310

Query: 575 YRTRVSDEFRKSKGLILVTSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKE 634
            R R  ++F+  +  +LV +DV+ARG+D PDV+ VI   LP D E Y+HR+GRTGR G++
Sbjct: 311 ERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRK 370

Query: 635 GQGILLLAPWEEF-----FLSTIKDLPILKAPVPSVDPDTKKKVERALSHVEMKNKEAAY 689
           G  I  +   EE          ++        +P  +P+  K ++     +E ++  +  
Sbjct: 371 GVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRPGLEEESDISDE 430

Query: 690 QAWLG-YYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRSK 747
              L     +  +    ++ L +L     + +            L +    +   +   
Sbjct: 431 IKKLKSSKKALLRGLGVRFTLSKLLANLGKEIPGAGDAVTIDPELERRSPNSADDIEYI 489

Length = 513

>gnl\|CDD\|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional	Back alignment and domain information

>gnl\|CDD\|238167 cd00268, DEADc, DEAD-box helicases	Back alignment and domain information

>gnl\|CDD\|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional	Back alignment and domain information

>gnl\|CDD\|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

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

>gnl\|CDD\|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional	Back alignment and domain information

>gnl\|CDD\|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional	Back alignment and domain information

>gnl\|CDD\|215832 pfam00270, DEAD, DEAD/DEAH box helicase	Back alignment and domain information

>gnl\|CDD\|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

>gnl\|CDD\|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional	Back alignment and domain information

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

>gnl\|CDD\|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional	Back alignment and domain information

>gnl\|CDD\|185609 PTZ00424, PTZ00424, helicase 45; Provisional	Back alignment and domain information

>gnl\|CDD\|238005 cd00046, DEXDc, DEAD-like helicases superfamily	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\|197757 smart00490, HELICc, helicase superfamily c-terminal domain	Back alignment and domain information

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

>gnl\|CDD\|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|224126 COG1205, 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

>gnl\|CDD\|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family	Back alignment and domain information

>gnl\|CDD\|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ	Back alignment and domain information

>gnl\|CDD\|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3	Back alignment and domain information

>gnl\|CDD\|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	Back alignment and domain information

>gnl\|CDD\|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3	Back alignment and domain information

>gnl\|CDD\|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|237496 PRK13766, PRK13766, Hef nuclease; Provisional	Back alignment and domain information

>gnl\|CDD\|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain	Back alignment and domain information

>gnl\|CDD\|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		747
KOG0342		543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0345		567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0343		758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0330		476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0348		708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338		691	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0340		442	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110		545	helicase; Provisional	100.0
KOG0333		673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0328		400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PRK04837		423	ATP-dependent RNA helicase RhlB; Provisional	100.0
PRK11776		460	ATP-dependent RNA helicase DbpA; Provisional	100.0
PRK10590		456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK04537		572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0326		459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0347		731	consensus RNA helicase [RNA processing and modific	100.0
KOG0335		482	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336		629	consensus ATP-dependent RNA helicase [RNA processi	100.0
PLN00206		518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0346		569	consensus RNA helicase [RNA processing and modific	100.0
PRK11192		434	ATP-dependent RNA helicase SrmB; Provisional	100.0
PRK01297		475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0341		610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0339		731	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424		401	helicase 45; Provisional	100.0
KOG0332		477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0334		997	consensus RNA helicase [RNA processing and modific	100.0
KOG0350		620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
TIGR03817		742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG0327		397	consensus Translation initiation factor 4F, helica	100.0
KOG0337		529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PLN03137		1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG4284		980	consensus DEAD box protein [Transcription]	100.0
TIGR00614		470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
PRK11057		607	ATP-dependent DNA helicase RecQ; Provisional	100.0
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR01389		591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
PRK13767		876	ATP-dependent helicase; Provisional	100.0
PRK02362		737	ski2-like helicase; Provisional	100.0
KOG0329		387	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR01970		819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK00254		720	ski2-like helicase; Provisional	100.0
PRK11664		812	ATP-dependent RNA helicase HrpB; Provisional	100.0
KOG0926		1172	consensus DEAH-box RNA helicase [RNA processing an	100.0
COG0514		590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
TIGR02621		844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
PHA02653		675	RNA helicase NPH-II; Provisional	100.0
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	100.0
COG1201		814	Lhr Lhr-like helicases [General function predictio	100.0
PRK01172		674	ski2-like helicase; Provisional	100.0
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	100.0
PRK10689		1147	transcription-repair coupling factor; Provisional	100.0
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	100.0
PRK09751		1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PRK11131		1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
KOG0352		641	consensus ATP-dependent DNA helicase [Replication,	100.0
PRK09401		1176	reverse gyrase; Reviewed	100.0
PRK14701		1638	reverse gyrase; Provisional	100.0
PRK12898		656	secA preprotein translocase subunit SecA; Reviewed	100.0
TIGR01967		1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
TIGR01587		358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
COG1111		542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
PHA02558		501	uvsW UvsW helicase; Provisional	100.0
PRK09200		790	preprotein translocase subunit SecA; Reviewed	100.0
KOG0922		674	consensus DEAH-box RNA helicase [RNA processing an	100.0
KOG0351		941	consensus ATP-dependent DNA helicase [Replication,	100.0
TIGR03714		762	secA2 accessory Sec system translocase SecA2. Memb	100.0
KOG0923		902	consensus mRNA splicing factor ATP-dependent RNA h	100.0
COG1643		845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
KOG0349		725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
TIGR01054		1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
TIGR00963		745	secA preprotein translocase, SecA subunit. The pro	100.0
PRK13766		773	Hef nuclease; Provisional	100.0
COG1202		830	Superfamily II helicase, archaea-specific [General	100.0
TIGR03158		357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
COG1205		851	Distinct helicase family with a unique C-terminal	100.0
COG1204		766	Superfamily II helicase [General function predicti	100.0
KOG0354		746	consensus DEAD-box like helicase [General function	100.0
KOG0353		695	consensus ATP-dependent DNA helicase [General func	100.0
KOG0924		1042	consensus mRNA splicing factor ATP-dependent RNA h	99.97
KOG0920		924	consensus ATP-dependent RNA helicase A [RNA proces	99.97
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	99.97
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.97
KOG2340		698	consensus Uncharacterized conserved protein [Funct	99.97
PRK05580		679	primosome assembly protein PriA; Validated	99.96
PRK13104		896	secA preprotein translocase subunit SecA; Reviewed	99.96
PRK04914		956	ATP-dependent helicase HepA; Validated	99.96
KOG0948		1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.96
KOG0947		1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.95
PF06862		442	DUF1253: Protein of unknown function (DUF1253); In	99.95
PRK09694		878	helicase Cas3; Provisional	99.95
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	99.95
PRK12899		970	secA preprotein translocase subunit SecA; Reviewed	99.95
PRK12904		830	preprotein translocase subunit SecA; Reviewed	99.95
PRK12906		796	secA preprotein translocase subunit SecA; Reviewed	99.95
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.95
COG1061		442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.95
TIGR00595		505	priA primosomal protein N'. All proteins in this f	99.95
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	99.94
COG4098		441	comFA Superfamily II DNA/RNA helicase required for	99.94
COG4581		1041	Superfamily II RNA helicase [DNA replication, reco	99.94
KOG0925		699	consensus mRNA splicing factor ATP-dependent RNA h	99.94
PRK13107		908	preprotein translocase subunit SecA; Reviewed	99.93
PRK11448		1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.92
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	99.91
PF00270		169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.91
PLN03142		1033	Probable chromatin-remodeling complex ATPase chain	99.91
KOG0950		1008	consensus DNA polymerase theta/eta, DEAD-box super	99.9
PRK12900		1025	secA preprotein translocase subunit SecA; Reviewed	99.88
COG1203		733	CRISPR-associated helicase Cas3 [Defense mechanism	99.87
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	99.86
KOG0385		971	consensus Chromatin remodeling complex WSTF-ISWI,	99.85
TIGR01407		850	dinG_rel DnaQ family exonuclease/DinG family helic	99.85
TIGR00631		655	uvrb excinuclease ABC, B subunit. This family is b	99.85
PRK12326		764	preprotein translocase subunit SecA; Reviewed	99.84
PRK05298		652	excinuclease ABC subunit B; Provisional	99.82
KOG0387		923	consensus Transcription-coupled repair protein CSB	99.81
PRK13103		913	secA preprotein translocase subunit SecA; Reviewed	99.8
KOG0949		1330	consensus Predicted helicase, DEAD-box superfamily	99.79
PRK12903		925	secA preprotein translocase subunit SecA; Reviewed	99.78
TIGR00348		667	hsdR type I site-specific deoxyribonuclease, HsdR	99.78
KOG0384		1373	consensus Chromodomain-helicase DNA-binding protei	99.78
COG1198		730	PriA Primosomal protein N' (replication factor Y)	99.77
COG4096		875	HsdR Type I site-specific restriction-modification	99.77
KOG1123		776	consensus RNA polymerase II transcription initiati	99.76
PRK07246		820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.76
smart00487		201	DEXDc DEAD-like helicases superfamily.	99.76
CHL00122		870	secA preprotein translocase subunit SecA; Validate	99.74
KOG4150		1034	consensus Predicted ATP-dependent RNA helicase [RN	99.74
PRK12902		939	secA preprotein translocase subunit SecA; Reviewed	99.72
cd00079		131	HELICc Helicase superfamily c-terminal domain; ass	99.69
KOG0390		776	consensus DNA repair protein, SNF2 family [Replica	99.69
KOG0389		941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.68
PRK08074		928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.67
KOG0953		700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.67
KOG0392		1549	consensus SNF2 family DNA-dependent ATPase domain-	99.67
COG0556		663	UvrB Helicase subunit of the DNA excision repair c	99.66
TIGR03117		636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.65
PF00271		78	Helicase_C: Helicase conserved C-terminal domain;	99.64
KOG0921		1282	consensus Dosage compensation complex, subunit MLE	99.63
PRK12901		1112	secA preprotein translocase subunit SecA; Reviewed	99.59
KOG1000		689	consensus Chromatin remodeling protein HARP/SMARCA	99.58
KOG0386		1157	consensus Chromatin remodeling complex SWI/SNF, co	99.58
cd00046		144	DEXDc DEAD-like helicases superfamily. A diverse f	99.56
COG1199		654	DinG Rad3-related DNA helicases [Transcription / D	99.55
PRK11747		697	dinG ATP-dependent DNA helicase DinG; Provisional	99.52
KOG0951		1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.52
COG4889		1518	Predicted helicase [General function prediction on	99.52
KOG1002		791	consensus Nucleotide excision repair protein RAD16	99.51
PF04851		184	ResIII: Type III restriction enzyme, res subunit;	99.5
TIGR00604		705	rad3 DNA repair helicase (rad3). All proteins in t	99.48
KOG0391		1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.46
TIGR02562		1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.46
smart00490		82	HELICc helicase superfamily c-terminal domain.	99.46
KOG0388		1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.43
PF02399		824	Herpes_ori_bp: Origin of replication binding prote	99.28
PRK14873		665	primosome assembly protein PriA; Provisional	99.22
KOG4439		901	consensus RNA polymerase II transcription terminat	99.18
COG0653		822	SecA Preprotein translocase subunit SecA (ATPase,	99.15
COG0553		866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.07
PF07652		148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.07
PF00176		299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.93
COG0610		962	Type I site-specific restriction-modification syst	98.93
smart00488		289	DEXDc2 DEAD-like helicases superfamily.	98.89
smart00489		289	DEXDc3 DEAD-like helicases superfamily.	98.89
KOG1015		1567	consensus Transcription regulator XNP/ATRX, DEAD-b	98.86
PF07517		266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.78
KOG1016		1387	consensus Predicted DNA helicase, DEAD-box superfa	98.49
PRK15483		986	type III restriction-modification system StyLTI en	98.32
TIGR00596		814	rad1 DNA repair protein (rad1). This family is bas	98.3
COG3587		985	Restriction endonuclease [Defense mechanisms]	98.3
PF13307		167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	98.09
PF13086		236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.09
KOG0952		1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.99
PF02562		205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.96
PF13604		196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.9
PF13959		65	DUF4217: Domain of unknown function (DUF4217)	97.79
PF12340		229	DUF3638: Protein of unknown function (DUF3638); In	97.76
PRK10536		262	hypothetical protein; Provisional	97.69
KOG1803		649	consensus DNA helicase [Replication, recombination	97.62
PRK10875		615	recD exonuclease V subunit alpha; Provisional	97.61
PF13872		303	AAA_34: P-loop containing NTP hydrolase pore-1	97.59
TIGR01448		720	recD_rel helicase, putative, RecD/TraA family. Thi	97.58
TIGR01447		586	recD exodeoxyribonuclease V, alpha subunit. This f	97.56
KOG1802		935	consensus RNA helicase nonsense mRNA reducing fact	97.45
PF09848		352	DUF2075: Uncharacterized conserved protein (DUF207	97.35
PF13245		76	AAA_19: Part of AAA domain	97.27
KOG1132		945	consensus Helicase of the DEAD superfamily [Replic	97.24
COG1875		436	NYN ribonuclease and ATPase of PhoH family domains	97.11
PF00580		315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.94
PF05970		364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.88
PF13401		131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	96.86
PRK12723		388	flagellar biosynthesis regulator FlhF; Provisional	96.85
PRK08181		269	transposase; Validated	96.81
smart00492		141	HELICc3 helicase superfamily c-terminal domain.	96.77
PRK14974		336	cell division protein FtsY; Provisional	96.77
PF00448		196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.76
TIGR02768		744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.68
smart00491		142	HELICc2 helicase superfamily c-terminal domain.	96.67
PRK14722		374	flhF flagellar biosynthesis regulator FlhF; Provis	96.64
PRK11889		436	flhF flagellar biosynthesis regulator FlhF; Provis	96.55
COG3421		812	Uncharacterized protein conserved in bacteria [Fun	96.53
KOG1805		1100	consensus DNA replication helicase [Replication, r	96.52
PRK13889		988	conjugal transfer relaxase TraA; Provisional	96.49
PRK06526		254	transposase; Provisional	96.47
cd00009		151	AAA The AAA+ (ATPases Associated with a wide varie	96.46
PRK04296		190	thymidine kinase; Provisional	96.43
PRK05703		424	flhF flagellar biosynthesis regulator FlhF; Valida	96.36
TIGR02760		1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.28
KOG1131		755	consensus RNA polymerase II transcription initiati	96.26
TIGR00376		637	DNA helicase, putative. The gene product may repre	96.25
PRK06921		266	hypothetical protein; Provisional	96.24
PRK07952		244	DNA replication protein DnaC; Validated	96.18
PF14617		252	CMS1: U3-containing 90S pre-ribosomal complex subu	96.12
TIGR01075		715	uvrD DNA helicase II. Designed to identify uvrD me	96.01
PRK13826		1102	Dtr system oriT relaxase; Provisional	95.99
smart00382		148	AAA ATPases associated with a variety of cellular	95.98
PF03354		477	Terminase_1: Phage Terminase ; InterPro: IPR005021	95.93
PRK08727		233	hypothetical protein; Validated	95.89
PRK08116		268	hypothetical protein; Validated	95.8
PRK12377		248	putative replication protein; Provisional	95.73
PF13871		278	Helicase_C_4: Helicase_C-like	95.71
COG1419		407	FlhF Flagellar GTP-binding protein [Cell motility	95.7
PRK06731		270	flhF flagellar biosynthesis regulator FlhF; Valida	95.61
PHA02533		534	17 large terminase protein; Provisional	95.54
PRK06893		229	DNA replication initiation factor; Validated	95.46
PRK05642		234	DNA replication initiation factor; Validated	95.43
PRK07764		824	DNA polymerase III subunits gamma and tau; Validat	95.4
cd01124		187	KaiC KaiC is a circadian clock protein primarily f	95.29
cd01120		165	RecA-like_NTPases RecA-like NTPases. This family i	95.27
PRK11054		684	helD DNA helicase IV; Provisional	95.26
PRK13709		1747	conjugal transfer nickase/helicase TraI; Provision	95.23
KOG1133		821	consensus Helicase of the DEAD superfamily [Replic	95.22
COG1484		254	DnaC DNA replication protein [DNA replication, rec	95.2
COG1444		758	Predicted P-loop ATPase fused to an acetyltransfer	95.18
PRK06835		329	DNA replication protein DnaC; Validated	95.1
PRK08084		235	DNA replication initiation factor; Provisional	95.06
PRK11773		721	uvrD DNA-dependent helicase II; Provisional	95.0
PF05876		557	Terminase_GpA: Phage terminase large subunit (GpA)	95.0
PRK12726		407	flagellar biosynthesis regulator FlhF; Provisional	94.99
PRK00149		450	dnaA chromosomal replication initiation protein; R	94.99
TIGR03420		226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	94.98
PF05127		177	Helicase_RecD: Helicase; InterPro: IPR007807 This	94.91
PRK10919		672	ATP-dependent DNA helicase Rep; Provisional	94.81
PRK14087		450	dnaA chromosomal replication initiation protein; P	94.72
KOG1001		674	consensus Helicase-like transcription factor HLTF/	94.72
PRK12724		432	flagellar biosynthesis regulator FlhF; Provisional	94.61
TIGR00362		405	DnaA chromosomal replication initiator protein Dna	94.5
KOG0989		346	consensus Replication factor C, subunit RFC4 [Repl	94.34
TIGR01074		664	rep ATP-dependent DNA helicase Rep. Designed to id	94.34
PRK14712		1623	conjugal transfer nickase/helicase TraI; Provision	94.33
PF05621		302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.32
PRK14721		420	flhF flagellar biosynthesis regulator FlhF; Provis	94.31
PHA03333		752	putative ATPase subunit of terminase; Provisional	94.28
PRK00771		437	signal recognition particle protein Srp54; Provisi	94.27
PRK07003		830	DNA polymerase III subunits gamma and tau; Validat	94.23
PRK12727		559	flagellar biosynthesis regulator FlhF; Provisional	94.23
PRK12323		700	DNA polymerase III subunits gamma and tau; Provisi	94.2
PRK09183		259	transposase/IS protein; Provisional	94.17
PRK14086		617	dnaA chromosomal replication initiation protein; P	94.17
KOG0298		1394	consensus DEAD box-containing helicase-like transc	94.16
PRK12422		445	chromosomal replication initiation protein; Provis	94.14
PRK14723		767	flhF flagellar biosynthesis regulator FlhF; Provis	94.09
PRK14964		491	DNA polymerase III subunits gamma and tau; Provisi	94.07
TIGR01073		726	pcrA ATP-dependent DNA helicase PcrA. Designed to	94.02
PRK14952		584	DNA polymerase III subunits gamma and tau; Provisi	93.97
PRK12402		337	replication factor C small subunit 2; Reviewed	93.95
PRK05707		328	DNA polymerase III subunit delta'; Validated	93.91
PRK08939		306	primosomal protein DnaI; Reviewed	93.89
PRK07994		647	DNA polymerase III subunits gamma and tau; Validat	93.84
PF00308		219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	93.82
PRK13833		323	conjugal transfer protein TrbB; Provisional	93.74
PRK09111		598	DNA polymerase III subunits gamma and tau; Validat	93.71
PRK14088		440	dnaA chromosomal replication initiation protein; P	93.7
PHA02544		316	44 clamp loader, small subunit; Provisional	93.69
PRK08903		227	DnaA regulatory inactivator Hda; Validated	93.68
TIGR00064		272	ftsY signal recognition particle-docking protein F	93.68
PHA03368		738	DNA packaging terminase subunit 1; Provisional	93.62
PRK07471		365	DNA polymerase III subunit delta'; Validated	93.57
COG4962		355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	93.54
PRK05580		679	primosome assembly protein PriA; Validated	93.35
PRK08769		319	DNA polymerase III subunit delta'; Validated	93.28
TIGR03499		282	FlhF flagellar biosynthetic protein FlhF.	93.21
TIGR01547		396	phage_term_2 phage terminase, large subunit, PBSX	93.13
PRK09112		351	DNA polymerase III subunit delta'; Validated	93.12
PRK10867		433	signal recognition particle protein; Provisional	93.11
PRK08691		709	DNA polymerase III subunits gamma and tau; Validat	93.1
TIGR02760		1960	TraI_TIGR conjugative transfer relaxase protein Tr	93.06
PRK14951		618	DNA polymerase III subunits gamma and tau; Provisi	92.97
TIGR02785		1232	addA_Gpos recombination helicase AddA, Firmicutes	92.96
TIGR03015		269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	92.94
COG1435		201	Tdk Thymidine kinase [Nucleotide transport and met	92.92
PF06745		226	KaiC: KaiC; InterPro: IPR014774 This entry represe	92.67
PRK14958		509	DNA polymerase III subunits gamma and tau; Provisi	92.66
PTZ00112		1164	origin recognition complex 1 protein; Provisional	92.64
TIGR02881		261	spore_V_K stage V sporulation protein K. Members o	92.63
TIGR00595		505	priA primosomal protein N'. All proteins in this f	92.56
PRK13894		319	conjugal transfer ATPase TrbB; Provisional	92.52
PTZ00293		211	thymidine kinase; Provisional	92.51
TIGR01425		429	SRP54_euk signal recognition particle protein SRP5	92.47
PF13177		162	DNA_pol3_delta2: DNA polymerase III, delta subunit	92.46
PRK14965		576	DNA polymerase III subunits gamma and tau; Provisi	92.45
cd00561		159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	92.39
PRK06645		507	DNA polymerase III subunits gamma and tau; Validat	92.25
PLN03025		319	replication factor C subunit; Provisional	92.24
PRK14873		665	primosome assembly protein PriA; Provisional	92.2
PRK10917		681	ATP-dependent DNA helicase RecG; Provisional	92.15
PRK10416		318	signal recognition particle-docking protein FtsY;	92.07
PF00004		132	AAA: ATPase family associated with various cellula	91.99
TIGR02782		299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	91.97
PRK14960		702	DNA polymerase III subunits gamma and tau; Provisi	91.89
TIGR00708		173	cobA cob(I)alamin adenosyltransferase. Alternate n	91.79
PRK14956		484	DNA polymerase III subunits gamma and tau; Provisi	91.74
PRK14949		944	DNA polymerase III subunits gamma and tau; Provisi	91.67
cd01122		271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	91.63
PRK05986		191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	91.61
PF05496		233	RuvB_N: Holliday junction DNA helicase ruvB N-term	91.57
PRK14961		363	DNA polymerase III subunits gamma and tau; Provisi	91.55
PRK14963		504	DNA polymerase III subunits gamma and tau; Provisi	91.51
PRK14959		624	DNA polymerase III subunits gamma and tau; Provisi	91.42
PRK11823		446	DNA repair protein RadA; Provisional	91.31
KOG0060		659	consensus Long-chain acyl-CoA transporter, ABC sup	91.31
KOG0991		333	consensus Replication factor C, subunit RFC2 [Repl	91.29
PF13173		128	AAA_14: AAA domain	91.21
PRK08533		230	flagellar accessory protein FlaH; Reviewed	91.15
PRK06871		325	DNA polymerase III subunit delta'; Validated	91.1
PRK06995		484	flhF flagellar biosynthesis regulator FlhF; Valida	91.08
PRK14955		397	DNA polymerase III subunits gamma and tau; Provisi	91.05
PRK06964		342	DNA polymerase III subunit delta'; Validated	91.0
PRK05563		559	DNA polymerase III subunits gamma and tau; Validat	90.99
PRK00411		394	cdc6 cell division control protein 6; Reviewed	90.99
PRK14962		472	DNA polymerase III subunits gamma and tau; Provisi	90.9
COG1110		1187	Reverse gyrase [DNA replication, recombination, an	90.86
PRK06620		214	hypothetical protein; Validated	90.73
PRK04195		482	replication factor C large subunit; Provisional	90.64
PRK07993		334	DNA polymerase III subunit delta'; Validated	90.61
TIGR03877		237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	90.59
PRK14969		527	DNA polymerase III subunits gamma and tau; Provisi	90.42
PRK13851		344	type IV secretion system protein VirB11; Provision	90.35
COG2804		500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	90.31
cd03115		173	SRP The signal recognition particle (SRP) mediates	90.28
PRK14957		546	DNA polymerase III subunits gamma and tau; Provisi	90.28
CHL00181		287	cbbX CbbX; Provisional	90.23
KOG1001		674	consensus Helicase-like transcription factor HLTF/	90.14
PF05729		166	NACHT: NACHT domain	90.14
PF01695		178	IstB_IS21: IstB-like ATP binding protein; InterPro	90.03
cd01121		372	Sms Sms (bacterial radA) DNA repair protein. This	90.03
PRK06067		234	flagellar accessory protein FlaH; Validated	89.99
PRK06090		319	DNA polymerase III subunit delta'; Validated	89.95
PRK13341		725	recombination factor protein RarA/unknown domain f	89.94
COG1474		366	CDC6 Cdc6-related protein, AAA superfamily ATPase	89.87
COG1198		730	PriA Primosomal protein N' (replication factor Y)	89.79
COG3973		747	Superfamily I DNA and RNA helicases [General funct	89.74
cd03239		178	ABC_SMC_head The structural maintenance of chromos	89.58
TIGR00959		428	ffh signal recognition particle protein. This mode	89.45
COG2909		894	MalT ATP-dependent transcriptional regulator [Tran	89.42
PRK14954		620	DNA polymerase III subunits gamma and tau; Provisi	89.38
TIGR00643		630	recG ATP-dependent DNA helicase RecG.	89.36
PRK08451		535	DNA polymerase III subunits gamma and tau; Validat	89.32
COG4626		546	Phage terminase-like protein, large subunit [Gener	89.31
PF01637		234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	89.24
COG0513		513	SrmB Superfamily II DNA and RNA helicases [DNA rep	89.23
COG0470		325	HolB ATPase involved in DNA replication [DNA repli	89.15
PF00437		270	T2SE: Type II/IV secretion system protein; InterPr	89.04
PRK00440		319	rfc replication factor C small subunit; Reviewed	89.0
TIGR00580		926	mfd transcription-repair coupling factor (mfd). Al	88.93
cd00267		157	ABC_ATPase ABC (ATP-binding cassette) transporter	88.92
COG1660		286	Predicted P-loop-containing kinase [General functi	88.71
KOG1133		821	consensus Helicase of the DEAD superfamily [Replic	88.64
COG0593		408	DnaA ATPase involved in DNA replication initiation	88.52
cd01130		186	VirB11-like_ATPase Type IV secretory pathway compo	88.5
TIGR02525		372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	88.49
PF03237		384	Terminase_6: Terminase-like family; InterPro: IPR0	88.47
PF03668		284	ATP_bind_2: P-loop ATPase protein family; InterPro	88.43
PRK08699		325	DNA polymerase III subunit delta'; Validated	88.31
PRK14950		585	DNA polymerase III subunits gamma and tau; Provisi	88.21
COG2256		436	MGS1 ATPase related to the helicase subunit of the	88.16
PRK07940		394	DNA polymerase III subunit delta'; Validated	88.09
PRK14948		620	DNA polymerase III subunits gamma and tau; Provisi	88.05
PRK10436		462	hypothetical protein; Provisional	88.04
PRK13342		413	recombination factor protein RarA; Reviewed	88.02
COG2109		198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	88.02
PRK05896		605	DNA polymerase III subunits gamma and tau; Validat	87.97
TIGR02868		529	CydC thiol reductant ABC exporter, CydC subunit. T	87.66
PRK13900		332	type IV secretion system ATPase VirB11; Provisiona	87.65
TIGR00678		188	holB DNA polymerase III, delta' subunit. At positi	87.6
PRK11034		758	clpA ATP-dependent Clp protease ATP-binding subuni	87.59
PF13555		62	AAA_29: P-loop containing region of AAA domain	87.38
COG0552		340	FtsY Signal recognition particle GTPase [Intracell	87.32
COG1132		567	MdlB ABC-type multidrug transport system, ATPase a	87.23
PRK09087		226	hypothetical protein; Validated	87.19
TIGR03878		259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	87.16
KOG0701		1606	consensus dsRNA-specific nuclease Dicer and relate	87.04
cd03221		144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	86.95
PF06733		174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	86.67
PF03969		362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	86.62
COG2805		353	PilT Tfp pilus assembly protein, pilus retraction	86.44
cd03228		171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	86.35
cd03246		173	ABCC_Protease_Secretion This family represents the	86.31
PRK07133		725	DNA polymerase III subunits gamma and tau; Validat	86.08
TIGR02655		484	circ_KaiC circadian clock protein KaiC. Members of	86.04
cd03247		178	ABCC_cytochrome_bd The CYD subfamily implicated in	86.04
cd00984		242	DnaB_C DnaB helicase C terminal domain. The hexame	86.02
PHA00729		226	NTP-binding motif containing protein	85.99
cd03229		178	ABC_Class3 This class is comprised of all BPD (Bin	85.95
COG2255		332	RuvB Holliday junction resolvasome, helicase subun	85.94
PF02572		172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	85.92
PRK05973		237	replicative DNA helicase; Provisional	85.84
cd03216		163	ABC_Carb_Monos_I This family represents the domain	85.8
TIGR02858		270	spore_III_AA stage III sporulation protein AA. Mem	85.79
TIGR02538		564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	85.77
PF10593		239	Z1: Z1 domain; InterPro: IPR018310 This entry repr	85.72
COG1074		1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	85.71
PRK10689		1147	transcription-repair coupling factor; Provisional	85.67
PRK14970		367	DNA polymerase III subunits gamma and tau; Provisi	85.4
TIGR03880		224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	85.39
COG0630		312	VirB11 Type IV secretory pathway, VirB11 component	85.39
TIGR02524		358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	85.38
PF14516		331	AAA_35: AAA-like domain	85.18
KOG0733		802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	85.02
cd01129		264	PulE-GspE PulE/GspE The type II secretory pathway	84.87
PF12846		304	AAA_10: AAA-like domain	84.85
PF03796		259	DnaB_C: DnaB-like helicase C terminal domain; Inte	84.74
PF02534		469	T4SS-DNA_transf: Type IV secretory system Conjugat	84.71
cd01126		384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	84.67
KOG0058		716	consensus Peptide exporter, ABC superfamily [Intra	84.66
KOG0331		519	consensus ATP-dependent RNA helicase [RNA processi	84.5
cd03215		182	ABC_Carb_Monos_II This family represents domain II	84.49
TIGR03819		340	heli_sec_ATPase helicase/secretion neighborhood AT	84.32
KOG0344		593	consensus ATP-dependent RNA helicase [RNA processi	84.2
TIGR03600		421	phage_DnaB phage replicative helicase, DnaB family	84.19
COG1219		408	ClpX ATP-dependent protease Clp, ATPase subunit [P	84.12
PRK06904		472	replicative DNA helicase; Validated	84.07
PRK14953		486	DNA polymerase III subunits gamma and tau; Provisi	84.05
cd03276		198	ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC protein	84.0
COG0210		655	UvrD Superfamily I DNA and RNA helicases [DNA repl	83.78
PRK13764		602	ATPase; Provisional	83.69
TIGR00416		454	sms DNA repair protein RadA. The gene protuct code	83.66
PRK07414		178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	83.62
cd03230		173	ABC_DR_subfamily_A This family of ATP-binding prot	83.31
KOG0347		731	consensus RNA helicase [RNA processing and modific	83.31
TIGR02012		321	tigrfam_recA protein RecA. This model describes or	82.93
TIGR02533		486	type_II_gspE general secretory pathway protein E.	82.87
KOG2028		554	consensus ATPase related to the helicase subunit o	82.81
TIGR00767		415	rho transcription termination factor Rho. Members	82.76
PHA03372		668	DNA packaging terminase subunit 1; Provisional	82.74
PRK06647		563	DNA polymerase III subunits gamma and tau; Validat	82.7
PRK08058		329	DNA polymerase III subunit delta'; Validated	82.57
COG4555		245	NatA ABC-type Na+ transport system, ATPase compone	82.56
PRK09354		349	recA recombinase A; Provisional	82.27
PRK03992		389	proteasome-activating nucleotidase; Provisional	82.17
PRK13897		606	type IV secretion system component VirD4; Provisio	82.14
cd00268		203	DEADc DEAD-box helicases. A diverse family of prot	82.12
TIGR02788		308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	82.07
cd03222		177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	81.96
KOG0741		744	consensus AAA+-type ATPase [Posttranslational modi	81.94
PRK14971		614	DNA polymerase III subunits gamma and tau; Provisi	81.88
TIGR01243		733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	81.86
COG1197		1139	Mfd Transcription-repair coupling factor (superfam	81.82
PRK11634		629	ATP-dependent RNA helicase DeaD; Provisional	81.79
PRK07399		314	DNA polymerase III subunit delta'; Validated	81.72
TIGR00763		775	lon ATP-dependent protease La. This protein is ind	81.59
TIGR01243		733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	81.3
PRK14701		1638	reverse gyrase; Provisional	81.26
cd00983		325	recA RecA is a bacterial enzyme which has roles in	81.2
PF02606		326	LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPr	81.11
COG4185		187	Uncharacterized protein conserved in bacteria [Fun	81.07
COG0541		451	Ffh Signal recognition particle GTPase [Intracellu	80.92
TIGR02639		731	ClpA ATP-dependent Clp protease ATP-binding subuni	80.85
TIGR03345		852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	80.85
PRK04841		903	transcriptional regulator MalT; Provisional	80.79
cd03289		275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	80.75
PHA00350		399	putative assembly protein	80.63
PRK06305		451	DNA polymerase III subunits gamma and tau; Validat	80.62
cd03278		197	ABC_SMC_barmotin Barmotin is a tight junction-asso	80.53
TIGR03689		512	pup_AAA proteasome ATPase. In the Actinobacteria,	80.51
TIGR02397		355	dnaX_nterm DNA polymerase III, subunit gamma and t	80.31
cd01131		198	PilT Pilus retraction ATPase PilT. PilT is a nucle	80.14
PRK08760		476	replicative DNA helicase; Provisional	80.07
COG1200		677	RecG RecG-like helicase [DNA replication, recombin	80.06

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

Probab=100.00  E-value=1.1e-81  Score=659.50  Aligned_cols=463  Identities=49%  Similarity=0.761  Sum_probs=430.6

Q ss_pred             CCCCCcCCcCCCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHHCCCcEEEEcCCCChhHHHHHHHHHHHHHcCCCCCCCCC
Q 004518          273 DSFMSESRFDQCSISALSLKGIKDAGYEKMTIVQEATLPVLLKGKDVLAKAKTGTGKTVAFLLPSIEVVIKSPPVDRDQR  352 (747)
Q Consensus       273 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~~i~~il~~~dvlv~a~TGsGKTl~~~lpil~~l~~~~~~~~~~~  352 (747)
                      +++.....|+.+.|++..+++++.+||+.+|++|+.+++.++.|+|+++.|.||+|||++|++|+++.+++.+...+   
T Consensus        76 ~s~~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r---  152 (543)
T KOG0342|consen   76 DSITTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPR---  152 (543)
T ss_pred             cchhhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCC---
Confidence            45666788999999999999999999999999999999999999999999999999999999999999999876543   


Q ss_pred             CCCeEEEEEcCcHHHHHHHHHHHHHHhhhCCCceEEEEeCCcchHHHHHHHhcCCCcEEEECchhHHHHHHccccccccC
Q 004518          353 RPPILVLVICPTRELATQAATEASTLLKYHPSIGVQVVIGGTRLALEQKRMQANPCQILVATPGRLRDHIENTAGFATRL  432 (747)
Q Consensus       353 ~~~~~vLIl~Ptr~La~Q~~~~~~~l~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tpg~Ll~~l~~~~~~~~~L  432 (747)
                       ++..+|||||||+||.|++.+++++..+++++.+++++||++...+..++.+ +++|+|||||+|++||++...|.+  
T Consensus       153 -~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k-~~niliATPGRLlDHlqNt~~f~~--  228 (543)
T KOG0342|consen  153 -NGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVK-GCNILIATPGRLLDHLQNTSGFLF--  228 (543)
T ss_pred             -CCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhc-cccEEEeCCchHHhHhhcCCcchh--
Confidence             5778999999999999999999999999999999999999999999988887 799999999999999999887653  


Q ss_pred             CCccEEEEeCCccccCCCcHHHHHHHHHHCCCCCeEEEEeccCChHHHHHHHHHhcCCceeeeeccCCccccccceeEEE
Q 004518          433 MGVKVLVLDEADHLLDMGFRKDIEKIIAAVPKQRQTLLFSATVPEEVRQICHIALKRDHEFINTVEEGSEETHEQVRQMH  512 (747)
Q Consensus       433 ~~i~~vIiDEAh~ll~~~f~~~l~~il~~~~~~~q~il~SATl~~~v~~l~~~~~~~~~~~i~~~~~~~~~~~~~i~~~~  512 (747)
                      .+++++|+||||+++++||++.+.+|+..+|+++|+++||||.++++..+++..++..+.+++++......++..+.|.|
T Consensus       229 r~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgy  308 (543)
T KOG0342|consen  229 RNLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGY  308 (543)
T ss_pred             hccceeEeecchhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceE
Confidence            56799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EecCcccchHHHHHHHHHHhhcCCCCeEEEEecchhHHHHHHHHHHhccccceeccCCCCHHHHHHHHHHHhcCCccEEE
Q 004518          513 LVAPLDLHFPLLYVLLREHVADNPEYKVLVFCTTAMVTRMVADLLGELKLNVREIHSRKPQSYRTRVSDEFRKSKGLILV  592 (747)
Q Consensus       513 ~~~~~~~k~~~l~~~l~~~~~~~~~~k~LVF~~s~~~~~~l~~~L~~~~~~v~~lh~~l~~~eR~~v~~~F~~g~~~VLv  592 (747)
                      ++++.+.++.+++.+++++...   +++||||+|+..+..++..|+...++|..|||+++|..|..++..|++.+..|||
T Consensus       309 vv~~~~~~f~ll~~~LKk~~~~---~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~  385 (543)
T KOG0342|consen  309 VVAPSDSRFSLLYTFLKKNIKR---YKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILV  385 (543)
T ss_pred             EeccccchHHHHHHHHHHhcCC---ceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEE
Confidence            9999999999999999987653   7999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCcccccCCCCccEEEEeCCCCChhhHHHhhccCCCCCCcceEEEEeCcchHHHHHHhhhCCCccCCCCCCCchhHHH
Q 004518          593 TSDVSARGVDYPDVTLVIQVGLPSDREQYIHRLGRTGRKGKEGQGILLLAPWEEFFLSTIKDLPILKAPVPSVDPDTKKK  672 (747)
Q Consensus       593 aT~v~~~GiDip~V~~VI~~d~p~s~~~y~Qr~GRagR~G~~G~~~~l~s~~e~~~l~~l~~~~i~~~~~~~~~~~~~~~  672 (747)
                      ||||++||+|+|+|++||+||+|.++.+|+||+|||||.|+.|++++|+.|||..|+..++++++.+.+++..+....+.
T Consensus       386 cTDVaARGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~G~alL~l~p~El~Flr~LK~lpl~~~e~~~~~~~~v~~  465 (543)
T KOG0342|consen  386 CTDVAARGLDIPDVDWVVQYDPPSDPEQYIHRVGRTAREGKEGKALLLLAPWELGFLRYLKKLPLEEFEFPPLKPEDVQS  465 (543)
T ss_pred             ecchhhccCCCCCceEEEEeCCCCCHHHHHHHhccccccCCCceEEEEeChhHHHHHHHHhhCCCcccCCCCCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999888877766


Q ss_pred             HHHHHHHHHHhcH---HHHHHHHHHHHhcccccccCcccHHHHHHHHHHHcCCCCCCCCChhhhhhcCCCCCCCCCC
Q 004518          673 VERALSHVEMKNK---EAAYQAWLGYYNSNKKVGRDKYKLVELANEYSRSMGLDNPPAIPKLVLGKMGLRNIPGLRS  746 (747)
Q Consensus       673 ~~~~~~~~~~~~~---~~a~~s~l~~y~~~~~~~~~~~~~~~~~~~~a~~~gl~~~p~i~~~~~~~~~~~~~pgl~~  746 (747)
                      +.+.+-+..+..+   ..||++|++||++|........+..+++ +++++||+..||.++....+++|+.+.+|++.
T Consensus       466 ~~~~li~~~y~~~~aak~ay~syl~~y~s~slk~~~~~~~l~La-~~~~s~gf~~pp~v~~~i~~~~~~k~~~~~~~  541 (543)
T KOG0342|consen  466 QLEKLISKNYSLKEAAKEAYKSYLGAYNSHSLKDIFNVNLLELA-AVAKSFGFSVPPAVDLKIDGKMGLKGNKGLRG  541 (543)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHhhhhhccchhhhcccccchhhHH-HHHHHcCCCCCccceeeccccccccCCCCCCC
Confidence            6555555444443   4667779999999987766667778888 99999999999999999999999999999875

>KOG0345 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

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

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

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

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

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

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

>PTZ00110 helicase; Provisional	Back alignment and domain information

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

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional	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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>PTZ00424 helicase 45; Provisional	Back alignment and domain information

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

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

>KOG0350 consensus DEAD-box 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

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

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

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

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

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

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

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

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

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

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

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

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

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

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional	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

>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

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

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

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

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

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

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

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

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

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

>KOG0352 consensus ATP-dependent DNA helicase [Replication, recombination and repair]	Back alignment and domain information

>PRK09401 reverse gyrase; Reviewed	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

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

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

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

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

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

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

>KOG0922 consensus DEAH-box 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

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

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

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

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

>TIGR01054 rgy reverse gyrase	Back alignment and domain information

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

>PRK13766 Hef nuclease; Provisional	Back alignment and domain information

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

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type	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

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

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

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

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

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

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

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

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]	Back alignment and domain information

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

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

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

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

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

>PRK09694 helicase Cas3; Provisional	Back alignment and domain information

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

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

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

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

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

>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

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

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

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

>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]	Back alignment and domain information

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

>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional	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

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]	Back alignment and domain information

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

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

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

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

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]	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

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

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

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

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

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

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

>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

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

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

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

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

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]	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

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4	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

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0388 consensus SNF2 family DNA-dependent ATPase [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

>PRK14873 primosome assembly protein PriA; 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

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

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain	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

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

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

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

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

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

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

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

>COG3587 Restriction endonuclease [Defense mechanisms]	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

>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

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

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

>PF13959 DUF4217: Domain of unknown function (DUF4217)	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

>PRK10536 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

>KOG1132 consensus Helicase of the DEAD superfamily [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

>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

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins	Back alignment and domain information

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

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

>PRK08181 transposase; Validated	Back alignment and domain information

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

>PRK14974 cell division protein FtsY; Provisional	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

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

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

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

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

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

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

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

>PRK06526 transposase; 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

>PRK04296 thymidine kinase; Provisional	Back alignment and domain information

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

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI	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

>TIGR00376 DNA helicase, putative	Back alignment and domain information

>PRK06921 hypothetical protein; Provisional	Back alignment and domain information

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

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit	Back alignment and domain information

>TIGR01075 uvrD DNA helicase II	Back alignment and domain information

>PRK13826 Dtr system oriT relaxase; Provisional	Back alignment and domain information

>smart00382 AAA ATPases associated with a variety of cellular activities	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

>PRK08727 hypothetical protein; Validated	Back alignment and domain information

>PRK08116 hypothetical protein; Validated	Back alignment and domain information

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

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

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]	Back alignment and domain information

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

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

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

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

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

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

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

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

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional	Back alignment and domain information

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

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

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]	Back alignment and domain information

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

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

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

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

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

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

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase	Back alignment and domain information

>PRK10919 ATP-dependent DNA helicase Rep; Provisional	Back alignment and domain information

>PRK14087 dnaA chromosomal replication initiation protein; Provisional	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

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

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

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

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

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional	Back alignment and domain information

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

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional	Back alignment and domain information

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

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

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

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

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

>PRK08939 primosomal protein DnaI; Reviewed	Back alignment and domain information

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

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

>PRK13833 conjugal transfer protein TrbB; Provisional	Back alignment and domain information

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

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

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

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

>TIGR00064 ftsY signal recognition particle-docking protein FtsY	Back alignment and domain information

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

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

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]	Back alignment and domain information

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

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

>TIGR03499 FlhF flagellar biosynthetic protein FlhF	Back alignment and domain information

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family	Back alignment and domain information

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

>PRK10867 signal recognition particle protein; Provisional	Back alignment and domain information

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

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI	Back alignment and domain information

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

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type	Back alignment and domain information

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

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]	Back alignment and domain information

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical	Back alignment and domain information

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

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

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

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

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

>PTZ00293 thymidine kinase; Provisional	Back alignment and domain information

>TIGR01425 SRP54_euk signal recognition particle protein SRP54	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

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

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

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

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

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

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

>PRK10416 signal recognition particle-docking protein FtsY; Provisional	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

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB	Back alignment and domain information

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

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

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

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

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases	Back alignment and domain information

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

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

>PRK14961 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

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

>PRK11823 DNA repair protein RadA; Provisional	Back alignment and domain information

>KOG0060 consensus Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism; General function prediction only]	Back alignment and domain information

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

>PF13173 AAA_14: AAA domain	Back alignment and domain information

>PRK08533 flagellar accessory protein FlaH; Reviewed	Back alignment and domain information

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

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated	Back alignment and domain information

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

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

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

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

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

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

>PRK06620 hypothetical protein; Validated	Back alignment and domain information

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

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

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family	Back alignment and domain information

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

>PRK13851 type IV secretion system protein VirB11; Provisional	Back alignment and domain information

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

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

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

>CHL00181 cbbX CbbX; Provisional	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

>PF05729 NACHT: NACHT domain	Back alignment and domain information

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif	Back alignment and domain information

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

>PRK06067 flagellar accessory protein FlaH; Validated	Back alignment and domain information

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

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed	Back alignment and domain information

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]	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

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

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms	Back alignment and domain information

>TIGR00959 ffh signal recognition particle protein	Back alignment and domain information

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]	Back alignment and domain information

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

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

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

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]	Back alignment and domain information

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP	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

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

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]	Back alignment and domain information

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

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

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules	Back alignment and domain information

>COG1660 Predicted P-loop-containing kinase [General function prediction only]	Back alignment and domain information

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]	Back alignment and domain information

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]	Back alignment and domain information

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases	Back alignment and domain information

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ	Back alignment and domain information

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []	Back alignment and domain information

>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins	Back alignment and domain information

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

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional	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

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

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

>PRK10436 hypothetical protein; Provisional	Back alignment and domain information

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

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]	Back alignment and domain information

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

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit	Back alignment and domain information

>PRK13900 type IV secretion system ATPase VirB11; Provisional	Back alignment and domain information

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

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional	Back alignment and domain information

>PF13555 AAA_29: P-loop containing region of AAA domain	Back alignment and domain information

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]	Back alignment and domain information

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	Back alignment and domain information

>PRK09087 hypothetical protein; Validated	Back alignment and domain information

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family	Back alignment and domain information

>KOG0701 consensus dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification]	Back alignment and domain information

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth	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

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP	Back alignment and domain information

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export	Back alignment and domain information

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain	Back alignment and domain information

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

>TIGR02655 circ_KaiC circadian clock protein KaiC	Back alignment and domain information

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis	Back alignment and domain information

>cd00984 DnaB_C DnaB helicase C terminal domain	Back alignment and domain information

>PHA00729 NTP-binding motif containing protein	Back alignment and domain information

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment	Back alignment and domain information

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]	Back alignment and domain information

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2	Back alignment and domain information

>PRK05973 replicative DNA helicase; Provisional	Back alignment and domain information

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)	Back alignment and domain information

>TIGR02858 spore_III_AA stage III sporulation protein AA	Back alignment and domain information

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB	Back alignment and domain information

>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases	Back alignment and domain information

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]	Back alignment and domain information

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

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family	Back alignment and domain information

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB	Back alignment and domain information

>PF14516 AAA_35: AAA-like domain	Back alignment and domain information

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)	Back alignment and domain information

>PF12846 AAA_10: AAA-like domain	Back alignment and domain information

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork	Back alignment and domain information

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues	Back alignment and domain information

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion	Back alignment and domain information

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]	Back alignment and domain information

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

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)	Back alignment and domain information

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase	Back alignment and domain information

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

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily	Back alignment and domain information

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>cd03276 ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains	Back alignment and domain information

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]	Back alignment and domain information

>PRK13764 ATPase; Provisional	Back alignment and domain information

>TIGR00416 sms DNA repair protein RadA	Back alignment and domain information

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated	Back alignment and domain information

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity	Back alignment and domain information

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

>TIGR02012 tigrfam_recA protein RecA	Back alignment and domain information

>TIGR02533 type_II_gspE general secretory pathway protein E	Back alignment and domain information

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]	Back alignment and domain information

>TIGR00767 rho transcription termination factor Rho	Back alignment and domain information

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

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

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

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]	Back alignment and domain information

>PRK09354 recA recombinase A; Provisional	Back alignment and domain information

>PRK03992 proteasome-activating nucleotidase; Provisional	Back alignment and domain information

>PRK13897 type IV secretion system component VirD4; Provisional	Back alignment and domain information

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

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11	Back alignment and domain information

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids	Back alignment and domain information

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily	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

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

>PRK07399 DNA polymerase III subunit delta'; Validated	Back alignment and domain information

>TIGR00763 lon ATP-dependent protease La	Back alignment and domain information

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily	Back alignment and domain information

>PRK14701 reverse gyrase; Provisional	Back alignment and domain information

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response	Back alignment and domain information

>PF02606 LpxK: Tetraacyldisaccharide-1-P 4'-kinase; InterPro: IPR003758 Tetraacyldisaccharide 4'-kinase phosphorylates the 4'-position of a tetraacyldisaccharide 1-phosphate precursor (DS-1-P) of lipid A, but the enzyme has not yet been purified because of instability []	Back alignment and domain information

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]	Back alignment and domain information

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]	Back alignment and domain information

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

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

>PRK04841 transcriptional regulator MalT; Provisional	Back alignment and domain information

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2	Back alignment and domain information

>PHA00350 putative assembly protein	Back alignment and domain information

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

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function	Back alignment and domain information

>TIGR03689 pup_AAA proteasome ATPase	Back alignment and domain information

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

>cd01131 PilT Pilus retraction ATPase PilT	Back alignment and domain information

>PRK08760 replicative DNA helicase; Provisional	Back alignment and domain information

>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]	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		747
1hv8_A		367	Crystal Structure Of A Dead Box Protein From The Hy		9e-51
3sqw_A		579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-49
3i5x_A		563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		5e-49
3sqx_A		512	Structure Of Mss116p (Nte And C-Tail Double Deletio		6e-49
1s2m_A		400	Crystal Structure Of The Dead Box Protein Dhh1p Len		1e-46
2db3_A		434	Structural Basis For Rna Unwinding By The Dead-Box		6e-44
2z0m_A		337	Crystal Structure Of Hypothetical Atp-Dependent Rna		7e-43
2j0q_A		410	The Crystal Structure Of The Exon Junction Complex		2e-42
2hyi_C		413	Structure Of The Human Exon Junction Complex With A		2e-42
2xb2_A		411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-42
2j0u_A		374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-42
2j0u_B		374	The Crystal Structure Of Eif4aiii-Barentsz Complex		4e-42
2hxy_A		391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		4e-42
2i4i_A		417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-40
1xtk_A		390	Structure Of Decd To Dead Mutation Of Human Uap56 L		4e-39
1xtj_A		386	Structure Of Human Uap56 In Complex With Adp Length		8e-39
1xti_A		391	Structure Of Wildtype Human Uap56 Length = 391		1e-38
3ly5_A		262	Ddx18 Dead-Domain Length = 262		4e-38
2vso_A		395	Crystal Structure Of A Translation Initiation Compl		7e-37
1fuu_A		394	Yeast Initiation Factor 4a Length = 394		4e-36
2pl3_A		236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-35
3eiq_A		414	Crystal Structure Of Pdcd4-eif4a Length = 414		9e-35
2zu6_A		388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-34
3ber_A		249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-32
3pew_A		395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		5e-32
3pey_A		395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		1e-31
3fmp_B		479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-30
3g0h_A		424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-30
3ews_A		445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-30
3fht_A		412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-30
2gxq_A		207	Hera N-Terminal Domain In Complex With Amp, Crystal		2e-28
1vec_A		206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-28
3mwj_A		207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		5e-28
1wrb_A		253	Crystal Structure Of The N-Terminal Reca-Like Domai		2e-27
1t6n_A		220	Crystal Structure Of The N-Terminal Domain Of Human		1e-26
3iuy_A		228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-25
1q0u_A		219	Crystal Structure Of The Bstdead N-Terminal Domain		4e-25
3fho_B		508	Structure Of S. Pombe Dbp5 Length = 508		7e-25
4a4d_A		253	Crystal Structure Of The N-Terminal Domain Of The H		1e-24
3fe2_A		242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-24
1qva_A		223	Yeast Initiation Factor 4a N-Terminal Domain Length		4e-23
1qde_A		224	Crystal Structure Of The Atpase Domain Of Translati		5e-23
3bor_A		237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-21
4db4_A		256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		2e-19
4db2_C		257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		2e-19
4db2_A		257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		2e-19
2g9n_A		221	Structure Of The Dead Domain Of Human Eukaryotic In		9e-19
2oxc_A		230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		2e-18
2hjv_A		163	Structure Of The Second Domain (Residues 207-368) O		8e-18
3dkp_A		245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-16
2kbe_A		226	Solution Structure Of Amino-Terminal Domain Of Dbp5		3e-16
3fhc_B		235	Crystal Structure Of Human Dbp5 In Complex With Nup		2e-15
3fmo_B		300	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-14
2wax_A		193	Structure Of The Human Ddx6 C-Terminal Domain In Co		7e-14
2jgn_A		185	Ddx3 Helicase Domain Length = 185		2e-12
2kbf_A		187	Solution Structure Of Carboxyl-Terminal Domain Of D		9e-12
2p6n_A		191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		2e-11
3peu_A		188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		2e-11
3gfp_A		189	Structure Of The C-Terminal Domain Of The Dead-Box		2e-11
2yjt_D		170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		3e-10
1fuk_A		165	Crystal Structure Of The Carboxy Terminal Domain Of		7e-10
2rb4_A		175	Crystal Structure Of The Helicase Domain Of Human D		2e-09
1t5i_A		172	Crystal Structure Of The C-Terminal Domain Of Uap56		5e-08
3i32_A		300	Dimeric Structure Of A Hera Helicase Fragment Inclu		3e-07
3eaq_A		212	Novel Dimerization Motif In The Dead Box Rna Helica		3e-07
1oyy_A		523	Structure Of The Recq Catalytic Core Bound To Atp-G		7e-07
1oyw_A		523	Structure Of The Recq Catalytic Core Length = 523		5e-06

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367