Citrus Sinensis ID: 006737

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Local Sequence Feature Prediction

Residue Number Marker
--------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---
Protein Sequence
MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTKLFDKADPDSETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFYIICFVYTISMY
Secondary Structure (PSIPRED)
ccHHHHHHcccccccccEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHHHHHcccccccccccccEEEEEcccHHHHHHHHHHHHHHHHccccccEEEEEcccccHHHHHHHHcccccEEEEcccHHHHHHccccccEEEcccccEEEEEccHHHHccccHHHHHHHHHHccccccEEEEEccccHHHHHHHcccccccccccccccccEEEEEEEEEEEEEHHHHccccEEEEEEEccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHccccccHHHHHHHEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHccccHHcccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccHccccccEEcccccccccccccHHHccccHHHHHHHHHcccccccHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHccccccccccccccEEEEEccHHHHHHHHHHHHHHHHHcccccEEEEEEccccccHHHHHHHccccEEEEEcccHHHHHHHcccccEEcHccEEEEEEcHHHHHHHccccHHHHHHHHHccHcccEEEEEccccHHHHHHHHHHHcccEEEEEEEEEEEccccHHHEEHHHHHHccccccEEEEEEEEEcc
Coil and Loop (DISEMBL)
msssvllqrskpltnilwfnrvfarpmgggprtfpgglnkWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTklfdkadpdsetnqhkpmspdeHVKALADRFMKEGaedlwneddgpvkseqrprsgaeanqrprlagapidlrglisdkrnsvnnsgnlnsgsnvktrnysvlseskfsdrsksaslifmpnlecndgetvipsrnvMDFVRRAyfsgtdkrnfcrndgsstrdkagfdtgnkakpfarnlgnnrengdsknmSEFMKKKcfvgkrrfkrnessssdddsdidsedvdekVEGWRDvkkmgssaslgkydmkitkrvplksledehdFEEQVELIRKEISKnklngngekkekreeepilsqkrfdecgispltIKALTAAGYIQMTRVQEATLSACLEGKDAVVKaktgtgksiAFLLPAIEAVLKATsssttqlvppiyvlILCPTRELASQIAAEAIALLKNHDGIGVLTLVggtrfkvdqrrlesdpcqilvatpgrlldhienksgLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYidtvglgsvetpvkvskYNIYVFVLVLSIKIQAFYIICFVYTISMY
Flexible Loop (DISEMBL)
msssvllqrskpltnilWFNRVFARPMgggprtfpgglnkWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTklfdkadpdsetnqhkpmspdEHVKALADRFMKEGAedlwneddgpvkseqrprsgaeanqrprlagapidLRGLISDKRNsvnnsgnlnsgsnvktrnySVLSeskfsdrsksaslifmpnlecndgetvipsrnvMDFVRRAYfsgtdkrnfcrndgsstrdkagfdtgnkakpfarnlgnnrengdsknmsefMKKKcfvgkrrfkrnessssdddsdidsedvdekvegwrdvkkmgssaslgkydmkitkrvplksledehDFEEQVELIRkeisknklngngekkekreeepilsqkrfdecgiSPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKAtsssttqlvpPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVdqrrlesdpcqilvatpgrlldhieNKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLprrrqsllfsatmpkelvlKREHTYIDTvglgsvetpvkvSKYNIYVFVLVLSIKIQAFYIICFVYTISMY
Low Complexity Region (SEG)
MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHekkakekekrlleqekqlyqARVRSQIRTKLFDKADPDSETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRnsvnnsgnlnsgsnvKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRRFKRNessssdddsdidsedvdeKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISknklngngekkekreeePILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFYIICFVYTISMY
Disordered region (IsUnstruct)
***********PLTNILWFNRVFARPMGGGPRTFPGGLNKWQWK****************************************************************************************************************************************************LIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNF******************************************************************************************************************************************************FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVL************PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFYIICFVYTI***
Disordered Region (DISOPRED)
*************TNILWFNRVFARPMGGGPRTFPGGLNKWQWK******************KQLYQARV**********************************************************************************************************************************************************************************************************************************************************************************************************************FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVL************PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTV*****E*PVKVSKYNIYVFVLVLSIKIQAFYIICFVYTISM*
Disordered Region (DISEMBL)
********RSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKR**********KRLLEQEKQLYQARVRSQIRTKLFDK***************DEHVKALADRFMKEGAEDLWNEDD****************QRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRR**********************KVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNG************ILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFYIICFVYTISMY
Disordered Region (DISPRO)
*SS**LLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTKLFD*******************VKALADRFMKEGAEDLWNEDDGPVK******************************************S*SNVKTRNYSVLSESK*******************************************K*****************************************************************************************************ITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFYIICFVYTISMY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiii
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWxxxxxxxxxxxxxxxxxxxxxxxxxxxxSQIRTKLFDKADPDSETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFYIICFVYTISMY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	633	2.2.26 [Sep-21-2011]
O80792	845	Putative DEAD-box ATP-dep	yes	no	0.838	0.628	0.514	1e-161
Q9C8S9	798	Probable DEAD-box ATP-dep	yes	no	0.868	0.689	0.516	1e-160
Q6K7R9	811	DEAD-box ATP-dependent RN	yes	no	0.862	0.673	0.477	1e-133
Q9FNM7	850	DEAD-box ATP-dependent RN	no	no	0.402	0.3	0.545	2e-76
Q0DBU5	547	DEAD-box ATP-dependent RN	no	no	0.472	0.546	0.475	8e-73
Q9FFQ1	716	DEAD-box ATP-dependent RN	no	no	0.380	0.336	0.522	7e-72
Q94C75	563	DEAD-box ATP-dependent RN	no	no	0.361	0.406	0.570	8e-72
Q5ZBH5	594	DEAD-box ATP-dependent RN	no	no	0.361	0.385	0.553	7e-70
Q0JL73	536	DEAD-box ATP-dependent RN	no	no	0.371	0.438	0.532	1e-67
Q8K9H6	601	Cold-shock DEAD box prote	yes	no	0.301	0.317	0.423	2e-34

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

 Score =  567 bits (1462), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 311/604 (51%), Positives = 407/604 (67%), Gaps = 73/604 (12%)

Query: 17  LWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRT 76
           LW NR+F+R MGGGPRTFPGGLNKWQWKRMHEKKA+EKE +LL+QEKQLY+AR+R++IR 
Sbjct: 67  LW-NRIFSRNMGGGPRTFPGGLNKWQWKRMHEKKAREKENKLLDQEKQLYEARIRTEIRA 125

Query: 77  KLFDKADPDSET----NQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKS-EQRPRS 131
           K++   D   +T      H PMSP EH+K LADRFMK GA+DLWN++DGPVK  +Q  RS
Sbjct: 126 KMWGHPDSGEKTAKLKQSHGPMSPKEHIKTLADRFMKAGADDLWNDNDGPVKKFDQGSRS 185

Query: 132 GAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSA 191
            +++     +   PID+R L+S   +S+     L+S      R +S +S  K ++ S   
Sbjct: 186 CSDS-----IDSTPIDVRRLVSATCDSMGKHRVLDSSR----RGFSSMSRFKRNESS--- 233

Query: 192 SLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAK 251
                    C++G+ V                                D    DT     
Sbjct: 234 ---------CDEGDDV--------------------------------DAKKLDT---LS 249

Query: 252 PFARNLGNNREN-GDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEKVEGW 310
           PF+      +E    S ++   ++ K   G+R+F++N+SS+ +D    D E  + K+ GW
Sbjct: 250 PFSPKFSGTKEKVKSSTSVVGVIRNKGLFGRRKFRKNDSSTEEDS---DEEGNEGKMIGW 306

Query: 311 RDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKR 370
            D++K GSSASLG +D+K+TKRV     ++E      +  +R+++SK +   N  ++++ 
Sbjct: 307 MDLRKTGSSASLGNHDIKLTKRVNRNVTDEELYPPLDINRVREDLSKKQSVDNVMEEKQE 366

Query: 371 EEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKS 430
             + I S KRFDE  ISPLT+KAL+A+G ++MTRVQ+ATLS CL+GKDA+VKAKTGTGKS
Sbjct: 367 PHDSIYSAKRFDESCISPLTLKALSASGIVKMTRVQDATLSECLDGKDALVKAKTGTGKS 426

Query: 431 IAFLLPAIEAVLKATSSST-TQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLT 489
           +AFLLPAIE VLKA +S      V PI+VLILCPTRELASQIAAE  ALLKNHDGIGV T
Sbjct: 427 MAFLLPAIETVLKAMNSGKGVHKVAPIFVLILCPTRELASQIAAEGKALLKNHDGIGVQT 486

Query: 490 LVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL 549
           L+GGTRF++DQ+RLES+PCQIL+ATPGRLLDHIENKSGL+ RLM LK+ ++DEAD LLDL
Sbjct: 487 LIGGTRFRLDQQRLESEPCQILIATPGRLLDHIENKSGLTSRLMALKLFIVDEADLLLDL 546

Query: 550 GFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVS 603
           GF++DVE I+DCLPR+RQSLLFSAT+PKE      LVLKR+H+YIDT+GLG VET  KV 
Sbjct: 547 GFKRDVEKIIDCLPRQRQSLLFSATIPKEVRRVSQLVLKRDHSYIDTIGLGCVETHDKVK 606

Query: 604 KYNI 607
           +  I
Sbjct: 607 QSCI 610

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

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

 Score =  567 bits (1461), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 320/620 (51%), Positives = 415/620 (66%), Gaps = 70/620 (11%)

Query: 1   MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLE 60
           M S +L +RS  +T  LW NR+ +R MGGGPRTFPGGLNKWQWKRMHEKKA+EKE +LL+
Sbjct: 1   MYSLILRERSGSITGSLW-NRISSRNMGGGPRTFPGGLNKWQWKRMHEKKAREKENKLLD 59

Query: 61  QEKQLYQARVRSQIRTKLFDKADPDSET----NQHKPMSPDEHVKALADRFMKEGAEDLW 116
           QEKQLY+AR+R++IR K++   D   +T      H PMSP EH+K LADRFMK GAED W
Sbjct: 60  QEKQLYEARIRTEIRAKMWGNPDSGEKTAKSKQSHGPMSPKEHIKTLADRFMKAGAEDFW 119

Query: 117 NEDDGPV-KSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRN 175
           NE+DGPV KS+Q  RSG+++      + +PID+R L+S   +S+  +    S      R 
Sbjct: 120 NENDGPVKKSDQGSRSGSDSID--STSNSPIDVRRLVSATCDSMGKNRVFGSSR----RG 173

Query: 176 YSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDG 235
           +S +S  K ++ S            C++G+         DF                   
Sbjct: 174 FSSMSRFKRNESS------------CDEGD---------DF------------------- 193

Query: 236 SSTRDKAGFDTGNKAKPFARNLGNNREN-GDSKNMSEFMKKKCFVGKRRFKRNESSSSDD 294
               D    DT     PF+      +E    S+++   ++ K   G+R+F++N+SS+   
Sbjct: 194 ----DAKKLDT---LSPFSPKFAGTKEKVKSSRSVVGVIRNKGLFGRRKFRKNDSSTE-- 244

Query: 295 DSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKE 354
             D D E  + K+ GW D++K GSSASLG +D+K+TKRV     ++E      +  +R++
Sbjct: 245 -EDSDEEGDEGKMIGWMDMRKTGSSASLGNHDIKLTKRVNRNVTDEELYPPLDINTVRED 303

Query: 355 ISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL 414
           +SK K   N  ++++   + I S KRFDE  ISPLT+KAL+A+G ++MTRVQ+ATLS CL
Sbjct: 304 LSKRKSVDNVMEEKQEPHDSIYSAKRFDESCISPLTLKALSASGILKMTRVQDATLSECL 363

Query: 415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST-TQLVPPIYVLILCPTRELASQIAA 473
           +GKDA+VKAKTGTGKS+AFLLPAIE VLKA +S      V PI+ LILCPTRELASQIAA
Sbjct: 364 DGKDALVKAKTGTGKSMAFLLPAIETVLKAMNSGKGVNKVAPIFALILCPTRELASQIAA 423

Query: 474 EAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM 533
           E  ALLK HDGIGV TL+GGTRFK+DQ+RLES+PCQIL+ATPGRLLDHIENKSGL+ RLM
Sbjct: 424 EGKALLKFHDGIGVQTLIGGTRFKLDQQRLESEPCQILIATPGRLLDHIENKSGLTSRLM 483

Query: 534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTY 587
            LK+ ++DEAD LLDLGFR+DVE I+DCLPR+RQSLLFSAT+PKE      LVLKR+H+Y
Sbjct: 484 ALKLFIVDEADLLLDLGFRRDVEKIIDCLPRQRQSLLFSATIPKEVRRVSQLVLKRDHSY 543

Query: 588 IDTVGLGSVETPVKVSKYNI 607
           IDT+GLG VET  KV +  I
Sbjct: 544 IDTIGLGCVETHDKVRQSCI 563

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  477 bits (1227), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 289/605 (47%), Positives = 365/605 (60%), Gaps = 59/605 (9%)

Query: 27  MGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTKLFDKADPDS 86
           MGGGPRTFPGGL+KWQ KRMHEK A+ KE+ LL  EKQLY AR+RS+IR      A    
Sbjct: 1   MGGGPRTFPGGLSKWQHKRMHEKLARHKERGLLRHEKQLYLARLRSEIRASRLPAAGASP 60

Query: 87  ETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKSEQRPRS-------GAEANQRP 139
             +   P S   H++ALADRF+  GAEDLWNEDDGP+    RPR        G     R 
Sbjct: 61  PDDGDGPTSSRAHIRALADRFLLPGAEDLWNEDDGPIHRADRPRPPRRIVSVGGNGGDRR 120

Query: 140 RLAGAPIDL-RGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSASLIF--- 195
           +L     +L RG    +  + N   +  + +    +  S  +      R+K AS  F   
Sbjct: 121 KLDSTKQELPRGGKEPRLAAFNPRRDFQTAAPWWWQWSSSSA---IPSRTKEASFCFFGP 177

Query: 196 ------MPNLECND---GETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDT 246
                 MP  + +    G +++P       + R   S   +    + +G      A    
Sbjct: 178 KRSYSVMPLFQAHQESSGTSMVP------LIARGLASA--RIAPSQLNGERFYSFAAGRF 229

Query: 247 GNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEK 306
           G K +P + +  +   +   K+M             RF R   +SS+++S  D      +
Sbjct: 230 GRKLRPDSSDEDDEDISTAKKDM-------------RFARF-GASSEEESGYD------E 269

Query: 307 VEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEH-DFEEQVELIRKEISKNKLNGNGE 365
           +E    ++K  SSA+L   DMK  +R  LKS E+E+ D       +R+EI   ++ G   
Sbjct: 270 LEARSAIRKKWSSAALRNCDMKKERRA-LKSYEEENNDLAGSFRELREEIKNREVLGAER 328

Query: 366 KKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKT 425
           ++ +   E + + KRF+ECGISPLT+KALT AGY+Q T VQE  L  CLEGKD +VKAKT
Sbjct: 329 RRYESRGESLFTNKRFEECGISPLTVKALTDAGYVQTTVVQETALPMCLEGKDVLVKAKT 388

Query: 426 GTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI 485
           GTGKS AFLLPAIE+VL A  S T   V PI+ LILCPTRELA Q+ AEA  LLK H GI
Sbjct: 389 GTGKSAAFLLPAIESVLNAMKSHTNHRVSPIFSLILCPTRELAIQLTAEANVLLKYHQGI 448

Query: 486 GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH 545
           GV +L+GGTRFK+DQRRLESDPCQILVATPGRLLDHIENKS  SVRLMGLK+LVLDEADH
Sbjct: 449 GVQSLIGGTRFKLDQRRLESDPCQILVATPGRLLDHIENKSSFSVRLMGLKLLVLDEADH 508

Query: 546 LLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETP 599
           LLDLGFR D+E IVD LPR+RQ+LLFSAT+PKE      LVLKR+H ++DTVGLG+VETP
Sbjct: 509 LLDLGFRTDIEKIVDSLPRQRQTLLFSATIPKEVRRVSQLVLKRDHVFVDTVGLGAVETP 568

Query: 600 VKVSK 604
            KV +
Sbjct: 569 TKVEQ 573

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9FNM7|RH26_ARATH DEAD-box ATP-dependent RNA helicase 26 OS=Arabidopsis thaliana GN=RH26 PE=1 SV=2

 Score =  287 bits (735), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/262 (54%), Positives = 191/262 (72%), Gaps = 7/262 (2%)

Query: 350 LIRKEISKNKLNGNGEKKEK-REEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEA 408
           LI+K  S   +  +    E  +  +  LS+ RFD+  +SPL++KA+  AG+  MT VQEA
Sbjct: 352 LIKKAASAKAVQTDKPTGEHVKTSDSYLSKTRFDQFPLSPLSLKAIKDAGFETMTVVQEA 411

Query: 409 TLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA 468
           TL   L+GKD + KAKTGTGK++AFLLPAIEAV+K+  +S     PPI VL++CPTRELA
Sbjct: 412 TLPIILQGKDVLAKAKTGTGKTVAFLLPAIEAVIKSPPASRDSRQPPIIVLVVCPTRELA 471

Query: 469 SQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGL 528
           SQ AAEA  LLK H  IGV  ++GGT+   +QRR++++PCQILVATPGRL DHIEN SG 
Sbjct: 472 SQAAAEANTLLKYHPSIGVQVVIGGTKLPTEQRRMQTNPCQILVATPGRLKDHIENTSGF 531

Query: 529 SVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLK 582
           + RLMG+K+LVLDEADHLLD+GFR+D+E I+  +P++RQ+ LFSAT+P+E      + LK
Sbjct: 532 ATRLMGVKVLVLDEADHLLDMGFRRDIERIIAAVPKQRQTFLFSATVPEEVRQICHVALK 591

Query: 583 REHTYIDTVGLGSVETPVKVSK 604
           R+H +I+ V  GS ET  KV++
Sbjct: 592 RDHEFINCVQEGSGETHQKVTQ 613

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  275 bits (703), Expect = 8e-73,   Method: Compositional matrix adjust.
 Identities = 154/324 (47%), Positives = 209/324 (64%), Gaps = 25/324 (7%)

Query: 292 SDDDSDIDSEDVDEKVEGWRD--VKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVE 349
           S+DDS++   D D+   G+ D      G   +L +   K     P +S++ E   +E V 
Sbjct: 7   SEDDSELGEVDEDDGPSGFEDDLFDDEGGEKNLVESPAK--NSAPFESIKGEPIDQEGVV 64

Query: 350 LIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEAT 409
             R+       +G G+          LSQ RFDEC +SPLT+K + AAGY +MT VQEAT
Sbjct: 65  HTRE-------SGGGDS--------YLSQTRFDECSLSPLTLKGVKAAGYERMTAVQEAT 109

Query: 410 LSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELAS 469
           L   L+GKD + KAKTGTGK++AFLLPAIE V K       +  PPI V+++CPTRELA 
Sbjct: 110 LPIILKGKDVLAKAKTGTGKTVAFLLPAIEVVSKLPPIDCDKKRPPISVVVVCPTRELAD 169

Query: 470 QIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLS 529
           Q AAEA  LLK H  IGV  ++GGTR  ++Q+R+ ++PCQILVATPGRL DH+EN  G +
Sbjct: 170 QAAAEANKLLKFHPSIGVQLVIGGTRMALEQKRMHTNPCQILVATPGRLKDHMENTPGFA 229

Query: 530 VRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKR 583
            RLMG+K+L+LDEAD LLD+GFR D+E IV  LP++RQ+LLFSAT+P E      + +KR
Sbjct: 230 TRLMGVKVLILDEADRLLDMGFRTDIERIVAALPKQRQTLLFSATVPDEVRQVCHIAMKR 289

Query: 584 EHTYIDTVGLGSVETPVKVSKYNI 607
           +  +++TV  GS ET  +V + ++
Sbjct: 290 DLEFVNTVEEGSEETHSQVKQMHV 313

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9FFQ1|RH31_ARATH DEAD-box ATP-dependent RNA helicase 31 OS=Arabidopsis thaliana GN=RH31 PE=2 SV=2

 Score =  272 bits (695), Expect = 7e-72,   Method: Compositional matrix adjust.
 Identities = 129/247 (52%), Positives = 180/247 (72%), Gaps = 6/247 (2%)

Query: 367 KEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTG 426
           K +   +  L++ RFD   +SPL++KA+  AGY  MT VQEATL   L+GKD + KAKTG
Sbjct: 236 KTRNANDSYLTKTRFDHYPLSPLSLKAIKDAGYETMTVVQEATLPIILKGKDVLAKAKTG 295

Query: 427 TGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIG 486
           TGK++AFLLP+IE V+K+  +S     PPI  L++CPTRELA+Q A EA  LLK H  IG
Sbjct: 296 TGKTVAFLLPSIEVVVKSPPTSPDNKRPPILALVICPTRELANQAATEANTLLKYHPSIG 355

Query: 487 VLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL 546
           V  ++GGTR  ++Q+R++++PCQILVATPGRL DHIEN  G + RL G+K+LVLDEADHL
Sbjct: 356 VQVVIGGTRLGLEQKRMQTNPCQILVATPGRLKDHIENTPGFATRLKGVKVLVLDEADHL 415

Query: 547 LDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPV 600
           LD+GFRKD+E I+  +P+ RQ+ LFSAT+P+E      + L+R+H +++ V  G++ET  
Sbjct: 416 LDMGFRKDIERIISAVPKERQTFLFSATVPEEVRQICLVALRRDHEFVNCVHEGTIETHQ 475

Query: 601 KVSKYNI 607
           +V + ++
Sbjct: 476 QVRQMHM 482

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q94C75|RH25_ARATH DEAD-box ATP-dependent RNA helicase 25 OS=Arabidopsis thaliana GN=RH25 PE=2 SV=2

 Score =  271 bits (694), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 134/235 (57%), Positives = 175/235 (74%), Gaps = 6/235 (2%)

Query: 376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLL 435
           LS+ RFD+  +SPLT+K +  AG+  MT VQEATL   L+GKD + KAKTGTGK++AFLL
Sbjct: 77  LSKTRFDQFPLSPLTLKGIEDAGFKTMTVVQEATLPLILQGKDILAKAKTGTGKTVAFLL 136

Query: 436 PAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
           P+IEAV+KA  +S     PPI VL++CPTRELA Q AAEA  LLK H  IGV  ++GGT+
Sbjct: 137 PSIEAVIKAPPASRDNRHPPIIVLVVCPTRELACQAAAEANILLKYHPSIGVQVVIGGTK 196

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
              +QRRL+  PCQILVATPGRL DHI+N SG + RLMG+K+LVLDEADHLLD+GFR+++
Sbjct: 197 LPTEQRRLQKSPCQILVATPGRLKDHIDNTSGFATRLMGVKVLVLDEADHLLDMGFRREI 256

Query: 556 ENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVSK 604
           E I+  +P++RQ+ LFSAT+  E      + LKR+H +++ V  G+ ET  KVS+
Sbjct: 257 ERIIAAVPKQRQTFLFSATVSDEVRQICHVALKRDHEFVNCVQEGAGETHQKVSQ 311

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  265 bits (677), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 130/235 (55%), Positives = 174/235 (74%), Gaps = 6/235 (2%)

Query: 376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLL 435
           LS  RFD+C ISPL++KA+  AGY +MT+VQEATL   L+GKD + KAKTGTGK++AFLL
Sbjct: 123 LSDTRFDQCTISPLSLKAVKDAGYERMTQVQEATLPVILQGKDVLAKAKTGTGKTVAFLL 182

Query: 436 PAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
           PAIE +    +S   QL P I +L++CPTRELA Q+A EA  LLK H  +GV  ++GGTR
Sbjct: 183 PAIEVLSALPNSRRDQLRPSINLLVMCPTRELAIQVAVEAKKLLKYHRSLGVQVVIGGTR 242

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
              +QR ++++PCQILVATPGRL DH+EN  G S RL G+K+LVLDEAD LLD+GFR+D+
Sbjct: 243 LTQEQRSMQANPCQILVATPGRLKDHVENTPGFSTRLKGVKVLVLDEADRLLDMGFRRDI 302

Query: 556 ENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVSK 604
           E I+  +P+ RQ+LLFSAT+P+E      + +K+ + +I+TV  G  ET  +VS+
Sbjct: 303 ERIIASVPKERQTLLFSATVPEEVRQISHIAMKKNYKFINTVKDGDEETHAQVSQ 357

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

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

 Score =  258 bits (658), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 132/248 (53%), Positives = 180/248 (72%), Gaps = 13/248 (5%)

Query: 376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLL 435
           LS+ RFD+C +SPL++KA+  AGY +MT+VQEATL   L+G+D + KAKTGTGK++AFLL
Sbjct: 71  LSETRFDQCPVSPLSLKAIKDAGYEKMTQVQEATLPIILQGEDVLAKAKTGTGKTVAFLL 130

Query: 436 PAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
           PAIE +      ST    P I +L++CPTRELA+Q+AAEA  LLK H  +GV  ++GGT+
Sbjct: 131 PAIELL------STLPRSPSINLLVICPTRELANQVAAEARKLLKYHRSLGVQVVIGGTK 184

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
              +QR ++S+PCQILVATPGRL DH+EN  G S R+ G+K+LVLDEAD LLD+GFR+D+
Sbjct: 185 LPQEQRSMQSNPCQILVATPGRLKDHLENTPGFSNRIKGVKVLVLDEADRLLDMGFRRDI 244

Query: 556 ENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVSK-YNIY 608
           E I+  +P+ RQ+LLFSAT+P+E      + +KR + +I+TV  G  ET  +VS+ Y + 
Sbjct: 245 EKIIAFIPKERQTLLFSATVPEEVRQISHIAMKRGYKFINTVKEGDEETHSQVSQMYMVA 304

Query: 609 VFVLVLSI 616
              L  SI
Sbjct: 305 PLDLHFSI 312

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8K9H6|DEAD_BUCAP Cold-shock DEAD box protein A homolog OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) GN=deaD PE=3 SV=1

 Score =  147 bits (372), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 86/203 (42%), Positives = 122/203 (60%), Gaps = 12/203 (5%)

Query: 377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLP 436
           ++  F   G++P  IK+L+  GY++ + +Q A +   LEG+D +  A+TG+GK+ AF LP
Sbjct: 4   TESTFSFLGLNPFIIKSLSKMGYVKPSPIQAACIPLLLEGRDVLGMAQTGSGKTAAFSLP 63

Query: 437 AIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF 496
            +  +          L  P  +L+L PTRELA Q+A       K   GI VL L GG R+
Sbjct: 64  LLHNL-------NINLKAP-QILVLAPTRELAVQVAEAFSDFSKYIMGIHVLPLYGGQRY 115

Query: 497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE 556
           +V  R L   P QI+V TPGRLLDH+  K G ++ L  L  LVLDEAD +L +GF +DVE
Sbjct: 116 EVQLRALRQGP-QIVVGTPGRLLDHL--KRG-TLNLSNLYALVLDEADEMLRMGFIEDVE 171

Query: 557 NIVDCLPRRRQSLLFSATMPKEL 579
            I+  +P+  Q+ LFSATMP+ +
Sbjct: 172 TIMSQIPKEHQTALFSATMPEAI 194

Has a helix-destabilizing activity.

Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) (taxid: 198804)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	633
255537383	771	dead box ATP-dependent RNA helicase, put	0.827	0.679	0.575	1e-177
449452480	813	PREDICTED: putative DEAD-box ATP-depende	0.911	0.709	0.525	1e-173
224074899	798	predicted protein [Populus trichocarpa]	0.849	0.674	0.573	1e-162
224053943	784	predicted protein [Populus trichocarpa]	0.834	0.673	0.570	1e-161
15226161	845	putative DEAD-box ATP-dependent RNA heli	0.838	0.628	0.514	1e-159
15221724	798	putative DEAD-box ATP-dependent RNA heli	0.868	0.689	0.516	1e-159
297837065	793	hypothetical protein ARALYDRAFT_315081 [	0.875	0.698	0.504	1e-155
297837071	808	hypothetical protein ARALYDRAFT_893124 [	0.872	0.683	0.504	1e-152
413939551	818	putative DEAD-box ATP-dependent RNA heli	0.883	0.683	0.484	1e-137
242067048	823	hypothetical protein SORBIDRAFT_04g03793	0.876	0.674	0.475	1e-136

>gi|255537383|ref|XP_002509758.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223549657|gb|EEF51145.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  629 bits (1622), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 356/619 (57%), Positives = 430/619 (69%), Gaps = 95/619 (15%)

Query: 2   SSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQ 61
           S SV+L+RSK +++ L   R+F R MGGGPRTFPGGLNKWQWKR+HEK+AKEKEK LLEQ
Sbjct: 4   SISVILRRSKTVSDHLQ-TRIFTRLMGGGPRTFPGGLNKWQWKRLHEKRAKEKEKSLLEQ 62

Query: 62  EKQLYQARVRSQIRTKLFDKADPDSETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDG 121
           EKQLYQAR+RSQIR+KL  + D +  TN +   SP +H+KALADRFMKEGAEDLWNEDDG
Sbjct: 63  EKQLYQARIRSQIRSKLAGEPDSNPNTNNYSATSPKDHIKALADRFMKEGAEDLWNEDDG 122

Query: 122 PVKSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSE 181
           P+ S Q P+S    NQR    G         S++R      G++N+  +++         
Sbjct: 123 PLTS-QLPKS----NQRSGSIG---------SNQR-----PGSINTPIDLR--------- 154

Query: 182 SKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDK 241
                                  + ++ +R+V +F   +Y + T  R +  N        
Sbjct: 155 -----------------------KVMLEARSVHNFENLSY-NYTKTREYSVN-------- 182

Query: 242 AGFDTGNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGK--RRFKRNESSSSDDDSDID 299
             F+ G K                  N S+ +KK+  + +  RRF+RNESSS +DD D D
Sbjct: 183 -SFNLGQK----------------QSNESDNLKKRGLISQKVRRFRRNESSSGEDDGDYD 225

Query: 300 SEDVDEKVEGWRDVKKM-GSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEI-SK 357
            ++  EK    R+V+++ GS A+LGKYD+KI+KRVPLK LE+E DFE     IR E+ +K
Sbjct: 226 CDNEREK--KGRNVREIIGSRAALGKYDVKISKRVPLKELEEETDFE----FIRYELENK 279

Query: 358 NKLNGNG-EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG 416
            KL+ N  EK E  E+E IL Q+RFDECGISPLT+KALT AGY+QMTRVQEATLSACLEG
Sbjct: 280 MKLDRNDREKSEIDEQESILGQRRFDECGISPLTVKALTTAGYVQMTRVQEATLSACLEG 339

Query: 417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI 476
           KDA+VKAKTGTGKS AFLLPAIEAVLKA SS+    V PIYVLILCPTRELASQIAAEA 
Sbjct: 340 KDALVKAKTGTGKSAAFLLPAIEAVLKAKSSNVKPRVSPIYVLILCPTRELASQIAAEAN 399

Query: 477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK 536
           A+LK HDGI V TLVGGTRFK DQ+RLE +PCQI+VATPGRLLDHIENK GLSV LMGLK
Sbjct: 400 AMLKYHDGISVQTLVGGTRFKDDQKRLEMNPCQIIVATPGRLLDHIENKGGLSVHLMGLK 459

Query: 537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDT 590
           ML+LDEADHLLDLGFRKDVE I+DCLPR R SL+FSAT+PKE      LVLKREH +IDT
Sbjct: 460 MLILDEADHLLDLGFRKDVEKIIDCLPRERHSLMFSATIPKEVRRISQLVLKREHAFIDT 519

Query: 591 VGLGSVETPVKVSKYNIYV 609
           VGLGSVETP KV ++++ V
Sbjct: 520 VGLGSVETPSKVKQFSVVV 538

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452480|ref|XP_004143987.1| PREDICTED: putative DEAD-box ATP-dependent RNA helicase 33-like [Cucumis sativus] gi|449495891|ref|XP_004159976.1| PREDICTED: putative DEAD-box ATP-dependent RNA helicase 33-like [Cucumis sativus]

 Score =  614 bits (1584), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 351/668 (52%), Positives = 446/668 (66%), Gaps = 91/668 (13%)

Query: 1   MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLE 60
           M+SSVLL R +  +++L    +F+R MGGGPRTFPGGLNKWQWKRMHEK+AKEKEKRLLE
Sbjct: 1   MTSSVLLDRHRTFSSLLC-KLIFSRSMGGGPRTFPGGLNKWQWKRMHEKRAKEKEKRLLE 59

Query: 61  QEKQLYQARVRSQIRTKLF-------DKADPDSETNQHKPMSPDEHVKALADRFMKEGAE 113
           QEKQLYQAR+RS IR+KL        + +DP   +  + P SP EH+  LA+RFMK+GA 
Sbjct: 60  QEKQLYQARIRSDIRSKLVGAHETSKNNSDP---STSYSPKSPSEHINDLANRFMKQGAI 116

Query: 114 DLWNEDDGPVKSEQRPRSGAEANQRPRLAG--------APIDLRGLISDKRNSVNNSGNL 165
           DLWNEDDGP+K+   PR  A      R+A         +PID++ L+++  +    S  +
Sbjct: 117 DLWNEDDGPLKTPL-PRPAALNEGSRRIASNVRSGSIRSPIDVKRLLAENHDGFVGSHYM 175

Query: 166 N-SGSNVKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSG 224
             +G NVK R+YSV S                                            
Sbjct: 176 GLNGDNVKGRSYSVQS-------------------------------------------- 191

Query: 225 TDKRNFCRNDGSSTRDKAGFDTG-NKAKPFARNLGNNRE-NGDSKNMSEFMKKKCFVGKR 282
             +R+F RN+ SS+ D   +++G +  KPFA  L  + + N  S+N++     +  V +R
Sbjct: 192 --RRSFRRNESSSSDDDMDYNSGVDSIKPFANKLARSPDRNAKSRNLNGISNDRKAVPQR 249

Query: 283 RFK--RNESSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLED 340
           + K  RN S SSDDDS+ +  +VD+ +  W+ +K  GSSASLGK D+++ KRVPLK  ++
Sbjct: 250 KMKFWRNGSLSSDDDSEEEFGNVDKDLRSWKGLK-TGSSASLGKCDVRMKKRVPLKPFDE 308

Query: 341 EHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYI 400
           E DF EQVEL+R E+SK       E++ ++ EE I ++KRFDECGISPLT+KAL+ +GY+
Sbjct: 309 ESDFAEQVELLRYELSKK---SAAEEEGEKREEIIFTEKRFDECGISPLTVKALSFSGYV 365

Query: 401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLI 460
           +MTRVQEATLS CLEGKD +VK+KTG+GKS+AFLLPAIEAVLKA  SS+ Q VPPI+VLI
Sbjct: 366 RMTRVQEATLSLCLEGKDTLVKSKTGSGKSVAFLLPAIEAVLKAACSSSNQRVPPIFVLI 425

Query: 461 LCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLD 520
           LCPTRELA QIAAEA  LLK HDGIGV TLVGGTRFK DQ+RLES P QI+VATPGRLLD
Sbjct: 426 LCPTRELACQIAAEANVLLKYHDGIGVQTLVGGTRFKDDQKRLESFPSQIIVATPGRLLD 485

Query: 521 HIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE-- 578
           H+EN+SGLS+RLMGLKML+LDEADHLLDLGFRKD+E IVDCLPR+RQSLLFSAT+P+E  
Sbjct: 486 HVENRSGLSLRLMGLKMLILDEADHLLDLGFRKDIEKIVDCLPRQRQSLLFSATIPREVR 545

Query: 579 ----LVLKREHTYIDTVGLGSVETPVKV----------SKYNIYVFVLVLSIKIQAFYII 624
               LVLKREH +++ VG+G VETPV+V          S + I   +L   I     Y +
Sbjct: 546 RISQLVLKREHVFVNNVGIGCVETPVQVKQSCLIAPHGSHFQIVCHLLKEHISCTPDYKV 605

Query: 625 CFVYTISM 632
               T  M
Sbjct: 606 IVFCTTGM 613

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074899|ref|XP_002304481.1| predicted protein [Populus trichocarpa] gi|222841913|gb|EEE79460.1| predicted protein [Populus trichocarpa]

 Score =  579 bits (1493), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 354/617 (57%), Positives = 424/617 (68%), Gaps = 79/617 (12%)

Query: 6   LLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQL 65
           LL+RSK L+  L   RV  R MGGGP +FPGGLNKWQWKR+HEKKAKEKEKRLL+QEKQL
Sbjct: 5   LLRRSKFLSEQLR-TRVVIRLMGGGPLSFPGGLNKWQWKRLHEKKAKEKEKRLLDQEKQL 63

Query: 66  YQARVRSQIRTKLFDKADPD--SETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDG-- 121
           +Q R+RSQIR+ L  ++ P+   + N++ PMSP+EH+KALADRFMK+GAEDLWNE+DG  
Sbjct: 64  FQDRMRSQIRSNLAGQSHPNLNPDPNKYNPMSPNEHLKALADRFMKDGAEDLWNENDGSL 123

Query: 122 -PVKSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLS 180
            P   EQ    G   NQ+P    +P+DLR LIS+                    +YS+L 
Sbjct: 124 KPPSDEQTEFVGT--NQQPGSIHSPVDLRKLISEG-------------------HYSMLR 162

Query: 181 ESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRD 240
           +  F                 + G++  P        RR       +R F  N+ SS+ D
Sbjct: 163 DLGFE----------------SGGDSTKP------LARR-------QRKFRINESSSSDD 193

Query: 241 KA--GFDTGNKAKPFARNLGNNREN-GDSKNMSEFMKKKC--FVGKRRFKRNESSSSDDD 295
               GF   +K K F  +  N R    + +N+S+FMK +    V +RRF+RNES   D  
Sbjct: 194 DEDHGF-VNDKVKNFVGDSWNERGGVSNLRNVSDFMKNRGSETVKQRRFQRNESDDED-- 250

Query: 296 SDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEI 355
                +         R    +GS A+LGKYDMK T+RVPLK L D++DF  +VELIR E+
Sbjct: 251 ----EDLEGGGDRRGRSATDIGSRAALGKYDMKKTRRVPLKEL-DKNDFANEVELIRYEL 305

Query: 356 S-KNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL 414
             K K  GN  + +K EE+ ILS+KRFDECG+SPLT+KAL AAGY+QMTRVQEATLS CL
Sbjct: 306 GRKKKFAGN--EGDKEEEDSILSEKRFDECGLSPLTVKALIAAGYVQMTRVQEATLSVCL 363

Query: 415 E-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAA 473
           E GKDA+VKAKTGTGKS AFLLPAIEAVLKATSS+    V PIY LILCPTRELASQIAA
Sbjct: 364 EAGKDAMVKAKTGTGKSAAFLLPAIEAVLKATSSNDKPQVSPIYALILCPTRELASQIAA 423

Query: 474 EAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM 533
           EA A+LK HDGIGVLTLVGGTRFK DQRRLESDP QI+VATPGRLLDHIENK GLSV LM
Sbjct: 424 EANAMLKYHDGIGVLTLVGGTRFKDDQRRLESDPYQIIVATPGRLLDHIENKGGLSVHLM 483

Query: 534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTY 587
           GLK+L+LDEADHLLDLGFRKD+E I+DCLPR+RQSLLFSAT+PKE      LVLKREH +
Sbjct: 484 GLKVLILDEADHLLDLGFRKDMEKILDCLPRQRQSLLFSATIPKEVRRISQLVLKREHAF 543

Query: 588 IDTVGLGSVETPVKVSK 604
           I+TVG+G VETP K+ +
Sbjct: 544 INTVGVGCVETPAKIKQ 560

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224053943|ref|XP_002298050.1| predicted protein [Populus trichocarpa] gi|222845308|gb|EEE82855.1| predicted protein [Populus trichocarpa]

 Score =  574 bits (1479), Expect = e-161,   Method: Compositional matrix adjust.
 Identities = 350/613 (57%), Positives = 420/613 (68%), Gaps = 85/613 (13%)

Query: 6   LLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQL 65
           L+ RSK L+  L   R+F R MGGGPRTFPGGLNKWQWKR+HEKKAKEKEKRLL+QEKQL
Sbjct: 5   LIHRSKSLSEQLR-TRIFIRLMGGGPRTFPGGLNKWQWKRLHEKKAKEKEKRLLDQEKQL 63

Query: 66  YQARVRSQIRTKLFDKADPD--SETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPV 123
           YQAR+RS IR+KL  + DP+   + ++  PMSP EH+KALADRFMKEGAEDLWNE DGP+
Sbjct: 64  YQARMRSNIRSKLAGQPDPNLNPDPSKFNPMSPKEHIKALADRFMKEGAEDLWNEMDGPL 123

Query: 124 KSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESK 183
           K        A +++RP   G         +++R      G++NS  +++     ++SE +
Sbjct: 124 K--------APSDERPGFVG---------TNQR-----PGSINSPLDLR----KLMSEGR 157

Query: 184 FSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAG 243
              R +  +                               G + R F  N+ SS+ D   
Sbjct: 158 NVSRHREEN-------------------------------GFNYRKFRINESSSSDDDED 186

Query: 244 FDTGN-KAKPFARNLGNNREN-GDSKNMSEFMKKKCF--VGKRRFKRNESSSSDDDSDID 299
           +   N K   F R+ GN R    +S+N+SEFMK K F    +RRF RNES        +D
Sbjct: 187 YGFVNDKVMNFGRDSGNERGAVSNSRNVSEFMKNKGFETQKQRRFGRNES--------VD 238

Query: 300 SEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEIS-KN 358
            E   E+    R  K++GS  +LGKYD+K T+RVP K LE ++DF  +VELIR E+  K 
Sbjct: 239 LEGGGER--RGRSAKEIGSRDALGKYDVKKTRRVPSKELE-KNDFANEVELIRYELGRKK 295

Query: 359 KLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE-GK 417
           KL GN    E  +E+ ILS KRFDECG+SPLT+KALTAAGY+QMTRVQEATLS CLE GK
Sbjct: 296 KLAGNDGDNE--DEDSILSDKRFDECGLSPLTVKALTAAGYVQMTRVQEATLSVCLEAGK 353

Query: 418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA 477
           DA+VKAKTG GKS AFLLPAIEAVLKA SS+    V PIYVLILCPTRELASQIAAEA A
Sbjct: 354 DAMVKAKTGKGKSAAFLLPAIEAVLKARSSNAKLRVSPIYVLILCPTRELASQIAAEANA 413

Query: 478 LLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM 537
           +LK HDGI + TLVGGTRFK DQR LESDPCQILVATPGRLLDHIENKSGLS+ L GLKM
Sbjct: 414 ILKYHDGIVMQTLVGGTRFKDDQRCLESDPCQILVATPGRLLDHIENKSGLSMHLKGLKM 473

Query: 538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTV 591
           L+LDEADHLLDLGFRKDVE IVDCLPR+RQSLLFSAT+PKE      LVLKREH +++TV
Sbjct: 474 LILDEADHLLDLGFRKDVEKIVDCLPRQRQSLLFSATIPKEVHRISQLVLKREHDFVNTV 533

Query: 592 GLGSVETPVKVSK 604
           G+  +ETP K+ +
Sbjct: 534 GVSCMETPAKIKQ 546

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226161|ref|NP_178818.1| putative DEAD-box ATP-dependent RNA helicase 33 [Arabidopsis thaliana] gi|75318697|sp|O80792.1|RH33_ARATH RecName: Full=Putative DEAD-box ATP-dependent RNA helicase 33 gi|3327394|gb|AAC26676.1| putative RNA helicase [Arabidopsis thaliana] gi|330251036|gb|AEC06130.1| putative DEAD-box ATP-dependent RNA helicase 33 [Arabidopsis thaliana]

 Score =  567 bits (1462), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 311/604 (51%), Positives = 407/604 (67%), Gaps = 73/604 (12%)

Query: 17  LWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRT 76
           LW NR+F+R MGGGPRTFPGGLNKWQWKRMHEKKA+EKE +LL+QEKQLY+AR+R++IR 
Sbjct: 67  LW-NRIFSRNMGGGPRTFPGGLNKWQWKRMHEKKAREKENKLLDQEKQLYEARIRTEIRA 125

Query: 77  KLFDKADPDSET----NQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKS-EQRPRS 131
           K++   D   +T      H PMSP EH+K LADRFMK GA+DLWN++DGPVK  +Q  RS
Sbjct: 126 KMWGHPDSGEKTAKLKQSHGPMSPKEHIKTLADRFMKAGADDLWNDNDGPVKKFDQGSRS 185

Query: 132 GAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSA 191
            +++     +   PID+R L+S   +S+     L+S      R +S +S  K ++ S   
Sbjct: 186 CSDS-----IDSTPIDVRRLVSATCDSMGKHRVLDSSR----RGFSSMSRFKRNESS--- 233

Query: 192 SLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAK 251
                    C++G+ V                                D    DT     
Sbjct: 234 ---------CDEGDDV--------------------------------DAKKLDT---LS 249

Query: 252 PFARNLGNNREN-GDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEKVEGW 310
           PF+      +E    S ++   ++ K   G+R+F++N+SS+ +D    D E  + K+ GW
Sbjct: 250 PFSPKFSGTKEKVKSSTSVVGVIRNKGLFGRRKFRKNDSSTEEDS---DEEGNEGKMIGW 306

Query: 311 RDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKR 370
            D++K GSSASLG +D+K+TKRV     ++E      +  +R+++SK +   N  ++++ 
Sbjct: 307 MDLRKTGSSASLGNHDIKLTKRVNRNVTDEELYPPLDINRVREDLSKKQSVDNVMEEKQE 366

Query: 371 EEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKS 430
             + I S KRFDE  ISPLT+KAL+A+G ++MTRVQ+ATLS CL+GKDA+VKAKTGTGKS
Sbjct: 367 PHDSIYSAKRFDESCISPLTLKALSASGIVKMTRVQDATLSECLDGKDALVKAKTGTGKS 426

Query: 431 IAFLLPAIEAVLKATSSST-TQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLT 489
           +AFLLPAIE VLKA +S      V PI+VLILCPTRELASQIAAE  ALLKNHDGIGV T
Sbjct: 427 MAFLLPAIETVLKAMNSGKGVHKVAPIFVLILCPTRELASQIAAEGKALLKNHDGIGVQT 486

Query: 490 LVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL 549
           L+GGTRF++DQ+RLES+PCQIL+ATPGRLLDHIENKSGL+ RLM LK+ ++DEAD LLDL
Sbjct: 487 LIGGTRFRLDQQRLESEPCQILIATPGRLLDHIENKSGLTSRLMALKLFIVDEADLLLDL 546

Query: 550 GFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVS 603
           GF++DVE I+DCLPR+RQSLLFSAT+PKE      LVLKR+H+YIDT+GLG VET  KV 
Sbjct: 547 GFKRDVEKIIDCLPRQRQSLLFSATIPKEVRRVSQLVLKRDHSYIDTIGLGCVETHDKVK 606

Query: 604 KYNI 607
           +  I
Sbjct: 607 QSCI 610

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221724|ref|NP_176514.1| putative DEAD-box ATP-dependent RNA helicase 48 [Arabidopsis thaliana] gi|75333533|sp|Q9C8S9.1|RH48_ARATH RecName: Full=Probable DEAD-box ATP-dependent RNA helicase 48 gi|12324351|gb|AAG52143.1|AC022355_4 putative RNA helicase; 42376-45543 [Arabidopsis thaliana] gi|332195955|gb|AEE34076.1| putative DEAD-box ATP-dependent RNA helicase 48 [Arabidopsis thaliana]

 Score =  567 bits (1461), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 320/620 (51%), Positives = 415/620 (66%), Gaps = 70/620 (11%)

Query: 1   MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLE 60
           M S +L +RS  +T  LW NR+ +R MGGGPRTFPGGLNKWQWKRMHEKKA+EKE +LL+
Sbjct: 1   MYSLILRERSGSITGSLW-NRISSRNMGGGPRTFPGGLNKWQWKRMHEKKAREKENKLLD 59

Query: 61  QEKQLYQARVRSQIRTKLFDKADPDSET----NQHKPMSPDEHVKALADRFMKEGAEDLW 116
           QEKQLY+AR+R++IR K++   D   +T      H PMSP EH+K LADRFMK GAED W
Sbjct: 60  QEKQLYEARIRTEIRAKMWGNPDSGEKTAKSKQSHGPMSPKEHIKTLADRFMKAGAEDFW 119

Query: 117 NEDDGPV-KSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNVKTRN 175
           NE+DGPV KS+Q  RSG+++      + +PID+R L+S   +S+  +    S      R 
Sbjct: 120 NENDGPVKKSDQGSRSGSDSID--STSNSPIDVRRLVSATCDSMGKNRVFGSSR----RG 173

Query: 176 YSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDG 235
           +S +S  K ++ S            C++G+         DF                   
Sbjct: 174 FSSMSRFKRNESS------------CDEGD---------DF------------------- 193

Query: 236 SSTRDKAGFDTGNKAKPFARNLGNNREN-GDSKNMSEFMKKKCFVGKRRFKRNESSSSDD 294
               D    DT     PF+      +E    S+++   ++ K   G+R+F++N+SS+   
Sbjct: 194 ----DAKKLDT---LSPFSPKFAGTKEKVKSSRSVVGVIRNKGLFGRRKFRKNDSSTE-- 244

Query: 295 DSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKE 354
             D D E  + K+ GW D++K GSSASLG +D+K+TKRV     ++E      +  +R++
Sbjct: 245 -EDSDEEGDEGKMIGWMDMRKTGSSASLGNHDIKLTKRVNRNVTDEELYPPLDINTVRED 303

Query: 355 ISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL 414
           +SK K   N  ++++   + I S KRFDE  ISPLT+KAL+A+G ++MTRVQ+ATLS CL
Sbjct: 304 LSKRKSVDNVMEEKQEPHDSIYSAKRFDESCISPLTLKALSASGILKMTRVQDATLSECL 363

Query: 415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST-TQLVPPIYVLILCPTRELASQIAA 473
           +GKDA+VKAKTGTGKS+AFLLPAIE VLKA +S      V PI+ LILCPTRELASQIAA
Sbjct: 364 DGKDALVKAKTGTGKSMAFLLPAIETVLKAMNSGKGVNKVAPIFALILCPTRELASQIAA 423

Query: 474 EAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM 533
           E  ALLK HDGIGV TL+GGTRFK+DQ+RLES+PCQIL+ATPGRLLDHIENKSGL+ RLM
Sbjct: 424 EGKALLKFHDGIGVQTLIGGTRFKLDQQRLESEPCQILIATPGRLLDHIENKSGLTSRLM 483

Query: 534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTY 587
            LK+ ++DEAD LLDLGFR+DVE I+DCLPR+RQSLLFSAT+PKE      LVLKR+H+Y
Sbjct: 484 ALKLFIVDEADLLLDLGFRRDVEKIIDCLPRQRQSLLFSATIPKEVRRVSQLVLKRDHSY 543

Query: 588 IDTVGLGSVETPVKVSKYNI 607
           IDT+GLG VET  KV +  I
Sbjct: 544 IDTIGLGCVETHDKVRQSCI 563

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297837065|ref|XP_002886414.1| hypothetical protein ARALYDRAFT_315081 [Arabidopsis lyrata subsp. lyrata] gi|297332255|gb|EFH62673.1| hypothetical protein ARALYDRAFT_315081 [Arabidopsis lyrata subsp. lyrata]

 Score =  556 bits (1433), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 316/626 (50%), Positives = 416/626 (66%), Gaps = 72/626 (11%)

Query: 1   MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLE 60
           M S +L +RS   T  LW +++F+R MGGGPRTFPGGLNKWQWKRMHEKKA+EKE +LL+
Sbjct: 1   MYSLILRERSGSFTGSLW-SQIFSRNMGGGPRTFPGGLNKWQWKRMHEKKAREKENKLLD 59

Query: 61  QEKQLYQARVRSQIRTKLFDKADPDSET----NQHKPMSPDEHVKALADRFMKEGAEDLW 116
           QEKQLY+AR+R++IR K++   D   +T      H PMSP EH+K LADRFMK GAEDLW
Sbjct: 60  QEKQLYEARIRTEIRAKMWGNPDSGEKTAKSKQSHGPMSPKEHIKTLADRFMKAGAEDLW 119

Query: 117 NEDDGPVKSE-------QRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGS 169
           NE+DGPVK         +R    + +N     + + ID+R L+S    S+ NS   +   
Sbjct: 120 NENDGPVKESDDGSGLTRRDNGRSGSNSIVSSSNSSIDVRKLVSGTCYSMGNSRVFDRSR 179

Query: 170 NVKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDKRN 229
               R +S +S  +F  R++S+         C++G+         DF             
Sbjct: 180 ----RGFSSMSRGRFK-RNESS---------CDEGD---------DF------------- 203

Query: 230 FCRNDGSSTRDKAGFDTGNKAKPFARNLGNNREN-GDSKNMSEFMKKKCFVGKRRFKRNE 288
                     D    DT     PF+      +E    S+++   ++ K   G+R+F++N+
Sbjct: 204 ----------DAKKLDT---LSPFSLKFAGTKEKVKSSRSVDGVIRNKGLFGRRKFRKND 250

Query: 289 SSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQV 348
           SS+     D + E  + K+ GW D++K GSSASLG +D+K+TKRV     ++E      +
Sbjct: 251 SSTE---EDSEEEGEEGKMIGWMDLRKTGSSASLGNHDIKLTKRVNRNVTDEELYPPLDI 307

Query: 349 ELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEA 408
             +R+++SK K   N  K+ +   +   S+KRFDE  ISPLT+KAL+A+G + MTRVQ+A
Sbjct: 308 NTVREDLSKRKSVDNVIKENREPHDSFYSRKRFDESSISPLTLKALSASGIVNMTRVQDA 367

Query: 409 TLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSS-STTQLVPPIYVLILCPTREL 467
           TLS CL+GKDA+VKAKTGTGKS+AFLLPAIE VLKA ++ ++   VPPI+ LILCPTREL
Sbjct: 368 TLSECLDGKDALVKAKTGTGKSMAFLLPAIETVLKAMNNGNSVHKVPPIFALILCPTREL 427

Query: 468 ASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG 527
           ASQI+AE +ALLK HDGIGV TL+GGTRFK+DQ+RLES+PCQIL+ATPGRLLDHIENKSG
Sbjct: 428 ASQISAEGMALLKYHDGIGVQTLIGGTRFKLDQQRLESEPCQILIATPGRLLDHIENKSG 487

Query: 528 LSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVL 581
           L+ RLM LK+ ++DEAD LLDLGFR+DVE I+DCLPR+RQSLLFSAT+PKE      LVL
Sbjct: 488 LTSRLMALKLFIVDEADLLLDLGFRRDVEKIIDCLPRQRQSLLFSATIPKEVRRVSQLVL 547

Query: 582 KREHTYIDTVGLGSVETPVKVSKYNI 607
           KR+H+YIDT+GLG VET  KV +  I
Sbjct: 548 KRDHSYIDTIGLGCVETHDKVKQSCI 573

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297837071|ref|XP_002886417.1| hypothetical protein ARALYDRAFT_893124 [Arabidopsis lyrata subsp. lyrata] gi|297332258|gb|EFH62676.1| hypothetical protein ARALYDRAFT_893124 [Arabidopsis lyrata subsp. lyrata]

 Score =  544 bits (1402), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 317/628 (50%), Positives = 409/628 (65%), Gaps = 76/628 (12%)

Query: 1   MSSSVLLQRSKPLTNILWFNRVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLE 60
           M S +L +RS   T  LW +R+F+R MGGGPRTFPGGLNKWQWKRMHEKKA+EKE +LL+
Sbjct: 1   MYSLILRERSGSFTGSLW-SRIFSRNMGGGPRTFPGGLNKWQWKRMHEKKAREKENKLLD 59

Query: 61  QEKQLYQARVRSQIRTKLFDKADPDSET----NQHKPMSPDEHVKALADRFMKEGAEDLW 116
           QEKQLY+AR+R++IR K++   D   +T      H PMSP EH+K LADRFMK GAEDLW
Sbjct: 60  QEKQLYEARIRTEIRAKMWGNPDSGEKTAKSKQSHGPMSPKEHIKTLADRFMKAGAEDLW 119

Query: 117 NE--------DDGPVKSEQ-RPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNS 167
           NE        DDG   S +   RSG+ +      +   +  R L+S    S+ NS   + 
Sbjct: 120 NENDGPMKESDDGSGLSRRDNGRSGSNSIDSSSNSSIDV--RKLVSGTCYSMGNSRVFDR 177

Query: 168 GSNVKTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRNVMDFVRRAYFSGTDK 227
                 R +S +S  +F  R++S+         C++G+         DF           
Sbjct: 178 SR----RGFSSMSRGRFK-RNESS---------CDEGD---------DF----------- 203

Query: 228 RNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNREN-GDSKNMSEFMKKKCFVGKRRFKR 286
                       D    DT     PF+      +E    SKN+   ++ K   G+R+F++
Sbjct: 204 ------------DAKKLDT---LSPFSPKFAGTKEKVKSSKNVVGVIRNKGLFGRRKFRK 248

Query: 287 NESSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEE 346
           N+SS+ +D      E  + K+  W D++KMGSSA+LG +D+K+TKRV     ++E     
Sbjct: 249 NDSSTEEDSE---EEGEEGKMNVWLDLRKMGSSAALGNHDIKLTKRVNRNVTDEELYPPL 305

Query: 347 QVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQ 406
            +  +R+++SK K   N  ++ +   + I S KRFDE  ISPLT+KAL+A+G ++MTRVQ
Sbjct: 306 DINTVREDLSKRKSVDNVIEENREPHDSIYSGKRFDESSISPLTLKALSASGIVKMTRVQ 365

Query: 407 EATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST-TQLVPPIYVLILCPTR 465
           +ATLS CL+GKDA+VKAKTGTGKS+AFLLPAIE VLKA +S      V PI+ LILCPTR
Sbjct: 366 DATLSECLDGKDALVKAKTGTGKSMAFLLPAIETVLKAMNSGNGVHKVAPIFALILCPTR 425

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENK 525
           ELASQIAAE  ALLK HDGIGV TL+GGTRFK+DQ+RLES+PCQIL+ATPGRLLDHIENK
Sbjct: 426 ELASQIAAEGKALLKYHDGIGVQTLIGGTRFKLDQQRLESEPCQILIATPGRLLDHIENK 485

Query: 526 SGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------L 579
           SGL+ RLM LK+ ++DEAD LLDLGFR+DVE I+DCLPR+RQSLLFSAT+PKE      L
Sbjct: 486 SGLTSRLMALKLFIVDEADLLLDLGFRRDVEKIIDCLPRQRQSLLFSATIPKEVRRVSQL 545

Query: 580 VLKREHTYIDTVGLGSVETPVKVSKYNI 607
           VLKR+H+YIDT+GLG VET  KV +  I
Sbjct: 546 VLKRDHSYIDTIGLGCVETHDKVKQSCI 573

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413939551|gb|AFW74102.1| putative DEAD-box ATP-dependent RNA helicase family protein [Zea mays]

 Score =  495 bits (1275), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 295/609 (48%), Positives = 386/609 (63%), Gaps = 50/609 (8%)

Query: 27  MGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTKLFDKADPDS 86
           MGGGPRTFPGGL+KWQ+KRMHEK A++K++ LL  EKQLY AR+RS+IR      A  ++
Sbjct: 1   MGGGPRTFPGGLSKWQYKRMHEKLARQKQRGLLRHEKQLYLARLRSEIRASRLPGAAAEA 60

Query: 87  ETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKSEQRP----RSGAEANQRPRLA 142
                 P S   H++ALADRF + GAEDLWNEDDGP++  +RP     SG    Q+   +
Sbjct: 61  PPGGEGPTSSRAHIRALADRFRRPGAEDLWNEDDGPLRRVKRPPTGIASGVRHQQQQLDS 120

Query: 143 GAPIDLRGLIS-DKRNSVNNSGNLNSGSNVKTRNYSVLSESKFSDRSKSASLI--FMPNL 199
           G P   RG  S +   S++    L+ G           + + F+ R +  +++  + P  
Sbjct: 121 GKP---RGGPSWEDLTSLDQPRPLDRGKGP--------TSAAFNPRREYLTVVAPWCPRW 169

Query: 200 ECNDGETVIPSRN--VMDFVRRAYFSGTDKRNFCRN----DGSSTRDK--AGFDTGN--- 248
           +      V P ++  VM     +     D R    +    DG+  +D   A F+      
Sbjct: 170 DPRPLGFVAPKKSYPVMTRCSVSCQPCVDLRPLVASGLTEDGNGRKDTPLAQFNQERFYS 229

Query: 249 -KAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEKV 307
             A+ F R    +  + D K  S   K        RF +   +SS++DS+ID E  D   
Sbjct: 230 VAARRFGRKWRPDSSDQDDKGTSAPKKNL------RFGKKFGASSEEDSEID-ESGDTGA 282

Query: 308 EGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDE-HDFEEQVELIRKEISKNKLNGNGEK 366
                +++  SSA+L   D+K  +RV LKS E+E +D   +++ +R+EI   ++ G   +
Sbjct: 283 -----IRRRWSSAALRNCDVKKERRV-LKSYEEESNDLAGRIQELREEIRNREVLGTERR 336

Query: 367 KEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTG 426
           + +   E +L+ KRFD+CG+S LT+KALT AGY+Q T VQEA L  CLEGKD +VKAKTG
Sbjct: 337 RYESRGESLLTSKRFDQCGVSALTVKALTDAGYVQTTVVQEAALPICLEGKDVLVKAKTG 396

Query: 427 TGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIG 486
           TGKS AFLLPAIE+VL A  S+T Q V PI+ L+LCPTRELA Q+ AEA  LLK H+GIG
Sbjct: 397 TGKSAAFLLPAIESVLNAMKSNTNQRVSPIFALVLCPTRELAIQLTAEANVLLKYHEGIG 456

Query: 487 VLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL 546
           V +L+GGTRFK+DQRRLESDPCQILVATPGRLLDHIENKS  SVRLM LK+LVLDEADHL
Sbjct: 457 VQSLIGGTRFKLDQRRLESDPCQILVATPGRLLDHIENKSSFSVRLMRLKLLVLDEADHL 516

Query: 547 LDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPV 600
           LDLGFRKD+E IVD LPR+RQ+LLFSAT+PKE      LVLKR+H ++DTVGLG+VETP 
Sbjct: 517 LDLGFRKDIEKIVDTLPRQRQTLLFSATIPKEVRRVSQLVLKRDHVFVDTVGLGAVETPT 576

Query: 601 KVSKYNIYV 609
           KV +  + V
Sbjct: 577 KVQQSCLVV 585

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242067048|ref|XP_002454813.1| hypothetical protein SORBIDRAFT_04g037930 [Sorghum bicolor] gi|241934644|gb|EES07789.1| hypothetical protein SORBIDRAFT_04g037930 [Sorghum bicolor]

 Score =  492 bits (1266), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 294/618 (47%), Positives = 376/618 (60%), Gaps = 63/618 (10%)

Query: 27  MGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTKLFDKADPDS 86
           MGGGPRTFPGGL+KWQ++RMHEK A++K++ LL  EKQLY AR+RS+IR      A  ++
Sbjct: 1   MGGGPRTFPGGLSKWQYRRMHEKLARQKQRGLLRHEKQLYLARLRSEIRASRLPGAAAEA 60

Query: 87  ETNQHKPMSPDEHVKALADRFMKEGAEDLWNEDDGPVKSEQRPRSGAEANQRPRLAGAPI 146
                 P S   H++ALADRF + GAEDLWNEDDGP++  +RP +G  +  R        
Sbjct: 61  PPQGEGPTSSRAHIRALADRFRRPGAEDLWNEDDGPLRRAKRPPTGIASGVR-------- 112

Query: 147 DLRGLISDKRNSVNNSGNLNSGSNVKTRNYSVLSESKFS----DRSKSASL-IFMPNLEC 201
                     +   +SG    G + +      L + +      DR K  +L  F P  E 
Sbjct: 113 --------HHHQQLDSGKPRGGPSWEDWEDLALGQPRPRKEPLDRGKGPTLAAFNPRREY 164

Query: 202 NDGETVI----PSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAKPFARNL 257
               TV+    P  N         F G  KR++      S   +   D           +
Sbjct: 165 L---TVVAPWCPRWNPGPL----RFVGP-KRSYSVMTPCSVSWQPCVDLRPLVARGLTEV 216

Query: 258 GNNRENGDSKNMSEFMKKKCF-VGKRRFKRNESSSSDDDSDID---------------SE 301
           GN R       +  F +++ + V  RRF R     S DD D                 S 
Sbjct: 217 GNGRREAP---LPLFNQERLYSVAARRFGRKWRPDSSDDDDEGTSAPKRNLRFGKFGASS 273

Query: 302 DVDEKVEGWRD---VKKMGSSASLGKYDMKITKRVPLKSLEDE-HDFEEQVELIRKEISK 357
           + D +++   D   +++  SSA+L   DMK  +RV LK  E+E +D   ++  +R+EI  
Sbjct: 274 EEDSEIDESGDTGAIRRRWSSAALRNCDMKKERRV-LKYYEEESNDLAGRIRELREEIRN 332

Query: 358 NKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGK 417
            ++ G   ++ +   E +L+ KRFDECG+SPLT+KALT AGY+  T VQEA L  CLEGK
Sbjct: 333 REVLGTERRRYESRGESLLTSKRFDECGVSPLTVKALTDAGYVHTTVVQEAALPICLEGK 392

Query: 418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA 477
           D +VKAKTGTGKS AFLLPAIE+VL A  ++T Q V PI+VL+LCPTRELA Q+AAEA  
Sbjct: 393 DVLVKAKTGTGKSAAFLLPAIESVLNAMKTNTNQRVSPIFVLVLCPTRELAIQLAAEANV 452

Query: 478 LLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM 537
           LLK H+GIGV TL+GGTRFK+DQRRLESDPCQILVATPGRLLDHIENKS  SVRLM LK+
Sbjct: 453 LLKYHEGIGVQTLIGGTRFKLDQRRLESDPCQILVATPGRLLDHIENKSSFSVRLMRLKL 512

Query: 538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE------LVLKREHTYIDTV 591
           LVLDEADHLLDLGFRKD+E IVD LPR+RQ+LLFSAT+PKE      LVLKR+H ++DTV
Sbjct: 513 LVLDEADHLLDLGFRKDIEKIVDSLPRQRQTLLFSATIPKEVRRVSQLVLKRDHVFVDTV 572

Query: 592 GLGSVETPVKVSKYNIYV 609
           GLG+VETP KV +  + V
Sbjct: 573 GLGAVETPTKVQQSCLVV 590

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	633
TAIR|locus:2054688	845	AT2G07750 [Arabidopsis thalian	0.608	0.455	0.539	7.1e-100
TAIR|locus:2038431	798	AT1G63250 [Arabidopsis thalian	0.597	0.473	0.544	1.7e-98
TAIR|locus:2159517	850	PDE340 "PIGMENT DEFECTIVE 340"	0.642	0.478	0.417	7.7e-71
TAIR|locus:2159527	563	STRS2 "STRESS RESPONSE SUPPRES	0.450	0.506	0.494	9.4e-66
UNIPROTKB|G4MSR4	717	MGG_07099 "Uncharacterized pro	0.333	0.294	0.431	1.5e-32
UNIPROTKB|Q2KEF1	568	MGCH7_ch7g1085 "Putative uncha	0.344	0.383	0.398	3.1e-32
UNIPROTKB|F1SV16	301	F1SV16 "Uncharacterized protei	0.360	0.757	0.388	3.3e-32
UNIPROTKB|Q81QF0	450	BAS2301 "ATP-dependent RNA hel	0.312	0.44	0.417	4.3e-32
TIGR_CMR|BA_2475	450	BA_2475 "ATP-dependent RNA hel	0.312	0.44	0.417	4.3e-32
UNIPROTKB|P21693	457	dbpA [Escherichia coli K-12 (t	0.287	0.398	0.432	7.5e-31

TAIR|locus:2054688 AT2G07750 [Arabidopsis thaliana (taxid:3702)]

 Score = 991 (353.9 bits), Expect = 7.1e-100, P = 7.1e-100
 Identities = 217/402 (53%), Positives = 275/402 (68%)

Query:   213 VMDFVRRAYFSGTD-KRNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNREN-GDSKNMS 270
             V+D  RR + S +  KRN    D     D    DT     PF+      +E    S ++ 
Sbjct:   213 VLDSSRRGFSSMSRFKRNESSCDEGDDVDAKKLDT---LSPFSPKFSGTKEKVKSSTSVV 269

Query:   271 EFMKKKCFVGKRRFKRNXXXXXXXXXXXXXXXXXXKVEGWRDVKKMGSSASLGKYDMKIT 330
               ++ K   G+R+F++N                  K+ GW D++K GSSASLG +D+K+T
Sbjct:   270 GVIRNKGLFGRRKFRKNDSSTEEDSDEEGNEG---KMIGWMDLRKTGSSASLGNHDIKLT 326

Query:   331 KRVPLKSLEDEHDFEE-QVELIRKEISXXXXXXXXXXXXXXXXXPILSQKRFDECGISPL 389
             KRV  +++ DE  +    +  +R+++S                  I S KRFDE  ISPL
Sbjct:   327 KRVN-RNVTDEELYPPLDINRVREDLSKKQSVDNVMEEKQEPHDSIYSAKRFDESCISPL 385

Query:   390 TIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST 449
             T+KAL+A+G ++MTRVQ+ATLS CL+GKDA+VKAKTGTGKS+AFLLPAIE VLKA +S  
Sbjct:   386 TLKALSASGIVKMTRVQDATLSECLDGKDALVKAKTGTGKSMAFLLPAIETVLKAMNSGK 445

Query:   450 -TQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPC 508
                 V PI+VLILCPTRELASQIAAE  ALLKNHDGIGV TL+GGTRF++DQ+RLES+PC
Sbjct:   446 GVHKVAPIFVLILCPTRELASQIAAEGKALLKNHDGIGVQTLIGGTRFRLDQQRLESEPC 505

Query:   509 QILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQS 568
             QIL+ATPGRLLDHIENKSGL+ RLM LK+ ++DEAD LLDLGF++DVE I+DCLPR+RQS
Sbjct:   506 QILIATPGRLLDHIENKSGLTSRLMALKLFIVDEADLLLDLGFKRDVEKIIDCLPRQRQS 565

Query:   569 LLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVSK 604
             LLFSAT+PKE      LVLKR+H+YIDT+GLG VET  KV +
Sbjct:   566 LLFSATIPKEVRRVSQLVLKRDHSYIDTIGLGCVETHDKVKQ 607

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

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

TAIR|locus:2038431 AT1G63250 [Arabidopsis thaliana (taxid:3702)]

 Score = 978 (349.3 bits), Expect = 1.7e-98, P = 1.7e-98
 Identities = 215/395 (54%), Positives = 270/395 (68%)

Query:   218 RRAYFSGTD-KRNFCRNDGSSTRDKAGFDTGNKAKPFARNLGNNREN-GDSKNMSEFMKK 275
             RR + S +  KRN    D     D    DT     PF+      +E    S+++   ++ 
Sbjct:   171 RRGFSSMSRFKRNESSCDEGDDFDAKKLDT---LSPFSPKFAGTKEKVKSSRSVVGVIRN 227

Query:   276 KCFVGKRRFKRNXXXXXXXXXXXXXXXXXXKVEGWRDVKKMGSSASLGKYDMKITKRVPL 335
             K   G+R+F++N                  K+ GW D++K GSSASLG +D+K+TKRV  
Sbjct:   228 KGLFGRRKFRKNDSSTEEDSDEEGDEG---KMIGWMDMRKTGSSASLGNHDIKLTKRVN- 283

Query:   336 KSLEDEHDFEE-QVELIRKEISXXXXXXXXXXXXXXXXXPILSQKRFDECGISPLTIKAL 394
             +++ DE  +    +  +R+++S                  I S KRFDE  ISPLT+KAL
Sbjct:   284 RNVTDEELYPPLDINTVREDLSKRKSVDNVMEEKQEPHDSIYSAKRFDESCISPLTLKAL 343

Query:   395 TAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST-TQLV 453
             +A+G ++MTRVQ+ATLS CL+GKDA+VKAKTGTGKS+AFLLPAIE VLKA +S      V
Sbjct:   344 SASGILKMTRVQDATLSECLDGKDALVKAKTGTGKSMAFLLPAIETVLKAMNSGKGVNKV 403

Query:   454 PPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVA 513
              PI+ LILCPTRELASQIAAE  ALLK HDGIGV TL+GGTRFK+DQ+RLES+PCQIL+A
Sbjct:   404 APIFALILCPTRELASQIAAEGKALLKFHDGIGVQTLIGGTRFKLDQQRLESEPCQILIA 463

Query:   514 TPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSA 573
             TPGRLLDHIENKSGL+ RLM LK+ ++DEAD LLDLGFR+DVE I+DCLPR+RQSLLFSA
Sbjct:   464 TPGRLLDHIENKSGLTSRLMALKLFIVDEADLLLDLGFRRDVEKIIDCLPRQRQSLLFSA 523

Query:   574 TMPKE------LVLKREHTYIDTVGLGSVETPVKV 602
             T+PKE      LVLKR+H+YIDT+GLG VET  KV
Sbjct:   524 TIPKEVRRVSQLVLKRDHSYIDTIGLGCVETHDKV 558

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISM

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

TAIR|locus:2159517 PDE340 "PIGMENT DEFECTIVE 340" [Arabidopsis thaliana (taxid:3702)]

 Score = 717 (257.5 bits), Expect = 7.7e-71, P = 7.7e-71
 Identities = 183/438 (41%), Positives = 247/438 (56%)

Query:   180 SESKF---SDRSKSASLIFMPNLECN-DGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDG 235
             SES F   SDR+  +   F    + N D  +    RN  +    + F G   RN   + G
Sbjct:   194 SESSFRGRSDRNVDSGSSFRGRSDKNVDSGSSFRGRNDRNVDSGSSFRGRSDRNV--DSG 251

Query:   236 SSTRDKA--GFDTGNKAKPFARNLGNNRENGDSKNMSEFMKKKCFVGKRRFKRNXXXXXX 293
             SS R ++    D+G+  +      G N  N DS   S F  +     +  F+R       
Sbjct:   252 SSFRGRSDRNVDSGSSFR------GRNDRNVDSG--SSFRGRNDRNVESGFRREPGSENN 303

Query:   294 XXXXXXXXXXXXKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRK 353
                         + E   D  +  +   LG  D      +P +   DE D E    LI+K
Sbjct:   304 RGLGKQTRGLSLEEEDSSDDDE--NRVGLGNID-----DLPSEDSSDEDD-ENDEPLIKK 355

Query:   354 EISXXXXXXXX-XXXXXXXXXPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSA 412
               S                    LS+ RFD+  +SPL++KA+  AG+  MT VQEATL  
Sbjct:   356 AASAKAVQTDKPTGEHVKTSDSYLSKTRFDQFPLSPLSLKAIKDAGFETMTVVQEATLPI 415

Query:   413 CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA 472
              L+GKD + KAKTGTGK++AFLLPAIEAV+K+  +S     PPI VL++CPTRELASQ A
Sbjct:   416 ILQGKDVLAKAKTGTGKTVAFLLPAIEAVIKSPPASRDSRQPPIIVLVVCPTRELASQAA 475

Query:   473 AEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRL 532
             AEA  LLK H  IGV  ++GGT+   +QRR++++PCQILVATPGRL DHIEN SG + RL
Sbjct:   476 AEANTLLKYHPSIGVQVVIGGTKLPTEQRRMQTNPCQILVATPGRLKDHIENTSGFATRL 535

Query:   533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL------VLKREHT 586
             MG+K+LVLDEADHLLD+GFR+D+E I+  +P++RQ+ LFSAT+P+E+       LKR+H 
Sbjct:   536 MGVKVLVLDEADHLLDMGFRRDIERIIAAVPKQRQTFLFSATVPEEVRQICHVALKRDHE 595

Query:   587 YIDTVGLGSVETPVKVSK 604
             +I+ V  GS ET  KV++
Sbjct:   596 FINCVQEGSGETHQKVTQ 613

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)]

 Score = 669 (240.6 bits), Expect = 9.4e-66, P = 9.4e-66
 Identities = 148/299 (49%), Positives = 196/299 (65%)

Query:   313 VKKMGSSAS-LGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISXXXXXXXXXXXXXXX 371
             VKK+ S     GK  +K   +   +  E + D +E   LI+K  S               
Sbjct:    20 VKKLTSDEDGSGKL-VKDNNKSLKRGREGKSDVDEP--LIKKPASTTPLVTQIAKTSDSY 76

Query:   372 XXPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSI 431
                 LS+ RFD+  +SPLT+K +  AG+  MT VQEATL   L+GKD + KAKTGTGK++
Sbjct:    77 ----LSKTRFDQFPLSPLTLKGIEDAGFKTMTVVQEATLPLILQGKDILAKAKTGTGKTV 132

Query:   432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
             AFLLP+IEAV+KA  +S     PPI VL++CPTRELA Q AAEA  LLK H  IGV  ++
Sbjct:   133 AFLLPSIEAVIKAPPASRDNRHPPIIVLVVCPTRELACQAAAEANILLKYHPSIGVQVVI 192

Query:   492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF 551
             GGT+   +QRRL+  PCQILVATPGRL DHI+N SG + RLMG+K+LVLDEADHLLD+GF
Sbjct:   193 GGTKLPTEQRRLQKSPCQILVATPGRLKDHIDNTSGFATRLMGVKVLVLDEADHLLDMGF 252

Query:   552 RKDVENIVDCLPRRRQSLLFSATMPKEL------VLKREHTYIDTVGLGSVETPVKVSK 604
             R+++E I+  +P++RQ+ LFSAT+  E+       LKR+H +++ V  G+ ET  KVS+
Sbjct:   253 RREIERIIAAVPKQRQTFLFSATVSDEVRQICHVALKRDHEFVNCVQEGAGETHQKVSQ 311

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0003723 "RNA binding" evidence=IDA

GO:0009409 "response to cold" evidence=IEP

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009651 "response to salt stress" evidence=IMP

GO:0042991 "transcription factor import into nucleus" evidence=RCA

UNIPROTKB|G4MSR4 MGG_07099 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 379 (138.5 bits), Expect = 1.5e-32, P = 1.5e-32
 Identities = 100/232 (43%), Positives = 137/232 (59%)

Query:   383 ECGISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAV 441
             +  I    IKA+T    Y  MT VQ  TL+  L+GKD V +AKTGTGK++AFL+P I+ +
Sbjct:    81 KANIDESIIKAITVDMRYEDMTDVQSMTLAPALKGKDLVAQAKTGTGKTLAFLIPVIQKI 140

Query:   442 LKATSS--STTQLVP-------PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG 492
             L A  S    ++  P        I  +I+ PTRELA QI  EA  L + + G+ V T VG
Sbjct:   141 LDADPSLKEVSRGRPRRFAQRQSIKAIIISPTRELAEQIGKEATRLCQRN-GVTVQTAVG 199

Query:   493 GTRFKVDQRRLESDPCQILVATPGRLLDHIENK-SGLSVRLMGLKMLVLDEADHLLDLGF 551
             GT  +   RR+  + C +LV TPGRL D + ++ SG+      ++ LVLDEAD +LD+GF
Sbjct:   200 GTGKRESLRRIHMEGCHLLVGTPGRLNDLLSDELSGIDAS--NVQALVLDEADRMLDVGF 257

Query:   552 RKDVENIVDCLPRR----RQSLLFSATMPKELV-LKREHTYIDTVGLGSVET 598
               ++ +IVD LP R    RQ+LLFSAT+PK +V L R   Y+D      V+T
Sbjct:   258 ENELRSIVDMLPDRQQVPRQTLLFSATLPKNVVGLAR--WYVDKQNFEFVQT 307

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0043581 "mycelium development" evidence=IEP

UNIPROTKB|Q2KEF1 MGCH7_ch7g1085 "Putative uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 372 (136.0 bits), Expect = 3.1e-32, P = 3.1e-32
 Identities = 94/236 (39%), Positives = 139/236 (58%)

Query:   386 ISPLTIKALTA-AGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIEAVLK 443
             + P+ +  +T    + +M+ VQ AT+   +  + D + +AKTGTGK+IAFLLPA++ +L+
Sbjct:    83 LDPVLLDTITQDLKFDRMSPVQAATIRHLIADRGDVLAQAKTGTGKTIAFLLPALQTLLR 142

Query:   444 ATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRL 503
               SS        + VL++ PTRELA QIA EA ALL+      V T +GGT    +QRR+
Sbjct:   143 RPSSRGND----VSVLVISPTRELALQIAKEAEALLQRLPQYKVCTAIGGTNKDAEQRRI 198

Query:   504 ESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP 563
                 CQIL+ TPGRL+DH+E +S ++  L  +   VLDEAD LLD+GF   ++ IV  LP
Sbjct:   199 LRG-CQILIGTPGRLMDHLEEQS-VAEMLQSVDTFVLDEADRLLDMGFMPQLKKIVAALP 256

Query:   564 RR----RQSLLFSATMPKE------LVLKREHTYIDTVGLGSVETPVKVSKYNIYV 609
              R    RQ +LFSAT+ +       + L  ++ +I T+  G   T  +V ++ I V
Sbjct:   257 NRQKVPRQGMLFSATVAEHVAKVSSIALAPDYKFISTIPKGESNTHERVPQHLIEV 312

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F1SV16 F1SV16 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 356 (130.4 bits), Expect = 3.3e-32, P = 3.3e-32
 Identities = 94/242 (38%), Positives = 137/242 (56%)

Query:   380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
             RF +  +S  T+K L  A Y  +T +Q+ T+   L+GKD +  AKTG+GK++AFL+P +E
Sbjct:    70 RFSDLPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLE 129

Query:   440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
             A+ +   +ST  L     VLI+ PTRELA Q       + KNHD    L ++GG   K +
Sbjct:   130 ALYRLQWTSTDGLG----VLIISPTRELAYQTFEVLRKVGKNHDFSAGL-IIGGKDLKHE 184

Query:   500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
               R+ +    ILV TPGRLL H++    +      L+MLVLDEAD +LD+GF   +  I+
Sbjct:   185 AERINN--INILVCTPGRLLQHMDET--ICFHATNLQMLVLDEADRILDMGFADTMNAII 240

Query:   560 DCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVL-SIKI 618
             + LP++RQ+LLFSAT  K +   ++   +       V    K +KY   +F  +  SIKI
Sbjct:   241 ENLPKKRQTLLFSATQTKSV---KDLARLSLKNPEYVWVHEK-AKYRYVLFETIFDSIKI 296

Query:   619 QA 620
              A
Sbjct:   297 SA 298

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q81QF0 BAS2301 "ATP-dependent RNA helicase, DEAD/DEAH box family" [Bacillus anthracis (taxid:1392)]

 Score = 355 (130.0 bits), Expect = 4.3e-32, P = 4.3e-32
 Identities = 88/211 (41%), Positives = 121/211 (57%)

Query:   379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAI 438
             K F E GIS      L   G  + T +QE  +   L GKD + +AKTGTGK++AF+LP +
Sbjct:     5 KNFLELGISETFNHTLRENGITEATPIQEKAIPVILSGKDIIGQAKTGTGKTLAFVLPIL 64

Query:   439 EAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV 498
             E +     SS  Q       LI+ PTRELA QI  E   +L   + I VL + GG     
Sbjct:    65 EKI--DPESSDVQ------ALIVAPTRELALQITTEIKKMLVQREDINVLAIYGGQDVAQ 116

Query:   499 DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI 558
               R+L+ +   I+VATPGRLLDHI  ++   + L  L  +VLDEAD +L  GF  D+E+I
Sbjct:   117 QLRKLKGNT-HIVVATPGRLLDHIRRET---IDLSNLSTIVLDEADQMLYFGFLYDIEDI 172

Query:   559 VDCLPRRRQSLLFSATMPKELVLKREHTYID 589
             +D  P  +Q++LFSAT+PK+ + K    Y+D
Sbjct:   173 LDETPGSKQTMLFSATIPKD-IKKLAKRYMD 202

GO:0008150 "biological_process" evidence=ND

TIGR_CMR|BA_2475 BA_2475 "ATP-dependent RNA helicase, DEAD/DEAH box family" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 355 (130.0 bits), Expect = 4.3e-32, P = 4.3e-32
 Identities = 88/211 (41%), Positives = 121/211 (57%)

Query:   379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAI 438
             K F E GIS      L   G  + T +QE  +   L GKD + +AKTGTGK++AF+LP +
Sbjct:     5 KNFLELGISETFNHTLRENGITEATPIQEKAIPVILSGKDIIGQAKTGTGKTLAFVLPIL 64

Query:   439 EAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV 498
             E +     SS  Q       LI+ PTRELA QI  E   +L   + I VL + GG     
Sbjct:    65 EKI--DPESSDVQ------ALIVAPTRELALQITTEIKKMLVQREDINVLAIYGGQDVAQ 116

Query:   499 DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI 558
               R+L+ +   I+VATPGRLLDHI  ++   + L  L  +VLDEAD +L  GF  D+E+I
Sbjct:   117 QLRKLKGNT-HIVVATPGRLLDHIRRET---IDLSNLSTIVLDEADQMLYFGFLYDIEDI 172

Query:   559 VDCLPRRRQSLLFSATMPKELVLKREHTYID 589
             +D  P  +Q++LFSAT+PK+ + K    Y+D
Sbjct:   173 LDETPGSKQTMLFSATIPKD-IKKLAKRYMD 202

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

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|P21693 dbpA [Escherichia coli K-12 (taxid:83333)]

 Score = 344 (126.2 bits), Expect = 7.5e-31, P = 7.5e-31
 Identities = 84/194 (43%), Positives = 115/194 (59%)

Query:   386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKAT 445
             + P  +  L   GY+ MT VQ A L A L GKD  V+AKTG+GK+ AF L  ++ +    
Sbjct:    10 LPPAQLTNLNELGYLTMTPVQAAALPAILAGKDVRVQAKTGSGKTAAFGLGLLQQI--DA 67

Query:   446 SSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLES 505
             S   TQ       L+LCPTRELA Q+A E   L +      +LTL GG  F + +  L+ 
Sbjct:    68 SLFQTQ------ALVLCPTRELADQVAGELRRLARFLPNTKILTLCGGQPFGMQRDSLQH 121

Query:   506 DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRR 565
              P  I+VATPGRLLDH++   G +V L  L  LV+DEAD +LD+GF   +++++   P  
Sbjct:   122 AP-HIIVATPGRLLDHLQK--G-TVSLDALNTLVMDEADRMLDMGFSDAIDDVIRFAPAS 177

Query:   566 RQSLLFSATMPKEL 579
             RQ+LLFSAT P+ +
Sbjct:   178 RQTLLFSATWPEAI 191

GO:0003724 "RNA helicase activity" evidence=IDA

GO:0016887 "ATPase activity" evidence=IDA

GO:0033677 "DNA/RNA helicase activity" evidence=IDA

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0000027 "ribosomal large subunit assembly" evidence=IMP

GO:0034459 "ATP-dependent 3'-5' RNA helicase activity" evidence=IDA

GO:0019843 "rRNA binding" evidence=IDA

GO:0043531 "ADP binding" evidence=IDA

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

GO:0005737 "cytoplasm" evidence=IEA

---

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)
O80792	RH33_ARATH	3, ., 6, ., 4, ., 1, 3	0.5149	0.8388	0.6284	yes	no
Q9C8S9	RH48_ARATH	3, ., 6, ., 4, ., 1, 3	0.5161	0.8688	0.6892	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	0.824
3rd Layer	3.6.4	0.766

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	633
cd00268	203	cd00268, DEADc, DEAD-box helicases	3e-73
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	6e-62
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	9e-55
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	4e-51
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	3e-43
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-40
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-37
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	3e-35
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	8e-34
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-33
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	7e-33
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	2e-30
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	4e-27
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	5e-27
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-23
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-09
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	2e-07
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	2e-07
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	5e-06
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	1e-05
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	1e-04
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	3e-04

>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases

 Score =  233 bits (598), Expect = 3e-73
 Identities = 83/199 (41%), Positives = 119/199 (59%), Gaps = 11/199 (5%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F+E G+SP  ++ + A G+ + T +Q   +   L G+D + +A+TG+GK+ AFL+P +E 
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +  +      Q       LIL PTRELA QIA  A  L K+   + V+ + GGT      
Sbjct: 61  LDPSPKKDGPQ------ALILAPTRELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQI 113

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
           R+L+     I+VATPGRLLD +E      + L  +K LVLDEAD +LD+GF   +  I+ 
Sbjct: 114 RKLKRG-PHIVVATPGRLLDLLERGK---LDLSKVKYLVLDEADRMLDMGFEDQIREILK 169

Query: 561 CLPRRRQSLLFSATMPKEL 579
            LP+ RQ+LLFSATMPKE+
Sbjct: 170 LLPKDRQTLLFSATMPKEV 188

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. Length = 203

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

 Score =  213 bits (545), Expect = 6e-62
 Identities = 91/226 (40%), Positives = 123/226 (54%), Gaps = 12/226 (5%)

Query: 354 EISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSAC 413
                KL         R EE       F   G+SP  ++AL   G+ + T +Q A +   
Sbjct: 6   YDRFVKLKSAHNVALSRGEEKT--PPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLI 63

Query: 414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAA 473
           L G+D + +A+TGTGK+ AFLLP ++ +LK+              LIL PTRELA QIA 
Sbjct: 64  LAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVS------ALILAPTRELAVQIAE 117

Query: 474 EAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM 533
           E   L KN  G+ V  + GG   +     L+     I+VATPGRLLD I+      + L 
Sbjct: 118 ELRKLGKNLGGLRVAVVYGGVSIRKQIEALK-RGVDIVVATPGRLLDLIKRGK---LDLS 173

Query: 534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL 579
           G++ LVLDEAD +LD+GF  D+E I+  LP  RQ+LLFSATMP ++
Sbjct: 174 GVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDI 219

Length = 513

>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase

 Score =  183 bits (467), Expect = 9e-55
 Identities = 79/177 (44%), Positives = 102/177 (57%), Gaps = 11/177 (6%)

Query: 403 TRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILC 462
           T +Q   + A L GKD +V+A TG+GK++AFLLP ++A+L                L+L 
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKG--------GPQALVLA 52

Query: 463 PTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHI 522
           PTRELA QI  E   L K   G+ V  L GGT  K   R+L+     ILV TPGRLLD +
Sbjct: 53  PTRELAEQIYEELKKLFKIL-GLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLL 111

Query: 523 ENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL 579
                  ++   LK+LVLDEA  LLD+GF  D+E I+  LP  RQ LL SAT+P+ L
Sbjct: 112 RRGKLKLLK--NLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNL 166

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. Length = 169

>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional

 Score =  183 bits (466), Expect = 4e-51
 Identities = 81/205 (39%), Positives = 109/205 (53%), Gaps = 18/205 (8%)

Query: 377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF--- 433
           S   F    + P  +  L   GY +MT +Q  +L A L GKD + +AKTG+GK+ AF   
Sbjct: 2   SMTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLG 61

Query: 434 LLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGG 493
           LL  ++       +           L+LCPTRELA Q+A E   L +    I VLTL GG
Sbjct: 62  LLQKLDVKRFRVQA-----------LVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGG 110

Query: 494 TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK 553
                    LE     I+V TPGR+LDH+   +   + L  L  LVLDEAD +LD+GF+ 
Sbjct: 111 VPMGPQIDSLEHGA-HIIVGTPGRILDHLRKGT---LDLDALNTLVLDEADRMLDMGFQD 166

Query: 554 DVENIVDCLPRRRQSLLFSATMPKE 578
            ++ I+   P RRQ+LLFSAT P+ 
Sbjct: 167 AIDAIIRQAPARRQTLLFSATYPEG 191

Length = 460

>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score =  153 bits (389), Expect = 3e-43
 Identities = 72/187 (38%), Positives = 103/187 (55%), Gaps = 14/187 (7%)

Query: 394 LTAAGYIQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQL 452
           +   G+  +   Q+  + A L G +D ++ A TG+GK++A LLPA+EA+ +         
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKR--------- 51

Query: 453 VPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILV 512
                VL+L PTRELA Q A E   L  +     V+ L GG   +   R+LES    ILV
Sbjct: 52  GKGGRVLVLVPTRELAEQWAEELKKLGPSLGLK-VVGLYGGDSKREQLRKLESGKTDILV 110

Query: 513 ATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS 572
            TPGRLLD +EN     + L  + +++LDEA  LLD GF   +E ++  LP+  Q LL S
Sbjct: 111 TTPGRLLDLLENDK---LSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLS 167

Query: 573 ATMPKEL 579
           AT P+E+
Sbjct: 168 ATPPEEI 174

Length = 201

>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional

 Score =  153 bits (388), Expect = 2e-40
 Identities = 85/204 (41%), Positives = 119/204 (58%), Gaps = 7/204 (3%)

Query: 373 EPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA 432
           EP   + RF +  ++P  + A+   G+   T +Q   L   L G DA+ +A+TGTGK+ A
Sbjct: 81  EPQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAA 140

Query: 433 FLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG 492
           FL+  I  +L+        +  P   LI+ PTREL  QIA +A AL K + G+ V+T VG
Sbjct: 141 FLISIINQLLQTPPPKERYMGEP-RALIIAPTRELVVQIAKDAAALTK-YTGLNVMTFVG 198

Query: 493 GTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFR 552
           G  F    ++LE+  C ILVATPGRLLD  +      V L  ++++VLDEAD +LD+GF 
Sbjct: 199 GMDFDKQLKQLEARFCDILVATPGRLLDFNQRG---EVHLDMVEVMVLDEADRMLDMGFI 255

Query: 553 KDVENIVDCLPRR--RQSLLFSAT 574
             V  I+   PR+  RQ+LLFSAT
Sbjct: 256 PQVRQIIRQTPRKEERQTLLFSAT 279

Length = 475

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score =  143 bits (363), Expect = 3e-37
 Identities = 78/205 (38%), Positives = 116/205 (56%), Gaps = 19/205 (9%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F E  +    ++AL   GY + T +Q   +   L+G+D +  A TGTGK+ AFLLPA++ 
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62

Query: 441 VLKATSSSTTQLVP-----PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
           +L           P     P  +LIL PTRELA Q+A +A  L K H  + + T+ GG  
Sbjct: 63  LLD---------FPRRKSGPPRILILTPTRELAMQVADQARELAK-HTHLDIATITGGVA 112

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
           +  +   + S+   I+VATPGRLL +I+ +     R   ++ L+LDEAD +LD+GF +D+
Sbjct: 113 YM-NHAEVFSENQDIVVATPGRLLQYIK-EENFDCR--AVETLILDEADRMLDMGFAQDI 168

Query: 556 ENIVDCLPRRRQSLLFSATMPKELV 580
           E I      R+Q+LLFSAT+  + V
Sbjct: 169 ETIAAETRWRKQTLLFSATLEGDAV 193

Length = 434

>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional

 Score =  140 bits (355), Expect = 3e-35
 Identities = 83/201 (41%), Positives = 116/201 (57%), Gaps = 20/201 (9%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPA--- 437
           F + G+    ++AL   GY + + +Q   +   L G+D +  A+TG+GK+ AF LP    
Sbjct: 8   FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67

Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH-DGIGVLTLVGGTRF 496
           ++  LKA             +L+L PTRELA Q+A EA+     H  G+ V+ L GG R+
Sbjct: 68  LDPELKAPQ-----------ILVLAPTRELAVQVA-EAMTDFSKHMRGVNVVALYGGQRY 115

Query: 497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE 556
            V  R L   P QI+V TPGRLLDH+  K G ++ L  L  LVLDEAD +L +GF +DVE
Sbjct: 116 DVQLRALRQGP-QIVVGTPGRLLDHL--KRG-TLDLSKLSGLVLDEADEMLRMGFIEDVE 171

Query: 557 NIVDCLPRRRQSLLFSATMPK 577
            I+  +P   Q+ LFSATMP+
Sbjct: 172 TIMAQIPEGHQTALFSATMPE 192

Length = 629

>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily

 Score =  125 bits (316), Expect = 8e-34
 Identities = 64/159 (40%), Positives = 86/159 (54%), Gaps = 15/159 (9%)

Query: 417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI 476
           +D ++ A TG+GK++A LLP +E +           +    VL+L PTRELA+Q+A    
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELLDS---------LKGGQVLVLAPTRELANQVAERLK 51

Query: 477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK 536
            L      +G L   GGT  K  Q +L S    I+V TPGRLLD +E    L + L  L 
Sbjct: 52  ELFGEGIKVGYLI--GGTSIK-QQEKLLSGKTDIVVGTPGRLLDELER---LKLSLKKLD 105

Query: 537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM 575
           +L+LDEA  LL+ GF      I+  LP+ RQ LL SAT 
Sbjct: 106 LLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 144

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Length = 144

>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional

 Score =  132 bits (333), Expect = 4e-33
 Identities = 78/199 (39%), Positives = 118/199 (59%), Gaps = 7/199 (3%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           FD  G+SP  ++A+   GY + T +Q+  + A LEG+D +  A+TGTGK+  F LP ++ 
Sbjct: 3   FDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ- 61

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
               T     +   P+  LIL PTRELA+QI  E +     +  I  L + GG       
Sbjct: 62  -HLITRQPHAKGRRPVRALILTPTRELAAQIG-ENVRDYSKYLNIRSLVVFGGVSINPQM 119

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
            +L      +LVATPGRLLD +E+++  +V+L  +++LVLDEAD +LD+GF  D+  ++ 
Sbjct: 120 MKLRGG-VDVLVATPGRLLD-LEHQN--AVKLDQVEILVLDEADRMLDMGFIHDIRRVLA 175

Query: 561 CLPRRRQSLLFSATMPKEL 579
            LP +RQ+LLFSAT   ++
Sbjct: 176 KLPAKRQNLLFSATFSDDI 194

Length = 456

>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional

 Score =  130 bits (330), Expect = 7e-33
 Identities = 70/202 (34%), Positives = 112/202 (55%), Gaps = 8/202 (3%)

Query: 376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLL 435
           L++++F +  + P  ++AL   G+   T +Q   L   L G+D   +A+TGTGK++AFL 
Sbjct: 5   LTEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLT 64

Query: 436 PAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
                +L   +    ++  P   LI+ PTRELA QI A+A  L +   G+ +    GG  
Sbjct: 65  ATFHYLLSHPAPEDRKVNQP-RALIMAPTRELAVQIHADAEPLAQ-ATGLKLGLAYGGDG 122

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
           +    + LES    IL+ T GRL+D+   K    + L  ++++VLDEAD + DLGF KD+
Sbjct: 123 YDKQLKVLESGV-DILIGTTGRLIDYA--KQNH-INLGAIQVVVLDEADRMFDLGFIKDI 178

Query: 556 ENIVDCLP--RRRQSLLFSATM 575
             +   +P   +R ++LFSAT+
Sbjct: 179 RWLFRRMPPANQRLNMLFSATL 200

Length = 423

>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score =  125 bits (316), Expect = 2e-30
 Identities = 90/267 (33%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 322 LGKYDMKITKRVPL-KSLEDEHD-----FEEQVELIRKEISKNKLNGNGEKKEKREEEPI 375
           L   D K    VP  K+   EH        ++V+ IRKE     + G    K      P+
Sbjct: 76  LQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPK------PV 129

Query: 376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLL 435
           +S   F+        +K+L  AG+ + T +Q       L G+D +  A+TG+GK++AFLL
Sbjct: 130 VS---FEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLL 186

Query: 436 PAIEAVLKATSSSTTQLVP---PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG 492
           PAI  +          L     PI VL+L PTRELA QI  +          I      G
Sbjct: 187 PAIVHINAQPL-----LRYGDGPI-VLVLAPTRELAEQIREQCNKF-GASSKIRNTVAYG 239

Query: 493 GTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFR 552
           G   +     L     +IL+A PGRL+D +E  S ++  L  +  LVLDEAD +LD+GF 
Sbjct: 240 GVPKRGQIYALRRG-VEILIACPGRLIDFLE--SNVT-NLRRVTYLVLDEADRMLDMGFE 295

Query: 553 KDVENIVDCLPRRRQSLLFSATMPKEL 579
             +  IV  +   RQ+L++SAT PKE+
Sbjct: 296 PQIRKIVSQIRPDRQTLMWSATWPKEV 322

Length = 545

>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional

 Score =  115 bits (290), Expect = 4e-27
 Identities = 76/213 (35%), Positives = 118/213 (55%), Gaps = 8/213 (3%)

Query: 376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLL 435
           L+   F    + P  +  L +AG+ + T +Q  TL   L G D   +A+TGTGK++AFL+
Sbjct: 6   LTDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLV 65

Query: 436 PAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
             +  +L   + +  +   P   LIL PTRELA QI  +A+    +  G+    + GG  
Sbjct: 66  AVMNRLLSRPALADRKPEDP-RALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVD 123

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
           +   QR L      +++ATPGRL+D+++    +S+     ++ VLDEAD + DLGF KD+
Sbjct: 124 YD-KQRELLQQGVDVIIATPGRLIDYVKQHKVVSLH--ACEICVLDEADRMFDLGFIKDI 180

Query: 556 ENIVDCLPRR--RQSLLFSATMP-KELVLKREH 585
             ++  +P R  RQ+LLFSAT+  + L L  EH
Sbjct: 181 RFLLRRMPERGTRQTLLFSATLSHRVLELAYEH 213

Length = 572

>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase; Provisional

 Score =  114 bits (288), Expect = 5e-27
 Identities = 75/208 (36%), Positives = 109/208 (52%), Gaps = 14/208 (6%)

Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF 433
           PILS   F  CG+ P  +  L  AGY   T +Q   + A L G+  +V A TG+GK+ +F
Sbjct: 119 PILS---FSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASF 175

Query: 434 LLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLT--LV 491
           L+P I       S   ++   P+  ++L PTREL  Q+  +A  L K   G+   T  +V
Sbjct: 176 LVPIISRCCTIRSGHPSEQRNPL-AMVLTPTRELCVQVEDQAKVLGK---GLPFKTALVV 231

Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF 551
           GG        R++    +++V TPGRL+D +   S   + L  + +LVLDE D +L+ GF
Sbjct: 232 GGDAMPQQLYRIQQG-VELIVGTPGRLIDLL---SKHDIELDNVSVLVLDEVDCMLERGF 287

Query: 552 RKDVENIVDCLPRRRQSLLFSATMPKEL 579
           R  V  I   L  + Q LLFSAT+  E+
Sbjct: 288 RDQVMQIFQALS-QPQVLLFSATVSPEV 314

Length = 518

>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional

 Score =  102 bits (257), Expect = 1e-23
 Identities = 64/205 (31%), Positives = 111/205 (54%), Gaps = 23/205 (11%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           FD   ++   ++ + + G+ + + +Q+  +   L+G D + +A++GTGK+  F++ A++ 
Sbjct: 30  FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQL 89

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL-----LKNHDGIGVLTLVGGTR 495
           +      +  Q       LIL PTRELA QI    +AL     ++ H        VGGT 
Sbjct: 90  I--DYDLNACQ------ALILAPTRELAQQIQKVVLALGDYLKVRCH------ACVGGTV 135

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
            + D  +L++    ++V TPGR+ D I+ +    +R+  LK+ +LDEAD +L  GF+  +
Sbjct: 136 VRDDINKLKAG-VHMVVGTPGRVYDMIDKRH---LRVDDLKLFILDEADEMLSRGFKGQI 191

Query: 556 ENIVDCLPRRRQSLLFSATMPKELV 580
            ++   LP   Q  LFSATMP E++
Sbjct: 192 YDVFKKLPPDVQVALFSATMPNEIL 216

Length = 401

>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

 Score = 61.3 bits (149), Expect = 1e-09
 Identities = 56/229 (24%), Positives = 88/229 (38%), Gaps = 31/229 (13%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAK 424
            +  K  E P L  +             AL  AG  ++   Q   L    EG++ VV   
Sbjct: 43  ARPGKTSEFPELRDESL---------KSALVKAGIERLYSHQVDALRLIREGRNVVVTTG 93

Query: 425 TGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL-KNHD 483
           TG+GK+ +FLLP ++ +L+  S+           L+L PT  LA+  A     L+     
Sbjct: 94  TGSGKTESFLLPILDHLLRDPSARA---------LLLYPTNALANDQAERLRELISDLPG 144

Query: 484 GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSGLSVRLMGLKMLVLDE 542
            +      G T  + ++R +  +P  IL+  P  L    + N       L  LK LV+DE
Sbjct: 145 KVTFGRYTGDTPPE-ERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDE 203

Query: 543 ADHLLDLGFRKDVENIVD-------CLPRRRQSLLFSATM--PKELVLK 582
             H        +V  ++              Q +  SAT+  P E   +
Sbjct: 204 L-HTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPGEFAEE 251

Length = 851

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 53.9 bits (130), Expect = 2e-07
 Identities = 48/179 (26%), Positives = 76/179 (42%), Gaps = 28/179 (15%)

Query: 404 RVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP 463
             QEA     L  ++ ++ A TG+GK++  LL  +  +L+            +Y+    P
Sbjct: 35  PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGGG-------KVVYI---VP 84

Query: 464 TRELASQIAAEA--IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDH 521
            + LA +   E   +  L    GI V    G      D  RL      ++V TP + LD 
Sbjct: 85  LKALAEEKYEEFSRLEEL----GIRVGISTGDYDL--DDERLAR--YDVIVTTPEK-LDS 135

Query: 522 IENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV-ENIVDCLPRRRQSLLF---SATMP 576
           +  K    +  + L  +V+DE  HLL    R  V E+IV  + R  + +     SAT+P
Sbjct: 136 LTRKRPSWIEEVDL--VVIDEI-HLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLP 191

Length = 766

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

 Score = 53.2 bits (128), Expect = 2e-07
 Identities = 46/180 (25%), Positives = 71/180 (39%), Gaps = 37/180 (20%)

Query: 406 QEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLIL 461
           QE  L A +      +  V+   TG GK++     A EA+ +   S           L+L
Sbjct: 41  QEEALDALVKNRRTERRGVIVLPTGAGKTVV----AAEAIAELKRS----------TLVL 86

Query: 462 CPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDH 521
            PT+EL  Q A      L  +D IG+    GG +        E +P ++ VAT    +  
Sbjct: 87  VPTKELLDQWAEALKKFLLLNDEIGIYG--GGEK--------ELEPAKVTVAT----VQT 132

Query: 522 IENKSGLSVRLMGLKML-VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV 580
           +  +  L   L     L + DE  HL    +R+    I++ L      L  +AT  +E  
Sbjct: 133 LARRQLLDEFLGNEFGLIIFDEVHHLPAPSYRR----ILELLSAAYPRLGLTATPEREDG 188

Length = 442

>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction only]

 Score = 49.6 bits (119), Expect = 5e-06
 Identities = 36/156 (23%), Positives = 67/156 (42%), Gaps = 7/156 (4%)

Query: 387 SPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATS 446
            P   +      +  +T  Q   +     G++ ++ A TG+GK+ A  LP I  +L    
Sbjct: 9   DPRVREWF-KRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLS--- 64

Query: 447 SSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESD 506
               +L   IY L + P + L + I       L+   GI V    G T  + +++++  +
Sbjct: 65  LGKGKLEDGIYALYISPLKALNNDIRRRLEEPLR-ELGIEVAVRHGDTP-QSEKQKMLKN 122

Query: 507 PCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDE 542
           P  IL+ TP  L   + +       L  ++ +++DE
Sbjct: 123 PPHILITTPESLAILLNSPK-FRELLRDVRYVIVDE 157

Length = 814

>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA ligase-associated

 Score = 48.3 bits (116), Expect = 1e-05
 Identities = 39/146 (26%), Positives = 61/146 (41%), Gaps = 24/146 (16%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           Q    +A LEG+  ++ A TG+GK++A  LP++  +              ++ L + P R
Sbjct: 18  QLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPK-----KGLHTLYITPLR 72

Query: 466 ELASQIA------AEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL- 518
            LA  IA       E + L      I V T  G T      R+ +  P  IL+ TP  L 
Sbjct: 73  ALAVDIARNLQAPIEELGL-----PIRVETRTGDTSSSERARQRKKPP-DILLTTPESLA 126

Query: 519 --LDHIENKSGLSVRLMGLKMLVLDE 542
             L + +           L+ +V+DE
Sbjct: 127 LLLSYPDAAR----LFKDLRCVVVDE 148

Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. Length = 803

>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 41/163 (25%), Positives = 69/163 (42%), Gaps = 22/163 (13%)

Query: 388 PLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSS 447
           P  + AL AAG  +  + Q         G+  VV   T +GKS+A+ LP + A+     +
Sbjct: 23  PDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPRA 82

Query: 448 STTQLVPPIYVLILCPTRELAS-QIAA-EAIALLKNHDGIGVLTLVGGTRFKVDQRRLES 505
           +          L L PT+ LA+ Q+ A   + L     G+   T  G T    ++RR   
Sbjct: 83  T---------ALYLAPTKALAADQLRAVRELTL----RGVRPATYDGDTPT--EERRWAR 127

Query: 506 DPCQILVATPGRLLDHI---ENKSGLSVRLMGLKMLVLDEADH 545
           +  + ++  P  L  H     + +  +  L  L+ +V+DE   
Sbjct: 128 EHARYVLTNPDML--HRGILPSHARWARFLRRLRYVVIDECHS 168

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA. Length = 742

>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication, recombination, and repair]

 Score = 43.4 bits (103), Expect = 3e-04
 Identities = 42/206 (20%), Positives = 75/206 (36%), Gaps = 47/206 (22%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           Q+  + A L GKD +V   TG GKS+ + +PA              L+     L++ P  
Sbjct: 22  QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPA--------------LLLEGLTLVVSP-- 65

Query: 466 ELAS----QIAAEAIALLKNHDGIGVLTLVGG-TRFKVDQ--RRLESDPCQILVATPGRL 518
            L S    Q+      L     GI    L    +R +  Q   +L+S   ++L  +P   
Sbjct: 66  -LISLMKDQVD----QLEAA--GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISP--- 115

Query: 519 LDHIENKSGLSVRLMG-LKMLVLDEADHLLDLG--FRKDVENIVD--CLPRRRQSLLFSA 573
            + + +   L +     + ++ +DEA  +   G  FR D   +            L  +A
Sbjct: 116 -ERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTA 174

Query: 574 TMPKELV--------LKREHTYIDTV 591
           T    +         L+  + +  + 
Sbjct: 175 TATPRVRDDIREQLGLQDANIFRGSF 200

Length = 590

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	633
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	99.97
KOG4284	980	consensus DEAD box protein [Transcription]	99.97
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.97
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.97
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.96
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.96
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK02362	737	ski2-like helicase; Provisional	99.95
PRK00254	720	ski2-like helicase; Provisional	99.95
PRK01172	674	ski2-like helicase; Provisional	99.93
PRK13767	876	ATP-dependent helicase; Provisional	99.93
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.93
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.93
PRK09401	1176	reverse gyrase; Reviewed	99.93
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.93
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.93
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.93
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.92
PRK14701	1638	reverse gyrase; Provisional	99.91
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.91
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.91
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.91
COG1205	851	Distinct helicase family with a unique C-terminal	99.89
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.88
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.87
PRK10689	1147	transcription-repair coupling factor; Provisional	99.87
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.87
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.86
COG1204	766	Superfamily II helicase [General function predicti	99.86
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.86
COG1202	830	Superfamily II helicase, archaea-specific [General	99.85
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.82
PHA02653	675	RNA helicase NPH-II; Provisional	99.82
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.82
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.81
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.81
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.81
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.8
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.8
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.78
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.74
PRK05580	679	primosome assembly protein PriA; Validated	99.73
PHA02558	501	uvsW UvsW helicase; Provisional	99.73
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.72
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.7
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.68
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.67
PRK13766	773	Hef nuclease; Provisional	99.65
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.62
KOG0354	746	consensus DEAD-box like helicase [General function	99.62
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.61
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.61
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.58
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.58
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.57
PRK09694	878	helicase Cas3; Provisional	99.57
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.57
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.55
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.54
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.53
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.53
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.5
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.47
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.39
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.36
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	99.32
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.31
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.31
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.3
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.28
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.27
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.27
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.27
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.21
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.17
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.17
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	99.17
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.14
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.12
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.11
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.09
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.06
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.04
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.04
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.01
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	99.0
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.97
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	98.91
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	98.91
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	98.9
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	98.84
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.78
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.73
PRK12326	764	preprotein translocase subunit SecA; Reviewed	98.72
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	98.71
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	98.66
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	98.66
COG4096	875	HsdR Type I site-specific restriction-modification	98.65
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.64
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.61
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	98.55
CHL00122	870	secA preprotein translocase subunit SecA; Validate	98.54
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	98.52
PRK14873	665	primosome assembly protein PriA; Provisional	98.5
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.47
PRK04914	956	ATP-dependent helicase HepA; Validated	98.4
PRK15483	986	type III restriction-modification system StyLTI en	98.39
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	98.37
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.28
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.21
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.05
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	98.0
COG4889	1518	Predicted helicase [General function prediction on	97.99
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	97.95
COG0610	962	Type I site-specific restriction-modification syst	97.93
KOG1123	776	consensus RNA polymerase II transcription initiati	97.9
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.89
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.88
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	97.87
KOG0387	923	consensus Transcription-coupled repair protein CSB	97.84
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.83
PRK10536	262	hypothetical protein; Provisional	97.66
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	97.65
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	97.53
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.46
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	97.46
KOG1803	649	consensus DNA helicase [Replication, recombination	97.44
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	97.42
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	97.42
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	97.39
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.39
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.37
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	97.36
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.3
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.3
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	97.29
PRK10875	615	recD exonuclease V subunit alpha; Provisional	97.26
KOG4439	901	consensus RNA polymerase II transcription terminat	97.16
COG3587	985	Restriction endonuclease [Defense mechanisms]	97.12
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.11
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.08
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.02
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.82
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.79
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	96.78
PF13245	76	AAA_19: Part of AAA domain	96.76
KOG1805	1100	consensus DNA replication helicase [Replication, r	96.71
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.65
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	96.64
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	96.59
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	96.54
PRK06921	266	hypothetical protein; Provisional	96.42
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	96.39
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.34
PRK08181	269	transposase; Validated	96.31
PRK13826	1102	Dtr system oriT relaxase; Provisional	96.24
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.14
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	96.12
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	96.11
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	96.03
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.0
PRK07952	244	DNA replication protein DnaC; Validated	95.97
smart00382	148	AAA ATPases associated with a variety of cellular	95.94
PRK04296	190	thymidine kinase; Provisional	95.93
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	95.86
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	95.83
PRK06526	254	transposase; Provisional	95.8
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	95.66
PRK08727	233	hypothetical protein; Validated	95.65
TIGR00376	637	DNA helicase, putative. The gene product may repre	95.64
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	95.61
PRK12377	248	putative replication protein; Provisional	95.59
PRK05642	234	DNA replication initiation factor; Validated	95.55
PHA02533	534	17 large terminase protein; Provisional	95.55
PRK14974	336	cell division protein FtsY; Provisional	95.53
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	95.53
PRK06893	229	DNA replication initiation factor; Validated	95.51
PRK08116	268	hypothetical protein; Validated	95.42
PRK06835	329	DNA replication protein DnaC; Validated	95.31
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	95.23
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	95.23
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	95.13
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.12
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	95.06
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	94.93
PRK00149	450	dnaA chromosomal replication initiation protein; R	94.9
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	94.76
COG1484	254	DnaC DNA replication protein [DNA replication, rec	94.73
PRK08084	235	DNA replication initiation factor; Provisional	94.72
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	94.68
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.53
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	94.5
PRK14087	450	dnaA chromosomal replication initiation protein; P	94.49
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	94.41
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	94.35
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	94.3
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	94.3
KOG1131	755	consensus RNA polymerase II transcription initiati	94.27
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	94.16
PRK14086	617	dnaA chromosomal replication initiation protein; P	94.09
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	94.05
PRK12402	337	replication factor C small subunit 2; Reviewed	94.02
PTZ00112	1164	origin recognition complex 1 protein; Provisional	94.01
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	93.97
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	93.95
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	93.94
PHA03368	738	DNA packaging terminase subunit 1; Provisional	93.89
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	93.78
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	93.77
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	93.74
PRK08903	227	DnaA regulatory inactivator Hda; Validated	93.66
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	93.62
PRK14088	440	dnaA chromosomal replication initiation protein; P	93.6
PHA02544	316	44 clamp loader, small subunit; Provisional	93.59
PRK11054	684	helD DNA helicase IV; Provisional	93.57
PHA03333	752	putative ATPase subunit of terminase; Provisional	93.47
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	93.45
PRK12422	445	chromosomal replication initiation protein; Provis	93.42
PRK00411	394	cdc6 cell division control protein 6; Reviewed	93.37
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	93.32
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	93.32
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.19
PRK05298	652	excinuclease ABC subunit B; Provisional	93.18
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	93.14
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	93.14
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	93.12
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	93.11
PRK09183	259	transposase/IS protein; Provisional	93.08
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	93.02
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	92.95
PF00004	132	AAA: ATPase family associated with various cellula	92.95
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	92.78
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	92.67
PRK05973	237	replicative DNA helicase; Provisional	92.67
PRK08533	230	flagellar accessory protein FlaH; Reviewed	92.56
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	92.52
PF13173	128	AAA_14: AAA domain	92.48
PRK07471	365	DNA polymerase III subunit delta'; Validated	92.45
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	92.45
PRK08769	319	DNA polymerase III subunit delta'; Validated	92.29
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	92.24
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	92.22
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	92.22
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	92.13
PRK11823	446	DNA repair protein RadA; Provisional	92.13
PRK04195	482	replication factor C large subunit; Provisional	92.09
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	92.03
PRK13833	323	conjugal transfer protein TrbB; Provisional	91.94
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	91.94
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	91.9
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	91.85
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	91.82
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	91.78
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	91.67
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	91.63
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	91.62
PRK08939	306	primosomal protein DnaI; Reviewed	91.6
PLN03025	319	replication factor C subunit; Provisional	91.58
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	91.44
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	91.38
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	91.26
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	91.2
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	91.13
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	91.12
PRK10689	1147	transcription-repair coupling factor; Provisional	91.1
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	91.1
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	91.04
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	91.02
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	91.02
PF05729	166	NACHT: NACHT domain	90.68
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	90.68
PRK05707	328	DNA polymerase III subunit delta'; Validated	90.55
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	90.52
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	90.5
COG0593	408	DnaA ATPase involved in DNA replication initiation	90.49
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	90.46
PRK06067	234	flagellar accessory protein FlaH; Validated	90.39
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	90.34
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	90.3
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	90.29
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	90.17
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	90.14
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	90.08
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	90.06
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	89.94
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	89.92
COG4626	546	Phage terminase-like protein, large subunit [Gener	89.9
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	89.87
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	89.74
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	89.56
PRK04328	249	hypothetical protein; Provisional	89.5
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	89.41
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	89.39
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	89.35
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	89.22
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	89.2
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	89.11
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	89.07
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	89.01
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	89.01
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	88.85
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	88.77
PRK00771	437	signal recognition particle protein Srp54; Provisi	88.67
CHL00181	287	cbbX CbbX; Provisional	88.44
PRK09112	351	DNA polymerase III subunit delta'; Validated	88.4
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	88.2
PRK13897	606	type IV secretion system component VirD4; Provisio	88.19
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	88.19
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	88.14
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	88.14
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	88.09
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	87.95
PRK06904	472	replicative DNA helicase; Validated	87.74
PRK00440	319	rfc replication factor C small subunit; Reviewed	87.69
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	87.66
PRK13342	413	recombination factor protein RarA; Reviewed	87.58
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	87.57
PRK13341	725	recombination factor protein RarA/unknown domain f	87.53
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	87.47
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	87.43
PRK08506	472	replicative DNA helicase; Provisional	87.37
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	87.28
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	87.23
PHA03372	668	DNA packaging terminase subunit 1; Provisional	87.21
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	87.21
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	87.16
PRK08699	325	DNA polymerase III subunit delta'; Validated	87.13
PRK09087	226	hypothetical protein; Validated	87.1
PRK06871	325	DNA polymerase III subunit delta'; Validated	87.05
TIGR00665	434	DnaB replicative DNA helicase. This model describe	87.04
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	87.04
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	86.91
TIGR02237	209	recomb_radB DNA repair and recombination protein R	86.89
TIGR00064	272	ftsY signal recognition particle-docking protein F	86.86
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	86.85
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	86.85
PRK07940	394	DNA polymerase III subunit delta'; Validated	86.82
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	86.81
PRK13851	344	type IV secretion system protein VirB11; Provision	86.72
PRK06964	342	DNA polymerase III subunit delta'; Validated	86.63
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	86.57
PRK07004	460	replicative DNA helicase; Provisional	86.54
PRK03992	389	proteasome-activating nucleotidase; Provisional	86.44
COG2256	436	MGS1 ATPase related to the helicase subunit of the	86.41
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	86.29
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	86.27
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	85.9
PRK07993	334	DNA polymerase III subunit delta'; Validated	85.89
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	85.82
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	85.82
PRK05748	448	replicative DNA helicase; Provisional	85.8
PRK08760	476	replicative DNA helicase; Provisional	85.77
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	85.71
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	85.54
PTZ00110	545	helicase; Provisional	85.29
PRK13850	670	type IV secretion system protein VirD4; Provisiona	85.28
PRK09165	497	replicative DNA helicase; Provisional	85.22
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	85.19
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	85.14
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	84.95
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	84.92
COG3973	747	Superfamily I DNA and RNA helicases [General funct	84.9
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	84.86
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	84.72
PRK04841	903	transcriptional regulator MalT; Provisional	84.5
PRK10416	318	signal recognition particle-docking protein FtsY;	84.49
PRK08840	464	replicative DNA helicase; Provisional	84.45
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	84.41
cd01394	218	radB RadB. The archaeal protein radB shares simila	84.28
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	84.27
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	84.26
PRK10436	462	hypothetical protein; Provisional	84.03
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	84.03
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	84.0
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	83.77
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	83.76
PRK09302	509	circadian clock protein KaiC; Reviewed	83.74
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	83.66
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	83.58
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	83.52
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	83.5
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	83.47
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	83.4
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	83.37
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	83.3
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	83.06
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	83.01
PRK13822	641	conjugal transfer coupling protein TraG; Provision	82.93
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	82.93
PF12846	304	AAA_10: AAA-like domain	82.92
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	82.74
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	82.65
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	82.57
PRK08006	471	replicative DNA helicase; Provisional	82.57
PRK05636	505	replicative DNA helicase; Provisional	82.52
cd03246	173	ABCC_Protease_Secretion This family represents the	82.51
PRK13880	636	conjugal transfer coupling protein TraG; Provision	82.45
KOG0060	659	consensus Long-chain acyl-CoA transporter, ABC sup	82.44
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	82.38
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	82.29
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	82.24
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	82.06
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	82.05
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	81.89
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	81.62
TIGR00959	428	ffh signal recognition particle protein. This mode	81.57
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	81.47
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	81.46
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	81.37
cd03239	178	ABC_SMC_head The structural maintenance of chromos	81.36
PRK10867	433	signal recognition particle protein; Provisional	81.14
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	81.01
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	80.96
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	80.9
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	80.81
TIGR00767	415	rho transcription termination factor Rho. Members	80.77
KOG1001	674	consensus Helicase-like transcription factor HLTF/	80.73
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	80.7
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	80.56
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	80.4
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	80.38
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	80.36
PRK06090	319	DNA polymerase III subunit delta'; Validated	80.3
PHA00729	226	NTP-binding motif containing protein	80.25
PTZ00424	401	helicase 45; Provisional	80.19
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	80.13

>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.5e-42  Score=367.70  Aligned_cols=241  Identities=37%  Similarity=0.532  Sum_probs=204.8

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|.+|+|+..|++++..+||..|||||..+||..+-|+|++.||.||||||.||+||+|++++-....     ....+
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~-----~~~TR  254 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK-----VAATR  254 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc-----Cccee
Confidence            4579999999999999999999999999999999999999999999999999999999999998765432     34468


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      ||||+||||||.|++.+.++++.+. .+.+++++||.+.+.|...+... +||+|+|||+|++||.+..  .++|++|.+
T Consensus       255 VLVL~PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LRs~-PDIVIATPGRlIDHlrNs~--sf~ldsiEV  330 (691)
T KOG0338|consen  255 VLVLVPTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLRSR-PDIVIATPGRLIDHLRNSP--SFNLDSIEV  330 (691)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHhhC-CCEEEecchhHHHHhccCC--CccccceeE
Confidence            9999999999999999999999877 69999999999999888777776 6999999999999998876  467999999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh----cc-ccce--EeeeccccccccCccceEEEeehh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV----LK-REHT--YIDTVGLGSVETPVKVSKYNIYVF  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~----l~-~~~~--~i~~~~~~~~~~~~~V~q~~i~v~  610 (633)
                      ||+||||+||+.+|..+|..|+..+|+++|+++||||++.++.    +. ..++  ++++    ...+...+.|.|+-+.
T Consensus       331 LvlDEADRMLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~----~~~~a~~LtQEFiRIR  406 (691)
T KOG0338|consen  331 LVLDEADRMLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDP----NKDTAPKLTQEFIRIR  406 (691)
T ss_pred             EEechHHHHHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCC----ccccchhhhHHHheec
Confidence            9999999999999999999999999999999999999999952    11 2222  3332    2456667888887432


Q ss_pred             ---------hH-HHHhhcCCceEEEEEcccc
Q 006737          611 ---------VL-VLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ---------~l-~~~~k~~~~~~LVFcnT~s  631 (633)
                               ++ .+....-...++||+.|+.
T Consensus       407 ~~re~dRea~l~~l~~rtf~~~~ivFv~tKk  437 (691)
T KOG0338|consen  407 PKREGDREAMLASLITRTFQDRTIVFVRTKK  437 (691)
T ss_pred             cccccccHHHHHHHHHHhcccceEEEEehHH
Confidence                     22 2233344568999999974

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=100.00  E-value=1.6e-41  Score=361.60  Aligned_cols=251  Identities=47%  Similarity=0.703  Sum_probs=224.9

Q ss_pred             CcccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCC
Q 006737          374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLV  453 (633)
Q Consensus       374 p~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~  453 (633)
                      .+.+...|+++.|++.+++++..+||..+|++|+.+|+.++.|+|+++.|.||||||+||+||+++.+.+......    
T Consensus        77 s~~~~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r----  152 (543)
T KOG0342|consen   77 SITTTFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPR----  152 (543)
T ss_pred             chhhhhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCC----
Confidence            3445567999999999999999999999999999999999999999999999999999999999999998765433    


Q ss_pred             CCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          454 PPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       454 ~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      .++.||||+||||||.|++.+++++..++..+.+.++.||+......+.+.. +|+|+|||||+|+++|++..+  +...
T Consensus       153 ~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k-~~niliATPGRLlDHlqNt~~--f~~r  229 (543)
T KOG0342|consen  153 NGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVK-GCNILIATPGRLLDHLQNTSG--FLFR  229 (543)
T ss_pred             CCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhc-cccEEEeCCchHHhHhhcCCc--chhh
Confidence            5678999999999999999999999999889999999999999988888887 799999999999999998865  3456


Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh------hccccceEeeeccccccccCccceEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL------VLKREHTYIDTVGLGSVETPVKVSKYNI  607 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el------~l~~~~~~i~~~~~~~~~~~~~V~q~~i  607 (633)
                      .++++||||||+++++||...|.+|+..+|+++|+++||||+|.++      .+..++.+++++..+...++..++|.|+
T Consensus       230 ~~k~lvlDEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyv  309 (543)
T KOG0342|consen  230 NLKCLVLDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYV  309 (543)
T ss_pred             ccceeEeecchhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEE
Confidence            7799999999999999999999999999999999999999999995      4677899999999888899999999999


Q ss_pred             ehh-------hHHHHhhcCC-ceEEEEEcccc
Q 006737          608 YVF-------VLVLSIKIQA-FYIICFVYTIS  631 (633)
Q Consensus       608 ~v~-------~l~~~~k~~~-~~~LVFcnT~s  631 (633)
                      ++.       ++..+.++.. ++++|||+|..
T Consensus       310 v~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~  341 (543)
T KOG0342|consen  310 VAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCM  341 (543)
T ss_pred             eccccchHHHHHHHHHHhcCCceEEEEechhh
Confidence            875       2223344444 89999999964

>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-41  Score=353.88  Aligned_cols=241  Identities=36%  Similarity=0.559  Sum_probs=208.3

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ...+|.+|++.+.+++++...||+.||+||+++||.++.|+|||+.|.||||||.+|+||++++++....        .+
T Consensus        59 ~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~--------~~  130 (476)
T KOG0330|consen   59 SFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPK--------LF  130 (476)
T ss_pred             hhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCC--------Cc
Confidence            3567999999999999999999999999999999999999999999999999999999999999998543        36


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||||||.||.+.+..+.... +++++++.||..+..+...+... +||||||||+|.+++.+..  .+.+..++
T Consensus       131 ~~lVLtPtRELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~kk-PhilVaTPGrL~dhl~~Tk--gf~le~lk  206 (476)
T KOG0330|consen  131 FALVLTPTRELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLSKK-PHILVATPGRLWDHLENTK--GFSLEQLK  206 (476)
T ss_pred             eEEEecCcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhhcC-CCEEEeCcHHHHHHHHhcc--CccHHHhH
Confidence            89999999999999999999998766 89999999999988777777654 7999999999999998765  36689999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhcc-----ccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLK-----REHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~-----~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      ++|+||||+++++.|...+..|+..+|..+|+++||||+|..+.-.     .++..+..  ...+.+...++|.|+.+. 
T Consensus       207 ~LVlDEADrlLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~--s~ky~tv~~lkQ~ylfv~~  284 (476)
T KOG0330|consen  207 FLVLDEADRLLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAV--SSKYQTVDHLKQTYLFVPG  284 (476)
T ss_pred             HHhhchHHhhhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEec--cchhcchHHhhhheEeccc
Confidence            9999999999999999999999999999999999999999996321     22222222  233567778999999875 


Q ss_pred             ------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                            ++.+++...+..+||||||.+
T Consensus       285 k~K~~yLV~ll~e~~g~s~iVF~~t~~  311 (476)
T KOG0330|consen  285 KDKDTYLVYLLNELAGNSVIVFCNTCN  311 (476)
T ss_pred             cccchhHHHHHHhhcCCcEEEEEeccc
Confidence                  444555666679999999975

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

Probab=100.00  E-value=8.1e-41  Score=366.03  Aligned_cols=245  Identities=33%  Similarity=0.438  Sum_probs=209.0

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      .|++++|++.+..+|...||..|||||.++||+++.|+|++..|.|||||||+|+||++.++....  .......+|++|
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~--~~~~~~~~P~vL  169 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQ--GKLSRGDGPIVL  169 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhcc--ccccCCCCCeEE
Confidence            699999999999999999999999999999999999999999999999999999999999998731  122334578999


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||+||||||.||..++..+.... .+++.|++||.....|...++.+ ++|+|||||+|+++|+..   ...|+++.|||
T Consensus       170 VL~PTRELA~QV~~~~~~~~~~~-~~~~~cvyGG~~~~~Q~~~l~~g-vdiviaTPGRl~d~le~g---~~~l~~v~ylV  244 (519)
T KOG0331|consen  170 VLAPTRELAVQVQAEAREFGKSL-RLRSTCVYGGAPKGPQLRDLERG-VDVVIATPGRLIDLLEEG---SLNLSRVTYLV  244 (519)
T ss_pred             EEcCcHHHHHHHHHHHHHHcCCC-CccEEEEeCCCCccHHHHHHhcC-CcEEEeCChHHHHHHHcC---CccccceeEEE
Confidence            99999999999999999998765 58899999999999988888775 899999999999999988   58899999999


Q ss_pred             EecccccCCcChHHHHHHHHHHC-CCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh---
Q 006737          540 LDEADHLLDLGFRKDVENIVDCL-PRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~l-pk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      +||||+|+++||.+++..|+..+ ++.+|++++|||+|.++.     +..++..+++..........+|.|...+|.   
T Consensus       245 LDEADrMldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~  324 (519)
T KOG0331|consen  245 LDEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETA  324 (519)
T ss_pred             eccHHhhhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHH
Confidence            99999999999999999999999 556799999999999963     223555555544434456667888888775   


Q ss_pred             -------hHHHHhhcCCceEEEEEcccc
Q 006737          611 -------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 -------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                             ++.........++||||+|+.
T Consensus       325 K~~~l~~lL~~~~~~~~~KvIIFc~tkr  352 (519)
T KOG0331|consen  325 KLRKLGKLLEDISSDSEGKVIIFCETKR  352 (519)
T ss_pred             HHHHHHHHHHHHhccCCCcEEEEecchh
Confidence                   222222334569999999985

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

Probab=100.00  E-value=1.4e-39  Score=344.84  Aligned_cols=248  Identities=35%  Similarity=0.519  Sum_probs=212.8

Q ss_pred             cCccccC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          379 KRFDECG--ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       379 ~~F~el~--L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ..|++++  |++++++++..+||..+||+|..+||.+++++||++.|+||||||+||++|++..+.......+..   .+
T Consensus         4 ~~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~---~v   80 (567)
T KOG0345|consen    4 KSFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPG---QV   80 (567)
T ss_pred             cchhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCcc---ce
Confidence            4677775  559999999999999999999999999999999999999999999999999999997654432221   25


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      -+|||+||||||.||.+++..+..+.+++++.+++||.....+...++..+++|+|||||+|.+++..... .+.+.+++
T Consensus        81 galIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~-~l~~rsLe  159 (567)
T KOG0345|consen   81 GALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAE-KLSFRSLE  159 (567)
T ss_pred             eEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhh-hccccccc
Confidence            69999999999999999999999988899999999999999999999999999999999999999987532 34566999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +||+||||+|+++||...++.|+..+|++++|-+||||.+.++.     -.++++.+.........+|+.+..+|++|. 
T Consensus       160 ~LVLDEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a  239 (567)
T KOG0345|consen  160 ILVLDEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEA  239 (567)
T ss_pred             eEEecchHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecH
Confidence            99999999999999999999999999999999999999999963     235566655444334458999999999986 


Q ss_pred             ------hHHHHhhcCCceEEEEEccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTI  630 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~  630 (633)
                            ++..+......++|||++|=
T Consensus       240 ~eK~~~lv~~L~~~~~kK~iVFF~TC  265 (567)
T KOG0345|consen  240 DEKLSQLVHLLNNNKDKKCIVFFPTC  265 (567)
T ss_pred             HHHHHHHHHHHhccccccEEEEecCc
Confidence                  33444556667999999884

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

Probab=100.00  E-value=4e-39  Score=361.23  Aligned_cols=243  Identities=39%  Similarity=0.563  Sum_probs=204.8

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ..|++|++++.++++|.++||..|||||..+||.++.|+|++++|+||||||+||+||+|+++......      ....+
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~------~~~~a  102 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVER------KYVSA  102 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhccccc------CCCce
Confidence            569999999999999999999999999999999999999999999999999999999999997643110      00119


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      |||+||||||.||++++..+..+..++++++++||.+...+...+..+ +||||||||||++++.+.   .+.++.+++|
T Consensus       103 Lil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~-~~ivVaTPGRllD~i~~~---~l~l~~v~~l  178 (513)
T COG0513         103 LILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRG-VDIVVATPGRLLDLIKRG---KLDLSGVETL  178 (513)
T ss_pred             EEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcC-CCEEEECccHHHHHHHcC---CcchhhcCEE
Confidence            999999999999999999999876578899999999999888888774 899999999999999887   5889999999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh---
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      |+||||+|+++||.+++..|+..+|.++|+++||||+|..+.     +..++..+.........+...|.|+|+.+.   
T Consensus       179 VlDEADrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~  258 (513)
T COG0513         179 VLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEE  258 (513)
T ss_pred             EeccHhhhhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHH
Confidence            999999999999999999999999999999999999999752     233444443322222337789999999885   


Q ss_pred             ----hHHH-HhhcCCceEEEEEcccc
Q 006737          611 ----VLVL-SIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ----~l~~-~~k~~~~~~LVFcnT~s  631 (633)
                          .+.. +......++||||+|+.
T Consensus       259 ~k~~~L~~ll~~~~~~~~IVF~~tk~  284 (513)
T COG0513         259 EKLELLLKLLKDEDEGRVIVFVRTKR  284 (513)
T ss_pred             HHHHHHHHHHhcCCCCeEEEEeCcHH
Confidence                2222 22334457999999975

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=4.8e-39  Score=345.11  Aligned_cols=246  Identities=35%  Similarity=0.546  Sum_probs=211.9

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ..+.|++|+|+..++++|.+.+|..||.||+.+||..|.|+|||..|.|||||||||++|+|++|+..+-..    ..|+
T Consensus        67 ~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kWs~----~DGl  142 (758)
T KOG0343|consen   67 TIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKWSP----TDGL  142 (758)
T ss_pred             hhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCCCC----CCCc
Confidence            456799999999999999999999999999999999999999999999999999999999999999876543    3466


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      -||||+||||||.|++.++.+.++++ .+..++++||........++.  .++|||||||+|+.+|....  .+..+++.
T Consensus       143 GalIISPTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi~--~mNILVCTPGRLLQHmde~~--~f~t~~lQ  217 (758)
T KOG0343|consen  143 GALIISPTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERIS--QMNILVCTPGRLLQHMDENP--NFSTSNLQ  217 (758)
T ss_pred             eeEEecchHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhhh--cCCeEEechHHHHHHhhhcC--CCCCCcce
Confidence            79999999999999999999999877 899999999999877666665  47999999999999998765  35678999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +||+||||+|+++||..++..|++.+|+.+|+++||||-++.+.     ...++.+|.+.......+|.++.|+|+.|. 
T Consensus       218 mLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~~atP~~L~Q~y~~v~l  297 (758)
T KOG0343|consen  218 MLVLDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAVAATPSNLQQSYVIVPL  297 (758)
T ss_pred             EEEeccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEeccccccChhhhhheEEEEeh
Confidence            99999999999999999999999999999999999999999852     225667776554445778999999999986 


Q ss_pred             -----hH-HHHhhcCCceEEEEEcccc
Q 006737          611 -----VL-VLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 -----~l-~~~~k~~~~~~LVFcnT~s  631 (633)
                           ++ .........+.|||+.|-.
T Consensus       298 ~~Ki~~L~sFI~shlk~K~iVF~SscK  324 (758)
T KOG0343|consen  298 EDKIDMLWSFIKSHLKKKSIVFLSSCK  324 (758)
T ss_pred             hhHHHHHHHHHHhccccceEEEEehhh
Confidence                 11 1222333468999998853

>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=6.6e-38  Score=335.59  Aligned_cols=257  Identities=33%  Similarity=0.511  Sum_probs=209.3

Q ss_pred             CCCCCcccccCccccCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCC
Q 006737          370 REEEPILSQKRFDECGISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSS  448 (633)
Q Consensus       370 ~~~~p~~~~~~F~el~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~  448 (633)
                      ...+.+++...|..|||++.++..|.. +++..||.+|+++||.+++|+|++|.++||||||+||+||+++.|.....  
T Consensus       127 ~v~e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~--  204 (708)
T KOG0348|consen  127 QVSEAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEP--  204 (708)
T ss_pred             cccccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCc--
Confidence            334455566789999999999999986 79999999999999999999999999999999999999999999987654  


Q ss_pred             CCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCc
Q 006737          449 TTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGL  528 (633)
Q Consensus       449 ~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~  528 (633)
                      ..++..|+.||||+||||||.|+|+.++++.+.+.-+..+.+.||...+.+..++..+ ++|||+|||||+++|.+..  
T Consensus       205 ki~Rs~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKG-iNILIgTPGRLvDHLknT~--  281 (708)
T KOG0348|consen  205 KIQRSDGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKG-INILIGTPGRLVDHLKNTK--  281 (708)
T ss_pred             cccccCCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcC-ceEEEcCchHHHHHHhccc--
Confidence            3456788999999999999999999999999888778889999999988888888765 8999999999999998875  


Q ss_pred             ccccCCeeEEEEecccccCCcChHHHHHHHHHHCC-------------CCCcEEEEeccCChhhh-----ccccceEeee
Q 006737          529 SVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP-------------RRRQSLLFSATMPKELV-----LKREHTYIDT  590 (633)
Q Consensus       529 ~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-------------k~~Q~IlfSATl~~el~-----l~~~~~~i~~  590 (633)
                      .+.++.+++||+||||+|++.||...|..|++.+.             ...|.+++|||++..+.     ...++++|..
T Consensus       282 ~i~~s~LRwlVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~l  361 (708)
T KOG0348|consen  282 SIKFSRLRWLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISL  361 (708)
T ss_pred             hheeeeeeEEEecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeec
Confidence            45688999999999999999999999999988772             23789999999999852     1234445440


Q ss_pred             c----------------c-------ccccccCccceEEEeehh----------hHHHHhh-cCCceEEEEEcccc
Q 006737          591 V----------------G-------LGSVETPVKVSKYNIYVF----------VLVLSIK-IQAFYIICFVYTIS  631 (633)
Q Consensus       591 ~----------------~-------~~~~~~~~~V~q~~i~v~----------~l~~~~k-~~~~~~LVFcnT~s  631 (633)
                      .                .       .+....|.++.|.|.+|+          ++....+ ....++|||+++..
T Consensus       362 d~s~~~~~p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d  436 (708)
T KOG0348|consen  362 DKSHSQLNPKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSD  436 (708)
T ss_pred             cchhhhcCcchhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechh
Confidence            0                0       011345677888888876          2222222 22348999998864

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=3.9e-36  Score=339.63  Aligned_cols=246  Identities=32%  Similarity=0.438  Sum_probs=198.5

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +..+|+++++++.++++|.++||.+||++|.++||.+++|+|+|++||||||||++|+||++.++......   ....++
T Consensus       128 p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~---~~~~gp  204 (545)
T PTZ00110        128 PVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLL---RYGDGP  204 (545)
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccc---cCCCCc
Confidence            34679999999999999999999999999999999999999999999999999999999999988764321   112357


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||||||.|+.+.+..+.... ++++.+++|+.....+...+.. +++|||+||++|++++...   ...|.+++
T Consensus       205 ~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg~~~~~q~~~l~~-~~~IlVaTPgrL~d~l~~~---~~~l~~v~  279 (545)
T PTZ00110        205 IVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGGVPKRGQIYALRR-GVEILIACPGRLIDFLESN---VTNLRRVT  279 (545)
T ss_pred             EEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCCCCHHHHHHHHHc-CCCEEEECHHHHHHHHHcC---CCChhhCc
Confidence            89999999999999999999987654 7889999999887777666655 4899999999999999865   36789999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhc------cccceEeeeccccccccCccceEEEeehh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVL------KREHTYIDTVGLGSVETPVKVSKYNIYVF  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l------~~~~~~i~~~~~~~~~~~~~V~q~~i~v~  610 (633)
                      +|||||||+|++++|..++..|+..+++++|+++||||+|.++..      ...+..+...... .....+++|.+.++.
T Consensus       280 ~lViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~-l~~~~~i~q~~~~~~  358 (545)
T PTZ00110        280 YLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLD-LTACHNIKQEVFVVE  358 (545)
T ss_pred             EEEeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCc-cccCCCeeEEEEEEe
Confidence            999999999999999999999999999999999999999988531      1223333221111 233456777776553


Q ss_pred             -------hHHHHhhc--CCceEEEEEcccc
Q 006737          611 -------VLVLSIKI--QAFYIICFVYTIS  631 (633)
Q Consensus       611 -------~l~~~~k~--~~~~~LVFcnT~s  631 (633)
                             +...+...  ...++||||+|+.
T Consensus       359 ~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~  388 (545)
T PTZ00110        359 EHEKRGKLKMLLQRIMRDGDKILIFVETKK  388 (545)
T ss_pred             chhHHHHHHHHHHHhcccCCeEEEEecChH
Confidence                   11111111  4569999999975

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=4.2e-37  Score=323.52  Aligned_cols=248  Identities=29%  Similarity=0.456  Sum_probs=205.7

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+|++|+|+++|++++.+.||.+||-||+.+||.++.|+|+++.|.||||||+||+||+++.++......  ....++.+
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~--~~e~~~sa   96 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTN--DGEQGPSA   96 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcc--ccccccee
Confidence            6899999999999999999999999999999999999999999999999999999999999999876543  33456789


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCC-CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHD-GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~-~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +||+||+|||.|++.++.++..++. .+++.-+....+..... ......++|+|+||++|+.++..+.  ...+..+++
T Consensus        97 ~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~-~~L~d~pdIvV~TP~~ll~~~~~~~--~~~~~~l~~  173 (569)
T KOG0346|consen   97 VILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNS-VALMDLPDIVVATPAKLLRHLAAGV--LEYLDSLSF  173 (569)
T ss_pred             EEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHH-HHHccCCCeEEeChHHHHHHHhhcc--chhhhheee
Confidence            9999999999999999999987764 45555555444444344 4444568999999999999998763  256889999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh--
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      ||+||||.++..||.+.+..|...+|+.+|.++||||++..+.     +..+++++.. .......+.++.|+++.|.  
T Consensus       174 LVvDEADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl-~e~el~~~dqL~Qy~v~cse~  252 (569)
T KOG0346|consen  174 LVVDEADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKL-TEGELPNPDQLTQYQVKCSEE  252 (569)
T ss_pred             EEechhhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEe-ccccCCCcccceEEEEEeccc
Confidence            9999999999999999999999999999999999999999963     3355555543 3334557789999999986  


Q ss_pred             ------hHHHHhhcCCceEEEEEccccC
Q 006737          611 ------VLVLSIKIQAFYIICFVYTISM  632 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s~  632 (633)
                            +..........++|||+||+.+
T Consensus       253 DKflllyallKL~LI~gKsliFVNtIdr  280 (569)
T KOG0346|consen  253 DKFLLLYALLKLRLIRGKSLIFVNTIDR  280 (569)
T ss_pred             hhHHHHHHHHHHHHhcCceEEEEechhh
Confidence                  2223344556799999999864

>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.8e-36  Score=314.53  Aligned_cols=311  Identities=27%  Similarity=0.353  Sum_probs=234.9

Q ss_pred             chhhhhcCCCcccCcccc--cccccCCCCCCCCccchHHHHHHHHHHhhccccCCCCCccccCCCCCcccccCccc-cCC
Q 006737          310 WRDVKKMGSSASLGKYDM--KITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDE-CGI  386 (633)
Q Consensus       310 ~~~~~~~~~s~~~~~~~~--k~~~~~~~~~~e~e~e~ee~ve~~~k~~~~~~~~~~~~~~~~~~~~p~~~~~~F~e-l~L  386 (633)
                      ++.+.+..-......|..  ..++..+..+.+.......++..++++..+.....  .+..+..+.|. +..+|++ ++.
T Consensus       151 we~~~~~~l~~e~~kW~~lpPi~knfYke~~e~s~ls~~q~~~~r~en~~it~dd--~K~gekrpIPn-P~ctFddAFq~  227 (629)
T KOG0336|consen  151 WESIREARLKDEKFKWAKLPPIKKNFYKESNETSNLSKEQLQEWRKENFNITCDD--LKEGEKRPIPN-PVCTFDDAFQC  227 (629)
T ss_pred             HHHHHHHHhhhhhcccccCCchhhhhhhcCchhccCCHHHHHHHHHcCCcEEecc--cccCCcccCCC-CcCcHHHHHhh
Confidence            333333333333445554  45555566677777778888888888766555432  23333333333 3456776 578


Q ss_pred             CHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHH
Q 006737          387 SPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRE  466 (633)
Q Consensus       387 ~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTRe  466 (633)
                      .+++++.+.+.||.+|||||.++||.+|.|.|++.+|.||+|||++||+|.+.|+.......  ....++.+|+++|||+
T Consensus       228 ~pevmenIkK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~--~qr~~p~~lvl~ptre  305 (629)
T KOG0336|consen  228 YPEVMENIKKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRR--EQRNGPGVLVLTPTRE  305 (629)
T ss_pred             hHHHHHHHHhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhh--hccCCCceEEEeccHH
Confidence            89999999999999999999999999999999999999999999999999998887654321  2445788999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccccc
Q 006737          467 LASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL  546 (633)
Q Consensus       467 La~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~L  546 (633)
                      ||.|+.-++.++.  +.+++..|++||.+...+.+.++.+ .+|+|+||++|.++...+   .++|.+|.||||||||+|
T Consensus       306 Lalqie~e~~kys--yng~ksvc~ygggnR~eqie~lkrg-veiiiatPgrlndL~~~n---~i~l~siTYlVlDEADrM  379 (629)
T KOG0336|consen  306 LALQIEGEVKKYS--YNGLKSVCVYGGGNRNEQIEDLKRG-VEIIIATPGRLNDLQMDN---VINLASITYLVLDEADRM  379 (629)
T ss_pred             HHHHHHhHHhHhh--hcCcceEEEecCCCchhHHHHHhcC-ceEEeeCCchHhhhhhcC---eeeeeeeEEEEecchhhh
Confidence            9999988887775  3489999999999988888888765 899999999999998776   588999999999999999


Q ss_pred             CCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh------hHHH-
Q 006737          547 LDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF------VLVL-  614 (633)
Q Consensus       547 ld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~------~l~~-  614 (633)
                      |++||..++.+|+--+.+++|+++.|||+|+.+.     ...++.++- ++.-.......|+|+.++-.      .+.. 
T Consensus       380 LDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~-vGsLdL~a~~sVkQ~i~v~~d~~k~~~~~~f  458 (629)
T KOG0336|consen  380 LDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVY-VGSLDLVAVKSVKQNIIVTTDSEKLEIVQFF  458 (629)
T ss_pred             hcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEE-ecccceeeeeeeeeeEEecccHHHHHHHHHH
Confidence            9999999999999999999999999999999963     223333321 11111223456888876432      1111 


Q ss_pred             -HhhcCCceEEEEEccccC
Q 006737          615 -SIKIQAFYIICFVYTISM  632 (633)
Q Consensus       615 -~~k~~~~~~LVFcnT~s~  632 (633)
                       .......++||||..+.+
T Consensus       459 ~~~ms~ndKvIiFv~~K~~  477 (629)
T KOG0336|consen  459 VANMSSNDKVIIFVSRKVM  477 (629)
T ss_pred             HHhcCCCceEEEEEechhh
Confidence             224455799999998754

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3.2e-37  Score=331.13  Aligned_cols=200  Identities=32%  Similarity=0.485  Sum_probs=171.8

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCC-----CCC
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSS-----STT  450 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~-----~~~  450 (633)
                      ....|..|+++..++++|.++||..||+||..+||++..| .|++..|.|||||||||-||+++.+......     ...
T Consensus       179 DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~  258 (731)
T KOG0347|consen  179 DVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTS  258 (731)
T ss_pred             ChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHH
Confidence            4456999999999999999999999999999999999999 5999999999999999999999966543211     111


Q ss_pred             CCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccc
Q 006737          451 QLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSV  530 (633)
Q Consensus       451 ~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~  530 (633)
                      .....+.+||++||||||.||.+.+..++.+ +++++..++||.....+++.+.. .++|+|||||||+.++........
T Consensus       259 ~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~-t~i~v~si~GGLavqKQqRlL~~-~p~IVVATPGRlweli~e~n~~l~  336 (731)
T KOG0347|consen  259 AKYVKPIALVVTPTRELAHQVKQHLKAIAEK-TQIRVASITGGLAVQKQQRLLNQ-RPDIVVATPGRLWELIEEDNTHLG  336 (731)
T ss_pred             hccCcceeEEecChHHHHHHHHHHHHHhccc-cCeEEEEeechhHHHHHHHHHhc-CCCEEEecchHHHHHHHhhhhhhh
Confidence            2223345999999999999999999998874 59999999999999988877776 579999999999999987644345


Q ss_pred             ccCCeeEEEEecccccCCcChHHHHHHHHHHCC-----CCCcEEEEeccCChh
Q 006737          531 RLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP-----RRRQSLLFSATMPKE  578 (633)
Q Consensus       531 ~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-----k~~Q~IlfSATl~~e  578 (633)
                      .+++|++|||||||+|++.|+...+..|++.++     ..+|+++||||++-.
T Consensus       337 ~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~  389 (731)
T KOG0347|consen  337 NFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLV  389 (731)
T ss_pred             hhhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehh
Confidence            688999999999999999999999999998886     368999999999765

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2e-35  Score=324.17  Aligned_cols=246  Identities=31%  Similarity=0.469  Sum_probs=197.4

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      .++|++++|++.++++|.++||..||++|.+|||.+++|+|++++||||||||++|++|+++.+....... .....+++
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~-~~~~~~~~   85 (423)
T PRK04837          7 EQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPE-DRKVNQPR   85 (423)
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhccccc-ccccCCce
Confidence            36799999999999999999999999999999999999999999999999999999999999987643211 11123578


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+|||+||.|+++.+..+.... ++.+.+++||.....+...+.. +++|||+||++|.+++...   .+.++++++
T Consensus        86 ~lil~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~-~~~IlV~TP~~l~~~l~~~---~~~l~~v~~  160 (423)
T PRK04837         86 ALIMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVLES-GVDILIGTTGRLIDYAKQN---HINLGAIQV  160 (423)
T ss_pred             EEEECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcC-CCCEEEECHHHHHHHHHcC---CcccccccE
Confidence            9999999999999999999998765 7999999999887776666654 5799999999999999765   467899999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCC--CCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPR--RRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk--~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~  610 (633)
                      |||||||+|++++|...+..++..++.  .+|+++||||++..+.     ...++.++.....  ......+.+.++++.
T Consensus       161 lViDEad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~--~~~~~~i~~~~~~~~  238 (423)
T PRK04837        161 VVLDEADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPE--QKTGHRIKEELFYPS  238 (423)
T ss_pred             EEEecHHHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCC--CcCCCceeEEEEeCC
Confidence            999999999999999999999999984  5788999999998753     1223344432211  223456777766653


Q ss_pred             ------hH-HHHhhcCCceEEEEEcccc
Q 006737          611 ------VL-VLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l-~~~~k~~~~~~LVFcnT~s  631 (633)
                            .+ .........++||||||+.
T Consensus       239 ~~~k~~~l~~ll~~~~~~~~lVF~~t~~  266 (423)
T PRK04837        239 NEEKMRLLQTLIEEEWPDRAIIFANTKH  266 (423)
T ss_pred             HHHHHHHHHHHHHhcCCCeEEEEECCHH
Confidence                  11 1222334578999999974

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

Probab=100.00  E-value=1.8e-36  Score=304.19  Aligned_cols=243  Identities=28%  Similarity=0.434  Sum_probs=207.0

Q ss_pred             cccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCC
Q 006737          375 ILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVP  454 (633)
Q Consensus       375 ~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~  454 (633)
                      +....+|+++||++.+++++.+.||++|+.||+.||++|+.|+||+++|.+|+|||.+|.+.+|+.+.-...        
T Consensus        23 ~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~~r--------   94 (400)
T KOG0328|consen   23 VKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDISVR--------   94 (400)
T ss_pred             cccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccccc--------
Confidence            334567999999999999999999999999999999999999999999999999999999999877644332        


Q ss_pred             CeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          455 PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       455 ~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      ..+||||+||||||.|+.+.+..++.++ ++.+..+.||.+...+.+.+. .+++++.+|||+++++++..   .+.-..
T Consensus        95 ~tQ~lilsPTRELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkld-~G~hvVsGtPGrv~dmikr~---~L~tr~  169 (400)
T KOG0328|consen   95 ETQALILSPTRELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKLD-YGQHVVSGTPGRVLDMIKRR---SLRTRA  169 (400)
T ss_pred             eeeEEEecChHHHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhhc-ccceEeeCCCchHHHHHHhc---cccccc
Confidence            2579999999999999999999998766 899999999999998888887 56899999999999999887   577889


Q ss_pred             eeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeeh
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYV  609 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v  609 (633)
                      +++||+||||.||+.||..++..|+..+|+..|++++|||+|.++.     +..+++.+-....  .-+...++|+|+.+
T Consensus       170 vkmlVLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrd--eltlEgIKqf~v~v  247 (400)
T KOG0328|consen  170 VKMLVLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRD--ELTLEGIKQFFVAV  247 (400)
T ss_pred             eeEEEeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecC--CCchhhhhhheeee
Confidence            9999999999999999999999999999999999999999999963     3445544432222  33556799999987


Q ss_pred             h--------hHHHHhhcCCceEEEEEccccC
Q 006737          610 F--------VLVLSIKIQAFYIICFVYTISM  632 (633)
Q Consensus       610 ~--------~l~~~~k~~~~~~LVFcnT~s~  632 (633)
                      .        +-.......-.+++|||||+.+
T Consensus       248 e~EewKfdtLcdLYd~LtItQavIFcnTk~k  278 (400)
T KOG0328|consen  248 EKEEWKFDTLCDLYDTLTITQAVIFCNTKRK  278 (400)
T ss_pred             chhhhhHhHHHHHhhhhehheEEEEecccch
Confidence            5        2223345556799999999853

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=1.9e-35  Score=327.54  Aligned_cols=243  Identities=35%  Similarity=0.525  Sum_probs=195.9

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      +|++|+|++.++++|.++||..||++|.++||.++.|+|+|++||||||||+||++|+++.+......  .....++++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~--~~~~~~~~aL   79 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPH--AKGRRPVRAL   79 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccc--cccCCCceEE
Confidence            69999999999999999999999999999999999999999999999999999999999998764321  1122346899


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||+||++||.|+++.+..+.... ++.+..++|+.....+...+. ..++|||+||++|++++...   ...++++++||
T Consensus        80 il~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~-~~~~IiV~TP~rL~~~~~~~---~~~l~~v~~lV  154 (456)
T PRK10590         80 ILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLR-GGVDVLVATPGRLLDLEHQN---AVKLDQVEILV  154 (456)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHHc-CCCcEEEEChHHHHHHHHcC---CcccccceEEE
Confidence            99999999999999999988755 788899999998777666554 45799999999999988765   36789999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh----
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF----  610 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~----  610 (633)
                      |||||+|++++|...+..++..++..+|+++||||+++++.     +..++..+....  .......+.+++.++.    
T Consensus       155 iDEah~ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~--~~~~~~~i~~~~~~~~~~~k  232 (456)
T PRK10590        155 LDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVAR--RNTASEQVTQHVHFVDKKRK  232 (456)
T ss_pred             eecHHHHhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEec--ccccccceeEEEEEcCHHHH
Confidence            99999999999999999999999999999999999998742     222333332211  1223456777776654    


Q ss_pred             --hHHHH-hhcCCceEEEEEcccc
Q 006737          611 --VLVLS-IKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 --~l~~~-~k~~~~~~LVFcnT~s  631 (633)
                        ++... ......++||||||+.
T Consensus       233 ~~~l~~l~~~~~~~~~lVF~~t~~  256 (456)
T PRK10590        233 RELLSQMIGKGNWQQVLVFTRTKH  256 (456)
T ss_pred             HHHHHHHHHcCCCCcEEEEcCcHH
Confidence              22222 2234468999999975

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.9e-35  Score=327.64  Aligned_cols=238  Identities=36%  Similarity=0.533  Sum_probs=198.4

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+|++|+|++.++++|.++||..|||+|.+|||.++.|+|++++||||||||++|++|+++++....        ..+++
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~~--------~~~~~   75 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKR--------FRVQA   75 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhcc--------CCceE
Confidence            5699999999999999999999999999999999999999999999999999999999999875332        13579


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      |||+||++||.|+.+.++.+.....++++..++||.+...+...+. .+++|+|+||++|.+++.+.   ...+.++++|
T Consensus        76 lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~-~~~~IvV~Tp~rl~~~l~~~---~~~l~~l~~l  151 (460)
T PRK11776         76 LVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE-HGAHIIVGTPGRILDHLRKG---TLDLDALNTL  151 (460)
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc-CCCCEEEEChHHHHHHHHcC---CccHHHCCEE
Confidence            9999999999999999999987766899999999999887777666 45799999999999999765   4678999999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh---
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      ||||||+|++++|...+..++..++..+|+++||||+++.+..     ...+..+....   ......+.|.++.+.   
T Consensus       152 ViDEad~~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~---~~~~~~i~~~~~~~~~~~  228 (460)
T PRK11776        152 VLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVES---THDLPAIEQRFYEVSPDE  228 (460)
T ss_pred             EEECHHHHhCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECc---CCCCCCeeEEEEEeCcHH
Confidence            9999999999999999999999999999999999999988532     23333333221   223445788777664   


Q ss_pred             ----hHHHHhhcCCceEEEEEcccc
Q 006737          611 ----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                          +...+......++||||||+.
T Consensus       229 k~~~l~~ll~~~~~~~~lVF~~t~~  253 (460)
T PRK11776        229 RLPALQRLLLHHQPESCVVFCNTKK  253 (460)
T ss_pred             HHHHHHHHHHhcCCCceEEEECCHH
Confidence                222233445568999999975

>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.6e-36  Score=311.01  Aligned_cols=244  Identities=37%  Similarity=0.480  Sum_probs=202.8

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +.+.|+.|||++++.+.|+.+|+.+|||+|..|||.|+.|+|+|.+|.||||||++|.||+|+++.+...        +.
T Consensus         5 t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP~--------gi   76 (442)
T KOG0340|consen    5 TAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDPY--------GI   76 (442)
T ss_pred             ccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCCC--------cc
Confidence            3467999999999999999999999999999999999999999999999999999999999999977654        46


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-cccccCCe
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-LSVRLMGL  535 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-~~~~Ls~l  535 (633)
                      .+||++||||||.|+.+.|..+.+.. ++++.+++||.+.-.+...+... +||||+|||+|.+++..... ...-+.++
T Consensus        77 FalvlTPTrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~r-PHvVvatPGRlad~l~sn~~~~~~~~~rl  154 (442)
T KOG0340|consen   77 FALVLTPTRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDR-PHVVVATPGRLADHLSSNLGVCSWIFQRL  154 (442)
T ss_pred             eEEEecchHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccC-CCeEecCccccccccccCCccchhhhhce
Confidence            89999999999999999999987755 89999999999987766666554 79999999999999976632 23348899


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhcc-ccc----eEeeeccccccccCccceEEEeehh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLK-REH----TYIDTVGLGSVETPVKVSKYNIYVF  610 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~-~~~----~~i~~~~~~~~~~~~~V~q~~i~v~  610 (633)
                      +++|+||||++++..|-..+..|.+.+|+.+|+++||||+++.+.-. ..+    .......+..+.++..+.|.|++|.
T Consensus       155 kflVlDEADrvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~  234 (442)
T KOG0340|consen  155 KFLVLDEADRVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVS  234 (442)
T ss_pred             eeEEecchhhhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecc
Confidence            99999999999999999999999999999999999999999986321 111    1111122234677888999999886


Q ss_pred             ----------hHHHHhhcCCceEEEEEccc
Q 006737          611 ----------VLVLSIKIQAFYIICFVYTI  630 (633)
Q Consensus       611 ----------~l~~~~k~~~~~~LVFcnT~  630 (633)
                                .+..........++||+||-
T Consensus       235 ~~vkdaYLv~~Lr~~~~~~~~simIFvntt  264 (442)
T KOG0340|consen  235 IDVKDAYLVHLLRDFENKENGSIMIFVNTT  264 (442)
T ss_pred             hhhhHHHHHHHHhhhhhccCceEEEEeehh
Confidence                      22222233566899999984

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.9e-35  Score=338.16  Aligned_cols=240  Identities=35%  Similarity=0.528  Sum_probs=198.9

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      .++|.+|+|++.++++|.++||..|||+|.++||.++.|+|+|++||||||||+||++|+++.+....        ..++
T Consensus         5 ~~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~~--------~~~~   76 (629)
T PRK11634          5 ETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPEL--------KAPQ   76 (629)
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhcc--------CCCe
Confidence            45699999999999999999999999999999999999999999999999999999999998875432        2358


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++||.|+++.+..+.....++.+..++||.....+...+.. .++|||+||++|++++...   .+.+++|.+
T Consensus        77 ~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~-~~~IVVgTPgrl~d~l~r~---~l~l~~l~~  152 (629)
T PRK11634         77 ILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ-GPQIVVGTPGRLLDHLKRG---TLDLSKLSG  152 (629)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcC-CCCEEEECHHHHHHHHHcC---CcchhhceE
Confidence            999999999999999999999887778999999999988777666654 4799999999999999765   467899999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh--
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      |||||||+|++++|...+..|+..+|..+|+++||||+|+.+.     +..++..+....  .......+.|.|+.+.  
T Consensus       153 lVlDEAd~ml~~gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~--~~~~~~~i~q~~~~v~~~  230 (629)
T PRK11634        153 LVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQS--SVTTRPDISQSYWTVWGM  230 (629)
T ss_pred             EEeccHHHHhhcccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccC--ccccCCceEEEEEEechh
Confidence            9999999999999999999999999999999999999998853     222333332221  1234456777776553  


Q ss_pred             -----hHHHHhhcCCceEEEEEcccc
Q 006737          611 -----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 -----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                           +...+......++||||||+.
T Consensus       231 ~k~~~L~~~L~~~~~~~~IVF~~tk~  256 (629)
T PRK11634        231 RKNEALVRFLEAEDFDAAIIFVRTKN  256 (629)
T ss_pred             hHHHHHHHHHHhcCCCCEEEEeccHH
Confidence                 222233344568999999975

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=6.8e-35  Score=330.99  Aligned_cols=246  Identities=31%  Similarity=0.480  Sum_probs=194.9

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+|++|+|++.++++|.++||..||+||.++||.++.|+|++++||||||||++|++|+++.+....... ......+++
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~-~~~~~~~ra   87 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALA-DRKPEDPRA   87 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhccccc-ccccCCceE
Confidence            4699999999999999999999999999999999999999999999999999999999999987542110 111124689


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      |||+||+|||.|+++.+..++... ++.+..++|+.....+...+.. +++|||+||++|++++.+..  .+.+..+++|
T Consensus        88 LIl~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l~~-~~dIiV~TP~rL~~~l~~~~--~~~l~~v~~l  163 (572)
T PRK04537         88 LILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQ-GVDVIIATPGRLIDYVKQHK--VVSLHACEIC  163 (572)
T ss_pred             EEEeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHHhC-CCCEEEECHHHHHHHHHhcc--ccchhheeee
Confidence            999999999999999999988765 7899999999988766665554 57999999999999987642  2457899999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCC--CCcEEEEeccCChhhhcc-----ccceEeeeccccccccCccceEEEeehh-
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPR--RRQSLLFSATMPKELVLK-----REHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk--~~Q~IlfSATl~~el~l~-----~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      ||||||+|++++|...+..|+..++.  .+|+++||||++..+...     ..+..+....  .......+.|.++++. 
T Consensus       164 ViDEAh~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~--~~~~~~~i~q~~~~~~~  241 (572)
T PRK04537        164 VLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVET--ETITAARVRQRIYFPAD  241 (572)
T ss_pred             EecCHHHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEecc--ccccccceeEEEEecCH
Confidence            99999999999999999999999987  789999999999874211     1221111111  1223456777776553 


Q ss_pred             ------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                            ++..+......++||||||+.
T Consensus       242 ~~k~~~L~~ll~~~~~~k~LVF~nt~~  268 (572)
T PRK04537        242 EEKQTLLLGLLSRSEGARTMVFVNTKA  268 (572)
T ss_pred             HHHHHHHHHHHhcccCCcEEEEeCCHH
Confidence                  222233345679999999974

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=100.00  E-value=1.6e-34  Score=324.85  Aligned_cols=246  Identities=30%  Similarity=0.444  Sum_probs=195.1

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +..+|++++|++.++++|.+.||..|||+|.++||.++.|+|++++||||||||++|++|++.++....... .....++
T Consensus       119 pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~-~~~~~~~  197 (518)
T PLN00206        119 PILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGH-PSEQRNP  197 (518)
T ss_pred             hhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhcccc-ccccCCc
Confidence            446799999999999999999999999999999999999999999999999999999999999887532211 1112457


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||||||.|+++.+..+.... ++++.+++||.....+...+.. +++|||+||++|.+++...   ...++++.
T Consensus       198 ~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~~q~~~l~~-~~~IiV~TPgrL~~~l~~~---~~~l~~v~  272 (518)
T PLN00206        198 LAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGGDAMPQQLYRIQQ-GVELIVGTPGRLIDLLSKH---DIELDNVS  272 (518)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHHHhcC-CCCEEEECHHHHHHHHHcC---Cccchhee
Confidence            89999999999999999999887655 6788889999887777666654 4799999999999999776   46789999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +|||||||+|++++|..++..|+..++ ..|+++||||+++++.     +..+...+.....  ......+.|.++++. 
T Consensus       273 ~lViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~--~~~~~~v~q~~~~~~~  349 (518)
T PLN00206        273 VLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNP--NRPNKAVKQLAIWVET  349 (518)
T ss_pred             EEEeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC--CCCCcceeEEEEeccc
Confidence            999999999999999999999999885 6899999999999853     2223333332111  223345777777654 


Q ss_pred             ------hHHHHhh--cCCceEEEEEcccc
Q 006737          611 ------VLVLSIK--IQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k--~~~~~~LVFcnT~s  631 (633)
                            ++..+..  ....++||||||+.
T Consensus       350 ~~k~~~l~~~l~~~~~~~~~~iVFv~s~~  378 (518)
T PLN00206        350 KQKKQKLFDILKSKQHFKPPAVVFVSSRL  378 (518)
T ss_pred             hhHHHHHHHHHHhhcccCCCEEEEcCCch
Confidence                  1111111  12357999999975

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

Probab=100.00  E-value=2.4e-36  Score=307.35  Aligned_cols=237  Identities=32%  Similarity=0.483  Sum_probs=204.6

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ..|+++.|...++..+.+.||++|+|+|.++||..+.|+|+++-|..|+|||.||++|+|+.+.....        .+++
T Consensus        85 ~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~~~--------~IQ~  156 (459)
T KOG0326|consen   85 NEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPKKN--------VIQA  156 (459)
T ss_pred             ccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCcccc--------ceeE
Confidence            35999999999999999999999999999999999999999999999999999999999998754432        4789


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      +|++||||||.|+.+.++.+.+++ ++.+...+||++...+..++.. ..|++|+|||+++++++.+   ...+++..++
T Consensus       157 ~ilVPtrelALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl~~-~VH~~vgTPGRIlDL~~Kg---Va~ls~c~~l  231 (459)
T KOG0326|consen  157 IILVPTRELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRLNQ-TVHLVVGTPGRILDLAKKG---VADLSDCVIL  231 (459)
T ss_pred             EEEeecchhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeeecC-ceEEEEcCChhHHHHHhcc---cccchhceEE
Confidence            999999999999999999999877 7999999999999988877765 4899999999999999887   4568999999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhcc-----ccceEeeeccccccccCccceEEEeehh---
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLK-----REHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~-----~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      |+||||.|+...|...+..++..+|+++|++++|||+|-.+.-.     ..+..|+..   ..-++..|.|+|.++.   
T Consensus       232 V~DEADKlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM---~eLtl~GvtQyYafV~e~q  308 (459)
T KOG0326|consen  232 VMDEADKLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLM---EELTLKGVTQYYAFVEERQ  308 (459)
T ss_pred             EechhhhhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehh---hhhhhcchhhheeeechhh
Confidence            99999999999999999999999999999999999999886422     223333322   2456788999999875   


Q ss_pred             ----hHHHHhhcCCceEEEEEcccc
Q 006737          611 ----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                          +-....+.+-.+.||||||..
T Consensus       309 KvhCLntLfskLqINQsIIFCNS~~  333 (459)
T KOG0326|consen  309 KVHCLNTLFSKLQINQSIIFCNSTN  333 (459)
T ss_pred             hhhhHHHHHHHhcccceEEEeccch
Confidence                112234666779999999974

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

Probab=100.00  E-value=5.5e-35  Score=311.29  Aligned_cols=251  Identities=31%  Similarity=0.427  Sum_probs=210.0

Q ss_pred             CCcccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCC
Q 006737          373 EPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQL  452 (633)
Q Consensus       373 ~p~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~  452 (633)
                      .|.-+.++|++++++..|..++.+..|.+|||+|.+++|..+.|+||+..|.||||||.||+.|++.|++....-   ..
T Consensus       217 s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~eL---~~  293 (731)
T KOG0339|consen  217 SPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPEL---KP  293 (731)
T ss_pred             CCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchhhh---cC
Confidence            344456789999999999999999999999999999999999999999999999999999999999999876431   22


Q ss_pred             CCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          453 VPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       453 ~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      ..+|.+||+||||+||.||+.+++++++.+ ++++.+++||.+...|...|+ .++.|||||||||++++...   ..++
T Consensus       294 g~gPi~vilvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk~eQ~k~Lk-~g~EivVaTPgRlid~VkmK---atn~  368 (731)
T KOG0339|consen  294 GEGPIGVILVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSKWEQSKELK-EGAEIVVATPGRLIDMVKMK---ATNL  368 (731)
T ss_pred             CCCCeEEEEeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcHHHHHHhhh-cCCeEEEechHHHHHHHHhh---cccc
Confidence            457889999999999999999999998877 899999999999999999998 56899999999999999876   4789


Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhccccceEeeeccc---cccccCccceEEEeeh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGL---GSVETPVKVSKYNIYV  609 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~~~~~~i~~~~~---~~~~~~~~V~q~~i~v  609 (633)
                      .++.||||||||+|+++||..++..|...+.+++|+|+||||++..+.-.....+.+++.+   ........|.|.+.+|
T Consensus       369 ~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dITQ~V~V~  448 (731)
T KOG0339|consen  369 SRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDITQTVSVC  448 (731)
T ss_pred             eeeeEEEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccchhheeeec
Confidence            9999999999999999999999999999999999999999999999743322222222221   2234566899998888


Q ss_pred             h--------hHHHHhh-cCCceEEEEEcccc
Q 006737          610 F--------VLVLSIK-IQAFYIICFVYTIS  631 (633)
Q Consensus       610 ~--------~l~~~~k-~~~~~~LVFcnT~s  631 (633)
                      .        ++..+.. .....+|||+..+.
T Consensus       449 ~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~  479 (731)
T KOG0339|consen  449 PSEEKKLNWLLRHLVEFSSEGKVLIFVTKKA  479 (731)
T ss_pred             cCcHHHHHHHHHHhhhhccCCcEEEEEeccC
Confidence            5        2222222 22348999987553

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=5e-34  Score=313.95  Aligned_cols=241  Identities=34%  Similarity=0.507  Sum_probs=194.9

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      +|++|+|++.++++|.++||..|+++|.++|+.++.|+|++++||||+|||+||++|+++++......    ...++++|
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~----~~~~~~~l   77 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRR----KSGPPRIL   77 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhcccc----CCCCceEE
Confidence            69999999999999999999999999999999999999999999999999999999999998764221    12246899


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||+||++||.|+++.+..+.... ++.+..++|+.....+...+. .+++|||+||++|++++...   .+.+.++++||
T Consensus        78 il~Pt~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~-~~~~IlV~Tp~rl~~~~~~~---~~~~~~v~~lV  152 (434)
T PRK11192         78 ILTPTRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFS-ENQDIVVATPGRLLQYIKEE---NFDCRAVETLI  152 (434)
T ss_pred             EECCcHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHhc-CCCCEEEEChHHHHHHHHcC---CcCcccCCEEE
Confidence            99999999999999999998765 789999999998776655554 45799999999999999765   36688999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh-hh-----ccccceEeeeccccccccCccceEEEeehh---
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE-LV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e-l~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      |||||+|++++|...+..+...++...|+++||||++.. +.     +...+..+....  ......++.|+++.+.   
T Consensus       153 iDEah~~l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~--~~~~~~~i~~~~~~~~~~~  230 (434)
T PRK11192        153 LDEADRMLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEP--SRRERKKIHQWYYRADDLE  230 (434)
T ss_pred             EECHHHHhCCCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecC--CcccccCceEEEEEeCCHH
Confidence            999999999999999999999999899999999999865 21     122333332211  1223456777777553   


Q ss_pred             ----hHHHHh-hcCCceEEEEEcccc
Q 006737          611 ----VLVLSI-KIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ----~l~~~~-k~~~~~~LVFcnT~s  631 (633)
                          ++.... .....++||||||+.
T Consensus       231 ~k~~~l~~l~~~~~~~~~lVF~~s~~  256 (434)
T PRK11192        231 HKTALLCHLLKQPEVTRSIVFVRTRE  256 (434)
T ss_pred             HHHHHHHHHHhcCCCCeEEEEeCChH
Confidence                222222 235579999999975

>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=3.8e-35  Score=316.99  Aligned_cols=246  Identities=36%  Similarity=0.486  Sum_probs=205.8

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCC--CeE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVP--PIY  457 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~--~~~  457 (633)
                      .|.+-.+.+.+..++...||..|||+|+.+||.+..|+|+++||+||||||.||++|++.+++............  .|+
T Consensus        75 ~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~  154 (482)
T KOG0335|consen   75 TFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPR  154 (482)
T ss_pred             cccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCCCc
Confidence            788888999999999999999999999999999999999999999999999999999999999886654443333  589


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +||++||||||.|++++++++.. ...++++..+|+.+...+...+.. +|||+|||||+|.++++..   .+.|..+++
T Consensus       155 ~lIlapTReL~~Qi~nea~k~~~-~s~~~~~~~ygg~~~~~q~~~~~~-gcdIlvaTpGrL~d~~e~g---~i~l~~~k~  229 (482)
T KOG0335|consen  155 ALILAPTRELVDQIYNEARKFSY-LSGMKSVVVYGGTDLGAQLRFIKR-GCDILVATPGRLKDLIERG---KISLDNCKF  229 (482)
T ss_pred             eEEEeCcHHHhhHHHHHHHhhcc-cccceeeeeeCCcchhhhhhhhcc-CccEEEecCchhhhhhhcc---eeehhhCcE
Confidence            99999999999999999998864 348899999999888877777665 4899999999999999887   588999999


Q ss_pred             EEEecccccCC-cChHHHHHHHHHHCCC----CCcEEEEeccCChhhh------ccccceEeeeccccccccCccceEEE
Q 006737          538 LVLDEADHLLD-LGFRKDVENIVDCLPR----RRQSLLFSATMPKELV------LKREHTYIDTVGLGSVETPVKVSKYN  606 (633)
Q Consensus       538 LVIDEAD~Lld-~gf~~~l~~Il~~lpk----~~Q~IlfSATl~~el~------l~~~~~~i~~~~~~~~~~~~~V~q~~  606 (633)
                      |||||||+|+| ++|.++|..|+..+..    .+|+++||||+|.++.      +..+++++....+  -.+..++.|..
T Consensus       230 ~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rv--g~~~~ni~q~i  307 (482)
T KOG0335|consen  230 LVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRV--GSTSENITQKI  307 (482)
T ss_pred             EEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeee--ccccccceeEe
Confidence            99999999999 9999999999987754    7999999999999953      2223555544333  35677899988


Q ss_pred             eehh-------hHHHHhhcC----Cc-----eEEEEEccccC
Q 006737          607 IYVF-------VLVLSIKIQ----AF-----YIICFVYTISM  632 (633)
Q Consensus       607 i~v~-------~l~~~~k~~----~~-----~~LVFcnT~s~  632 (633)
                      .+|.       ++.++.+..    ..     .++|||.|+.+
T Consensus       308 ~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~  349 (482)
T KOG0335|consen  308 LFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRG  349 (482)
T ss_pred             eeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccch
Confidence            8875       333333222    22     79999999864

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.5e-33  Score=313.90  Aligned_cols=247  Identities=35%  Similarity=0.522  Sum_probs=195.4

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ...|.+++|++.++++|.++||..|+++|.++|+.++.|+|+|+++|||||||+||++|+++.+....... ......++
T Consensus        86 ~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~-~~~~~~~~  164 (475)
T PRK01297         86 KTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPK-ERYMGEPR  164 (475)
T ss_pred             CCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCccc-ccccCCce
Confidence            35689999999999999999999999999999999999999999999999999999999999987653211 11122468


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++||.|+++.+..+.... ++.+..++||.....+...+....++|||+||++|+.++...   ...++++++
T Consensus       165 aLil~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~---~~~l~~l~~  240 (475)
T PRK01297        165 ALIIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRG---EVHLDMVEV  240 (475)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcC---CcccccCce
Confidence            9999999999999999999998765 788999999988877777777777899999999999988765   467899999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCC--CCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPR--RRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk--~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~  610 (633)
                      |||||||++++++|...+..|+..++.  .+|+|+||||++..+..     ...+..+.....  ......+.++++.+.
T Consensus       241 lViDEah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~--~~~~~~~~~~~~~~~  318 (475)
T PRK01297        241 MVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPE--NVASDTVEQHVYAVA  318 (475)
T ss_pred             EEechHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccC--cCCCCcccEEEEEec
Confidence            999999999999999999999998864  57999999999887431     122233222111  122344566555442


Q ss_pred             ------hHHH-HhhcCCceEEEEEcccc
Q 006737          611 ------VLVL-SIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~-~~k~~~~~~LVFcnT~s  631 (633)
                            .+.. .......++||||+|+.
T Consensus       319 ~~~k~~~l~~ll~~~~~~~~IVF~~s~~  346 (475)
T PRK01297        319 GSDKYKLLYNLVTQNPWERVMVFANRKD  346 (475)
T ss_pred             chhHHHHHHHHHHhcCCCeEEEEeCCHH
Confidence                  1222 22333458999999974

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=100.00  E-value=2.9e-33  Score=299.66  Aligned_cols=248  Identities=31%  Similarity=0.504  Sum_probs=206.3

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCC-CCCCCC
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST-TQLVPP  455 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~-~~~~~~  455 (633)
                      +..+|++.+++..+++.+.+.||..|+|||..+||..+.++|+|..|.||||||++|++|++..|.....-.. .....+
T Consensus       243 plrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~g  322 (673)
T KOG0333|consen  243 PLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEG  322 (673)
T ss_pred             cccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccC
Confidence            3567999999999999999999999999999999999999999999999999999999999988876543222 234568


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      |+++|++|||+||+||..+..+++... ++++..++||.+..++--.+.. +|+|+|||||+|++.|.+.   .+-++++
T Consensus       323 pyaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~EEq~fqls~-gceiviatPgrLid~Lenr---~lvl~qc  397 (673)
T KOG0333|consen  323 PYAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSFEEQGFQLSM-GCEIVIATPGRLIDSLENR---YLVLNQC  397 (673)
T ss_pred             ceeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccchhhhhhhhhc-cceeeecCchHHHHHHHHH---HHHhccC
Confidence            999999999999999999999998766 7999999999998876555544 5899999999999999887   4679999


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCC-------------------------CcEEEEeccCChhhh-----ccccc
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRR-------------------------RQSLLFSATMPKELV-----LKREH  585 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~-------------------------~Q~IlfSATl~~el~-----l~~~~  585 (633)
                      .+||+||||+|+|+||.+++..|+..+|..                         +|+++||||+|+.+.     +...+
T Consensus       398 tyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~p  477 (673)
T KOG0333|consen  398 TYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRP  477 (673)
T ss_pred             ceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCC
Confidence            999999999999999999999999999731                         799999999999963     33444


Q ss_pred             eEeeeccccccccCccceEEEeehh-------hHHHHhhcCCceEEEEEcccc
Q 006737          586 TYIDTVGLGSVETPVKVSKYNIYVF-------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       586 ~~i~~~~~~~~~~~~~V~q~~i~v~-------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      +++. ++. .......|+|..+.+.       ++..+......++|||+|++.
T Consensus       478 v~vt-ig~-~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~~ppiIIFvN~kk  528 (673)
T KOG0333|consen  478 VVVT-IGS-AGKPTPRVEQKVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKK  528 (673)
T ss_pred             eEEE-ecc-CCCCccchheEEEEecchHHHHHHHHHHHhCCCCCEEEEEechh
Confidence            5442 221 1234567888887764       444444556779999999974

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.2e-33  Score=323.34  Aligned_cols=248  Identities=32%  Similarity=0.467  Sum_probs=207.7

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ++++|.++|++..++..|+++||..|++||.+|||+|+.|+|||.+|.||||||++|+||++.|+..+..-   ....+|
T Consensus       363 pv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~---~~gdGP  439 (997)
T KOG0334|consen  363 PVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPL---EEGDGP  439 (997)
T ss_pred             ccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCCh---hhCCCc
Confidence            35679999999999999999999999999999999999999999999999999999999999887665432   223478


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      .+||++|||+||.||.+.+..+++. .++++++++|+.....++..++.+ +.|+|||||++++++....+...+|.++.
T Consensus       440 i~li~aPtrela~QI~r~~~kf~k~-l~ir~v~vygg~~~~~qiaelkRg-~eIvV~tpGRmiD~l~~n~grvtnlrR~t  517 (997)
T KOG0334|consen  440 IALILAPTRELAMQIHREVRKFLKL-LGIRVVCVYGGSGISQQIAELKRG-AEIVVCTPGRMIDILCANSGRVTNLRRVT  517 (997)
T ss_pred             eEEEEcCCHHHHHHHHHHHHHHHhh-cCceEEEecCCccHHHHHHHHhcC-CceEEeccchhhhhHhhcCCccccccccc
Confidence            9999999999999999999999987 599999999999999988888887 89999999999999977766666788888


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhcc-----ccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLK-----REHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~-----~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +||+||||+|++++|.+++..|++.+++.+|+++||||+|..+...     .-++-  .+..........|+|.+.+|. 
T Consensus       518 ~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pve--iiv~~~svV~k~V~q~v~V~~~  595 (997)
T KOG0334|consen  518 YLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVE--IIVGGRSVVCKEVTQVVRVCAI  595 (997)
T ss_pred             eeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCee--EEEccceeEeccceEEEEEecC
Confidence            9999999999999999999999999999999999999999985211     12222  222233445667889888875 


Q ss_pred             --------hHHHHhhcCCceEEEEEcccc
Q 006737          611 --------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 --------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                              +.++-..-...++||||.+..
T Consensus       596 e~eKf~kL~eLl~e~~e~~~tiiFv~~qe  624 (997)
T KOG0334|consen  596 ENEKFLKLLELLGERYEDGKTIIFVDKQE  624 (997)
T ss_pred             chHHHHHHHHHHHHHhhcCCEEEEEcCch
Confidence                    111112333679999998754

>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]

Probab=100.00  E-value=1.8e-34  Score=299.38  Aligned_cols=250  Identities=30%  Similarity=0.443  Sum_probs=207.1

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +..+|.++.++..+++.|++.|+..|||||.+-||.+++|+|+|..|-||||||++|.||++...+......+-....+|
T Consensus       168 PIksF~eMKFP~~~L~~lk~KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP  247 (610)
T KOG0341|consen  168 PIKSFKEMKFPKPLLRGLKKKGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGP  247 (610)
T ss_pred             chhhhhhccCCHHHHHHHHhcCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCC
Confidence            45789999999999999999999999999999999999999999999999999999999999988887766666667789


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHh-----cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccc
Q 006737          457 YVLILCPTRELASQIAAEAIALLK-----NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVR  531 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~-----~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~  531 (633)
                      .+|||||+||||.|++..+..++.     .++.++.+++.||.+...+......+ .||+|+|||+|.++|...   ...
T Consensus       248 ~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~G-vHivVATPGRL~DmL~KK---~~s  323 (610)
T KOG0341|consen  248 YGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRG-VHIVVATPGRLMDMLAKK---IMS  323 (610)
T ss_pred             eeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcC-eeEEEcCcchHHHHHHHh---hcc
Confidence            999999999999999999888874     33568889999999999888777665 899999999999999876   477


Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhccccceEeeeccc--ccccc-Ccc-------
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREHTYIDTVGL--GSVET-PVK-------  601 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~~~~~~i~~~~~--~~~~~-~~~-------  601 (633)
                      |.-++||++||||+|+++||...+..|+..+..++|+++||||+|..+.+....-.+.++.+  +.... .-+       
T Consensus       324 Ld~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEy  403 (610)
T KOG0341|consen  324 LDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEY  403 (610)
T ss_pred             HHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHH
Confidence            88899999999999999999999999999999999999999999999865543333322222  11111 112       


Q ss_pred             ceEEEeehhhHHHHhhcCCceEEEEEcccc
Q 006737          602 VSKYNIYVFVLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       602 V~q~~i~v~~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      |+|..-.+.++.++.+. ..++||||..+.
T Consensus       404 VkqEaKiVylLeCLQKT-~PpVLIFaEkK~  432 (610)
T KOG0341|consen  404 VKQEAKIVYLLECLQKT-SPPVLIFAEKKA  432 (610)
T ss_pred             HHhhhhhhhHHHHhccC-CCceEEEecccc
Confidence            34444444456665554 458999998764

>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5e-33  Score=291.77  Aligned_cols=240  Identities=32%  Similarity=0.450  Sum_probs=197.1

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      -.|..+||+..+++++.+.||..|||||+++||.|+.++|++..|.||||||.||+||+++++....       ..+.++
T Consensus        21 g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s-------~~g~Ra   93 (529)
T KOG0337|consen   21 GGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS-------QTGLRA   93 (529)
T ss_pred             CCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc-------ccccce
Confidence            4599999999999999999999999999999999999999999999999999999999999986653       246789


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      ||++|||+||.|..+.++.+++.. ++++.+++||....++...+..+ +|||||||++++++...-   .+.|+.|+||
T Consensus        94 lilsptreLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l~~n-pDii~ATpgr~~h~~vem---~l~l~sveyV  168 (529)
T KOG0337|consen   94 LILSPTRELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILLNEN-PDIIIATPGRLLHLGVEM---TLTLSSVEYV  168 (529)
T ss_pred             eeccCcHHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHhccC-CCEEEecCceeeeeehhe---eccccceeee
Confidence            999999999999999999998866 78999999999998888777654 699999999998876544   4779999999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhccc-----cceEeeeccccccccCccceEEEeehh---
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKR-----EHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~~-----~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      |+||||.|+++||.+++..++..+|..+|+++||||+|..+.-+.     ++..+. +.+ .......++..+..+.   
T Consensus       169 VfdEadrlfemgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVR-ldv-etkise~lk~~f~~~~~a~  246 (529)
T KOG0337|consen  169 VFDEADRLFEMGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVR-LDV-ETKISELLKVRFFRVRKAE  246 (529)
T ss_pred             eehhhhHHHhhhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEE-eeh-hhhcchhhhhheeeeccHH
Confidence            999999999999999999999999999999999999999854221     222222 111 1223344555555443   


Q ss_pred             ---hHHHHhhcC--CceEEEEEccccC
Q 006737          611 ---VLVLSIKIQ--AFYIICFVYTISM  632 (633)
Q Consensus       611 ---~l~~~~k~~--~~~~LVFcnT~s~  632 (633)
                         .++.+....  +.+++|||.|+.+
T Consensus       247 K~aaLl~il~~~~~~~~t~vf~~tk~h  273 (529)
T KOG0337|consen  247 KEAALLSILGGRIKDKQTIVFVATKHH  273 (529)
T ss_pred             HHHHHHHHHhccccccceeEEecccch
Confidence               333333333  3489999999754

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=2.3e-31  Score=289.00  Aligned_cols=239  Identities=29%  Similarity=0.440  Sum_probs=190.2

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.++++|.++||..|+++|.++|+.+++|+|++++||||||||++|++|+++.+....        .+.+
T Consensus        27 ~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~~--------~~~~   98 (401)
T PTZ00424         27 VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDL--------NACQ   98 (401)
T ss_pred             cCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCCC--------CCce
Confidence            46799999999999999999999999999999999999999999999999999999999998774221        2357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++||.|+.+.+..++... .+.+..+.|+.....+...+.. +++|+|+||++|.+++...   ...++++++
T Consensus        99 ~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~Ivv~Tp~~l~~~l~~~---~~~l~~i~l  173 (401)
T PTZ00424         99 ALILAPTRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKA-GVHMVVGTPGRVYDMIDKR---HLRVDDLKL  173 (401)
T ss_pred             EEEECCCHHHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHHcC-CCCEEEECcHHHHHHHHhC---CcccccccE
Confidence            9999999999999999998887644 6777788888877666655554 4799999999999988765   356899999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh--
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      |||||||++++.+|...+..++..++.+.|++++|||+++.+.     ....+..+....  .......+.++++.+.  
T Consensus       174 vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  251 (401)
T PTZ00424        174 FILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKK--DELTLEGIRQFYVAVEKE  251 (401)
T ss_pred             EEEecHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCC--CCcccCCceEEEEecChH
Confidence            9999999999999999999999999999999999999998742     112222221111  1223456677776553  


Q ss_pred             ------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                            +..........++||||+|+.
T Consensus       252 ~~~~~~l~~~~~~~~~~~~ivF~~t~~  278 (401)
T PTZ00424        252 EWKFDTLCDLYETLTITQAIIYCNTRR  278 (401)
T ss_pred             HHHHHHHHHHHHhcCCCeEEEEecCcH
Confidence                  111222334568999999975

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

Probab=99.97  E-value=1.7e-31  Score=278.70  Aligned_cols=238  Identities=31%  Similarity=0.487  Sum_probs=203.9

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+|++|+|++.|++.++..||++|+.||+.||.++..|.|+++++++|+|||.+|++++++++.....        ..+|
T Consensus        26 dsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~~k--------e~qa   97 (397)
T KOG0327|consen   26 DSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMSVK--------ETQA   97 (397)
T ss_pred             hhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcchH--------HHHH
Confidence            47999999999999999999999999999999999999999999999999999999999998743322        2469


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      ||++|||+||.|+.++...++... ++++..+.||.....+...++...++|+|+|||++.+++...   .+....++++
T Consensus        98 lilaPtreLa~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~---~l~~~~iKmf  173 (397)
T KOG0327|consen   98 LILAPTRELAQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRG---SLSTDGIKMF  173 (397)
T ss_pred             HHhcchHHHHHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccc---cccccceeEE
Confidence            999999999999998888887765 789999999998887777777777899999999999999776   4667889999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh---
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      |+||||.|+..||.+++..|++.+|.+.|++++|||+|+++.     +..++..+.....+  -+...++|+|+.+.   
T Consensus       174 vlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~--ltl~gikq~~i~v~k~~  251 (397)
T KOG0327|consen  174 VLDEADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDE--LTLEGIKQFYINVEKEE  251 (397)
T ss_pred             eecchHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchh--hhhhheeeeeeeccccc
Confidence            999999999999999999999999999999999999999963     44556655444332  45678999999764   


Q ss_pred             ---hHHHHhhcCCceEEEEEcccc
Q 006737          611 ---VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ---~l~~~~k~~~~~~LVFcnT~s  631 (633)
                         .+..+.. ...+++|||||+.
T Consensus       252 k~~~l~dl~~-~~~q~~if~nt~r  274 (397)
T KOG0327|consen  252 KLDTLCDLYR-RVTQAVIFCNTRR  274 (397)
T ss_pred             cccHHHHHHH-hhhcceEEecchh
Confidence               3333333 6679999999975

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.97  E-value=2.3e-31  Score=289.65  Aligned_cols=238  Identities=29%  Similarity=0.439  Sum_probs=201.4

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ..|+++-|...++..|+..+|..||+||.+|||+++.+-|+||+|..|+|||++|.+.+++.+...        ...+++
T Consensus        25 ~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~--------~~~~q~   96 (980)
T KOG4284|consen   25 PGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSR--------SSHIQK   96 (980)
T ss_pred             CCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcc--------cCccee
Confidence            469999999999999999999999999999999999999999999999999999998888766433        234689


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      +||+||||+|.||...+..++..+.++++.+++||+....+..+++.  |+|+|+|||+|..+++.+   .++.++|+++
T Consensus        97 ~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk~--~rIvIGtPGRi~qL~el~---~~n~s~vrlf  171 (980)
T KOG4284|consen   97 VIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLKQ--TRIVIGTPGRIAQLVELG---AMNMSHVRLF  171 (980)
T ss_pred             EEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhhh--ceEEecCchHHHHHHHhc---CCCccceeEE
Confidence            99999999999999999999998899999999999999988888876  689999999999999887   5789999999


Q ss_pred             EEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh--
Q 006737          539 VLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       539 VIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      ||||||.|++ ..|..+|..|++.+|+.+|+++||||.|..+.     +++++.++.....  ....-.|+|+++.+.  
T Consensus       172 VLDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~--d~~L~GikQyv~~~~s~  249 (980)
T KOG4284|consen  172 VLDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNAD--DVQLFGIKQYVVAKCSP  249 (980)
T ss_pred             EeccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccC--CceeechhheeeeccCC
Confidence            9999999998 55999999999999999999999999999863     4456665543221  334557888887643  


Q ss_pred             ------------hHH-HHhhcCCceEEEEEcccc
Q 006737          611 ------------VLV-LSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------------~l~-~~~k~~~~~~LVFcnT~s  631 (633)
                                  .|. ....+...++||||+..+
T Consensus       250 nnsveemrlklq~L~~vf~~ipy~QAlVF~~~~s  283 (980)
T KOG4284|consen  250 NNSVEEMRLKLQKLTHVFKSIPYVQALVFCDQIS  283 (980)
T ss_pred             cchHHHHHHHHHHHHHHHhhCchHHHHhhhhhhh
Confidence                        111 122333448999999865

>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.97  E-value=3.5e-30  Score=274.97  Aligned_cols=242  Identities=32%  Similarity=0.462  Sum_probs=185.1

Q ss_pred             CccccCCCHH----------HHHHHHHcCCCCCcHHHHHHHHHHhC---------CCcEEEEccCCCCchhhhHHHHHHH
Q 006737          380 RFDECGISPL----------TIKALTAAGYIQMTRVQEATLSACLE---------GKDAVVKAKTGTGKSIAFLLPAIEA  440 (633)
Q Consensus       380 ~F~el~L~~~----------Ll~~L~~~g~~~pt~iQ~~aIp~il~---------grDvLv~ApTGSGKTlaylLPiL~~  440 (633)
                      .|+.+++++.          +..+|.+++++...|+|..++|.++.         .+|++|.||||||||+||.|||++.
T Consensus       128 ~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~  207 (620)
T KOG0350|consen  128 IFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQL  207 (620)
T ss_pred             eeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHHH
Confidence            3566665554          44558999999999999999999853         5899999999999999999999998


Q ss_pred             HHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCC----cEEEECch
Q 006737          441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPC----QILVATPG  516 (633)
Q Consensus       441 l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~----dILIaTPg  516 (633)
                      +....       ...++||||+||++|+.|++..|..+.... ++.|+.+.|..+...+...+.....    ||||+|||
T Consensus       208 L~~R~-------v~~LRavVivPtr~L~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPG  279 (620)
T KOG0350|consen  208 LSSRP-------VKRLRAVVIVPTRELALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPG  279 (620)
T ss_pred             HccCC-------ccceEEEEEeeHHHHHHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCch
Confidence            86542       235799999999999999999999998765 8899999999999988888887766    99999999


Q ss_pred             hhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC---------------------------------
Q 006737          517 RLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP---------------------------------  563 (633)
Q Consensus       517 rLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp---------------------------------  563 (633)
                      ||.++|.+..  .++|++++|+||||||+|++..|..++-.+...+.                                 
T Consensus       280 RLVDHl~~~k--~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~  357 (620)
T KOG0350|consen  280 RLVDHLNNTK--SFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKL  357 (620)
T ss_pred             HHHHhccCCC--CcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCc
Confidence            9999998754  47899999999999999998776666554443331                                 


Q ss_pred             -CCCcEEEEeccCChhh----hcccc-ceEeeec--cccccccCccceEEEeehh-------hHHHHhhcCCceEEEEEc
Q 006737          564 -RRRQSLLFSATMPKEL----VLKRE-HTYIDTV--GLGSVETPVKVSKYNIYVF-------VLVLSIKIQAFYIICFVY  628 (633)
Q Consensus       564 -k~~Q~IlfSATl~~el----~l~~~-~~~i~~~--~~~~~~~~~~V~q~~i~v~-------~l~~~~k~~~~~~LVFcn  628 (633)
                       +..+.++||||++..-    .+... +....+.  .+.....|..+.+.++++.       +..........++|||+|
T Consensus       358 ~~~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~  437 (620)
T KOG0350|consen  358 YPPLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVN  437 (620)
T ss_pred             CchhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHhhcceEEEEec
Confidence             1135788899987651    11111 1111111  1344677888999888775       222333455569999999


Q ss_pred             ccc
Q 006737          629 TIS  631 (633)
Q Consensus       629 T~s  631 (633)
                      |.+
T Consensus       438 S~~  440 (620)
T KOG0350|consen  438 SVS  440 (620)
T ss_pred             chH
Confidence            975

>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase

Probab=99.97  E-value=1.5e-29  Score=294.59  Aligned_cols=182  Identities=24%  Similarity=0.282  Sum_probs=148.4

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEccc
Q 006737          385 GISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT  464 (633)
Q Consensus       385 ~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPT  464 (633)
                      .+++.+.++|.++||.+|+++|.++|+.++.|+|+++++|||||||+||+||+++.+....         ++++|||+||
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~~---------~~~aL~l~Pt   90 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP---------RATALYLAPT   90 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhCC---------CcEEEEEcCh
Confidence            3789999999999999999999999999999999999999999999999999999987531         3579999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHh-cccCcccccCCeeEEEEecc
Q 006737          465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIE-NKSGLSVRLMGLKMLVLDEA  543 (633)
Q Consensus       465 ReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~-~~~~~~~~Ls~l~~LVIDEA  543 (633)
                      ||||.|+++.++.+.  ..++++..+.|++... +...+.. +++|||+||+.|...+. ....+...+++|++||||||
T Consensus        91 raLa~q~~~~l~~l~--~~~i~v~~~~Gdt~~~-~r~~i~~-~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEa  166 (742)
T TIGR03817        91 KALAADQLRAVRELT--LRGVRPATYDGDTPTE-ERRWARE-HARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDEC  166 (742)
T ss_pred             HHHHHHHHHHHHHhc--cCCeEEEEEeCCCCHH-HHHHHhc-CCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeCh
Confidence            999999999999986  3378888888887743 4444444 47999999999975432 22112234889999999999


Q ss_pred             cccCCcChHHHHHHHHHH-------CCCCCcEEEEeccCChhhh
Q 006737          544 DHLLDLGFRKDVENIVDC-------LPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~-------lpk~~Q~IlfSATl~~el~  580 (633)
                      |.+.+. |..++..++..       ++.++|+|+||||+++...
T Consensus       167 h~~~g~-fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~  209 (742)
T TIGR03817       167 HSYRGV-FGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA  209 (742)
T ss_pred             hhccCc-cHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH
Confidence            999763 66665555443       4567899999999998854

A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.

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

Probab=99.96  E-value=9e-30  Score=264.10  Aligned_cols=244  Identities=28%  Similarity=0.383  Sum_probs=196.9

Q ss_pred             CCCCcccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCC
Q 006737          371 EEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSS  448 (633)
Q Consensus       371 ~~~p~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~  448 (633)
                      +..|+.+.++|++|+|+|+++++|..|+|.+|+.||..++|.++..  +|+|.++.+|+|||.||.|.+|.++.-.    
T Consensus        82 pnsPlyS~ksFeeL~LkPellkgly~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~----  157 (477)
T KOG0332|consen   82 PNSPLYSAKSFEELRLKPELLKGLYAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD----  157 (477)
T ss_pred             CCCCccccccHHhhCCCHHHHhHHHHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc----
Confidence            6678999999999999999999999999999999999999999986  6999999999999999999999876433    


Q ss_pred             CCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCc
Q 006737          449 TTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGL  528 (633)
Q Consensus       449 ~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~  528 (633)
                          ...|++|.|+||||||.|+.+++.+++++. ++.+....-+....... .+   ..+|+|+|||.+++++..-.  
T Consensus       158 ----~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~rG~-~i---~eqIviGTPGtv~Dlm~klk--  226 (477)
T KOG0332|consen  158 ----VVVPQCICLAPTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKRGN-KL---TEQIVIGTPGTVLDLMLKLK--  226 (477)
T ss_pred             ----ccCCCceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccccCC-cc---hhheeeCCCccHHHHHHHHH--
Confidence                234679999999999999999999999877 78887777666333211 11   24899999999999997632  


Q ss_pred             ccccCCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccc
Q 006737          529 SVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKV  602 (633)
Q Consensus       529 ~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V  602 (633)
                      .+.+..++++|+||||.|++ .||.++-..|...+|+++|+|+||||+...+.     +..++..+...  ...-...+|
T Consensus       227 ~id~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk--~eel~L~~I  304 (477)
T KOG0332|consen  227 CIDLEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILK--REELALDNI  304 (477)
T ss_pred             hhChhhceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeee--hhhccccch
Confidence            57789999999999999986 57999999999999999999999999998853     12222221111  123356789


Q ss_pred             eEEEeehh--------hHHHHhhcCCceEEEEEcccc
Q 006737          603 SKYNIYVF--------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       603 ~q~~i~v~--------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      +|+|+.|.        +..++-.....++||||.|+.
T Consensus       305 kQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~  341 (477)
T KOG0332|consen  305 KQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKA  341 (477)
T ss_pred             hhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehh
Confidence            99999986        222333455579999999974

>cd00268 DEADc DEAD-box helicases

Probab=99.96  E-value=3.1e-28  Score=239.92  Aligned_cols=188  Identities=44%  Similarity=0.680  Sum_probs=166.8

Q ss_pred             ccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 006737          381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLI  460 (633)
Q Consensus       381 F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLI  460 (633)
                      |+++++++.+.+.|.++|+..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....      ..++++||
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~~------~~~~~vii   74 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPK------KDGPQALI   74 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhcc------cCCceEEE
Confidence            678999999999999999999999999999999999999999999999999999999999877531      12468999


Q ss_pred             EcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEE
Q 006737          461 LCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVL  540 (633)
Q Consensus       461 LvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVI  540 (633)
                      ++||++|+.|+...+..+.... ++.+..++|+.........+. ..++|+|+||+.|..++.+.   ...+.++++|||
T Consensus        75 i~p~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~~iiv~T~~~l~~~l~~~---~~~~~~l~~lIv  149 (203)
T cd00268          75 LAPTRELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLK-RGPHIVVATPGRLLDLLERG---KLDLSKVKYLVL  149 (203)
T ss_pred             EcCCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhc-CCCCEEEEChHHHHHHHHcC---CCChhhCCEEEE
Confidence            9999999999999999987654 788899999888766555554 45899999999999998766   356789999999


Q ss_pred             ecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          541 DEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       541 DEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      ||||.+.+.++...+..++..+++.+|++++|||+++.+
T Consensus       150 DE~h~~~~~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~  188 (203)
T cd00268         150 DEADRMLDMGFEDQIREILKLLPKDRQTLLFSATMPKEV  188 (203)
T ss_pred             eChHHhhccChHHHHHHHHHhCCcccEEEEEeccCCHHH
Confidence            999999988899999999999999999999999999875

A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.96  E-value=2.7e-29  Score=249.56  Aligned_cols=241  Identities=29%  Similarity=0.446  Sum_probs=200.9

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..-|.++-|+|++++++...||..|+.+|.+|||...-|.|++++|.+|.|||.+|.|..|+.+--.        ...+-
T Consensus        41 ssgfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv--------~g~vs  112 (387)
T KOG0329|consen   41 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV--------DGQVS  112 (387)
T ss_pred             ccchhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC--------CCeEE
Confidence            3558999999999999999999999999999999999999999999999999999999998876322        22367


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|++|.|||||.||.++...+.++++.+++.+++||...+.+.+.+++ .++|+|+|||+++.+..+.   .+.|+++++
T Consensus       113 vlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~-~PhivVgTPGrilALvr~k---~l~lk~vkh  188 (387)
T KOG0329|consen  113 VLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKN-CPHIVVGTPGRILALVRNR---SLNLKNVKH  188 (387)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhC-CCeEEEcCcHHHHHHHHhc---cCchhhcce
Confidence            999999999999999999999999999999999999999998888887 6799999999999999877   588999999


Q ss_pred             EEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh-
Q 006737          538 LVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       538 LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +||||+|.|++ .+.+..+..|+...|.+.|+++||||+++++.     +..++.-+-. .....-+.-.+.|+|+.+. 
T Consensus       189 FvlDEcdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~v-DdE~KLtLHGLqQ~YvkLke  267 (387)
T KOG0329|consen  189 FVLDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFV-DDEAKLTLHGLQQYYVKLKE  267 (387)
T ss_pred             eehhhHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhc-cchhhhhhhhHHHHHHhhhh
Confidence            99999999985 45899999999999999999999999999963     2333222111 1112234456778887653 


Q ss_pred             ------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                            +...+......+++||+.|+.
T Consensus       268 ~eKNrkl~dLLd~LeFNQVvIFvKsv~  294 (387)
T KOG0329|consen  268 NEKNRKLNDLLDVLEFNQVVIFVKSVQ  294 (387)
T ss_pred             hhhhhhhhhhhhhhhhcceeEeeehhh
Confidence                  333344555679999998864

>PRK02362 ski2-like helicase; Provisional

Probab=99.95  E-value=2.3e-27  Score=277.30  Aligned_cols=179  Identities=22%  Similarity=0.239  Sum_probs=153.0

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .|++++|++.++++|.+.||.+|+|+|.+|++. ++.|+|++++||||||||++|.+|+++++...           .++
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~~-----------~ka   70 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARG-----------GKA   70 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhcC-----------CcE
Confidence            588999999999999999999999999999998 78899999999999999999999999988532           369


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      |||+||++||.|+++.+..+.. . ++++..++|+......  .+  ..++|+||||+++..++.+..   ..+.++++|
T Consensus        71 l~i~P~raLa~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~~--~l--~~~~IiV~Tpek~~~llr~~~---~~l~~v~lv  141 (737)
T PRK02362         71 LYIVPLRALASEKFEEFERFEE-L-GVRVGISTGDYDSRDE--WL--GDNDIIVATSEKVDSLLRNGA---PWLDDITCV  141 (737)
T ss_pred             EEEeChHHHHHHHHHHHHHhhc-C-CCEEEEEeCCcCcccc--cc--CCCCEEEECHHHHHHHHhcCh---hhhhhcCEE
Confidence            9999999999999999997643 2 7889999998754321  22  236999999999998887642   347899999


Q ss_pred             EEecccccCCcChHHHHHHHHHHC---CCCCcEEEEeccCChh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCL---PRRRQSLLFSATMPKE  578 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~l---pk~~Q~IlfSATl~~e  578 (633)
                      ||||||.+.+.+++..++.++..+   +.+.|+|+||||+++.
T Consensus       142 ViDE~H~l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n~  184 (737)
T PRK02362        142 VVDEVHLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNA  184 (737)
T ss_pred             EEECccccCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCCH
Confidence            999999999888888888776544   5689999999999874

>PRK00254 ski2-like helicase; Provisional

Probab=99.95  E-value=3.6e-27  Score=275.04  Aligned_cols=180  Identities=23%  Similarity=0.267  Sum_probs=157.2

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      +|+++++++.+.+.|.+.||..|+|+|.++++. ++.|+|+++++|||||||++|.+|+++++...          +.++
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~----------~~~~   71 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE----------GGKA   71 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc----------CCeE
Confidence            578999999999999999999999999999986 88999999999999999999999999987643          2369


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      |||+|+++||.|+++.+..+.. . ++++..++|+......  .+  ..++|+|+||+++..++...   ...+++|++|
T Consensus        72 l~l~P~~aLa~q~~~~~~~~~~-~-g~~v~~~~Gd~~~~~~--~~--~~~~IiV~Tpe~~~~ll~~~---~~~l~~l~lv  142 (720)
T PRK00254         72 VYLVPLKALAEEKYREFKDWEK-L-GLRVAMTTGDYDSTDE--WL--GKYDIIIATAEKFDSLLRHG---SSWIKDVKLV  142 (720)
T ss_pred             EEEeChHHHHHHHHHHHHHHhh-c-CCEEEEEeCCCCCchh--hh--ccCCEEEEcHHHHHHHHhCC---chhhhcCCEE
Confidence            9999999999999999987643 2 7899999998764422  22  34799999999998888654   2457899999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ||||+|.+.+.++...+..++..+....|+|++|||+++.
T Consensus       143 ViDE~H~l~~~~rg~~le~il~~l~~~~qiI~lSATl~n~  182 (720)
T PRK00254        143 VADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVGNA  182 (720)
T ss_pred             EEcCcCccCCccchHHHHHHHHhcCcCCcEEEEEccCCCH
Confidence            9999999999899999999999998899999999999875

>PRK01172 ski2-like helicase; Provisional

Probab=99.93  E-value=3.9e-25  Score=256.34  Aligned_cols=179  Identities=17%  Similarity=0.227  Sum_probs=150.3

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      .|++++|++.+++.+.+.+|. ++++|.++++.++.++|++++||||||||+++.++++..+...           .++|
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~~-----------~k~v   69 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAG-----------LKSI   69 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHhC-----------CcEE
Confidence            588999999999999999987 9999999999999999999999999999999999999887542           2599


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||+|+++||.|+++.+.++..  .++.+..++|+......  .+  ..++|+|+||+++..++.+.   ...+.++++||
T Consensus        70 ~i~P~raLa~q~~~~~~~l~~--~g~~v~~~~G~~~~~~~--~~--~~~dIiv~Tpek~~~l~~~~---~~~l~~v~lvV  140 (674)
T PRK01172         70 YIVPLRSLAMEKYEELSRLRS--LGMRVKISIGDYDDPPD--FI--KRYDVVILTSEKADSLIHHD---PYIINDVGLIV  140 (674)
T ss_pred             EEechHHHHHHHHHHHHHHhh--cCCeEEEEeCCCCCChh--hh--ccCCEEEECHHHHHHHHhCC---hhHHhhcCEEE
Confidence            999999999999999987643  27888888887654322  22  23699999999998888664   24578999999


Q ss_pred             EecccccCCcChHHHHHHHHH---HCCCCCcEEEEeccCChhh
Q 006737          540 LDEADHLLDLGFRKDVENIVD---CLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~---~lpk~~Q~IlfSATl~~el  579 (633)
                      |||||++.+.++...+..++.   .++.+.|+|+||||+++..
T Consensus       141 iDEaH~l~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n~~  183 (674)
T PRK01172        141 ADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSNAN  183 (674)
T ss_pred             EecchhccCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCCHH
Confidence            999999998877777776654   4566899999999998753

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.93  E-value=3.7e-25  Score=262.33  Aligned_cols=188  Identities=21%  Similarity=0.292  Sum_probs=144.5

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      +++.+.+.+. .+|..|||+|.++|+.++.|+|++++||||||||+||++|+++.+.......  ....++++|||+||+
T Consensus        18 l~~~v~~~~~-~~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~--~~~~~~~~LyIsPtr   94 (876)
T PRK13767         18 LRPYVREWFK-EKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREG--ELEDKVYCLYVSPLR   94 (876)
T ss_pred             cCHHHHHHHH-HccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhcccc--CCCCCeEEEEEcCHH
Confidence            4566666554 4799999999999999999999999999999999999999999987643211  112357899999999


Q ss_pred             HHHHHHHHHHHHH-------H----hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          466 ELASQIAAEAIAL-------L----KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       466 eLa~Qi~~~l~~l-------~----~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      +||.|+++.+...       +    ...+++.+.+.+|++........+. .+++|||+||++|..++.... ....+.+
T Consensus        95 aLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~-~~p~IlVtTPE~L~~ll~~~~-~~~~l~~  172 (876)
T PRK13767         95 ALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLK-KPPHILITTPESLAILLNSPK-FREKLRT  172 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHh-CCCCEEEecHHHHHHHhcChh-HHHHHhc
Confidence            9999998876532       2    1223678899999988665544443 457999999999988875432 1235789


Q ss_pred             eeEEEEecccccCCcChHHHHH----HHHHHCCCCCcEEEEeccCChh
Q 006737          535 LKMLVLDEADHLLDLGFRKDVE----NIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~----~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +++|||||||.+++..+..++.    ++....+...|+|+||||+++.
T Consensus       173 l~~VVIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~  220 (876)
T PRK13767        173 VKWVIVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL  220 (876)
T ss_pred             CCEEEEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH
Confidence            9999999999999766555444    4444455678999999999874

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

Probab=99.93  E-value=3e-25  Score=211.25  Aligned_cols=164  Identities=37%  Similarity=0.599  Sum_probs=138.9

Q ss_pred             cHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcC
Q 006737          403 TRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH  482 (633)
Q Consensus       403 t~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~  482 (633)
                      ||+|.++++.+.+|+|++++||||+|||++|++|+++.+.....         .++||++|+++|+.|+++.+..++.. 
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~~~---------~~~lii~P~~~l~~q~~~~~~~~~~~-   70 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEGKD---------ARVLIIVPTRALAEQQFERLRKFFSN-   70 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTTSS---------SEEEEEESSHHHHHHHHHHHHHHTTT-
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccCCC---------ceEEEEeecccccccccccccccccc-
Confidence            79999999999999999999999999999999999998876521         26999999999999999999999876 


Q ss_pred             CCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHC
Q 006737          483 DGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCL  562 (633)
Q Consensus       483 ~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~l  562 (633)
                      .++++..++++............++++|+|+||++|.+++...   ...+.++.+|||||+|.+..+.+...+..|+..+
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~---~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~  147 (169)
T PF00270_consen   71 TNVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNG---KINISRLSLIVIDEAHHLSDETFRAMLKSILRRL  147 (169)
T ss_dssp             TTSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTT---SSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHS
T ss_pred             cccccccccccccccccccccccccccccccCcchhhcccccc---ccccccceeeccCcccccccccHHHHHHHHHHHh
Confidence            4788999999887553333333456899999999999999874   2356679999999999999888899999999887


Q ss_pred             CC--CCcEEEEeccCChhh
Q 006737          563 PR--RRQSLLFSATMPKEL  579 (633)
Q Consensus       563 pk--~~Q~IlfSATl~~el  579 (633)
                      ..  +.|+|++|||+++.+
T Consensus       148 ~~~~~~~~i~~SAT~~~~~  166 (169)
T PF00270_consen  148 KRFKNIQIILLSATLPSNV  166 (169)
T ss_dssp             HTTTTSEEEEEESSSTHHH
T ss_pred             cCCCCCcEEEEeeCCChhH
Confidence            43  599999999999544

Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....

>COG1201 Lhr Lhr-like helicases [General function prediction only]

Probab=99.93  E-value=3.8e-25  Score=254.59  Aligned_cols=186  Identities=23%  Similarity=0.312  Sum_probs=156.5

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      |++.+.+.+... |..||+.|.+|||.|..|+|+|++||||||||+|..||+++.+.+..   ......++.||||+|.|
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~---~~~~~~~i~~lYIsPLk   83 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG---KGKLEDGIYALYISPLK   83 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhcc---CCCCCCceEEEEeCcHH
Confidence            678888888887 99999999999999999999999999999999999999999999874   11223468999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc
Q 006737          466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH  545 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~  545 (633)
                      +|.+++...+...+... |+.+.+-+|++..... +....+++||||+||+.|.-+|... .....|.++++|||||+|.
T Consensus        84 ALn~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er-~r~~~~PPdILiTTPEsL~lll~~~-~~r~~l~~vr~VIVDEiHe  160 (814)
T COG1201          84 ALNNDIRRRLEEPLREL-GIEVAVRHGDTPQSEK-QKMLKNPPHILITTPESLAILLNSP-KFRELLRDVRYVIVDEIHA  160 (814)
T ss_pred             HHHHHHHHHHHHHHHHc-CCccceecCCCChHHh-hhccCCCCcEEEeChhHHHHHhcCH-HHHHHhcCCcEEEeehhhh
Confidence            99999999999998866 8999999999987754 4444567899999999998888654 2335699999999999999


Q ss_pred             cCCcChH----HHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          546 LLDLGFR----KDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       546 Lld~gf~----~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +.+...+    -.++++....+ +.|.|++|||+.+..
T Consensus       161 l~~sKRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~~~  197 (814)
T COG1201         161 LAESKRGVQLALSLERLRELAG-DFQRIGLSATVGPPE  197 (814)
T ss_pred             hhccccchhhhhhHHHHHhhCc-ccEEEeehhccCCHH
Confidence            9865433    34455556666 899999999998773

>PRK09401 reverse gyrase; Reviewed

Probab=99.93  E-value=1.2e-24  Score=262.52  Aligned_cols=215  Identities=23%  Similarity=0.191  Sum_probs=158.9

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|+ .|+++|..++|.++.|+|++++||||+|||+ |.++++..+...          +.++|||+|||+||.|+++.++
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~~----------g~~alIL~PTreLa~Qi~~~l~  144 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAKK----------GKKSYIIFPTRLLVEQVVEKLE  144 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHhc----------CCeEEEEeccHHHHHHHHHHHH
Confidence            466 8999999999999999999999999999996 556665544321          3579999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccc-----hHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC---
Q 006737          477 ALLKNHDGIGVLTLVGGTRF-----KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD---  548 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~-----~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld---  548 (633)
                      .++... ++.+.+++|+...     ......+..+.++|+|+||++|.+++..     +.+..+++|||||||+|++   
T Consensus       145 ~l~~~~-~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~-----l~~~~~~~lVvDEaD~~L~~~k  218 (1176)
T PRK09401        145 KFGEKV-GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDE-----LPKKKFDFVFVDDVDAVLKSSK  218 (1176)
T ss_pred             HHhhhc-CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHh-----ccccccCEEEEEChHHhhhccc
Confidence            998755 6777777776542     2233445556689999999999998762     4456799999999999996   


Q ss_pred             --------cChH-HHHHHHHHHCCC------------------------CCcEEEEeccCChh-hh--ccccceEeeecc
Q 006737          549 --------LGFR-KDVENIVDCLPR------------------------RRQSLLFSATMPKE-LV--LKREHTYIDTVG  592 (633)
Q Consensus       549 --------~gf~-~~l~~Il~~lpk------------------------~~Q~IlfSATl~~e-l~--l~~~~~~i~~~~  592 (633)
                              .||. ..+..++..++.                        ..|+++||||+++. +.  +..+...+....
T Consensus       219 ~id~~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~~l~~~ll~~~v~~  298 (1176)
T PRK09401        219 NIDKLLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFEVGS  298 (1176)
T ss_pred             chhhHHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHHHHhhccceEEecC
Confidence                    5774 678888887765                        68999999999875 32  223332222211


Q ss_pred             ccccccCccceEEEeehh----hHHHHhhcCCceEEEEEcccc
Q 006737          593 LGSVETPVKVSKYNIYVF----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       593 ~~~~~~~~~V~q~~i~v~----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                        ......+|.|.|+.+.    .+..+.+.....+||||||..
T Consensus       299 --~~~~~rnI~~~yi~~~~k~~~L~~ll~~l~~~~LIFv~t~~  339 (1176)
T PRK09401        299 --PVFYLRNIVDSYIVDEDSVEKLVELVKRLGDGGLIFVPSDK  339 (1176)
T ss_pred             --cccccCCceEEEEEcccHHHHHHHHHHhcCCCEEEEEeccc
Confidence              1234567899888762    222233333468999999864

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

Probab=99.93  E-value=1.3e-25  Score=245.04  Aligned_cols=241  Identities=24%  Similarity=0.309  Sum_probs=181.5

Q ss_pred             cCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          384 CGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       384 l~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      +.+++.+++.+...+|..|+|+|.+|||.++.++|+++|||||||||++|++|+++++.....   .....+.+++||.|
T Consensus       141 ~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~---~~~~~gl~a~Il~p  217 (593)
T KOG0344|consen  141 YSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQ---EKHKVGLRALILSP  217 (593)
T ss_pred             hhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhc---ccCccceEEEEecc
Confidence            678999999999999999999999999999999999999999999999999999999987653   23345789999999


Q ss_pred             cHHHHHHHHHHHHHHH--hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEe
Q 006737          464 TRELASQIAAEAIALL--KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLD  541 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~--~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVID  541 (633)
                      ||+||.|++.++.++.  ... .+.+..+............+....++|+|.||-+|..++.... ..++++.|.++|+|
T Consensus       218 treLa~Qi~re~~k~~~~~~t-~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~-~~idl~~V~~lV~d  295 (593)
T KOG0344|consen  218 TRELAAQIYREMRKYSIDEGT-SLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGK-LNIDLSKVEWLVVD  295 (593)
T ss_pred             hHHHHHHHHHHHHhcCCCCCC-chhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCC-ccchhheeeeEeec
Confidence            9999999999999997  222 3333333333222222222223347999999999999997652 23679999999999


Q ss_pred             cccccCCc-ChHHHHHHHHHHCC-CCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh----
Q 006737          542 EADHLLDL-GFRKDVENIVDCLP-RRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF----  610 (633)
Q Consensus       542 EAD~Lld~-gf~~~l~~Il~~lp-k~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~----  610 (633)
                      |||.+++. .|..++..|+..+. ++..+-+||||++..+.     .+.+...+ +++.. ......|.|..++|-    
T Consensus       296 EaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~v-ivg~~-~sa~~~V~QelvF~gse~~  373 (593)
T KOG0344|consen  296 EADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRV-IVGLR-NSANETVDQELVFCGSEKG  373 (593)
T ss_pred             hHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeE-EEecc-hhHhhhhhhhheeeecchh
Confidence            99999998 89999999998654 57888999999999853     22222222 22221 233457888888774    


Q ss_pred             ----hHHHHhhcCCceEEEEEcccc
Q 006737          611 ----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                          +..........++|||+.|+.
T Consensus       374 K~lA~rq~v~~g~~PP~lIfVQs~e  398 (593)
T KOG0344|consen  374 KLLALRQLVASGFKPPVLIFVQSKE  398 (593)
T ss_pred             HHHHHHHHHhccCCCCeEEEEecHH
Confidence                222233445679999998864

>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional

Probab=99.93  E-value=6.9e-25  Score=257.27  Aligned_cols=180  Identities=20%  Similarity=0.239  Sum_probs=137.3

Q ss_pred             ccc--cCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          381 FDE--CGISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       381 F~e--l~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      |..  ++....+...+.. +||..|+|+|.++|++++.|+|+|+++|||+|||+||+||+|..   .           ..
T Consensus       437 W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~---~-----------Gi  502 (1195)
T PLN03137        437 WSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC---P-----------GI  502 (1195)
T ss_pred             ccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc---C-----------Cc
Confidence            553  4556667666665 69999999999999999999999999999999999999999842   1           24


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhc-----CCCcEEEECchhhHH--HHhcccCccc
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLES-----DPCQILVATPGRLLD--HIENKSGLSV  530 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~-----~~~dILIaTPgrLl~--lL~~~~~~~~  530 (633)
                      +|||+|+++|+.+++..+...     ++.+..+.++.....+...+..     +.++|||+||++|..  .+.+......
T Consensus       503 TLVISPLiSLmqDQV~~L~~~-----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~  577 (1195)
T PLN03137        503 TLVISPLVSLIQDQIMNLLQA-----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLN  577 (1195)
T ss_pred             EEEEeCHHHHHHHHHHHHHhC-----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhh
Confidence            999999999998766555443     7888899998877665544332     568999999999852  1211100001


Q ss_pred             ccCCeeEEEEecccccCCcC--hHHHHHHH--HHHCCCCCcEEEEeccCChhh
Q 006737          531 RLMGLKMLVLDEADHLLDLG--FRKDVENI--VDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       531 ~Ls~l~~LVIDEAD~Lld~g--f~~~l~~I--l~~lpk~~Q~IlfSATl~~el  579 (633)
                      ....|.+|||||||++++||  |+..+..+  +....+.+|+++||||++..+
T Consensus       578 ~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V  630 (1195)
T PLN03137        578 SRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASV  630 (1195)
T ss_pred             hccccceeccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHH
Confidence            23458899999999999998  88887764  333445789999999999874

>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype

Probab=99.93  E-value=1.4e-24  Score=251.17  Aligned_cols=216  Identities=19%  Similarity=0.117  Sum_probs=151.1

Q ss_pred             cCCCCCcHHHHHHHHHHhCCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEE-EcccHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLI-LCPTRELASQIAAE  474 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLI-LvPTReLa~Qi~~~  474 (633)
                      .||. |||+|.++||.++.|+ ++++++|||||||.+|.++++.. ...        ...+++|| ++|||+||.|+++.
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~~--------~~~~~rLv~~vPtReLa~Qi~~~   81 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EIG--------AKVPRRLVYVVNRRTVVDQVTEE   81 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-ccc--------ccccceEEEeCchHHHHHHHHHH
Confidence            5888 9999999999999998 67788999999999776555522 111        12244555 77999999999999


Q ss_pred             HHHHHhcCC----------------------CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-----
Q 006737          475 AIALLKNHD----------------------GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-----  527 (633)
Q Consensus       475 l~~l~~~~~----------------------~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-----  527 (633)
                      +.++.+.+.                      .+++.+++||.....+...+.. +++|||+|+    +++.+..-     
T Consensus        82 ~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~-~p~IIVgT~----D~i~sr~L~~gYg  156 (844)
T TIGR02621        82 AEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPH-RPAVIVGTV----DMIGSRLLFSGYG  156 (844)
T ss_pred             HHHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCC-CCcEEEECH----HHHcCCccccccc
Confidence            999987552                      4889999999998888877765 479999995    55544310     


Q ss_pred             cc-----c---ccCCeeEEEEecccccCCcChHHHHHHHHHHC--CCC---CcEEEEeccCChhhh-----ccccceEee
Q 006737          528 LS-----V---RLMGLKMLVLDEADHLLDLGFRKDVENIVDCL--PRR---RQSLLFSATMPKELV-----LKREHTYID  589 (633)
Q Consensus       528 ~~-----~---~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~l--pk~---~Q~IlfSATl~~el~-----l~~~~~~i~  589 (633)
                      ..     +   .|+++++|||||||  ++++|...+..|+..+  ++.   +|+++||||++.++.     +..++..+.
T Consensus       157 ~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~  234 (844)
T TIGR02621       157 CGFKSRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHP  234 (844)
T ss_pred             cccccccchhhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceee
Confidence            00     0   26889999999999  6789999999999975  442   799999999997632     122222222


Q ss_pred             eccccccccCccceEEEeehh---------hHHHHhhcCCceEEEEEcccc
Q 006737          590 TVGLGSVETPVKVSKYNIYVF---------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       590 ~~~~~~~~~~~~V~q~~i~v~---------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      ...  ...+..++.|++....         .+.........++||||||+.
T Consensus       235 V~~--~~l~a~ki~q~v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~NTv~  283 (844)
T TIGR02621       235 VLK--KRLAAKKIVKLVPPSDEKFLSTMVKELNLLMKDSGGAILVFCRTVK  283 (844)
T ss_pred             ccc--ccccccceEEEEecChHHHHHHHHHHHHHHHhhCCCcEEEEECCHH
Confidence            111  1123335555433211         111122345578999999975

This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.92  E-value=1.4e-24  Score=241.73  Aligned_cols=162  Identities=23%  Similarity=0.320  Sum_probs=126.8

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          396 AAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       396 ~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .+||..|+|+|.++|+.+++|+|+++++|||+|||+||++|++..              +..+|||+||++|+.|++..+
T Consensus         6 ~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~--------------~~~~lVi~P~~~L~~dq~~~l   71 (470)
T TIGR00614         6 VFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS--------------DGITLVISPLISLMEDQVLQL   71 (470)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc--------------CCcEEEEecHHHHHHHHHHHH
Confidence            369999999999999999999999999999999999999999742              124899999999999998888


Q ss_pred             HHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccc-ccCCeeEEEEecccccCCcC-
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSV-RLMGLKMLVLDEADHLLDLG-  550 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~-~Ls~l~~LVIDEAD~Lld~g-  550 (633)
                      ..+     ++.+..+.++.......   ..+..+.++|||+||+++........  .+ .+.++.+|||||||++++|| 
T Consensus        72 ~~~-----gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~--~l~~~~~i~~iViDEaH~i~~~g~  144 (470)
T TIGR00614        72 KAS-----GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQ--TLEERKGITLIAVDEAHCISQWGH  144 (470)
T ss_pred             HHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHH--HHHhcCCcCEEEEeCCcccCcccc
Confidence            754     67777777776544222   23455668999999999754221000  01 46789999999999999987 


Q ss_pred             -hHHHHHHH---HHHCCCCCcEEEEeccCChhh
Q 006737          551 -FRKDVENI---VDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       551 -f~~~l~~I---l~~lpk~~Q~IlfSATl~~el  579 (633)
                       |+..+..|   ...+ ++.|+++||||+++.+
T Consensus       145 ~fr~~~~~l~~l~~~~-~~~~~l~lTAT~~~~~  176 (470)
T TIGR00614       145 DFRPDYKALGSLKQKF-PNVPIMALTATASPSV  176 (470)
T ss_pred             ccHHHHHHHHHHHHHc-CCCceEEEecCCCHHH
Confidence             67776654   3344 5789999999999874

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK14701 reverse gyrase; Provisional

Probab=99.91  E-value=1.6e-23  Score=257.87  Aligned_cols=225  Identities=20%  Similarity=0.189  Sum_probs=162.2

Q ss_pred             HHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHH
Q 006737          388 PLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRE  466 (633)
Q Consensus       388 ~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTRe  466 (633)
                      ..+.+.+.+ +|| .|+++|+.+|+.++.|+|++++||||+|||++++++++....           .+.++|||+||++
T Consensus        66 ~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~-----------~g~~aLVl~PTre  133 (1638)
T PRK14701         66 EEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL-----------KGKKCYIILPTTL  133 (1638)
T ss_pred             HHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh-----------cCCeEEEEECHHH
Confidence            345555665 799 699999999999999999999999999999977766654321           1347999999999


Q ss_pred             HHHHHHHHHHHHHhcCC-CceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEec
Q 006737          467 LASQIAAEAIALLKNHD-GIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDE  542 (633)
Q Consensus       467 La~Qi~~~l~~l~~~~~-~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDE  542 (633)
                      |+.|+++.++.++.... ++.+..++|+.+...+.   ..+..+.++|||+||++|.+++...    . ..++++|||||
T Consensus       134 La~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l----~-~~~i~~iVVDE  208 (1638)
T PRK14701        134 LVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM----K-HLKFDFIFVDD  208 (1638)
T ss_pred             HHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH----h-hCCCCEEEEEC
Confidence            99999999999886542 56778888998766543   3455666899999999998876542    1 26799999999


Q ss_pred             ccccCC-----------cChHHHHHH----HHH----------------------HCCCCCc-EEEEeccCChh---hhc
Q 006737          543 ADHLLD-----------LGFRKDVEN----IVD----------------------CLPRRRQ-SLLFSATMPKE---LVL  581 (633)
Q Consensus       543 AD~Lld-----------~gf~~~l~~----Il~----------------------~lpk~~Q-~IlfSATl~~e---l~l  581 (633)
                      ||+|++           .||.+++..    |+.                      .+++..| ++++|||++..   +.+
T Consensus       209 AD~ml~~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~~~~l  288 (1638)
T PRK14701        209 VDAFLKASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGDRVKL  288 (1638)
T ss_pred             ceeccccccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhHHHHH
Confidence            999987           478887764    332                      2345566 57799999963   233


Q ss_pred             cccceEeeeccccccccCccceEEEeehh-----hHHHHhhcCCceEEEEEcccc
Q 006737          582 KREHTYIDTVGLGSVETPVKVSKYNIYVF-----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       582 ~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      ..+...+.. +. ......++.|.|+.+.     .+..+.+.....+||||||..
T Consensus       289 ~~~~l~f~v-~~-~~~~lr~i~~~yi~~~~~~k~~L~~ll~~~g~~gIVF~~t~~  341 (1638)
T PRK14701        289 YRELLGFEV-GS-GRSALRNIVDVYLNPEKIIKEHVRELLKKLGKGGLIFVPIDE  341 (1638)
T ss_pred             hhcCeEEEe-cC-CCCCCCCcEEEEEECCHHHHHHHHHHHHhCCCCeEEEEeccc
Confidence            333333322 11 1234567888888553     222223333568999999864

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.91  E-value=9.9e-24  Score=241.72  Aligned_cols=171  Identities=22%  Similarity=0.311  Sum_probs=131.0

Q ss_pred             CCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEccc
Q 006737          386 ISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT  464 (633)
Q Consensus       386 L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPT  464 (633)
                      +.......|.+ +||..|+|+|.++|+.+++|+|+++++|||+|||+||++|++..   .           ..+|||+|+
T Consensus         9 ~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~---~-----------g~tlVisPl   74 (607)
T PRK11057          9 LESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL---D-----------GLTLVVSPL   74 (607)
T ss_pred             chhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc---C-----------CCEEEEecH
Confidence            34444455554 69999999999999999999999999999999999999999842   1           148999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEe
Q 006737          465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLD  541 (633)
Q Consensus       465 ReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVID  541 (633)
                      ++|+.|++..+..+     ++.+.++.++.......   ..+..+..+|+|+||++|....-..   .+...++.+||||
T Consensus        75 ~sL~~dqv~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~---~l~~~~l~~iVID  146 (607)
T PRK11057         75 ISLMKDQVDQLLAN-----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLE---HLAHWNPALLAVD  146 (607)
T ss_pred             HHHHHHHHHHHHHc-----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHH---HHhhCCCCEEEEe
Confidence            99999999888765     67777777766544332   2344566899999999987321111   1334578999999


Q ss_pred             cccccCCcC--hHHHHHHH---HHHCCCCCcEEEEeccCChhh
Q 006737          542 EADHLLDLG--FRKDVENI---VDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       542 EAD~Lld~g--f~~~l~~I---l~~lpk~~Q~IlfSATl~~el  579 (633)
                      |||++++||  |...+..|   ...+ ++.|+++||||+++.+
T Consensus       147 EaH~i~~~G~~fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~  188 (607)
T PRK11057        147 EAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTT  188 (607)
T ss_pred             CccccccccCcccHHHHHHHHHHHhC-CCCcEEEEecCCChhH
Confidence            999999987  67666544   3344 4789999999999874

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.91  E-value=8.7e-24  Score=241.68  Aligned_cols=164  Identities=24%  Similarity=0.359  Sum_probs=130.3

Q ss_pred             HHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          393 ALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       393 ~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      .|.+ +||..|+++|.++|+.+++|+|+++++|||+|||+||++|++..   .           ..+|||+|+++|+.|+
T Consensus         4 ~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~---~-----------g~~lVisPl~sL~~dq   69 (591)
T TIGR01389         4 VLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL---K-----------GLTVVISPLISLMKDQ   69 (591)
T ss_pred             HHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc---C-----------CcEEEEcCCHHHHHHH
Confidence            3444 79999999999999999999999999999999999999999732   1           1489999999999999


Q ss_pred             HHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC
Q 006737          472 AAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       472 ~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      +..++.+     ++.+..+.++.......   ..+..+.++|+++||++|.......   .....++.+|||||||++++
T Consensus        70 ~~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~---~l~~~~l~~iViDEaH~i~~  141 (591)
T TIGR01389        70 VDQLRAA-----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLN---MLQRIPIALVAVDEAHCVSQ  141 (591)
T ss_pred             HHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHH---HHhcCCCCEEEEeCCccccc
Confidence            9888775     67788888877655433   3345567899999999986432222   23456899999999999999


Q ss_pred             cC--hHHHHHHHH---HHCCCCCcEEEEeccCChhh
Q 006737          549 LG--FRKDVENIV---DCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       549 ~g--f~~~l~~Il---~~lpk~~Q~IlfSATl~~el  579 (633)
                      ||  |+..+..+.   ..++ ..++++||||.+..+
T Consensus       142 ~g~~frp~y~~l~~l~~~~~-~~~vi~lTAT~~~~~  176 (591)
T TIGR01389       142 WGHDFRPEYQRLGSLAERFP-QVPRIALTATADAET  176 (591)
T ss_pred             ccCccHHHHHHHHHHHHhCC-CCCEEEEEeCCCHHH
Confidence            87  777776654   3444 456999999999885

The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.

>TIGR01054 rgy reverse gyrase

Probab=99.91  E-value=2.5e-23  Score=251.25  Aligned_cols=222  Identities=23%  Similarity=0.246  Sum_probs=155.8

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          389 LTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       389 ~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      .+.+.+.+.....|+++|+.+++.++.|+|++++||||+|||+ |.+|++..+...          ++++|||+|||+||
T Consensus        66 ~f~~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~----------g~~vLIL~PTreLa  134 (1171)
T TIGR01054        66 EFEEFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKK----------GKRCYIILPTTLLV  134 (1171)
T ss_pred             HHHHHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhc----------CCeEEEEeCHHHHH
Confidence            4445555544558999999999999999999999999999997 777777665432          35799999999999


Q ss_pred             HHHHHHHHHHHhcCCCce---EEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEec
Q 006737          469 SQIAAEAIALLKNHDGIG---VLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDE  542 (633)
Q Consensus       469 ~Qi~~~l~~l~~~~~~i~---v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDE  542 (633)
                      .|+++.+..++... ++.   +.+++|+.+...+   ...+..++++|||+||++|.+++...     .. .+++|||||
T Consensus       135 ~Qi~~~l~~l~~~~-~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l-----~~-~~~~iVvDE  207 (1171)
T TIGR01054       135 IQVAEKISSLAEKA-GVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDEL-----GP-KFDFIFVDD  207 (1171)
T ss_pred             HHHHHHHHHHHHhc-CCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHh-----cC-CCCEEEEeC
Confidence            99999999998754 343   3457788776543   23455566899999999999887542     12 899999999


Q ss_pred             ccccCC-----------cChHHH-HHHHH----------------------HHCCCCCc--EEEEecc-CChhhh--ccc
Q 006737          543 ADHLLD-----------LGFRKD-VENIV----------------------DCLPRRRQ--SLLFSAT-MPKELV--LKR  583 (633)
Q Consensus       543 AD~Lld-----------~gf~~~-l~~Il----------------------~~lpk~~Q--~IlfSAT-l~~el~--l~~  583 (633)
                      ||+|++           .||..+ +..++                      ..+++.+|  +++|||| .|..+.  +..
T Consensus       208 aD~~L~~~k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~~l~r  287 (1171)
T TIGR01054       208 VDALLKASKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRAKLFR  287 (1171)
T ss_pred             hHhhhhccccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHHHHcc
Confidence            999998           577664 44443                      23455566  5678999 555432  223


Q ss_pred             cceEeeeccccccccCccceEEEeehhh----HHHHhhcCCceEEEEEccc
Q 006737          584 EHTYIDTVGLGSVETPVKVSKYNIYVFV----LVLSIKIQAFYIICFVYTI  630 (633)
Q Consensus       584 ~~~~i~~~~~~~~~~~~~V~q~~i~v~~----l~~~~k~~~~~~LVFcnT~  630 (633)
                      +...+.. + .......+|.|.|+.+..    +..+.+.....+||||||+
T Consensus       288 ~ll~~~v-~-~~~~~~r~I~~~~~~~~~~~~~L~~ll~~l~~~~IVFv~t~  336 (1171)
T TIGR01054       288 ELLGFEV-G-GGSDTLRNVVDVYVEDEDLKETLLEIVKKLGTGGIVYVSID  336 (1171)
T ss_pred             cccceEe-c-CccccccceEEEEEecccHHHHHHHHHHHcCCCEEEEEecc
Confidence            3222222 1 123345678888875432    2223333356899999997

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]

Probab=99.89  E-value=3e-22  Score=235.35  Aligned_cols=183  Identities=27%  Similarity=0.323  Sum_probs=150.9

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      ....+..+|.+.|+..|+.+|.+|+..+.+|+|+||+.+||||||+||++||++++++....         ++|+|.||+
T Consensus        55 ~~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a---------~AL~lYPtn  125 (851)
T COG1205          55 RDESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA---------RALLLYPTN  125 (851)
T ss_pred             hhhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCcCc---------cEEEEechh
Confidence            45567888999999999999999999999999999999999999999999999999987543         599999999


Q ss_pred             HHHHHHHHHHHHHHhcCC-CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHH-hcccCcccccCCeeEEEEecc
Q 006737          466 ELASQIAAEAIALLKNHD-GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHI-ENKSGLSVRLMGLKMLVLDEA  543 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~-~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL-~~~~~~~~~Ls~l~~LVIDEA  543 (633)
                      +||+++.+.+.++....+ .+.+..++|++.... .+.+..++++||++||..|..++ .....+...++++++|||||+
T Consensus       126 ALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~-r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDEl  204 (851)
T COG1205         126 ALANDQAERLRELISDLPGKVTFGRYTGDTPPEE-RRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDEL  204 (851)
T ss_pred             hhHhhHHHHHHHHHHhCCCcceeeeecCCCChHH-HHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecc
Confidence            999999999999998876 578888888887654 33556677899999999998844 444445556889999999999


Q ss_pred             cccCCcChHHHH----HHHHH---HCCCCCcEEEEeccCChhh
Q 006737          544 DHLLDLGFRKDV----ENIVD---CLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       544 D~Lld~gf~~~l----~~Il~---~lpk~~Q~IlfSATl~~el  579 (633)
                      |..-.. |+..|    .+++.   ..+...|+|+.|||+.+..
T Consensus       205 HtYrGv-~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np~  246 (851)
T COG1205         205 HTYRGV-QGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPG  246 (851)
T ss_pred             eecccc-chhHHHHHHHHHHHHHhccCCCceEEEEeccccChH
Confidence            987532 44433    33333   3345789999999998874

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.88  E-value=1.4e-21  Score=231.20  Aligned_cols=167  Identities=22%  Similarity=0.184  Sum_probs=132.6

Q ss_pred             CCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          386 ISPLTIKALTA-AGYIQMTRVQEATLSACLEG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       386 L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+..++..+.+ ++| .||++|..||+.++++      +|++++|+||||||++|++|++..+...           .++
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~g-----------~qv  503 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDG-----------KQV  503 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHhC-----------CeE
Confidence            44566666655 578 5999999999999985      7999999999999999999999877532           369


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      +||+||++||.|+++.+++++... ++++..++|+......   ...+..+.++|||+||.    ++..    ...+.++
T Consensus       504 lvLvPT~~LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~----ll~~----~v~f~~L  574 (926)
T TIGR00580       504 AVLVPTTLLAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK----LLQK----DVKFKDL  574 (926)
T ss_pred             EEEeCcHHHHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH----HhhC----CCCcccC
Confidence            999999999999999999988765 6888888887764432   33455667899999994    2322    2568899


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+|||||+|++.     ......+..++.+.|+++||||..+.
T Consensus       575 ~llVIDEahrfg-----v~~~~~L~~~~~~~~vL~~SATpipr  612 (926)
T TIGR00580       575 GLLIIDEEQRFG-----VKQKEKLKELRTSVDVLTLSATPIPR  612 (926)
T ss_pred             CEEEeecccccc-----hhHHHHHHhcCCCCCEEEEecCCCHH
Confidence            999999999953     23445566677889999999997665

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.87  E-value=2.5e-21  Score=224.57  Aligned_cols=165  Identities=21%  Similarity=0.268  Sum_probs=130.1

Q ss_pred             HHHHHHHH-HcCCCCCcHHHHHHHHHHhCC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 006737          388 PLTIKALT-AAGYIQMTRVQEATLSACLEG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLI  460 (633)
Q Consensus       388 ~~Ll~~L~-~~g~~~pt~iQ~~aIp~il~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLI  460 (633)
                      ..+.+.+. .++| +||++|..+|+.|..+      .++|++|+||||||++|++|++..+..           +.++||
T Consensus       248 ~~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~-----------g~q~li  315 (681)
T PRK10917        248 GELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA-----------GYQAAL  315 (681)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc-----------CCeEEE
Confidence            34445444 4566 6999999999999987      489999999999999999999987642           347999


Q ss_pred             EcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH---HHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          461 LCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       461 LvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      ++||++||.|+++.+++++... ++++.+++|+.....   ....+..+.++||||||+.+.+        ...+.++.+
T Consensus       316 laPT~~LA~Q~~~~l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~--------~v~~~~l~l  386 (681)
T PRK10917        316 MAPTEILAEQHYENLKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD--------DVEFHNLGL  386 (681)
T ss_pred             EeccHHHHHHHHHHHHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc--------cchhcccce
Confidence            9999999999999999998765 789999999987543   3345556679999999987743        245789999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      |||||+|++..     .....+.......++++||||..+.
T Consensus       387 vVIDE~Hrfg~-----~qr~~l~~~~~~~~iL~~SATp~pr  422 (681)
T PRK10917        387 VIIDEQHRFGV-----EQRLALREKGENPHVLVMTATPIPR  422 (681)
T ss_pred             EEEechhhhhH-----HHHHHHHhcCCCCCEEEEeCCCCHH
Confidence            99999999632     2223333445568999999997655

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.87  E-value=3.1e-21  Score=232.56  Aligned_cols=164  Identities=22%  Similarity=0.203  Sum_probs=130.3

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEc
Q 006737          389 LTIKALTAAGYIQMTRVQEATLSACLEG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILC  462 (633)
Q Consensus       389 ~Ll~~L~~~g~~~pt~iQ~~aIp~il~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILv  462 (633)
                      ...+....++| .||++|.+||+.++.+      +|+++||+||+|||.+|+++++..+..           +.+||||+
T Consensus       589 ~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~~-----------g~qvlvLv  656 (1147)
T PRK10689        589 QYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVEN-----------HKQVAVLV  656 (1147)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHHc-----------CCeEEEEe
Confidence            34445566788 7999999999999997      899999999999999999888766532           24799999


Q ss_pred             ccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHH---HhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          463 PTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRR---LESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       463 PTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~---l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||++||.|+++.+.+.+... ++++.+++|+.+...+...   +..+.++|||+||+.|    ..    ...+.++.+||
T Consensus       657 PT~eLA~Q~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~~----~v~~~~L~lLV  727 (1147)
T PRK10689        657 PTTLLAQQHYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----QS----DVKWKDLGLLI  727 (1147)
T ss_pred             CcHHHHHHHHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----hC----CCCHhhCCEEE
Confidence            99999999999999887655 6788888888776655443   3446789999999643    22    24578999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      |||+|++   |+.  ....+..++.++|+++||||..+.
T Consensus       728 IDEahrf---G~~--~~e~lk~l~~~~qvLl~SATpipr  761 (1147)
T PRK10689        728 VDEEHRF---GVR--HKERIKAMRADVDILTLTATPIPR  761 (1147)
T ss_pred             Eechhhc---chh--HHHHHHhcCCCCcEEEEcCCCCHH
Confidence            9999997   332  234566778899999999997765

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.87  E-value=1.6e-21  Score=236.83  Aligned_cols=155  Identities=22%  Similarity=0.314  Sum_probs=120.5

Q ss_pred             EEccCCCCchhhhHHHHHHHHHHhcCCCC--CCCCCCeEEEEEcccHHHHHHHHHHHHHHHh-----------cCCCceE
Q 006737          421 VKAKTGTGKSIAFLLPAIEAVLKATSSST--TQLVPPIYVLILCPTRELASQIAAEAIALLK-----------NHDGIGV  487 (633)
Q Consensus       421 v~ApTGSGKTlaylLPiL~~l~~~~~~~~--~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~-----------~~~~i~v  487 (633)
                      |+||||||||+||.||+|+.++.......  .....++++|||+|+++|++|+++.++..+.           ...+++|
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            57999999999999999999986431100  0112357899999999999999998875321           1236899


Q ss_pred             EEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcC----hHHHHHHHHHHCC
Q 006737          488 LTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG----FRKDVENIVDCLP  563 (633)
Q Consensus       488 ~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g----f~~~l~~Il~~lp  563 (633)
                      ..++|++....+.+.++ .++||||+||++|..+|.+..  ...|++|++|||||+|.|++..    +...+.+|...++
T Consensus        81 ~vrtGDt~~~eR~rll~-~ppdILVTTPEsL~~LLtsk~--r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~  157 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTR-NPPDILITTPESLYLMLTSRA--RETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLH  157 (1490)
T ss_pred             EEEECCCCHHHHHHHhc-CCCCEEEecHHHHHHHHhhhh--hhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCC
Confidence            99999998776554444 468999999999998886432  2458999999999999999653    4556677777778


Q ss_pred             CCCcEEEEeccCChh
Q 006737          564 RRRQSLLFSATMPKE  578 (633)
Q Consensus       564 k~~Q~IlfSATl~~e  578 (633)
                      .+.|+|+||||+++.
T Consensus       158 ~~~QrIgLSATI~n~  172 (1490)
T PRK09751        158 TSAQRIGLSATVRSA  172 (1490)
T ss_pred             CCCeEEEEEeeCCCH
Confidence            889999999999985

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.86  E-value=6.9e-21  Score=219.23  Aligned_cols=165  Identities=22%  Similarity=0.276  Sum_probs=130.0

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEc
Q 006737          389 LTIKALTAAGYIQMTRVQEATLSACLEG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILC  462 (633)
Q Consensus       389 ~Ll~~L~~~g~~~pt~iQ~~aIp~il~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILv  462 (633)
                      .+.+.+...+| +||++|..||+.|+++      .+.+++|+||||||++|++|++..+..           +.+++|++
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~-----------g~qvlila  291 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA-----------GYQVALMA  291 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc-----------CCcEEEEC
Confidence            34556667788 7999999999999986      368999999999999999999987643           24699999


Q ss_pred             ccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH---HHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          463 PTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       463 PTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||++||.|+++.+.+++... ++++.+++|+.....   ....+..+.++|||+||+.|.+        ...+.++.+||
T Consensus       292 PT~~LA~Q~~~~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~--------~~~~~~l~lvV  362 (630)
T TIGR00643       292 PTEILAEQHYNSLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE--------KVEFKRLALVI  362 (630)
T ss_pred             CHHHHHHHHHHHHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc--------cccccccceEE
Confidence            99999999999999998765 789999999987654   3345566678999999987753        24578999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCC--CCCcEEEEeccCChh
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLP--RRRQSLLFSATMPKE  578 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lp--k~~Q~IlfSATl~~e  578 (633)
                      |||+|++...    +...+.....  ...|+++||||..+.
T Consensus       363 IDEaH~fg~~----qr~~l~~~~~~~~~~~~l~~SATp~pr  399 (630)
T TIGR00643       363 IDEQHRFGVE----QRKKLREKGQGGFTPHVLVMSATPIPR  399 (630)
T ss_pred             EechhhccHH----HHHHHHHhcccCCCCCEEEEeCCCCcH
Confidence            9999996422    2223333332  268999999997554

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.86  E-value=1.7e-21  Score=226.41  Aligned_cols=177  Identities=23%  Similarity=0.298  Sum_probs=143.7

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          385 GISPLTIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       385 ~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      .+.+.+.+.+...++.++.+-|+.++.. ++.++|+|||+|||||||++.++.+++.+.+..          .++|||||
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~~----------~k~vYivP   84 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGG----------GKVVYIVP   84 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhcC----------CcEEEEeC
Confidence            3677888888888887877777777766 455699999999999999999999999988752          25999999


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecc
Q 006737          464 TRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEA  543 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEA  543 (633)
                      +++||.++++.+..+.. + |++|...+|+.....  ..+.  .++|||+||+++-.++.+...   .+..|++|||||+
T Consensus        85 lkALa~Ek~~~~~~~~~-~-GirV~~~TgD~~~~~--~~l~--~~~ViVtT~EK~Dsl~R~~~~---~~~~V~lvViDEi  155 (766)
T COG1204          85 LKALAEEKYEEFSRLEE-L-GIRVGISTGDYDLDD--ERLA--RYDVIVTTPEKLDSLTRKRPS---WIEEVDLVVIDEI  155 (766)
T ss_pred             hHHHHHHHHHHhhhHHh-c-CCEEEEecCCcccch--hhhc--cCCEEEEchHHhhHhhhcCcc---hhhcccEEEEeee
Confidence            99999999999994433 3 899999999987554  2222  379999999999888877643   5779999999999


Q ss_pred             cccCCcChHHHHHHHHHHCC---CCCcEEEEeccCChhhh
Q 006737          544 DHLLDLGFRKDVENIVDCLP---RRRQSLLFSATMPKELV  580 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~lp---k~~Q~IlfSATl~~el~  580 (633)
                      |.+.+...+..++.|+..++   ..+|++++|||+|+...
T Consensus       156 H~l~d~~RG~~lE~iv~r~~~~~~~~rivgLSATlpN~~e  195 (766)
T COG1204         156 HLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNAEE  195 (766)
T ss_pred             eecCCcccCceehhHHHHHHhhCcceEEEEEeeecCCHHH
Confidence            99998766777777766544   34899999999999843

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

Probab=99.86  E-value=4e-21  Score=219.67  Aligned_cols=229  Identities=19%  Similarity=0.243  Sum_probs=160.4

Q ss_pred             HcCCCCCcHHHHHHHHHHhC-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          396 AAGYIQMTRVQEATLSACLE-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       396 ~~g~~~pt~iQ~~aIp~il~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      -++|..++.+|..++|.+.. +.|+|||||||+|||..|+|.||+.+.+. .+.........++|||+|+++||.++++.
T Consensus       105 ~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~-~~~~~i~k~~fKiVYIaPmKALa~Em~~~  183 (1230)
T KOG0952|consen  105 FFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEH-EEQGDIAKDDFKIVYIAPMKALAAEMVDK  183 (1230)
T ss_pred             cccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhh-ccccccccCCceEEEEechHHHHHHHHHH
Confidence            36788999999999999876 45999999999999999999999988763 22233344567899999999999999988


Q ss_pred             HHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHH
Q 006737          475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       475 l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                      +.+.+... ++.|..++|++......  +.  .|+|||+||+.+--.-....+....++.|++|||||+|.|-+. .++.
T Consensus       184 ~~kkl~~~-gi~v~ELTGD~ql~~te--i~--~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHlLhd~-RGpv  257 (1230)
T KOG0952|consen  184 FSKKLAPL-GISVRELTGDTQLTKTE--IA--DTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHLLHDD-RGPV  257 (1230)
T ss_pred             Hhhhcccc-cceEEEecCcchhhHHH--HH--hcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehhhcCc-ccch
Confidence            88777655 89999999998766443  22  3799999999974332222222344778999999999998754 4555


Q ss_pred             HHHHHH-------HCCCCCcEEEEeccCChhhhccccc---eEeeeccccccccCccceEEEeehh--------------
Q 006737          555 VENIVD-------CLPRRRQSLLFSATMPKELVLKREH---TYIDTVGLGSVETPVKVSKYNIYVF--------------  610 (633)
Q Consensus       555 l~~Il~-------~lpk~~Q~IlfSATl~~el~l~~~~---~~i~~~~~~~~~~~~~V~q~~i~v~--------------  610 (633)
                      ++.|+.       ......++|++|||+|+-+.+...-   .+...........|..+++.++-+.              
T Consensus       258 lEtiVaRtlr~vessqs~IRivgLSATlPN~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d~~  337 (1230)
T KOG0952|consen  258 LETIVARTLRLVESSQSMIRIVGLSATLPNYEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNIDEV  337 (1230)
T ss_pred             HHHHHHHHHHHHHhhhhheEEEEeeccCCCHHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHHHH
Confidence            555544       3345688999999999985433211   1111111122334445555554321              


Q ss_pred             --hHHHHhhcCCceEEEEEcccc
Q 006737          611 --VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 --~l~~~~k~~~~~~LVFcnT~s  631 (633)
                        .-.......+.+++|||.|.+
T Consensus       338 ~~~kv~e~~~~g~qVlvFvhsR~  360 (1230)
T KOG0952|consen  338 CYDKVVEFLQEGHQVLVFVHSRN  360 (1230)
T ss_pred             HHHHHHHHHHcCCeEEEEEecCh
Confidence              122233456789999999875

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

Probab=99.85  E-value=1.1e-20  Score=205.16  Aligned_cols=234  Identities=23%  Similarity=0.215  Sum_probs=177.6

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ...++|.|++.+.+.|...|++.+.|+|..++.. ++.|.|++|+++|+||||++.-|.-+..++..+.          +
T Consensus       194 ~~vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~g~----------K  263 (830)
T COG1202         194 VPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSGGK----------K  263 (830)
T ss_pred             ccccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhCCC----------e
Confidence            4568999999999999999999999999999988 7899999999999999999999988888877543          5


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHH---HHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQR---RLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~---~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      .|+|+|..+||+|.++.|+...... ++++.+-+|.........   .-....+||||+|.+.+-.+|..+    ..+.+
T Consensus       264 mlfLvPLVALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg----~~lgd  338 (830)
T COG1202         264 MLFLVPLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG----KDLGD  338 (830)
T ss_pred             EEEEehhHHhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC----Ccccc
Confidence            8999999999999999999887665 788888887765554322   112235799999999998888765    56889


Q ss_pred             eeEEEEecccccCCcChHHHHHHHH---HHCCCCCcEEEEeccCChhhhccccceEeeeccccccccCccceEEEeehh-
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIV---DCLPRRRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il---~~lpk~~Q~IlfSATl~~el~l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      |..|||||+|.|-+...+..+.-++   ..+-+..|+|.+|||+.|...+......- .  +.....|..++.+.+++. 
T Consensus       339 iGtVVIDEiHtL~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp~elA~~l~a~-l--V~y~~RPVplErHlvf~~~  415 (830)
T COG1202         339 IGTVVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNPEELAKKLGAK-L--VLYDERPVPLERHLVFARN  415 (830)
T ss_pred             cceEEeeeeeeccchhcccchhhHHHHHHHhCCCCeEEEEEeecCChHHHHHHhCCe-e--EeecCCCCChhHeeeeecC
Confidence            9999999999998765555555443   44456899999999998875443211110 0  112345666777766653 


Q ss_pred             ----------hH-----HHHhhcCCceEEEEEccc
Q 006737          611 ----------VL-----VLSIKIQAFYIICFVYTI  630 (633)
Q Consensus       611 ----------~l-----~~~~k~~~~~~LVFcnT~  630 (633)
                                +.     ....+.--.++|||.||.
T Consensus       416 e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SR  450 (830)
T COG1202         416 ESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSR  450 (830)
T ss_pred             chHHHHHHHHHHHHHHhhhhccCcCCceEEEecch
Confidence                      11     112233346899999986

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.82  E-value=1.5e-19  Score=212.26  Aligned_cols=199  Identities=20%  Similarity=0.186  Sum_probs=138.8

Q ss_pred             HHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCc
Q 006737          406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI  485 (633)
Q Consensus       406 Q~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i  485 (633)
                      -.+.+..+.++++++++|+||||||++|.+|+++....           ..++||++|||++|.|+++.+........+.
T Consensus        10 ~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~-----------~~~ilvlqPrR~aA~qia~rva~~l~~~~g~   78 (812)
T PRK11664         10 LPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI-----------NGKIIMLEPRRLAARNVAQRLAEQLGEKPGE   78 (812)
T ss_pred             HHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc-----------CCeEEEECChHHHHHHHHHHHHHHhCcccCc
Confidence            34556677788999999999999999999998864211           1369999999999999999987665444466


Q ss_pred             eEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc-cCCcCh-HHHHHHHHHHCC
Q 006737          486 GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH-LLDLGF-RKDVENIVDCLP  563 (633)
Q Consensus       486 ~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~-Lld~gf-~~~l~~Il~~lp  563 (633)
                      .|+..+++....       ....+|+|+|||+|++++...    ..|+++++|||||||. .++.++ ...+..++..++
T Consensus        79 ~VGy~vr~~~~~-------~~~t~I~v~T~G~Llr~l~~d----~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr  147 (812)
T PRK11664         79 TVGYRMRAESKV-------GPNTRLEVVTEGILTRMIQRD----PELSGVGLVILDEFHERSLQADLALALLLDVQQGLR  147 (812)
T ss_pred             eEEEEecCcccc-------CCCCcEEEEChhHHHHHHhhC----CCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCC
Confidence            777766654422       123589999999999998764    5689999999999997 455443 334456677788


Q ss_pred             CCCcEEEEeccCChhhh--ccccceEeeeccccccccCccceEEEeehh-----------hHHHHhhcCCceEEEEEccc
Q 006737          564 RRRQSLLFSATMPKELV--LKREHTYIDTVGLGSVETPVKVSKYNIYVF-----------VLVLSIKIQAFYIICFVYTI  630 (633)
Q Consensus       564 k~~Q~IlfSATl~~el~--l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-----------~l~~~~k~~~~~~LVFcnT~  630 (633)
                      ++.|+|+||||++.+..  +..+...+...+     ....|+++|+.+.           .+..........+|||||++
T Consensus       148 ~~lqlilmSATl~~~~l~~~~~~~~~I~~~g-----r~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg~  222 (812)
T PRK11664        148 DDLKLLIMSATLDNDRLQQLLPDAPVIVSEG-----RSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGV  222 (812)
T ss_pred             ccceEEEEecCCCHHHHHHhcCCCCEEEecC-----ccccceEEeccCchhhhHHHHHHHHHHHHHHhCCCCEEEEcCCH
Confidence            89999999999997732  111222222111     1123666665332           12222333467899999986


Q ss_pred             c
Q 006737          631 S  631 (633)
Q Consensus       631 s  631 (633)
                      .
T Consensus       223 ~  223 (812)
T PRK11664        223 G  223 (812)
T ss_pred             H
Confidence            4

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.82  E-value=1.7e-19  Score=207.13  Aligned_cols=158  Identities=17%  Similarity=0.201  Sum_probs=115.3

Q ss_pred             cHHHHHHHHHHhCCCcEEEEccCCCCchhh---------hHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHH
Q 006737          403 TRVQEATLSACLEGKDAVVKAKTGTGKSIA---------FLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAA  473 (633)
Q Consensus       403 t~iQ~~aIp~il~grDvLv~ApTGSGKTla---------ylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~  473 (633)
                      ..+|.++++.++.|+|+|++|+||||||.+         |++|.+..+..-..     .....+++|++|||+||.|+..
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~-----~~~~~~ilvt~PrreLa~qi~~  240 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDP-----NFIERPIVLSLPRVALVRLHSI  240 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhccc-----ccCCcEEEEECcHHHHHHHHHH
Confidence            358999999999999999999999999996         45555554422110     1123479999999999999999


Q ss_pred             HHHHHHhc--CCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcCh
Q 006737          474 EAIALLKN--HDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF  551 (633)
Q Consensus       474 ~l~~l~~~--~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf  551 (633)
                      .+.+..++  ..+..+.+.+|+...  ..........+|||+|++..          ...|+++++|||||||.++..+ 
T Consensus       241 ~i~~~vg~~~~~g~~v~v~~Gg~~~--~~~~t~~k~~~Ilv~T~~L~----------l~~L~~v~~VVIDEaHEr~~~~-  307 (675)
T PHA02653        241 TLLKSLGFDEIDGSPISLKYGSIPD--ELINTNPKPYGLVFSTHKLT----------LNKLFDYGTVIIDEVHEHDQIG-  307 (675)
T ss_pred             HHHHHhCccccCCceEEEEECCcch--HHhhcccCCCCEEEEeCccc----------ccccccCCEEEccccccCccch-
Confidence            98877654  246778889999762  22122222469999997631          1347899999999999998764 


Q ss_pred             HHHHHHHHHHC-CCCCcEEEEeccCChhh
Q 006737          552 RKDVENIVDCL-PRRRQSLLFSATMPKEL  579 (633)
Q Consensus       552 ~~~l~~Il~~l-pk~~Q~IlfSATl~~el  579 (633)
                       +.+..++..+ ++.+|+++||||++.++
T Consensus       308 -DllL~llk~~~~~~rq~ILmSATl~~dv  335 (675)
T PHA02653        308 -DIIIAVARKHIDKIRSLFLMTATLEDDR  335 (675)
T ss_pred             -hHHHHHHHHhhhhcCEEEEEccCCcHhH
Confidence             4455555544 34469999999998764

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.82  E-value=2.8e-19  Score=209.65  Aligned_cols=200  Identities=23%  Similarity=0.197  Sum_probs=138.8

Q ss_pred             HHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCC
Q 006737          405 VQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDG  484 (633)
Q Consensus       405 iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~  484 (633)
                      +-.+.+..+.+++++|++|+||||||++|.+++++....           ..++||++|||++|.|+++.+........+
T Consensus         6 ~~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~~-----------~~~ilvlqPrR~aA~qiA~rva~~~~~~~g   74 (819)
T TIGR01970         6 VLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGI-----------GGKIIMLEPRRLAARSAAQRLASQLGEAVG   74 (819)
T ss_pred             HHHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhcc-----------CCeEEEEeCcHHHHHHHHHHHHHHhCCCcC
Confidence            334566677788999999999999999999999876521           246999999999999999988665543335


Q ss_pred             ceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc-ccCCcChHHH-HHHHHHHC
Q 006737          485 IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD-HLLDLGFRKD-VENIVDCL  562 (633)
Q Consensus       485 i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD-~Lld~gf~~~-l~~Il~~l  562 (633)
                      ..|+..+++...       ....++|+|+|||+|++++.+.    ..|+++++||||||| ++++.++... +..+...+
T Consensus        75 ~~VGy~vr~~~~-------~s~~t~I~v~T~G~Llr~l~~d----~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~l  143 (819)
T TIGR01970        75 QTVGYRVRGENK-------VSRRTRLEVVTEGILTRMIQDD----PELDGVGALIFDEFHERSLDADLGLALALDVQSSL  143 (819)
T ss_pred             cEEEEEEccccc-------cCCCCcEEEECCcHHHHHHhhC----cccccCCEEEEeccchhhhccchHHHHHHHHHHhc
Confidence            556555544321       1234699999999999999764    568999999999999 4777666443 45566678


Q ss_pred             CCCCcEEEEeccCChhhh--ccccceEeeeccccccccCccceEEEeehh-----------hHHHHhhcCCceEEEEEcc
Q 006737          563 PRRRQSLLFSATMPKELV--LKREHTYIDTVGLGSVETPVKVSKYNIYVF-----------VLVLSIKIQAFYIICFVYT  629 (633)
Q Consensus       563 pk~~Q~IlfSATl~~el~--l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-----------~l~~~~k~~~~~~LVFcnT  629 (633)
                      +++.|+|+||||++.+..  +..+...+...     .....|+++|+.+.           .+..........+|||||+
T Consensus       144 r~dlqlIlmSATl~~~~l~~~l~~~~vI~~~-----gr~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~~~g~iLVFlpg  218 (819)
T TIGR01970       144 REDLKILAMSATLDGERLSSLLPDAPVVESE-----GRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPG  218 (819)
T ss_pred             CCCceEEEEeCCCCHHHHHHHcCCCcEEEec-----CcceeeeeEEeecchhhhHHHHHHHHHHHHHHhcCCcEEEEECC
Confidence            889999999999998742  11122222211     11223666665432           1222223345789999998


Q ss_pred             cc
Q 006737          630 IS  631 (633)
Q Consensus       630 ~s  631 (633)
                      ..
T Consensus       219 ~~  220 (819)
T TIGR01970       219 QA  220 (819)
T ss_pred             HH
Confidence            64

This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]

Probab=99.81  E-value=9.3e-20  Score=192.24  Aligned_cols=120  Identities=33%  Similarity=0.449  Sum_probs=101.7

Q ss_pred             CeEEEEEcccHHHHHHHHHHHHHHHhcCC--CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          455 PIYVLILCPTRELASQIAAEAIALLKNHD--GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       455 ~~~vLILvPTReLa~Qi~~~l~~l~~~~~--~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .|.+||+-|.|||+.|+++.++++-.+..  .++..++.||.....+...++.+ .+|+|+||++|.+++...   .+.|
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g-~~ivvGtpgRl~~~is~g---~~~l  361 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDG-THIVVGTPGRLLQPISKG---LVTL  361 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcC-ceeeecCchhhhhhhhcc---ceee
Confidence            47899999999999999998888765543  45666888888877777777664 799999999999999876   4778


Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCC------CCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPR------RRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk------~~Q~IlfSATl~~e  578 (633)
                      ..+.++|+||||.++..++-+.|.++...+|+      ..|.+++|||+..-
T Consensus       362 t~crFlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~f  413 (725)
T KOG0349|consen  362 THCRFLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIF  413 (725)
T ss_pred             eeeEEEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEE
Confidence            99999999999999998999999888887774      57999999998754

>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]

Probab=99.81  E-value=7.1e-20  Score=204.80  Aligned_cols=165  Identities=26%  Similarity=0.383  Sum_probs=132.5

Q ss_pred             HHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHH
Q 006737          392 KALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQ  470 (633)
Q Consensus       392 ~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Q  470 (633)
                      ..|.. +||..+.+-|.++|..+++|+|+++..|||+||++||+||++-.   .+           -+|||+|..+|+.+
T Consensus         7 ~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~---~G-----------~TLVVSPLiSLM~D   72 (590)
T COG0514           7 QVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL---EG-----------LTLVVSPLISLMKD   72 (590)
T ss_pred             HHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc---CC-----------CEEEECchHHHHHH
Confidence            44554 69999999999999999999999999999999999999999832   11           28999999999999


Q ss_pred             HHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccC
Q 006737          471 IAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       471 i~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      +++.++..     |+.+.++.+..+..+..   ..+..+..+||+-+|++|..---..   .+.--.|.++|||||||++
T Consensus        73 QV~~l~~~-----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~---~L~~~~i~l~vIDEAHCiS  144 (590)
T COG0514          73 QVDQLEAA-----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLE---LLKRLPISLVAIDEAHCIS  144 (590)
T ss_pred             HHHHHHHc-----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHH---HHHhCCCceEEechHHHHh
Confidence            99888876     78888888876555433   4455566899999999985421111   1223478899999999999


Q ss_pred             CcC--hHHHHHHHHH---HCCCCCcEEEEeccCChhh
Q 006737          548 DLG--FRKDVENIVD---CLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       548 d~g--f~~~l~~Il~---~lpk~~Q~IlfSATl~~el  579 (633)
                      +||  |++.+..+-.   .+| +.++++||||.++.+
T Consensus       145 qWGhdFRP~Y~~lg~l~~~~~-~~p~~AlTATA~~~v  180 (590)
T COG0514         145 QWGHDFRPDYRRLGRLRAGLP-NPPVLALTATATPRV  180 (590)
T ss_pred             hcCCccCHhHHHHHHHHhhCC-CCCEEEEeCCCChHH
Confidence            998  9998887754   444 789999999999985

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=1.7e-19  Score=208.61  Aligned_cols=148  Identities=21%  Similarity=0.339  Sum_probs=128.5

Q ss_pred             cccCCCHHHHHHHH-----HcCCCCC---cHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCC
Q 006737          382 DECGISPLTIKALT-----AAGYIQM---TRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLV  453 (633)
Q Consensus       382 ~el~L~~~Ll~~L~-----~~g~~~p---t~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~  453 (633)
                      +.|.+...+.+.+.     .+||..|   +|+|.++|+.++.+++++++++||+|||++|+||++..++...        
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g~--------  136 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTGK--------  136 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhcC--------
Confidence            67888898888887     6899998   9999999999999999999999999999999999998876431        


Q ss_pred             CCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccCccccc
Q 006737          454 PPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSGLSVRL  532 (633)
Q Consensus       454 ~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~~~~~L  532 (633)
                         .++||+||++||.|+.+.+..+..+. ++++.+++||.....+...+   .|||+||||++| .++|....   +.+
T Consensus       137 ---~v~IVTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y---~~DIVygTPgRLgfDyLrd~~---~~~  206 (970)
T PRK12899        137 ---PVHLVTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIY---QCDVVYGTASEFGFDYLRDNS---IAT  206 (970)
T ss_pred             ---CeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHc---CCCEEEECCChhHHHHhhCCC---CCc
Confidence               28899999999999999999998876 79999999999988766544   389999999999 99997652   333


Q ss_pred             C-------CeeEEEEecccccC
Q 006737          533 M-------GLKMLVLDEADHLL  547 (633)
Q Consensus       533 s-------~l~~LVIDEAD~Ll  547 (633)
                      +       .+.++||||||.||
T Consensus       207 ~~~~~vqr~~~~~IIDEADsmL  228 (970)
T PRK12899        207 RKEEQVGRGFYFAIIDEVDSIL  228 (970)
T ss_pred             CHHHhhcccccEEEEechhhhh
Confidence            3       56899999999987

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.80  E-value=3.9e-19  Score=190.70  Aligned_cols=148  Identities=25%  Similarity=0.239  Sum_probs=102.9

Q ss_pred             cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccch
Q 006737          418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK  497 (633)
Q Consensus       418 DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~  497 (633)
                      |++++||||||||++|++|++..+....         ..++||++|+++|+.|+++.+..++..    .+..++++....
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~~---------~~~ii~v~P~~~L~~q~~~~l~~~f~~----~~~~~~~~~~~~   67 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQK---------ADRVIIALPTRATINAMYRRAKELFGS----NLGLLHSSSSFK   67 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhCC---------CCeEEEEeehHHHHHHHHHHHHHHhCc----ccEEeeccHHHH
Confidence            6899999999999999999998764321         236999999999999999999998642    344445443211


Q ss_pred             H------------HHHHHhc-----CCCcEEEECchhhHHHHhccc-CcccccC--CeeEEEEecccccCCcChHHHHHH
Q 006737          498 V------------DQRRLES-----DPCQILVATPGRLLDHIENKS-GLSVRLM--GLKMLVLDEADHLLDLGFRKDVEN  557 (633)
Q Consensus       498 ~------------~~~~l~~-----~~~dILIaTPgrLl~lL~~~~-~~~~~Ls--~l~~LVIDEAD~Lld~gf~~~l~~  557 (633)
                      .            .......     ...+|+|+||++++..+.... .....+.  ..++|||||||.++++++.. +..
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~  146 (358)
T TIGR01587        68 RIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILA  146 (358)
T ss_pred             HHhccCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHH
Confidence            0            0000001     135799999999988776521 1111122  23789999999999865443 555


Q ss_pred             HHHHCC-CCCcEEEEeccCChhh
Q 006737          558 IVDCLP-RRRQSLLFSATMPKEL  579 (633)
Q Consensus       558 Il~~lp-k~~Q~IlfSATl~~el  579 (633)
                      ++..+. .+.|+++||||+|+.+
T Consensus       147 ~l~~l~~~~~~~i~~SATlp~~l  169 (358)
T TIGR01587       147 VLEVLKDNDVPILLMSATLPKFL  169 (358)
T ss_pred             HHHHHHHcCCCEEEEecCchHHH
Confidence            555554 4789999999999764

This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.80  E-value=1.3e-18  Score=187.57  Aligned_cols=161  Identities=19%  Similarity=0.194  Sum_probs=115.3

Q ss_pred             HHHHHHHHHhCCCc--EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcC
Q 006737          405 VQEATLSACLEGKD--AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH  482 (633)
Q Consensus       405 iQ~~aIp~il~grD--vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~  482 (633)
                      +|.++++.+.++.+  ++++||||||||+||++|++..    .          .++||++|+++|+.|+++.+..++...
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~----~----------~~~~~~~P~~aL~~~~~~~~~~~~~~~   66 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG----E----------NDTIALYPTNALIEDQTEAIKEFVDVF   66 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc----C----------CCEEEEeChHHHHHHHHHHHHHHHHhc
Confidence            59999999999874  7899999999999999998841    1          248999999999999999999987543


Q ss_pred             ---CCceEEEEECCccchH--H-----------------HHHHhcCCCcEEEECchhhHHHHhcccC-----cccccCCe
Q 006737          483 ---DGIGVLTLVGGTRFKV--D-----------------QRRLESDPCQILVATPGRLLDHIENKSG-----LSVRLMGL  535 (633)
Q Consensus       483 ---~~i~v~~l~Gg~~~~~--~-----------------~~~l~~~~~dILIaTPgrLl~lL~~~~~-----~~~~Ls~l  535 (633)
                         .++.+..+.|.+....  .                 ........++|+++||+.|..++.....     ....+.++
T Consensus        67 ~~~~~~~v~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~  146 (357)
T TIGR03158        67 KPERDVNLLHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKF  146 (357)
T ss_pred             CCCCCceEEEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCC
Confidence               2556666666532210  0                 1111223578999999999776643211     11135789


Q ss_pred             eEEEEecccccCCcC-----hHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLG-----FRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~g-----f~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      ++|||||+|.+..++     +...+..++.......++|++|||+++.+
T Consensus       147 ~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~  195 (357)
T TIGR03158       147 STVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPAL  195 (357)
T ss_pred             CEEEEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHH
Confidence            999999999987543     22234455555455689999999999884

subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.78  E-value=5.9e-18  Score=162.02  Aligned_cols=171  Identities=43%  Similarity=0.645  Sum_probs=137.5

Q ss_pred             HcCCCCCcHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          396 AAGYIQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       396 ~~g~~~pt~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      ..++..++++|.+++..++.. +.++++++||+|||.+++.+++..+....         ..++||++|++.++.|+...
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~---------~~~~l~~~p~~~~~~~~~~~   73 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK---------GKRVLVLVPTRELAEQWAEE   73 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC---------CCcEEEEeCCHHHHHHHHHH
Confidence            356789999999999999999 99999999999999999999888765432         12599999999999999999


Q ss_pred             HHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHH
Q 006737          475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       475 l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                      +..++... ........++.........+.....+|+++|++.|...+....   .....+.+|||||||.+....+...
T Consensus        74 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~---~~~~~~~~iIiDE~h~~~~~~~~~~  149 (201)
T smart00487       74 LKKLGPSL-GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDL---LELSNVDLVILDEAHRLLDGGFGDQ  149 (201)
T ss_pred             HHHHhccC-CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCC---cCHhHCCEEEEECHHHHhcCCcHHH
Confidence            98887543 2233444444443444555555545999999999999887652   4567889999999999997678899


Q ss_pred             HHHHHHHCCCCCcEEEEeccCChhh
Q 006737          555 VENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +..++..+++..+++++|||.++..
T Consensus       150 ~~~~~~~~~~~~~~v~~saT~~~~~  174 (201)
T smart00487      150 LEKLLKLLPKNVQLLLLSATPPEEI  174 (201)
T ss_pred             HHHHHHhCCccceEEEEecCCchhH
Confidence            9999998888899999999998764

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

Probab=99.74  E-value=4e-17  Score=185.40  Aligned_cols=185  Identities=18%  Similarity=0.222  Sum_probs=144.7

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ..| ++...|++||-++..|.+|+|.|+|.+|||++.-..+...- ..          ..++||.+|.++|.+|-++.|+
T Consensus       294 ~pF-elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq-~h----------~TR~iYTSPIKALSNQKfRDFk  361 (1248)
T KOG0947|consen  294 YPF-ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQ-KH----------MTRTIYTSPIKALSNQKFRDFK  361 (1248)
T ss_pred             CCC-CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHH-hh----------ccceEecchhhhhccchHHHHH
Confidence            344 79999999999999999999999999999998554443211 11          2469999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      ..+..     +.+++|+.....        .+.++|+|.+.|..+|.++.   --++++++||+||+|.+.|...+-.++
T Consensus       362 ~tF~D-----vgLlTGDvqinP--------eAsCLIMTTEILRsMLYrga---dliRDvE~VIFDEVHYiND~eRGvVWE  425 (1248)
T KOG0947|consen  362 ETFGD-----VGLLTGDVQINP--------EASCLIMTTEILRSMLYRGA---DLIRDVEFVIFDEVHYINDVERGVVWE  425 (1248)
T ss_pred             Hhccc-----cceeecceeeCC--------CcceEeehHHHHHHHHhccc---chhhccceEEEeeeeecccccccccce
Confidence            88653     348888876553        26899999999999998874   337789999999999999999999999


Q ss_pred             HHHHHCCCCCcEEEEeccCChhhhccccceEeee--cc-ccccccCccceEEEeeh
Q 006737          557 NIVDCLPRRRQSLLFSATMPKELVLKREHTYIDT--VG-LGSVETPVKVSKYNIYV  609 (633)
Q Consensus       557 ~Il~~lpk~~Q~IlfSATl~~el~l~~~~~~i~~--~~-~~~~~~~~~V~q~~i~v  609 (633)
                      .++-++|+..++|++|||+|+...+..+-..+..  ++ +.....|..++|+..+-
T Consensus       426 EViIMlP~HV~~IlLSATVPN~~EFA~WIGRtK~K~IyViST~kRPVPLEh~l~t~  481 (1248)
T KOG0947|consen  426 EVIIMLPRHVNFILLSATVPNTLEFADWIGRTKQKTIYVISTSKRPVPLEHYLYTK  481 (1248)
T ss_pred             eeeeeccccceEEEEeccCCChHHHHHHhhhccCceEEEEecCCCccceEEEEEec
Confidence            9999999999999999999999766533211111  11 11234566777776643

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.73  E-value=1.8e-16  Score=183.94  Aligned_cols=153  Identities=21%  Similarity=0.249  Sum_probs=118.3

Q ss_pred             CCcHHHHHHHHHHhCC---CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG---KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g---rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      .+|+.|++++..++++   ++++++++||||||.+|+.++...+...           .++|||+||++|+.|+++.+++
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~g-----------~~vLvLvPt~~L~~Q~~~~l~~  212 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQG-----------KQALVLVPEIALTPQMLARFRA  212 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHcC-----------CeEEEEeCcHHHHHHHHHHHHH
Confidence            6899999999999984   7999999999999999988776665432           3699999999999999999988


Q ss_pred             HHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcCh---
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF---  551 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf---  551 (633)
                      .+    +..+..++|+.+.....   ..+..+.++|||+|++.+.          ..+.++.+|||||+|...-+..   
T Consensus       213 ~f----g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~----------~p~~~l~liVvDEeh~~s~~~~~~p  278 (679)
T PRK05580        213 RF----GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF----------LPFKNLGLIIVDEEHDSSYKQQEGP  278 (679)
T ss_pred             Hh----CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc----------ccccCCCEEEEECCCccccccCcCC
Confidence            65    56788999987765433   3445566899999998763          3467899999999998763321   


Q ss_pred             ---HHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          552 ---RKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       552 ---~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                         ...+. ++.....+.|+|++|||.+.+.
T Consensus       279 ~y~~r~va-~~ra~~~~~~~il~SATps~~s  308 (679)
T PRK05580        279 RYHARDLA-VVRAKLENIPVVLGSATPSLES  308 (679)
T ss_pred             CCcHHHHH-HHHhhccCCCEEEEcCCCCHHH
Confidence               12222 2333446799999999987663

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.73  E-value=2.8e-17  Score=184.69  Aligned_cols=151  Identities=17%  Similarity=0.175  Sum_probs=114.5

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ...|+++|.++++.++.+++.++++|||+|||+++.+. ...+....         ..++|||+||++|+.|+.+.+.++
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l-~~~~~~~~---------~~~vLilvpt~eL~~Q~~~~l~~~  181 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLL-SRYYLENY---------EGKVLIIVPTTSLVTQMIDDFVDY  181 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHH-HHHHHhcC---------CCeEEEEECcHHHHHHHHHHHHHh
Confidence            35899999999999999999999999999999976432 22222221         126999999999999999999987


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                      +... ...+..+.+|....        ...+|+|+||++|.....      ..+.++++|||||||++...    .+..+
T Consensus       182 ~~~~-~~~~~~i~~g~~~~--------~~~~I~VaT~qsl~~~~~------~~~~~~~~iIvDEaH~~~~~----~~~~i  242 (501)
T PHA02558        182 RLFP-REAMHKIYSGTAKD--------TDAPIVVSTWQSAVKQPK------EWFDQFGMVIVDECHLFTGK----SLTSI  242 (501)
T ss_pred             cccc-ccceeEEecCcccC--------CCCCEEEeeHHHHhhchh------hhccccCEEEEEchhcccch----hHHHH
Confidence            6432 34455566665422        235899999999876432      23678999999999999754    45677


Q ss_pred             HHHCCCCCcEEEEeccCChh
Q 006737          559 VDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~~e  578 (633)
                      +..+++.+|+++||||+...
T Consensus       243 l~~~~~~~~~lGLTATp~~~  262 (501)
T PHA02558        243 ITKLDNCKFKFGLTGSLRDG  262 (501)
T ss_pred             HHhhhccceEEEEeccCCCc
Confidence            77777778999999999753

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

Probab=99.72  E-value=3e-17  Score=192.24  Aligned_cols=165  Identities=19%  Similarity=0.209  Sum_probs=139.4

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHH
Q 006737          394 LTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAA  473 (633)
Q Consensus       394 L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~  473 (633)
                      ....+| .+.++|++++-+|..|.+|++|||||+|||++.-..+...+...           -+++|++|.++|.+|.++
T Consensus       113 ~~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~~-----------qrviYTsPIKALsNQKyr  180 (1041)
T COG4581         113 AREYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRDG-----------QRVIYTSPIKALSNQKYR  180 (1041)
T ss_pred             HHhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHcC-----------CceEeccchhhhhhhHHH
Confidence            344566 79999999999999999999999999999998666555444333           249999999999999999


Q ss_pred             HHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHH
Q 006737          474 EAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK  553 (633)
Q Consensus       474 ~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~  553 (633)
                      .+...+... .-.+++++|+....        ..+.|+|+|.+.|..++..+   ...+..+..||+||+|.|.+...+.
T Consensus       181 dl~~~fgdv-~~~vGL~TGDv~IN--------~~A~clvMTTEILRnMlyrg---~~~~~~i~~ViFDEvHyi~D~eRG~  248 (1041)
T COG4581         181 DLLAKFGDV-ADMVGLMTGDVSIN--------PDAPCLVMTTEILRNMLYRG---SESLRDIEWVVFDEVHYIGDRERGV  248 (1041)
T ss_pred             HHHHHhhhh-hhhccceecceeeC--------CCCceEEeeHHHHHHHhccC---cccccccceEEEEeeeeccccccch
Confidence            998887543 33467888887754        34789999999999999877   3558899999999999999999999


Q ss_pred             HHHHHHHHCCCCCcEEEEeccCChhhhcc
Q 006737          554 DVENIVDCLPRRRQSLLFSATMPKELVLK  582 (633)
Q Consensus       554 ~l~~Il~~lpk~~Q~IlfSATl~~el~l~  582 (633)
                      .++.++-++|...|+|+||||+|+...+.
T Consensus       249 VWEE~Ii~lP~~v~~v~LSATv~N~~EF~  277 (1041)
T COG4581         249 VWEEVIILLPDHVRFVFLSATVPNAEEFA  277 (1041)
T ss_pred             hHHHHHHhcCCCCcEEEEeCCCCCHHHHH
Confidence            99999999999999999999999996543

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

Probab=99.70  E-value=8.4e-17  Score=186.48  Aligned_cols=239  Identities=21%  Similarity=0.241  Sum_probs=168.4

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          385 GISPLTIKALTAAGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       385 ~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      .++.+-..++  .|...+..+|..+..+.+.+. ++++|||||+|||...++-+|+.+-........-.....+++|++|
T Consensus       295 elP~Wnq~aF--~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYIAP  372 (1674)
T KOG0951|consen  295 ELPKWNQPAF--FGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYIAP  372 (1674)
T ss_pred             CCcchhhhhc--ccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEEee
Confidence            3445555555  466779999999999998875 9999999999999999999999987765533333344568999999


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecc
Q 006737          464 TRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEA  543 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEA  543 (633)
                      +.+|+..++..+.+.+..+ ++.|..++|+.....++  +  ...+||||||+..- .+.+..+......-++++||||.
T Consensus       373 mKaLvqE~VgsfSkRla~~-GI~V~ElTgD~~l~~~q--i--eeTqVIV~TPEK~D-iITRk~gdraY~qlvrLlIIDEI  446 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPL-GITVLELTGDSQLGKEQ--I--EETQVIVTTPEKWD-IITRKSGDRAYEQLVRLLIIDEI  446 (1674)
T ss_pred             HHHHHHHHHHHHHhhcccc-CcEEEEecccccchhhh--h--hcceeEEeccchhh-hhhcccCchhHHHHHHHHhhhhh
Confidence            9999999999888887776 89999999987654322  1  13689999999963 34333222233456789999999


Q ss_pred             cccCCcChHHHHHHHHHHC-------CCCCcEEEEeccCChhhhcccc--ceEeeeccccccccCccceEEEeehh----
Q 006737          544 DHLLDLGFRKDVENIVDCL-------PRRRQSLLFSATMPKELVLKRE--HTYIDTVGLGSVETPVKVSKYNIYVF----  610 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~l-------pk~~Q~IlfSATl~~el~l~~~--~~~i~~~~~~~~~~~~~V~q~~i~v~----  610 (633)
                      |.+-|. .++.++.|+...       ...++++++|||+||-......  ...-+.-..+..-.|..+.|.||-+-    
T Consensus       447 HLLhDd-RGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~  525 (1674)
T KOG0951|consen  447 HLLHDD-RGPVLESIVARTFRRSESTEEGSRLVGLSATLPNYEDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKP  525 (1674)
T ss_pred             hhcccc-cchHHHHHHHHHHHHhhhcccCceeeeecccCCchhhhHHHhccCcccccccCcccCcCCccceEeccccCCc
Confidence            998653 455555554432       2368999999999998533221  00111122233456778888888653    


Q ss_pred             -----------hHHHHhhcCCceEEEEEccccC
Q 006737          611 -----------VLVLSIKIQAFYIICFVYTISM  632 (633)
Q Consensus       611 -----------~l~~~~k~~~~~~LVFcnT~s~  632 (633)
                                 +-+.+......++||||.|+++
T Consensus       526 ~~~~qamNe~~yeKVm~~agk~qVLVFVHsRkE  558 (1674)
T KOG0951|consen  526 LKRFQAMNEACYEKVLEHAGKNQVLVFVHSRKE  558 (1674)
T ss_pred             hHHHHHHHHHHHHHHHHhCCCCcEEEEEEechH
Confidence                       2233444555799999998753

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

Probab=99.68  E-value=1.3e-16  Score=168.65  Aligned_cols=168  Identities=21%  Similarity=0.264  Sum_probs=124.4

Q ss_pred             HHHHHHHH-cCCCCC-cHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          389 LTIKALTA-AGYIQM-TRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       389 ~Ll~~L~~-~g~~~p-t~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      .+..+|++ +|+..+ +++|.+++..+..+ +||.|++|||+||+|||+||+|.+   .          + .+||++|..
T Consensus         6 ~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~---~----------g-ITIV~SPLi   71 (641)
T KOG0352|consen    6 KVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH---G----------G-ITIVISPLI   71 (641)
T ss_pred             HHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh---C----------C-eEEEehHHH
Confidence            45667776 477765 89999999998776 599999999999999999999843   1          1 589999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHH---HHh--cCCCcEEEECchhh-----HHHHhcccCcccccCCe
Q 006737          466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQR---RLE--SDPCQILVATPGRL-----LDHIENKSGLSVRLMGL  535 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~---~l~--~~~~dILIaTPgrL-----l~lL~~~~~~~~~Ls~l  535 (633)
                      +|+.++...+..+     .+.+..+....+..+..+   .+.  .....||+.||+.-     ..+|+.-    ..-.-+
T Consensus        72 ALIkDQiDHL~~L-----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L----~~r~~L  142 (641)
T KOG0352|consen   72 ALIKDQIDHLKRL-----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGL----ANRDVL  142 (641)
T ss_pred             HHHHHHHHHHHhc-----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHH----hhhcee
Confidence            9999998888777     444444555444443222   122  23467999999874     3333322    234568


Q ss_pred             eEEEEecccccCCcC--hHHHHHHHHH--HCCCCCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLG--FRKDVENIVD--CLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~g--f~~~l~~Il~--~lpk~~Q~IlfSATl~~el  579 (633)
                      .|+|||||||+.+||  |++++..+-.  ..-.....++++||.+.++
T Consensus       143 ~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~V  190 (641)
T KOG0352|consen  143 RYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKV  190 (641)
T ss_pred             eeEEechhhhHhhhccccCcchhhhhhHHhhCCCCceEEeecccChhH
Confidence            999999999999998  8888887733  2234788999999999985

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=99.67  E-value=2.4e-16  Score=185.33  Aligned_cols=171  Identities=23%  Similarity=0.252  Sum_probs=128.9

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          389 LTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       389 ~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      ........+|+..+++-|.++|..++.|+|++|.+|||.||++||+||++  +..            ..+|||.|.++|+
T Consensus       252 ~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~--l~~------------gitvVISPL~SLm  317 (941)
T KOG0351|consen  252 LELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPAL--LLG------------GVTVVISPLISLM  317 (941)
T ss_pred             HHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccc--ccC------------CceEEeccHHHHH
Confidence            33334445799999999999999999999999999999999999999997  211            2489999999999


Q ss_pred             HHHHHHHHHHHhcCCCceEEEEECCccchH---HHHHHhcC--CCcEEEECchhhHHHHhcccCcccccCC---eeEEEE
Q 006737          469 SQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQRRLESD--PCQILVATPGRLLDHIENKSGLSVRLMG---LKMLVL  540 (633)
Q Consensus       469 ~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~~~l~~~--~~dILIaTPgrLl~lL~~~~~~~~~Ls~---l~~LVI  540 (633)
                      ..+...+...     ++....+.++.....   ..+.+..+  .++|++.||+.+...-.-. .....|..   |.++||
T Consensus       318 ~DQv~~L~~~-----~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~-~~~~~L~~~~~lal~vI  391 (941)
T KOG0351|consen  318 QDQVTHLSKK-----GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLL-ESLADLYARGLLALFVI  391 (941)
T ss_pred             HHHHHhhhhc-----CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchh-hHHHhccCCCeeEEEEe
Confidence            9877665333     777888887766542   23344444  6899999999985421100 00123444   899999


Q ss_pred             ecccccCCcC--hHHHHHHHHHHCC--CCCcEEEEeccCChhh
Q 006737          541 DEADHLLDLG--FRKDVENIVDCLP--RRRQSLLFSATMPKEL  579 (633)
Q Consensus       541 DEAD~Lld~g--f~~~l~~Il~~lp--k~~Q~IlfSATl~~el  579 (633)
                      |||||++.||  |++.+..+-....  ....+|++|||.+..+
T Consensus       392 DEAHCVSqWgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v  434 (941)
T KOG0351|consen  392 DEAHCVSQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERV  434 (941)
T ss_pred             cHHHHhhhhcccccHHHHHHHHHHhhCCCCCeEEeehhccHHH
Confidence            9999999998  8998887744322  2489999999999885

>PRK13766 Hef nuclease; Provisional

Probab=99.65  E-value=3e-15  Score=176.56  Aligned_cols=160  Identities=22%  Similarity=0.203  Sum_probs=123.3

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .-+++++|..++..++.+ |+|+++|||+|||+++++++...+...          +.++|||+||++|+.|+.+.++.+
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~~----------~~~vLvl~Pt~~L~~Q~~~~~~~~   81 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHKK----------GGKVLILAPTKPLVEQHAEFFRKF   81 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHhC----------CCeEEEEeCcHHHHHHHHHHHHHH
Confidence            447899999999988887 999999999999999999888776311          236999999999999999999887


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                      +.. ....+..++|+........ +.. .++|+|+||+.+...+...   ...+.++++|||||||++........+...
T Consensus        82 ~~~-~~~~v~~~~g~~~~~~r~~-~~~-~~~iiv~T~~~l~~~l~~~---~~~~~~~~liVvDEaH~~~~~~~~~~i~~~  155 (773)
T PRK13766         82 LNI-PEEKIVVFTGEVSPEKRAE-LWE-KAKVIVATPQVIENDLIAG---RISLEDVSLLIFDEAHRAVGNYAYVYIAER  155 (773)
T ss_pred             hCC-CCceEEEEeCCCCHHHHHH-HHh-CCCEEEECHHHHHHHHHcC---CCChhhCcEEEEECCccccccccHHHHHHH
Confidence            642 2457788888876553332 222 3589999999998776544   356789999999999998755444445444


Q ss_pred             HHHCCCCCcEEEEeccC
Q 006737          559 VDCLPRRRQSLLFSATM  575 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl  575 (633)
                      +....+..++++||||.
T Consensus       156 ~~~~~~~~~il~lTaTP  172 (773)
T PRK13766        156 YHEDAKNPLVLGLTASP  172 (773)
T ss_pred             HHhcCCCCEEEEEEcCC
Confidence            44455567899999996

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=99.62  E-value=1.2e-15  Score=159.09  Aligned_cols=180  Identities=22%  Similarity=0.321  Sum_probs=135.2

Q ss_pred             cccCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEE
Q 006737          382 DECGISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLI  460 (633)
Q Consensus       382 ~el~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLI  460 (633)
                      ++++.+....+.|.+ +...+++|+|..+|.+.+.|.|+++..|||.||++||+||+|-.   .           -.+||
T Consensus        74 d~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a---d-----------g~alv  139 (695)
T KOG0353|consen   74 DDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA---D-----------GFALV  139 (695)
T ss_pred             CCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc---C-----------CceEe
Confidence            567888888888876 46789999999999999999999999999999999999999722   1           14899


Q ss_pred             EcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHH--hcCCCcEEEECchhhHHH--HhcccCcccccC
Q 006737          461 LCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRL--ESDPCQILVATPGRLLDH--IENKSGLSVRLM  533 (633)
Q Consensus       461 LvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l--~~~~~dILIaTPgrLl~l--L~~~~~~~~~Ls  533 (633)
                      |+|...|+.++.-+++.+     ++....+...++.....   ..+  +.....+|+.||+.+...  +.+.-...+...
T Consensus       140 i~plislmedqil~lkql-----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~  214 (695)
T KOG0353|consen  140 ICPLISLMEDQILQLKQL-----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAG  214 (695)
T ss_pred             echhHHHHHHHHHHHHHh-----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhcc
Confidence            999999999988888888     45555554444433211   111  223467999999998531  111111124456


Q ss_pred             CeeEEEEecccccCCcC--hHHHHHH--HHHHCCCCCcEEEEeccCChhhh
Q 006737          534 GLKMLVLDEADHLLDLG--FRKDVEN--IVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g--f~~~l~~--Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      .+.+|.|||+||...||  |++.+..  |+...-+...+|.++||.++.+.
T Consensus       215 ~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl  265 (695)
T KOG0353|consen  215 FFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVL  265 (695)
T ss_pred             eeEEEeecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchh
Confidence            78899999999999998  7877764  46655678999999999999853

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=99.62  E-value=3.4e-15  Score=169.61  Aligned_cols=178  Identities=19%  Similarity=0.206  Sum_probs=130.1

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      +.+.....+.-...-.++.+|.+.....| |+|+||++|||+|||++.+.-+++++.....         -++|+++||+
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p~---------~KiVF~aP~~  116 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRPK---------GKVVFLAPTR  116 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCCc---------ceEEEeeCCc
Confidence            33444444433445578999999998888 9999999999999999999989988866543         3799999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc
Q 006737          466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH  545 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~  545 (633)
                      -|+.|+...+..++.   +..+....||.........+.. ..+|+|+||..|.+.|.....  ..|+.+.++||||||+
T Consensus       117 pLv~QQ~a~~~~~~~---~~~~T~~l~~~~~~~~r~~i~~-s~~vff~TpQil~ndL~~~~~--~~ls~fs~iv~DE~Hr  190 (746)
T KOG0354|consen  117 PLVNQQIACFSIYLI---PYSVTGQLGDTVPRSNRGEIVA-SKRVFFRTPQILENDLKSGLH--DELSDFSLIVFDECHR  190 (746)
T ss_pred             hHHHHHHHHHhhccC---cccceeeccCccCCCchhhhhc-ccceEEeChHhhhhhcccccc--cccceEEEEEEccccc
Confidence            999999866666653   2445555555333322223322 359999999999999977643  2378999999999999


Q ss_pred             cCCcChHHHHH-HHHHHCCCCCcEEEEeccCChhh
Q 006737          546 LLDLGFRKDVE-NIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       546 Lld~gf~~~l~-~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      -....-+..+. .++..-....|+|++|||..+..
T Consensus       191 a~kn~~Y~~Vmr~~l~~k~~~~qILgLTASpG~~~  225 (746)
T KOG0354|consen  191 TSKNHPYNNIMREYLDLKNQGNQILGLTASPGSKL  225 (746)
T ss_pred             ccccccHHHHHHHHHHhhhccccEEEEecCCCccH
Confidence            88655445554 44444444459999999998763

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.61  E-value=2e-14  Score=129.54  Aligned_cols=144  Identities=44%  Similarity=0.613  Sum_probs=106.4

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccc
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF  496 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~  496 (633)
                      +++++.++||+|||..++..+........         ..++||++|++.++.|+...+......  .+.+..+.+....
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~~~---------~~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~   69 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDSLK---------GGQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSI   69 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhccc---------CCCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcch
Confidence            46899999999999998887776554311         235999999999999999988887653  5667777776554


Q ss_pred             hHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       497 ~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      .... .......+|+|+|++.+...+....   .....+.+|||||+|.+....+...............+++++|||.
T Consensus        70 ~~~~-~~~~~~~~i~i~t~~~~~~~~~~~~---~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          70 KQQE-KLLSGKTDIVVGTPGRLLDELERLK---LSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             hHHH-HHhcCCCCEEEECcHHHHHHHHcCC---cchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            4333 2334457999999999988776542   3355788999999999987654444333445556788999999995

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.61  E-value=6.8e-15  Score=177.05  Aligned_cols=147  Identities=27%  Similarity=0.329  Sum_probs=97.4

Q ss_pred             HHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc----cHHHHHHHHHHHHHHHhc
Q 006737          406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP----TRELASQIAAEAIALLKN  481 (633)
Q Consensus       406 Q~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP----TReLa~Qi~~~l~~l~~~  481 (633)
                      -.+.+..|..++.++|+|+||||||+  ++|.+-  +......      ...+++..|    +++||.+|.+++......
T Consensus        79 r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~l--le~g~g~------~g~I~~TQPRRlAArsLA~RVA~El~~~lG~  148 (1294)
T PRK11131         79 KQDILEAIRDHQVVIVAGETGSGKTT--QLPKIC--LELGRGV------KGLIGHTQPRRLAARTVANRIAEELETELGG  148 (1294)
T ss_pred             HHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHH--HHcCCCC------CCceeeCCCcHHHHHHHHHHHHHHHhhhhcc
Confidence            34555666677788999999999999  788653  2222110      113445567    567888887777653322


Q ss_pred             CCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc-ccCCcChHHH-HHHHH
Q 006737          482 HDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD-HLLDLGFRKD-VENIV  559 (633)
Q Consensus       482 ~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD-~Lld~gf~~~-l~~Il  559 (633)
                          .|+.-+   ....+    ....++|+|+|||+|++.+...    ..|+++++||||||| ++++.+|... +..++
T Consensus       149 ----~VGY~v---rf~~~----~s~~t~I~v~TpG~LL~~l~~d----~~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL  213 (1294)
T PRK11131        149 ----CVGYKV---RFNDQ----VSDNTMVKLMTDGILLAEIQQD----RLLMQYDTIIIDEAHERSLNIDFILGYLKELL  213 (1294)
T ss_pred             ----eeceee---cCccc----cCCCCCEEEEChHHHHHHHhcC----CccccCcEEEecCccccccccchHHHHHHHhh
Confidence                222111   11111    1235799999999999999765    458999999999999 5788887653 33333


Q ss_pred             HHCCCCCcEEEEeccCChh
Q 006737          560 DCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       560 ~~lpk~~Q~IlfSATl~~e  578 (633)
                      .. .++.|+|+||||++.+
T Consensus       214 ~~-rpdlKvILmSATid~e  231 (1294)
T PRK11131        214 PR-RPDLKVIITSATIDPE  231 (1294)
T ss_pred             hc-CCCceEEEeeCCCCHH
Confidence            22 2478999999999866

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.58  E-value=9.3e-15  Score=167.66  Aligned_cols=131  Identities=23%  Similarity=0.244  Sum_probs=107.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|..+.+.++.|+  |+.++||+|||++|++|++...+..           ..|+|++||++||.|.++.+..++.
T Consensus        56 ~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~G-----------~~V~VvTpt~~LA~qdae~~~~l~~  122 (745)
T TIGR00963        56 RPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALTG-----------KGVHVVTVNDYLAQRDAEWMGQVYR  122 (745)
T ss_pred             CccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHhC-----------CCEEEEcCCHHHHHHHHHHHHHHhc
Confidence            78999999999988886  9999999999999999996443332           1489999999999999999999998


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccCC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      +. ++++++++|+..........   .++|+|+||++| .++|...-.   ....++.+.++||||||.|+-
T Consensus       123 ~L-GLsv~~i~g~~~~~~r~~~y---~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LI  190 (745)
T TIGR00963       123 FL-GLSVGLILSGMSPEERREAY---ACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILI  190 (745)
T ss_pred             cC-CCeEEEEeCCCCHHHHHHhc---CCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhH
Confidence            76 89999999998865433333   379999999999 888865411   124578999999999999873

The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.58  E-value=1.4e-14  Score=165.29  Aligned_cols=130  Identities=28%  Similarity=0.315  Sum_probs=104.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|..+++.++.|+  |+.+.||+|||++|++|++.....           +..|+||+||++||.|.++.+..++.
T Consensus       103 ~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~-----------G~~v~VvTptreLA~qdae~~~~l~~  169 (656)
T PRK12898        103 RHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA-----------GLPVHVITVNDYLAERDAELMRPLYE  169 (656)
T ss_pred             CCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc-----------CCeEEEEcCcHHHHHHHHHHHHHHHh
Confidence            78999999999999999  999999999999999999977543           24699999999999999999999988


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC----------------------cccccCCeeE
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG----------------------LSVRLMGLKM  537 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~----------------------~~~~Ls~l~~  537 (633)
                      +. ++++++++|+....  .+... ..|||+|+|...| .++|...-.                      .......+.+
T Consensus       170 ~l-Glsv~~i~gg~~~~--~r~~~-y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~  245 (656)
T PRK12898        170 AL-GLTVGCVVEDQSPD--ERRAA-YGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHF  245 (656)
T ss_pred             hc-CCEEEEEeCCCCHH--HHHHH-cCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccce
Confidence            66 89999999997643  22222 3589999999988 555543311                      0122456789


Q ss_pred             EEEecccccC
Q 006737          538 LVLDEADHLL  547 (633)
Q Consensus       538 LVIDEAD~Ll  547 (633)
                      .||||||.++
T Consensus       246 aIvDEvDSiL  255 (656)
T PRK12898        246 AIVDEADSVL  255 (656)
T ss_pred             eEeeccccee
Confidence            9999999876

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.57  E-value=1.9e-14  Score=167.15  Aligned_cols=134  Identities=20%  Similarity=0.213  Sum_probs=108.4

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|. .|+++|..+++.++.|+  |+.+.||+|||++|++|++...+..           ..|+|++||++||.|.++.+.
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~G-----------~~v~VvTpt~~LA~qd~e~~~  140 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALEG-----------KGVHLITVNDYLAKRDAEEMG  140 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHcC-----------CCeEEEeCCHHHHHHHHHHHH
Confidence            355 89999999999999887  9999999999999999998655532           359999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhccc---CcccccCCeeEEEEecccccC
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKS---GLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~---~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .++... ++.+++++|+.....+.+..  ..+||+|+||++| .++|...-   .....+..+.++||||||.|+
T Consensus       141 ~l~~~l-Gl~v~~i~g~~~~~~~r~~~--y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        141 QVYEFL-GLTVGLNFSDIDDASEKKAI--YEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             HHHhhc-CCeEEEEeCCCCcHHHHHHh--cCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            999876 89999999998843333333  3489999999999 55554321   011346889999999999887

>PRK09694 helicase Cas3; Provisional

Probab=99.57  E-value=5.3e-14  Score=165.85  Aligned_cols=171  Identities=22%  Similarity=0.182  Sum_probs=114.4

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ...|+|+|..+........-+|+.||||+|||.+.++.+.. +.....        .-+++|.+||+++++|+++++.++
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~-l~~~~~--------~~gi~~aLPT~Atan~m~~Rl~~~  354 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWR-LIDQGL--------ADSIIFALPTQATANAMLSRLEAL  354 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHH-HHHhCC--------CCeEEEECcHHHHHHHHHHHHHHH
Confidence            45899999988665555667899999999999998776553 333221        125899999999999999999875


Q ss_pred             HhcC-CCceEEEEECCccchHHH---------------------HHHh-----cCCCcEEEECchhhHHHHhcccCcccc
Q 006737          479 LKNH-DGIGVLTLVGGTRFKVDQ---------------------RRLE-----SDPCQILVATPGRLLDHIENKSGLSVR  531 (633)
Q Consensus       479 ~~~~-~~i~v~~l~Gg~~~~~~~---------------------~~l~-----~~~~dILIaTPgrLl~lL~~~~~~~~~  531 (633)
                      +... ....+.+++|........                     ..+.     ..-.+|+|||..+++..+-......+.
T Consensus       355 ~~~~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR  434 (878)
T PRK09694        355 ASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIR  434 (878)
T ss_pred             HHHhcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHH
Confidence            5422 235677788765432111                     0111     012589999999998655332211111


Q ss_pred             cC--CeeEEEEecccccCCcChHHHHHHHHHHCC-CCCcEEEEeccCChhh
Q 006737          532 LM--GLKMLVLDEADHLLDLGFRKDVENIVDCLP-RRRQSLLFSATMPKEL  579 (633)
Q Consensus       532 Ls--~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSATl~~el  579 (633)
                      +-  .-++|||||+|.+- ..+...+..+++.+. ....+|+||||+|..+
T Consensus       435 ~~~La~svvIiDEVHAyD-~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~  484 (878)
T PRK09694        435 GFGLGRSVLIVDEVHAYD-AYMYGLLEAVLKAQAQAGGSVILLSATLPATL  484 (878)
T ss_pred             HHhhccCeEEEechhhCC-HHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHH
Confidence            11  12589999999984 334555666666543 3578999999999874

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

Probab=99.57  E-value=3.8e-14  Score=153.80  Aligned_cols=163  Identities=19%  Similarity=0.128  Sum_probs=130.5

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .-+++.+|.......+.+ |+|++.|||-|||++.++-+.+.+...+         + ++|+|+||+-|+.|.+..|.+.
T Consensus        13 ~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~~---------~-kvlfLAPTKPLV~Qh~~~~~~v   81 (542)
T COG1111          13 TIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWFG---------G-KVLFLAPTKPLVLQHAEFCRKV   81 (542)
T ss_pred             cccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhcC---------C-eEEEecCCchHHHHHHHHHHHH
Confidence            346788888888777766 9999999999999998888877776543         2 6999999999999999999988


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                      +. .+.-.++.++|.............  .+|+|+||..+.+-|..+   .+++.++.+||+||||+-....-+..+...
T Consensus        82 ~~-ip~~~i~~ltGev~p~~R~~~w~~--~kVfvaTPQvveNDl~~G---rid~~dv~~lifDEAHRAvGnyAYv~Va~~  155 (542)
T COG1111          82 TG-IPEDEIAALTGEVRPEEREELWAK--KKVFVATPQVVENDLKAG---RIDLDDVSLLIFDEAHRAVGNYAYVFVAKE  155 (542)
T ss_pred             hC-CChhheeeecCCCChHHHHHHHhh--CCEEEeccHHHHhHHhcC---ccChHHceEEEechhhhccCcchHHHHHHH
Confidence            75 335678899999887755555444  489999999998888766   588999999999999997755444455554


Q ss_pred             HHHCCCCCcEEEEeccCChh
Q 006737          559 VDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~~e  578 (633)
                      .....+++.++++|||-...
T Consensus       156 y~~~~k~~~ilgLTASPGs~  175 (542)
T COG1111         156 YLRSAKNPLILGLTASPGSD  175 (542)
T ss_pred             HHHhccCceEEEEecCCCCC
Confidence            44556678899999999876

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.55  E-value=1.6e-14  Score=166.65  Aligned_cols=134  Identities=21%  Similarity=0.234  Sum_probs=98.4

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      |. .|+++|...+..+..|  .|+.++||+|||++|++|++.+.+..           ..|+||+|+++||.|..+.+..
T Consensus        68 gl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~g-----------~~V~VVTpn~yLA~Rdae~m~~  133 (762)
T TIGR03714        68 GM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALTG-----------KGAMLVTTNDYLAKRDAEEMGP  133 (762)
T ss_pred             CC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhcC-----------CceEEeCCCHHHHHHHHHHHHH
Confidence            44 5666666555555555  79999999999999999987665432           2499999999999999999999


Q ss_pred             HHhcCCCceEEEEECCcc---chHHHHHHhcCCCcEEEECchhh-HHHHhcc---cCcccccCCeeEEEEecccccC
Q 006737          478 LLKNHDGIGVLTLVGGTR---FKVDQRRLESDPCQILVATPGRL-LDHIENK---SGLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~---~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~---~~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      +..++ ++.+.+++++..   ......... ..|+|+|+||++| .++|...   ......+..+.++||||||.||
T Consensus       134 l~~~L-GLsv~~~~~~s~~~~~~~~~rr~~-y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsIL  208 (762)
T TIGR03714       134 VYEWL-GLTVSLGVVDDPDEEYDANEKRKI-YNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVL  208 (762)
T ss_pred             HHhhc-CCcEEEEECCCCccccCHHHHHHh-CCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHh
Confidence            98876 888988877632   222222222 3589999999999 5555322   0112346789999999999986

Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.

>TIGR00595 priA primosomal protein N'

Probab=99.54  E-value=9.3e-14  Score=156.26  Aligned_cols=133  Identities=23%  Similarity=0.227  Sum_probs=96.5

Q ss_pred             EEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH
Q 006737          420 VVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD  499 (633)
Q Consensus       420 Lv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~  499 (633)
                      |+.|+||||||++|+..+. .++..+          .++|||+|+++|+.|+++.+++.+    +..+..++++......
T Consensus         1 LL~g~TGsGKT~v~l~~i~-~~l~~g----------~~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er   65 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIE-KVLALG----------KSVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEK   65 (505)
T ss_pred             CccCCCCCCHHHHHHHHHH-HHHHcC----------CeEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHH
Confidence            4689999999999965543 333322          259999999999999999998875    4567888888765432


Q ss_pred             ---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcC------hHHHHHHHHHHCCCCCcEEE
Q 006737          500 ---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG------FRKDVENIVDCLPRRRQSLL  570 (633)
Q Consensus       500 ---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g------f~~~l~~Il~~lpk~~Q~Il  570 (633)
                         +..+..+.++|||+|+..|.          ..+.++.+|||||+|...-++      ....+..+.... .+.++|+
T Consensus        66 ~~~~~~~~~g~~~IVVGTrsalf----------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~-~~~~vil  134 (505)
T TIGR00595        66 LQAWRKVKNGEILVVIGTRSALF----------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKK-FNCPVVL  134 (505)
T ss_pred             HHHHHHHHcCCCCEEECChHHHc----------CcccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHh-cCCCEEE
Confidence               34455567899999998663          346789999999999877432      112233333333 4789999


Q ss_pred             EeccCChh
Q 006737          571 FSATMPKE  578 (633)
Q Consensus       571 fSATl~~e  578 (633)
                      +|||.+.+
T Consensus       135 ~SATPsle  142 (505)
T TIGR00595       135 GSATPSLE  142 (505)
T ss_pred             EeCCCCHH
Confidence            99997765

All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.53  E-value=3.8e-14  Score=164.84  Aligned_cols=130  Identities=22%  Similarity=0.240  Sum_probs=104.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.-.--.+..|+  |+.++||+|||++|.+|++..++..           ..|+||+||++||.|.++.+..+..
T Consensus        82 ~~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~G-----------~~V~VvTpn~yLA~qd~e~m~~l~~  148 (896)
T PRK13104         82 RHFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAISG-----------RGVHIVTVNDYLAKRDSQWMKPIYE  148 (896)
T ss_pred             CcchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhcC-----------CCEEEEcCCHHHHHHHHHHHHHHhc
Confidence            67788876666666665  8999999999999999999776543           1389999999999999999999988


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccCccc---ccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSGLSV---RLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~~~~---~Ls~l~~LVIDEAD~Ll  547 (633)
                      ++ ++.+.+++|+..........   .+||+|+||++| .++|...-....   ....+.++||||||.||
T Consensus       149 ~l-GLtv~~i~gg~~~~~r~~~y---~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        149 FL-GLTVGVIYPDMSHKEKQEAY---KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             cc-CceEEEEeCCCCHHHHHHHh---CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            76 89999999998766554443   479999999999 999876521111   12589999999999887

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

Probab=99.53  E-value=8e-15  Score=163.57  Aligned_cols=156  Identities=19%  Similarity=0.228  Sum_probs=133.9

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+.|.|..+|-.+-++.+|+|.|.|.+|||++.-..|.+.+....           +|||.+|-++|.+|-|+++..-+
T Consensus       128 F~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~kQ-----------RVIYTSPIKALSNQKYREl~~EF  196 (1041)
T KOG0948|consen  128 FTLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLREKQ-----------RVIYTSPIKALSNQKYRELLEEF  196 (1041)
T ss_pred             cccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHhcC-----------eEEeeChhhhhcchhHHHHHHHh
Confidence            3689999999999999999999999999999997776666654432           69999999999999999998876


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHH
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV  559 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il  559 (633)
                      +.     |++.+|+.....        .+..||+|.+.|..+|.++.   --+..|.+||+||+|.|-|...+-.++.-+
T Consensus       197 ~D-----VGLMTGDVTInP--------~ASCLVMTTEILRsMLYRGS---EvmrEVaWVIFDEIHYMRDkERGVVWEETI  260 (1041)
T KOG0948|consen  197 KD-----VGLMTGDVTINP--------DASCLVMTTEILRSMLYRGS---EVMREVAWVIFDEIHYMRDKERGVVWEETI  260 (1041)
T ss_pred             cc-----cceeecceeeCC--------CCceeeeHHHHHHHHHhccc---hHhheeeeEEeeeehhccccccceeeeeeE
Confidence            53     677888877553        36799999999999998874   447889999999999999988888888888


Q ss_pred             HHCCCCCcEEEEeccCChhhhcc
Q 006737          560 DCLPRRRQSLLFSATMPKELVLK  582 (633)
Q Consensus       560 ~~lpk~~Q~IlfSATl~~el~l~  582 (633)
                      -.+|++.+.+++|||+|+...+.
T Consensus       261 IllP~~vr~VFLSATiPNA~qFA  283 (1041)
T KOG0948|consen  261 ILLPDNVRFVFLSATIPNARQFA  283 (1041)
T ss_pred             EeccccceEEEEeccCCCHHHHH
Confidence            89999999999999999996554

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.50  E-value=3e-13  Score=163.49  Aligned_cols=148  Identities=23%  Similarity=0.255  Sum_probs=104.4

Q ss_pred             HHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceE
Q 006737          408 ATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGV  487 (633)
Q Consensus       408 ~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v  487 (633)
                      +.+..|..++.+|++|+||||||.  ++|.+-  +.....      ...+++++.|.|-.|..+...+.....    ..+
T Consensus        74 ~Il~~l~~~~vvii~g~TGSGKTT--qlPq~l--le~~~~------~~~~I~~tQPRRlAA~svA~RvA~elg----~~l  139 (1283)
T TIGR01967        74 DIAEAIAENQVVIIAGETGSGKTT--QLPKIC--LELGRG------SHGLIGHTQPRRLAARTVAQRIAEELG----TPL  139 (1283)
T ss_pred             HHHHHHHhCceEEEeCCCCCCcHH--HHHHHH--HHcCCC------CCceEecCCccHHHHHHHHHHHHHHhC----CCc
Confidence            455666677789999999999999  778763  332211      112567788999888888877766553    333


Q ss_pred             EEEECC-ccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc-ccCCcChHHH-HHHHHHHCCC
Q 006737          488 LTLVGG-TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD-HLLDLGFRKD-VENIVDCLPR  564 (633)
Q Consensus       488 ~~l~Gg-~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD-~Lld~gf~~~-l~~Il~~lpk  564 (633)
                      +..+|. ......    .+..+.|+|+|||+|+..+...    ..|+++++||||||| ++++.+|... +..++... +
T Consensus       140 G~~VGY~vR~~~~----~s~~T~I~~~TdGiLLr~l~~d----~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-p  210 (1283)
T TIGR01967       140 GEKVGYKVRFHDQ----VSSNTLVKLMTDGILLAETQQD----RFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-P  210 (1283)
T ss_pred             ceEEeeEEcCCcc----cCCCceeeeccccHHHHHhhhC----cccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-C
Confidence            334442 122111    1234789999999999998765    458999999999999 5888887764 55665444 5


Q ss_pred             CCcEEEEeccCChh
Q 006737          565 RRQSLLFSATMPKE  578 (633)
Q Consensus       565 ~~Q~IlfSATl~~e  578 (633)
                      +.|+|+||||++.+
T Consensus       211 dLKlIlmSATld~~  224 (1283)
T TIGR01967       211 DLKIIITSATIDPE  224 (1283)
T ss_pred             CCeEEEEeCCcCHH
Confidence            78999999999865

This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.

>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

Probab=99.47  E-value=2.7e-13  Score=129.94  Aligned_cols=157  Identities=18%  Similarity=0.207  Sum_probs=101.8

Q ss_pred             CCcHHHHHHHHHHhC-------CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLE-------GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAA  473 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~-------grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~  473 (633)
                      +|++.|.+++..+..       .+.+++.+|||||||.+++..+.... .             ++||++|+..|+.|..+
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~-~-------------~~l~~~p~~~l~~Q~~~   68 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELA-R-------------KVLIVAPNISLLEQWYD   68 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHH-C-------------EEEEEESSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhccc-c-------------ceeEecCHHHHHHHHHH
Confidence            578999999999884       58999999999999998775444332 2             48999999999999999


Q ss_pred             HHHHHHhcCCCceEE---------EEECCccchHHHHHHhcCCCcEEEECchhhHHHHhccc--------CcccccCCee
Q 006737          474 EAIALLKNHDGIGVL---------TLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKS--------GLSVRLMGLK  536 (633)
Q Consensus       474 ~l~~l~~~~~~i~v~---------~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~--------~~~~~Ls~l~  536 (633)
                      .+..+..........         ....................+|+++|...|........        ..........
T Consensus        69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  148 (184)
T PF04851_consen   69 EFDDFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFD  148 (184)
T ss_dssp             HHHHHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSES
T ss_pred             HHHHhhhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCC
Confidence            996665422111000         00011111112223334456899999999987765321        1112345678


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      +||+||||++....-   +..++.  .+...+|+||||..
T Consensus       149 ~vI~DEaH~~~~~~~---~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  149 LVIIDEAHHYPSDSS---YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             EEEEETGGCTHHHHH---HHHHHH--SSCCEEEEEESS-S
T ss_pred             EEEEehhhhcCCHHH---HHHHHc--CCCCeEEEEEeCcc
Confidence            999999999864321   444544  45677999999974

1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.39  E-value=4.6e-13  Score=145.25  Aligned_cols=179  Identities=26%  Similarity=0.268  Sum_probs=123.1

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccC-CCCc--hhhhHHHHHHHHHHhc--------------------CCCCCCCCCCe
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKT-GTGK--SIAFLLPAIEAVLKAT--------------------SSSTTQLVPPI  456 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApT-GSGK--TlaylLPiL~~l~~~~--------------------~~~~~~~~~~~  456 (633)
                      ..+|+.|.+.+-.+.+++|+++.-.| +.|+  +-.|+|++|+|+++..                    ....+++.++|
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            46899999999999999999876544 2344  5679999999998731                    11245788899


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceE--------EEEECC--------ccchHHHHHHhc---------------
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGV--------LTLVGG--------TRFKVDQRRLES---------------  505 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v--------~~l~Gg--------~~~~~~~~~l~~---------------  505 (633)
                      +||||||+|+.|..+++.+..++.....-++        .--++|        .+...+.+.+..               
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftk  374 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTK  374 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHH
Confidence            9999999999999999999988533221010        001111        000011111111               


Q ss_pred             ---------CCCcEEEECchhhHHHHhcccCccc---ccCCeeEEEEecccccCC--cChHHHHHHHHHHCCCC------
Q 006737          506 ---------DPCQILVATPGRLLDHIENKSGLSV---RLMGLKMLVLDEADHLLD--LGFRKDVENIVDCLPRR------  565 (633)
Q Consensus       506 ---------~~~dILIaTPgrLl~lL~~~~~~~~---~Ls~l~~LVIDEAD~Lld--~gf~~~l~~Il~~lpk~------  565 (633)
                               ..+|||||+|..|..+|.+.+....   .|++|.++|||.||.|+.  |.+..++..-++.+|.+      
T Consensus       375 KtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QNwEhl~~ifdHLn~~P~k~h~~Df  454 (698)
T KOG2340|consen  375 KTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQNWEHLLHIFDHLNLQPSKQHDVDF  454 (698)
T ss_pred             HHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhhHHHHHHHHHHhhcCcccccCCCh
Confidence                     2579999999999999985443222   389999999999999883  43444444444555542      


Q ss_pred             ---------------CcEEEEeccCChh
Q 006737          566 ---------------RQSLLFSATMPKE  578 (633)
Q Consensus       566 ---------------~Q~IlfSATl~~e  578 (633)
                                     +|+++||+-..+.
T Consensus       455 SRVR~wyL~~qsr~~rQtl~Fs~y~~~~  482 (698)
T KOG2340|consen  455 SRVRMWYLDGQSRYFRQTLLFSRYSHPL  482 (698)
T ss_pred             hheehheeccHHHHHHHHHHHHhhccHH
Confidence                           6999999988776

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.36  E-value=4e-12  Score=147.90  Aligned_cols=130  Identities=24%  Similarity=0.258  Sum_probs=104.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.-..-.+..|+  |+.++||+|||+++.+|++-..+...           .|-|++||..||.|.++.+..++.
T Consensus        81 ~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~G~-----------~V~IvTpn~yLA~rd~e~~~~l~~  147 (830)
T PRK12904         81 RHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALTGK-----------GVHVVTVNDYLAKRDAEWMGPLYE  147 (830)
T ss_pred             CCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHcCC-----------CEEEEecCHHHHHHHHHHHHHHHh
Confidence            68889988777777775  89999999999999999963333221           267999999999999999999988


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccCc---ccccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSGL---SVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~~---~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .. ++.+++++|+.+........   .+||+|+||+.| .++|...-..   ...+..+.++||||||.||
T Consensus       148 ~L-Glsv~~i~~~~~~~er~~~y---~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiL  214 (830)
T PRK12904        148 FL-GLSVGVILSGMSPEERREAY---AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSIL  214 (830)
T ss_pred             hc-CCeEEEEcCCCCHHHHHHhc---CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhhe
Confidence            76 89999999998877655544   379999999999 8898755211   1236789999999999887

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

Probab=99.32  E-value=5.1e-11  Score=134.36  Aligned_cols=152  Identities=23%  Similarity=0.253  Sum_probs=110.1

Q ss_pred             HHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH-HHHhcCCCc
Q 006737          407 EATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI-ALLKNHDGI  485 (633)
Q Consensus       407 ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~-~l~~~~~~i  485 (633)
                      ++++++|..+--|||||.||||||.  ++|.+  |+..+........+++.+ |..|.|-.|..+.+++- ++......+
T Consensus       262 q~IMEaIn~n~vvIIcGeTGsGKTT--QvPQF--LYEAGf~s~~~~~~gmIG-ITqPRRVAaiamAkRVa~EL~~~~~eV  336 (1172)
T KOG0926|consen  262 QRIMEAINENPVVIICGETGSGKTT--QVPQF--LYEAGFASEQSSSPGMIG-ITQPRRVAAIAMAKRVAFELGVLGSEV  336 (1172)
T ss_pred             HHHHHHhhcCCeEEEecCCCCCccc--cchHH--HHHcccCCccCCCCCeee-ecCchHHHHHHHHHHHHHHhccCccce
Confidence            4566777778889999999999998  88866  888776655444455655 89999988888776654 443322234


Q ss_pred             eEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC-----cChHHHHHHHHH
Q 006737          486 GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-----LGFRKDVENIVD  560 (633)
Q Consensus       486 ~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld-----~gf~~~l~~Il~  560 (633)
                      ...+-+.++-..         ...|.++|.|.|+.-|.++    +.|.....|||||||.-.-     .|+...+..|..
T Consensus       337 sYqIRfd~ti~e---------~T~IkFMTDGVLLrEi~~D----flL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~  403 (1172)
T KOG0926|consen  337 SYQIRFDGTIGE---------DTSIKFMTDGVLLREIEND----FLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQ  403 (1172)
T ss_pred             eEEEEeccccCC---------CceeEEecchHHHHHHHHh----HhhhhceeEEechhhhccchHHHHHHHHHHHHHHHH
Confidence            455555554322         3689999999999999886    6789999999999997652     245555556655


Q ss_pred             HCCC------CCcEEEEeccCC
Q 006737          561 CLPR------RRQSLLFSATMP  576 (633)
Q Consensus       561 ~lpk------~~Q~IlfSATl~  576 (633)
                      .+.+      ....|+||||+-
T Consensus       404 k~~ke~~~~kpLKLIIMSATLR  425 (1172)
T KOG0926|consen  404 KYYKEQCQIKPLKLIIMSATLR  425 (1172)
T ss_pred             HHhhhhcccCceeEEEEeeeEE
Confidence            5444      467899999984

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

Probab=99.31  E-value=8.7e-12  Score=138.37  Aligned_cols=146  Identities=23%  Similarity=0.294  Sum_probs=100.3

Q ss_pred             CCCCcHHHHHHHHHHhC----CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLE----GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~----grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      ...++++|.+++..+.+    .+..++++|||+|||++++..+ ..+.             ..+||||||++|+.|..+.
T Consensus        34 ~~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~-~~~~-------------~~~Lvlv~~~~L~~Qw~~~   99 (442)
T COG1061          34 EFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAI-AELK-------------RSTLVLVPTKELLDQWAEA   99 (442)
T ss_pred             CCCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHH-HHhc-------------CCEEEEECcHHHHHHHHHH
Confidence            34699999999999998    8899999999999998765433 2221             1299999999999999877


Q ss_pred             HHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHH--HhcccCcccccCCeeEEEEecccccCCcChH
Q 006737          475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDH--IENKSGLSVRLMGLKMLVLDEADHLLDLGFR  552 (633)
Q Consensus       475 l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~l--L~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~  552 (633)
                      +...+...  ..+..+.|+.....      .  ..|.|+|-..+...  +..     .......+|||||||++....+.
T Consensus       100 ~~~~~~~~--~~~g~~~~~~~~~~------~--~~i~vat~qtl~~~~~l~~-----~~~~~~~liI~DE~Hh~~a~~~~  164 (442)
T COG1061         100 LKKFLLLN--DEIGIYGGGEKELE------P--AKVTVATVQTLARRQLLDE-----FLGNEFGLIIFDEVHHLPAPSYR  164 (442)
T ss_pred             HHHhcCCc--cccceecCceeccC------C--CcEEEEEhHHHhhhhhhhh-----hcccccCEEEEEccccCCcHHHH
Confidence            76665321  12344444333211      0  26999998888764  221     22346899999999999876444


Q ss_pred             HHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          553 KDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       553 ~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      .    +...+.....+++||||.+-
T Consensus       165 ~----~~~~~~~~~~~LGLTATp~R  185 (442)
T COG1061         165 R----ILELLSAAYPRLGLTATPER  185 (442)
T ss_pred             H----HHHhhhcccceeeeccCcee
Confidence            3    33333322228999999763

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=99.31  E-value=7.5e-12  Score=143.35  Aligned_cols=165  Identities=22%  Similarity=0.239  Sum_probs=123.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|..+|.+.+..+-.+..++|+|||.+|||++- ..+++++++....        --+|+++||.+|++|+...+...+.
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfis-fY~iEKVLResD~--------~VVIyvaPtKaLVnQvsa~VyaRF~  581 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFIS-FYAIEKVLRESDS--------DVVIYVAPTKALVNQVSANVYARFD  581 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceecc-HHHHHHHHhhcCC--------CEEEEecchHHHhhhhhHHHHHhhc
Confidence            588999999999999999999999999999863 3455666654322        1489999999999999988888774


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                      ...-.+...+.|......++.   .-.|+|+|+-|+.|..+|............|++||+||+|++....-...++.++.
T Consensus       582 ~~t~~rg~sl~g~ltqEYsin---p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~  658 (1330)
T KOG0949|consen  582 TKTFLRGVSLLGDLTQEYSIN---PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLL  658 (1330)
T ss_pred             cCccccchhhHhhhhHHhcCC---chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHH
Confidence            332233333444433222221   23589999999999998876433345678999999999999987665666667776


Q ss_pred             HCCCCCcEEEEeccCChhh
Q 006737          561 CLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl~~el  579 (633)
                      .++  |.++++|||+.+..
T Consensus       659 li~--CP~L~LSATigN~~  675 (1330)
T KOG0949|consen  659 LIP--CPFLVLSATIGNPN  675 (1330)
T ss_pred             hcC--CCeeEEecccCCHH
Confidence            664  89999999998873

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

Probab=99.30  E-value=1e-10  Score=121.98  Aligned_cols=148  Identities=20%  Similarity=0.231  Sum_probs=111.9

Q ss_pred             CCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ++++.|+.+-..    +.+.+++|+.|-||+|||.. +.+.++..++.+          .++.|.+|....|.+++.+++
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEM-if~~i~~al~~G----------~~vciASPRvDVclEl~~Rlk  165 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEM-IFQGIEQALNQG----------GRVCIASPRVDVCLELYPRLK  165 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhh-hHHHHHHHHhcC----------CeEEEecCcccchHHHHHHHH
Confidence            689999877655    44568999999999999974 556676666653          368899999999999999998


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      ..+.   +..+.+++|+......        .+++|||..+|+++-.          .+++|||||+|..--..-.....
T Consensus       166 ~aF~---~~~I~~Lyg~S~~~fr--------~plvVaTtHQLlrFk~----------aFD~liIDEVDAFP~~~d~~L~~  224 (441)
T COG4098         166 QAFS---NCDIDLLYGDSDSYFR--------APLVVATTHQLLRFKQ----------AFDLLIIDEVDAFPFSDDQSLQY  224 (441)
T ss_pred             Hhhc---cCCeeeEecCCchhcc--------ccEEEEehHHHHHHHh----------hccEEEEeccccccccCCHHHHH
Confidence            8875   5678899998775431        5899999999987643          46789999999876332222222


Q ss_pred             HHHHHCCCCCcEEEEeccCChhhh
Q 006737          557 NIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       557 ~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      .+-+...+.--+|++|||-++++.
T Consensus       225 Av~~ark~~g~~IylTATp~k~l~  248 (441)
T COG4098         225 AVKKARKKEGATIYLTATPTKKLE  248 (441)
T ss_pred             HHHHhhcccCceEEEecCChHHHH
Confidence            333444556789999999998864

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.28  E-value=3.2e-11  Score=143.88  Aligned_cols=98  Identities=24%  Similarity=0.299  Sum_probs=74.1

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHH----HHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEE
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLS----ACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLIL  461 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp----~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLIL  461 (633)
                      +++.+...+...||+ +++.|.+.+.    .+..++++++.||||+|||++|++|++.... ..          .++||.
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~~----------~~vvi~  298 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-TE----------KPVVIS  298 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-CC----------CeEEEE
Confidence            345677788888886 7899998665    5667899999999999999999999987654 11          259999


Q ss_pred             cccHHHHHHHHH-HHHHHHhcCC-CceEEEEECCcc
Q 006737          462 CPTRELASQIAA-EAIALLKNHD-GIGVLTLVGGTR  495 (633)
Q Consensus       462 vPTReLa~Qi~~-~l~~l~~~~~-~i~v~~l~Gg~~  495 (633)
                      +||++|+.|++. .+..+.+... .+++.++.|+..
T Consensus       299 t~t~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~~~  334 (850)
T TIGR01407       299 TNTKVLQSQLLEKDIPLLNEILNFKINAALIKGKSN  334 (850)
T ss_pred             eCcHHHHHHHHHHHHHHHHHHcCCCceEEEEEcchh
Confidence            999999999875 4554443321 367777776543

This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.27  E-value=1.6e-11  Score=141.27  Aligned_cols=176  Identities=20%  Similarity=0.187  Sum_probs=132.3

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHH--HHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATL--SACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aI--p~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      ++....-.....|...++.+|.+|+  |.++.++|+|+.+||+.|||++.-|-++..++....          .++.+.|
T Consensus       208 ~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr----------~~llilp  277 (1008)
T KOG0950|consen  208 PTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR----------NVLLILP  277 (1008)
T ss_pred             chHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh----------ceeEecc
Confidence            3333344445578999999999998  668889999999999999999998888877766543          3888889


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecc
Q 006737          464 TRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEA  543 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEA  543 (633)
                      ....+..-...+..++... |+.|-+++|........   +  .-++.|||-++-..++..-.. .-.+..+.+|||||.
T Consensus       278 ~vsiv~Ek~~~l~~~~~~~-G~~ve~y~g~~~p~~~~---k--~~sv~i~tiEkanslin~lie-~g~~~~~g~vvVdEl  350 (1008)
T KOG0950|consen  278 YVSIVQEKISALSPFSIDL-GFPVEEYAGRFPPEKRR---K--RESVAIATIEKANSLINSLIE-QGRLDFLGMVVVDEL  350 (1008)
T ss_pred             eeehhHHHHhhhhhhcccc-CCcchhhcccCCCCCcc---c--ceeeeeeehHhhHhHHHHHHh-cCCccccCcEEEeee
Confidence            8888888777777776655 78888887665533211   1  248999999887665543211 134778999999999


Q ss_pred             cccCCcChHHHHHHHHHHC-----CCCCcEEEEeccCChh
Q 006737          544 DHLLDLGFRKDVENIVDCL-----PRRRQSLLFSATMPKE  578 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~l-----pk~~Q~IlfSATl~~e  578 (633)
                      |.+.+.+....++.++..+     ....|+|+||||++|-
T Consensus       351 hmi~d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~  390 (1008)
T KOG0950|consen  351 HMIGDKGRGAILELLLAKILYENLETSVQIIGMSATIPNN  390 (1008)
T ss_pred             eeeeccccchHHHHHHHHHHHhccccceeEeeeecccCCh
Confidence            9999998888877776532     2346799999999987

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

Probab=99.27  E-value=2.4e-10  Score=129.00  Aligned_cols=168  Identities=20%  Similarity=0.266  Sum_probs=127.7

Q ss_pred             CCCHHHHHHH-HHcCCCCCcHHHHHHHHHHhCC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          385 GISPLTIKAL-TAAGYIQMTRVQEATLSACLEG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       385 ~L~~~Ll~~L-~~~g~~~pt~iQ~~aIp~il~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      .....+++.+ ....| ++|.-|+.++..|...      .+=++++--|||||++.++.++..+...           .+
T Consensus       246 ~~~~~l~~~~~~~LPF-~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~G-----------~Q  313 (677)
T COG1200         246 PANGELLAKFLAALPF-KLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAG-----------YQ  313 (677)
T ss_pred             CccHHHHHHHHHhCCC-CccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHcC-----------Ce
Confidence            3445555555 44555 8999999999998864      3568999999999999999998876443           36


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH---HHHHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      +..++||--||.|-++.+.+++... ++.|..++|...-..   ....+.++..+|+|+|-.-+    ..    ...+++
T Consensus       314 ~ALMAPTEILA~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALi----Qd----~V~F~~  384 (677)
T COG1200         314 AALMAPTEILAEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALI----QD----KVEFHN  384 (677)
T ss_pred             eEEeccHHHHHHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhh----hc----ceeecc
Confidence            8999999999999999999999876 799999999876554   34566677899999995433    32    367889


Q ss_pred             eeEEEEecccccCCcChHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      +.++||||-|++.     -.=+..+..-.. ..-+++||||-=+-
T Consensus       385 LgLVIiDEQHRFG-----V~QR~~L~~KG~~~Ph~LvMTATPIPR  424 (677)
T COG1200         385 LGLVIIDEQHRFG-----VHQRLALREKGEQNPHVLVMTATPIPR  424 (677)
T ss_pred             eeEEEEecccccc-----HHHHHHHHHhCCCCCcEEEEeCCCchH
Confidence            9999999999954     233333333333 56799999996443

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.27  E-value=1.4e-11  Score=143.41  Aligned_cols=130  Identities=22%  Similarity=0.226  Sum_probs=102.5

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.-.--.+..|+  |+.++||.|||++|.+|++...+...           .|.||+|+.+||.+..+.+..++.
T Consensus        82 ~~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~g~-----------~VhIvT~ndyLA~RD~e~m~~l~~  148 (908)
T PRK13107         82 RHFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALTGK-----------GVHVITVNDYLARRDAENNRPLFE  148 (908)
T ss_pred             CcCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhcCC-----------CEEEEeCCHHHHHHHHHHHHHHHH
Confidence            57778876555555554  89999999999999999987665432           399999999999999999999998


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccCcc---cccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSGLS---VRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~~~---~~Ls~l~~LVIDEAD~Ll  547 (633)
                      ++ ++.|.++.++....   .......|||+++||+.| .++|...-...   .....+.++||||||.+|
T Consensus       149 ~l-Glsv~~i~~~~~~~---~r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiL  215 (908)
T PRK13107        149 FL-GLTVGINVAGLGQQ---EKKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSIL  215 (908)
T ss_pred             hc-CCeEEEecCCCCHH---HHHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhc
Confidence            76 99999999987753   233344589999999999 88886551111   123778999999999887

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

Probab=99.21  E-value=1.3e-10  Score=140.82  Aligned_cols=162  Identities=17%  Similarity=0.188  Sum_probs=105.4

Q ss_pred             CCcHHHHHHHHHHh----C-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACL----E-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~il----~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .++++|..||..+.    . .+.+|++++||||||++. +.++..+++...        ..++|||+|+++|+.|..+.|
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~~--------~~rVLfLvDR~~L~~Qa~~~F  483 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAKR--------FRRILFLVDRSALGEQAEDAF  483 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcCc--------cCeEEEEecHHHHHHHHHHHH
Confidence            58999999998775    2 368999999999999874 345555554321        136999999999999999988


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC--cccccCCeeEEEEecccccCC-----
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG--LSVRLMGLKMLVLDEADHLLD-----  548 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~--~~~~Ls~l~~LVIDEAD~Lld-----  548 (633)
                      ..+.... ...+..+++....   ..........|+|+|...|...+.....  ....+..+++|||||||+-..     
T Consensus       484 ~~~~~~~-~~~~~~i~~i~~L---~~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~  559 (1123)
T PRK11448        484 KDTKIEG-DQTFASIYDIKGL---EDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEM  559 (1123)
T ss_pred             Hhccccc-ccchhhhhchhhh---hhhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCcccccc
Confidence            8763211 1111111111111   1111223468999999998776532211  113467788999999998531     


Q ss_pred             ----c------ChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          549 ----L------GFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       549 ----~------gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                          .      .+...+..++..+  +.-.|+||||.-.
T Consensus       560 ~~~~~~~~~~~~~~~~yr~iL~yF--dA~~IGLTATP~r  596 (1123)
T PRK11448        560 SEGELQFRDQLDYVSKYRRVLDYF--DAVKIGLTATPAL  596 (1123)
T ss_pred             ccchhccchhhhHHHHHHHHHhhc--CccEEEEecCCcc
Confidence                0      1246677777765  3568999999753

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.17  E-value=1e-10  Score=135.24  Aligned_cols=153  Identities=17%  Similarity=0.193  Sum_probs=103.9

Q ss_pred             CCCcHHHHHHHHHHhC-C--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLE-G--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~-g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ..++++|.+++..++. |  +..++++|||+|||+..+..+ ..+   .          -++|||||+..|+.|..+++.
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa-~~l---~----------k~tLILvps~~Lv~QW~~ef~  319 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAA-CTV---K----------KSCLVLCTSAVSVEQWKQQFK  319 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHH-HHh---C----------CCEEEEeCcHHHHHHHHHHHH
Confidence            3689999999999874 4  378999999999999865433 222   1          138999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-----cccccCCeeEEEEecccccCCcCh
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-----LSVRLMGLKMLVLDEADHLLDLGF  551 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-----~~~~Ls~l~~LVIDEAD~Lld~gf  551 (633)
                      +++.. ....+..++|+.....      .....|+|+|...+.....+...     ..+.-....+||+||||++..   
T Consensus       320 ~~~~l-~~~~I~~~tg~~k~~~------~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA---  389 (732)
T TIGR00603       320 MWSTI-DDSQICRFTSDAKERF------HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA---  389 (732)
T ss_pred             HhcCC-CCceEEEEecCccccc------ccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH---
Confidence            87532 2455666666543211      12258999999876532211100     001123577999999999864   


Q ss_pred             HHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          552 RKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       552 ~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                       ..+..++..+. ....++||||.-.+
T Consensus       390 -~~fr~il~~l~-a~~RLGLTATP~Re  414 (732)
T TIGR00603       390 -AMFRRVLTIVQ-AHCKLGLTATLVRE  414 (732)
T ss_pred             -HHHHHHHHhcC-cCcEEEEeecCccc
Confidence             34555666664 34579999998643

All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=99.17  E-value=2.7e-10  Score=130.45  Aligned_cols=77  Identities=21%  Similarity=0.281  Sum_probs=58.4

Q ss_pred             HHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH-hcC-CCc
Q 006737          408 ATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL-KNH-DGI  485 (633)
Q Consensus       408 ~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~-~~~-~~i  485 (633)
                      .+...+..++.+++.|+||+|||++|++|++..+....         +.++||++||++|+.|+++.+..+. +.. ..+
T Consensus         8 ~i~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~~---------~~rvlIstpT~~Lq~Ql~~~l~~l~~~~l~~~i   78 (636)
T TIGR03117         8 NCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERP---------DQKIAIAVPTLALMGQLWSELERLTAEGLAGPV   78 (636)
T ss_pred             HHHHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhcc---------CceEEEECCcHHHHHHHHHHHHHHHHhhcCCCe
Confidence            34455667889999999999999999999998765321         2369999999999999999888776 322 145


Q ss_pred             eEEEEECC
Q 006737          486 GVLTLVGG  493 (633)
Q Consensus       486 ~v~~l~Gg  493 (633)
                      ++.++.|+
T Consensus        79 ~~~~lkGr   86 (636)
T TIGR03117        79 QAGFFPGS   86 (636)
T ss_pred             eEEEEECC
Confidence            55555554

Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.

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

Probab=99.17  E-value=8.1e-10  Score=129.44  Aligned_cols=152  Identities=22%  Similarity=0.236  Sum_probs=107.2

Q ss_pred             HHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCc
Q 006737          406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI  485 (633)
Q Consensus       406 Q~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i  485 (633)
                      ..+.+.++.+.+-+||+|+||||||.  ++|.+  ++......      .-.+.++.|.|-.|..+.+.+-+.+....|-
T Consensus        55 ~~~i~~ai~~~~vvii~getGsGKTT--qlP~~--lle~g~~~------~g~I~~tQPRRlAArsvA~RvAeel~~~~G~  124 (845)
T COG1643          55 RDEILKAIEQNQVVIIVGETGSGKTT--QLPQF--LLEEGLGI------AGKIGCTQPRRLAARSVAERVAEELGEKLGE  124 (845)
T ss_pred             HHHHHHHHHhCCEEEEeCCCCCChHH--HHHHH--HHhhhccc------CCeEEecCchHHHHHHHHHHHHHHhCCCcCc
Confidence            34455566677789999999999999  66654  44443211      1247789999988888888777666543343


Q ss_pred             eEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccC-CcChH-HHHHHHHHHCC
Q 006737          486 GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL-DLGFR-KDVENIVDCLP  563 (633)
Q Consensus       486 ~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll-d~gf~-~~l~~Il~~lp  563 (633)
                      .|+.-+-.       .........|-++|.|.|+..+.++    ..|+.+++|||||||.-+ +.+|. ..+..++...+
T Consensus       125 ~VGY~iRf-------e~~~s~~Trik~mTdGiLlrei~~D----~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr  193 (845)
T COG1643         125 TVGYSIRF-------ESKVSPRTRIKVMTDGILLREIQND----PLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRR  193 (845)
T ss_pred             eeeEEEEe-------eccCCCCceeEEeccHHHHHHHhhC----cccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcC
Confidence            34322211       1112234689999999999999876    569999999999999654 44443 34455677777


Q ss_pred             CCCcEEEEeccCChh
Q 006737          564 RRRQSLLFSATMPKE  578 (633)
Q Consensus       564 k~~Q~IlfSATl~~e  578 (633)
                      .+..+|+||||+..+
T Consensus       194 ~DLKiIimSATld~~  208 (845)
T COG1643         194 DDLKLIIMSATLDAE  208 (845)
T ss_pred             CCceEEEEecccCHH
Confidence            789999999999988

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=99.14  E-value=1.3e-09  Score=126.51  Aligned_cols=135  Identities=24%  Similarity=0.305  Sum_probs=100.5

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      |+ .|...|+....-++.|++.-+.||||.|||.--++..   ++-...        +-+++||+||..|+.|+++.+..
T Consensus        80 G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~s---l~~a~k--------gkr~yii~PT~~Lv~Q~~~kl~~  147 (1187)
T COG1110          80 GF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMS---LYLAKK--------GKRVYIIVPTTTLVRQVYERLKK  147 (1187)
T ss_pred             CC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHH---HHHHhc--------CCeEEEEecCHHHHHHHHHHHHH
Confidence            44 8999999999999999999999999999997433322   222211        13699999999999999999999


Q ss_pred             HHhcCCCceEEE-EECCccchH---HHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCc
Q 006737          478 LLKNHDGIGVLT-LVGGTRFKV---DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL  549 (633)
Q Consensus       478 l~~~~~~i~v~~-l~Gg~~~~~---~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~  549 (633)
                      +.....+..+.+ +++..+.+.   ..+.+.++..||+|+|..-|...+..-.     --++++|++|.+|.++..
T Consensus       148 ~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~-----~~kFdfifVDDVDA~Lka  218 (1187)
T COG1110         148 FAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELS-----KLKFDFIFVDDVDAILKA  218 (1187)
T ss_pred             HHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhc-----ccCCCEEEEccHHHHHhc
Confidence            986654344444 555544333   3456777889999999888776654331     126789999999998853

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

Probab=99.12  E-value=3.1e-10  Score=134.49  Aligned_cols=85  Identities=26%  Similarity=0.384  Sum_probs=64.9

Q ss_pred             cCCCCCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      .|| ++++.|.+....    +..+..+++.|+||+|||++|++|++...  .          +.++||++||++|+.|+.
T Consensus       242 ~~~-e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~--~----------~~~vvI~t~T~~Lq~Ql~  308 (820)
T PRK07246        242 LGL-EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS--D----------QRQIIVSVPTKILQDQIM  308 (820)
T ss_pred             CCC-ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc--C----------CCcEEEEeCcHHHHHHHH
Confidence            355 688999885544    44578999999999999999999988653  1          246999999999999995


Q ss_pred             -HHHHHHHhcCCCceEEEEECCcc
Q 006737          473 -AEAIALLKNHDGIGVLTLVGGTR  495 (633)
Q Consensus       473 -~~l~~l~~~~~~i~v~~l~Gg~~  495 (633)
                       +.+..+.+.. ++.+.++.|+..
T Consensus       309 ~~~i~~l~~~~-~~~~~~~kg~~~  331 (820)
T PRK07246        309 AEEVKAIQEVF-HIDCHSLKGPQN  331 (820)
T ss_pred             HHHHHHHHHhc-CCcEEEEECCcc
Confidence             5666665543 677777777654

>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 [, ]

Probab=99.11  E-value=5.9e-10  Score=122.35  Aligned_cols=187  Identities=21%  Similarity=0.168  Sum_probs=114.7

Q ss_pred             CCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCc----eEEEEEC--------------CccchHHHHHHhcC--
Q 006737          447 SSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI----GVLTLVG--------------GTRFKVDQRRLESD--  506 (633)
Q Consensus       447 ~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i----~v~~l~G--------------g~~~~~~~~~l~~~--  506 (633)
                      ..++|+.++|+||||+|+|..|.++++.+..++.....+    +...-+|              ......+...+..+  
T Consensus        29 ~~RDQGftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~  108 (442)
T PF06862_consen   29 EFRDQGFTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNN  108 (442)
T ss_pred             hhhccCCCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCc
Confidence            456789999999999999999999999998887431000    0000011              00111122222221  


Q ss_pred             ----------------------CCcEEEECchhhHHHHhcc---cCcccccCCeeEEEEecccccC--CcChHHHHHHHH
Q 006737          507 ----------------------PCQILVATPGRLLDHIENK---SGLSVRLMGLKMLVLDEADHLL--DLGFRKDVENIV  559 (633)
Q Consensus       507 ----------------------~~dILIaTPgrLl~lL~~~---~~~~~~Ls~l~~LVIDEAD~Ll--d~gf~~~l~~Il  559 (633)
                                            .+|||||+|..|...+...   ....-.|++|+++|||.||.|+  +|.+...+...+
T Consensus       109 DD~FrlGik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~l  188 (442)
T PF06862_consen  109 DDCFRLGIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHL  188 (442)
T ss_pred             cceEEEeEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHh
Confidence                                  5799999999999999852   1222359999999999999887  455555555555


Q ss_pred             HHCCCC---------------------CcEEEEeccCChhhh-cc-------ccceEeeeccc---cccccCccceEEEe
Q 006737          560 DCLPRR---------------------RQSLLFSATMPKELV-LK-------REHTYIDTVGL---GSVETPVKVSKYNI  607 (633)
Q Consensus       560 ~~lpk~---------------------~Q~IlfSATl~~el~-l~-------~~~~~i~~~~~---~~~~~~~~V~q~~i  607 (633)
                      +..|++                     +|+|+||+..++++. +.       ...+.+.....   ........|+|.+.
T Consensus       189 N~~P~~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~  268 (442)
T PF06862_consen  189 NLQPKKSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQ  268 (442)
T ss_pred             ccCCCCCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEE
Confidence            555542                     899999999999852 11       11111111111   11234556777766


Q ss_pred             ehh------------------hHHHHh-hcCCceEEEEEccccCC
Q 006737          608 YVF------------------VLVLSI-KIQAFYIICFVYTISMY  633 (633)
Q Consensus       608 ~v~------------------~l~~~~-k~~~~~~LVFcnT~s~~  633 (633)
                      -+.                  ++-.+. ......+||||+|.-.|
T Consensus       269 r~~~~s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDf  313 (442)
T PF06862_consen  269 RFDCSSPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDF  313 (442)
T ss_pred             EecCCCcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhh
Confidence            421                  222222 34456899999997554

; GO: 0005634 nucleus

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

Probab=99.09  E-value=1.6e-09  Score=125.27  Aligned_cols=153  Identities=26%  Similarity=0.303  Sum_probs=115.9

Q ss_pred             CCCcHHHHHHHHHHhCC----CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG----KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g----rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      ..+++-|..++..|...    .-.++.+.||||||.+|+= ++...+..+.          +||||+|-++|..|+.+.|
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~-~i~~~L~~Gk----------qvLvLVPEI~Ltpq~~~rf  265 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLE-AIAKVLAQGK----------QVLVLVPEIALTPQLLARF  265 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHH-HHHHHHHcCC----------EEEEEeccccchHHHHHHH
Confidence            36788999999998765    5789999999999999864 5555555432          5999999999999999999


Q ss_pred             HHHHhcCCCceEEEEECCccchH---HHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC---c
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKV---DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD---L  549 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~---~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld---~  549 (633)
                      +..+    +.++.+++++.+...   .+.....+...|+|+|=..|          ...+.++.+|||||-|.-.-   .
T Consensus       266 ~~rF----g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAl----------F~Pf~~LGLIIvDEEHD~sYKq~~  331 (730)
T COG1198         266 KARF----GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSAL----------FLPFKNLGLIIVDEEHDSSYKQED  331 (730)
T ss_pred             HHHh----CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhh----------cCchhhccEEEEeccccccccCCc
Confidence            9998    467888888876544   45566678899999994333          35688999999999997652   1


Q ss_pred             C---hHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          550 G---FRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       550 g---f~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +   +..++-...... .++++|+-|||-+-+
T Consensus       332 ~prYhARdvA~~Ra~~-~~~pvvLgSATPSLE  362 (730)
T COG1198         332 GPRYHARDVAVLRAKK-ENAPVVLGSATPSLE  362 (730)
T ss_pred             CCCcCHHHHHHHHHHH-hCCCEEEecCCCCHH
Confidence            2   333333333333 478999999999877

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.06  E-value=1.5e-09  Score=127.07  Aligned_cols=157  Identities=21%  Similarity=0.239  Sum_probs=115.5

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHH--HHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAI--EAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       402 pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL--~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ....+...|.+|.+.+.++|+|.||+|||.  ++|.+  ......+        ..+.+|+..|.|-.|..+++++..--
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTT--QvpQfiLd~~~~~~--------~~~~IicTQPRRIsAIsvAeRVa~ER  243 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTT--QVPQFILDEAIESG--------AACNIICTQPRRISAISVAERVAKER  243 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchh--hhhHHHHHHHHhcC--------CCCeEEecCCchHHHHHHHHHHHHHh
Confidence            456788889999999999999999999998  56544  3322222        34568999999999988887775554


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccC-CcChHHHHHHH
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL-DLGFRKDVENI  558 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll-d~gf~~~l~~I  558 (633)
                      ....+-.|+.-.+..+.       ......+++||.|.|++.|...    ..+..+.+||+||+|.-. +.+|.-.+.+.
T Consensus       244 ~~~~g~~VGYqvrl~~~-------~s~~t~L~fcTtGvLLr~L~~~----~~l~~vthiivDEVHER~i~~DflLi~lk~  312 (924)
T KOG0920|consen  244 GESLGEEVGYQVRLESK-------RSRETRLLFCTTGVLLRRLQSD----PTLSGVTHIIVDEVHERSINTDFLLILLKD  312 (924)
T ss_pred             ccccCCeeeEEEeeecc-------cCCceeEEEecHHHHHHHhccC----cccccCceeeeeeEEEccCCcccHHHHHHH
Confidence            33334333332222111       1223689999999999999774    568899999999999765 55677777777


Q ss_pred             HHHCCCCCcEEEEeccCChhh
Q 006737          559 VDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~~el  579 (633)
                      +-..+++.++|+||||+..+.
T Consensus       313 lL~~~p~LkvILMSAT~dae~  333 (924)
T KOG0920|consen  313 LLPRNPDLKVILMSATLDAEL  333 (924)
T ss_pred             HhhhCCCceEEEeeeecchHH
Confidence            666678999999999999873

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.04  E-value=6.7e-10  Score=130.51  Aligned_cols=170  Identities=21%  Similarity=0.186  Sum_probs=108.6

Q ss_pred             CcHHHHHHHHHHhCC---C-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSACLEG---K-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       402 pt~iQ~~aIp~il~g---r-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ..+.|..++..++..   . .+++.||||+|||.+.+++++..+....       ....+++++.|++.++.++++.++.
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~~-------~~~~r~i~vlP~~t~ie~~~~r~~~  268 (733)
T COG1203         196 GYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKI-------KLKSRVIYVLPFRTIIEDMYRRAKE  268 (733)
T ss_pred             hhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhccc-------cccceEEEEccHHHHHHHHHHHHHh
Confidence            488898888887753   3 7889999999999999999887765521       1234799999999999999999998


Q ss_pred             HHhcCCCceEEEEECCccchHHHH-------------HHhcCCCcEEEECchhhHHHHhcccCccc-ccCCeeEEEEecc
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQR-------------RLESDPCQILVATPGRLLDHIENKSGLSV-RLMGLKMLVLDEA  543 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~-------------~l~~~~~dILIaTPgrLl~lL~~~~~~~~-~Ls~l~~LVIDEA  543 (633)
                      .+... .+.....+|.........             .....-..++++||-.+............ .+-...++|+||+
T Consensus       269 ~~~~~-~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~  347 (733)
T COG1203         269 IFGLF-SVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEV  347 (733)
T ss_pred             hhccc-ccccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccH
Confidence            87543 111111233322111100             01111235666676666553322221111 1113468999999


Q ss_pred             cccCCcChHHHHHHHHHHCC-CCCcEEEEeccCChhh
Q 006737          544 DHLLDLGFRKDVENIVDCLP-RRRQSLLFSATMPKEL  579 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSATl~~el  579 (633)
                      |.+.+......+..++..+. .+..+|++|||+|+.+
T Consensus       348 h~~~~~~~~~~l~~~i~~l~~~g~~ill~SATlP~~~  384 (733)
T COG1203         348 HLYADETMLAALLALLEALAEAGVPVLLMSATLPPFL  384 (733)
T ss_pred             HhhcccchHHHHHHHHHHHHhCCCCEEEEecCCCHHH
Confidence            99987644444445544443 3688999999999984

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=99.04  E-value=1.9e-09  Score=125.51  Aligned_cols=153  Identities=18%  Similarity=0.221  Sum_probs=95.9

Q ss_pred             CcHHHHHHHHHHh----C------CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          402 MTRVQEATLSACL----E------GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       402 pt~iQ~~aIp~il----~------grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      +...|..|+..+.    .      .+..+++.+||||||++.+.-+ ..+....        ..+++|||+|+.+|..|+
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la-~~l~~~~--------~~~~vl~lvdR~~L~~Q~  309 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAA-RKALELL--------KNPKVFFVVDRRELDYQL  309 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHH-HHHHhhc--------CCCeEEEEECcHHHHHHH
Confidence            6778888776643    2      2479999999999998765433 3333221        235799999999999999


Q ss_pred             HHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-cccccCCeeEEEEecccccCCcC
Q 006737          472 AAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-LSVRLMGLKMLVLDEADHLLDLG  550 (633)
Q Consensus       472 ~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-~~~~Ls~l~~LVIDEAD~Lld~g  550 (633)
                      .+.+..+....  +     .+..+...-...+......|+|+|...|...+..... ......++ +||+||||+.... 
T Consensus       310 ~~~f~~~~~~~--~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~-lvIvDEaHrs~~~-  380 (667)
T TIGR00348       310 MKEFQSLQKDC--A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEV-VVIFDEAHRSQYG-  380 (667)
T ss_pred             HHHHHhhCCCC--C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCE-EEEEEcCccccch-
Confidence            99998875311  0     1111112222334444468999999999864432110 00111122 8999999996533 


Q ss_pred             hHHHHHHHH-HHCCCCCcEEEEeccCC
Q 006737          551 FRKDVENIV-DCLPRRRQSLLFSATMP  576 (633)
Q Consensus       551 f~~~l~~Il-~~lpk~~Q~IlfSATl~  576 (633)
                         .+..++ ..+| +...++||||.-
T Consensus       381 ---~~~~~l~~~~p-~a~~lGfTaTP~  403 (667)
T TIGR00348       381 ---ELAKNLKKALK-NASFFGFTGTPI  403 (667)
T ss_pred             ---HHHHHHHhhCC-CCcEEEEeCCCc
Confidence               233333 3454 578999999984

Members of this family are assumed to differ from each other in DNA site specificity.

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

Probab=99.01  E-value=8.5e-09  Score=122.34  Aligned_cols=169  Identities=20%  Similarity=0.193  Sum_probs=125.8

Q ss_pred             cCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhC----C--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          384 CGISPLTIKALTA-AGYIQMTRVQEATLSACLE----G--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       384 l~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~----g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +..+......+.. ++| .-|+=|..||..+..    +  .|=|+||--|-|||.+.+=.++..+...           .
T Consensus       577 f~~d~~~q~~F~~~FPy-eET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~G-----------K  644 (1139)
T COG1197         577 FPPDTEWQEEFEASFPY-EETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMDG-----------K  644 (1139)
T ss_pred             CCCChHHHHHHHhcCCC-cCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcCC-----------C
Confidence            3344555555555 344 569999999999875    3  3899999999999998877777665443           4


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH---HHHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      +|.|||||--||.|-++.|++.++.+ .++|..+.-=.+.++   -.+.++.+..||||+|    ..+|...    +.++
T Consensus       645 QVAvLVPTTlLA~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT----HrLL~kd----v~Fk  715 (1139)
T COG1197         645 QVAVLVPTTLLAQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT----HRLLSKD----VKFK  715 (1139)
T ss_pred             eEEEEcccHHhHHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEec----hHhhCCC----cEEe
Confidence            69999999999999999999999877 577777655444333   3456777899999999    3455443    6789


Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ++.+|||||-|+..- ...+.+..+    ..+.-++-||||-=+-
T Consensus       716 dLGLlIIDEEqRFGV-k~KEkLK~L----r~~VDvLTLSATPIPR  755 (1139)
T COG1197         716 DLGLLIIDEEQRFGV-KHKEKLKEL----RANVDVLTLSATPIPR  755 (1139)
T ss_pred             cCCeEEEechhhcCc-cHHHHHHHH----hccCcEEEeeCCCCcc
Confidence            999999999999653 244444444    4566799999995433

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=99.00  E-value=1.3e-08  Score=114.38  Aligned_cols=149  Identities=22%  Similarity=0.213  Sum_probs=102.4

Q ss_pred             HHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCc
Q 006737          406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI  485 (633)
Q Consensus       406 Q~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i  485 (633)
                      -.+.+..+..++-+||.|.||||||.  ++|-+  +.+.+....     + ++.+..|.|-.|..+++++..-.....|-
T Consensus        56 r~~il~~ve~nqvlIviGeTGsGKST--QipQy--L~eaG~~~~-----g-~I~~TQPRRVAavslA~RVAeE~~~~lG~  125 (674)
T KOG0922|consen   56 RDQILYAVEDNQVLIVIGETGSGKST--QIPQY--LAEAGFASS-----G-KIACTQPRRVAAVSLAKRVAEEMGCQLGE  125 (674)
T ss_pred             HHHHHHHHHHCCEEEEEcCCCCCccc--cHhHH--HHhcccccC-----C-cEEeecCchHHHHHHHHHHHHHhCCCcCc
Confidence            35566677788899999999999998  78865  655543221     2 26799999999888887765554333233


Q ss_pred             eEEE--EECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHC-
Q 006737          486 GVLT--LVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCL-  562 (633)
Q Consensus       486 ~v~~--l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~l-  562 (633)
                      .|+.  -+.+..         .....|.++|.|.|++.+..+    ..|+..++|||||||.-.-  .-+.+..+++.+ 
T Consensus       126 ~VGY~IRFed~t---------s~~TrikymTDG~LLRE~l~D----p~LskYsvIIlDEAHERsl--~TDiLlGlLKki~  190 (674)
T KOG0922|consen  126 EVGYTIRFEDST---------SKDTRIKYMTDGMLLREILKD----PLLSKYSVIILDEAHERSL--HTDILLGLLKKIL  190 (674)
T ss_pred             eeeeEEEecccC---------CCceeEEEecchHHHHHHhcC----CccccccEEEEechhhhhh--HHHHHHHHHHHHH
Confidence            3332  222221         223689999999999988765    5689999999999997542  123333333322 


Q ss_pred             --CCCCcEEEEeccCChhh
Q 006737          563 --PRRRQSLLFSATMPKEL  579 (633)
Q Consensus       563 --pk~~Q~IlfSATl~~el  579 (633)
                        +++..+|++|||+..+.
T Consensus       191 ~~R~~LklIimSATlda~k  209 (674)
T KOG0922|consen  191 KKRPDLKLIIMSATLDAEK  209 (674)
T ss_pred             hcCCCceEEEEeeeecHHH
Confidence              24678999999999874

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

Probab=98.97  E-value=2.1e-09  Score=126.27  Aligned_cols=156  Identities=15%  Similarity=0.261  Sum_probs=122.2

Q ss_pred             CCCCcHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      |....++|.++++.+.+. .+|++++|+|||||.|.-+.++.    .        .+-.+++++.|..+.+..++..+.+
T Consensus      1141 f~~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----~--------~~~~~~vyi~p~~~i~~~~~~~w~~ 1208 (1674)
T KOG0951|consen 1141 FQDFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----P--------DTIGRAVYIAPLEEIADEQYRDWEK 1208 (1674)
T ss_pred             ccccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----C--------ccceEEEEecchHHHHHHHHHHHHH
Confidence            334589999999998775 57999999999999998887764    1        2235799999999999999999988


Q ss_pred             HHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcC------h
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG------F  551 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g------f  551 (633)
                      .+....|+.+..+.|......  +.+..  .+|||+||+++-.+ .       ....+++.|.||+|.+.+..      .
T Consensus      1209 ~f~~~~G~~~~~l~ge~s~~l--kl~~~--~~vii~tpe~~d~l-q-------~iQ~v~l~i~d~lh~igg~~g~v~evi 1276 (1674)
T KOG0951|consen 1209 KFSKLLGLRIVKLTGETSLDL--KLLQK--GQVIISTPEQWDLL-Q-------SIQQVDLFIVDELHLIGGVYGAVYEVI 1276 (1674)
T ss_pred             hhccccCceEEecCCccccch--HHhhh--cceEEechhHHHHH-h-------hhhhcceEeeehhhhhcccCCceEEEE
Confidence            888777888888888776542  22322  48999999998554 2       24578899999999998432      2


Q ss_pred             HHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          552 RKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       552 ~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      .. +..|-..+-++.+++++|..+++.-
T Consensus      1277 ~S-~r~ia~q~~k~ir~v~ls~~lana~ 1303 (1674)
T KOG0951|consen 1277 CS-MRYIASQLEKKIRVVALSSSLANAR 1303 (1674)
T ss_pred             ee-HHHHHHHHHhheeEEEeehhhccch
Confidence            23 6677777778899999999998873

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=98.91  E-value=1e-08  Score=107.86  Aligned_cols=73  Identities=19%  Similarity=0.164  Sum_probs=57.6

Q ss_pred             CCcHHHHH----HHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEA----TLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~----aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|+|.|.+    ++..+..|.++++.||||+|||++|++|++..+.......     .+.+++|+++|..+..|....++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~-----~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI-----QKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccc-----cccceeEEeccHHHHHHHHHHHH
Confidence            36999998    5555667899999999999999999999998766543210     12469999999999999877776


Q ss_pred             HH
Q 006737          477 AL  478 (633)
Q Consensus       477 ~l  478 (633)
                      ++
T Consensus        83 ~~   84 (289)
T smart00488       83 KL   84 (289)
T ss_pred             hc
Confidence            65

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=98.91  E-value=1e-08  Score=107.86  Aligned_cols=73  Identities=19%  Similarity=0.164  Sum_probs=57.6

Q ss_pred             CCcHHHHH----HHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEA----TLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~----aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|+|.|.+    ++..+..|.++++.||||+|||++|++|++..+.......     .+.+++|+++|..+..|....++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~~-----~~~kvi~~t~T~~~~~q~i~~l~   82 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPERI-----QKIKLIYLSRTVSEIEKRLEELR   82 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCcccc-----cccceeEEeccHHHHHHHHHHHH
Confidence            36999998    5555667899999999999999999999998766543210     12469999999999999877776


Q ss_pred             HH
Q 006737          477 AL  478 (633)
Q Consensus       477 ~l  478 (633)
                      ++
T Consensus        83 ~~   84 (289)
T smart00489       83 KL   84 (289)
T ss_pred             hc
Confidence            65

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

Probab=98.90  E-value=1.1e-08  Score=123.34  Aligned_cols=82  Identities=27%  Similarity=0.310  Sum_probs=59.8

Q ss_pred             CCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH--
Q 006737          401 QMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE--  474 (633)
Q Consensus       401 ~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~--  474 (633)
                      ++++-|.+.+..    +..++.+++.|+||+|||++|++|++.......          -++||-++|+.|..|+...  
T Consensus       257 e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~~~----------~~vvIsT~T~~LQ~Ql~~kDi  326 (928)
T PRK08074        257 EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKKKE----------EPVVISTYTIQLQQQLLEKDI  326 (928)
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhccC----------CeEEEEcCCHHHHHHHHHhhH
Confidence            789999886654    445789999999999999999999986543322          2599999999999998763  


Q ss_pred             --HHHHHhcCCCceEEEEECCc
Q 006737          475 --AIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       475 --l~~l~~~~~~i~v~~l~Gg~  494 (633)
                        +.+++..  .++++++.|..
T Consensus       327 P~L~~~~~~--~~~~~~lKGr~  346 (928)
T PRK08074        327 PLLQKIFPF--PVEAALLKGRS  346 (928)
T ss_pred             HHHHHHcCC--CceEEEEEccc
Confidence              3333321  35555555543

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=98.84  E-value=1.4e-08  Score=118.78  Aligned_cols=131  Identities=21%  Similarity=0.171  Sum_probs=99.1

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      -.|+++|.-.--.+..|+  |+.+.||.|||++..+|++-..+...           .|-|++||-.||.+-++.+..++
T Consensus        81 m~~ydVQliGg~~Lh~G~--iaEM~TGEGKTLvA~l~a~l~al~G~-----------~VhvvT~ndyLA~RD~e~m~~l~  147 (913)
T PRK13103         81 MRHFDVQLIGGMTLHEGK--IAEMRTGEGKTLVGTLAVYLNALSGK-----------GVHVVTVNDYLARRDANWMRPLY  147 (913)
T ss_pred             CCcchhHHHhhhHhccCc--cccccCCCCChHHHHHHHHHHHHcCC-----------CEEEEeCCHHHHHHHHHHHHHHh
Confidence            367888876655566664  88999999999999999986655432           48899999999999999999998


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      ..+ ++.|.++.++...........   |||+++|..-| .++|...-.   .......+.++||||+|.+|
T Consensus       148 ~~l-Gl~v~~i~~~~~~~err~~Y~---~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        148 EFL-GLSVGIVTPFQPPEEKRAAYA---ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             ccc-CCEEEEECCCCCHHHHHHHhc---CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            876 899999988876554433332   79999999886 344432210   01124788999999999887

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

Probab=98.78  E-value=2.7e-08  Score=93.67  Aligned_cols=135  Identities=21%  Similarity=0.274  Sum_probs=78.3

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCcc
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR  495 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~  495 (633)
                      |+=.++-..+|+|||--.+--++...+..          +.++|||.|||.++..+.+.++..     .+++..   ...
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~----------~~rvLvL~PTRvva~em~~aL~~~-----~~~~~t---~~~   65 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKR----------RLRVLVLAPTRVVAEEMYEALKGL-----PVRFHT---NAR   65 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHT----------T--EEEEESSHHHHHHHHHHTTTS-----SEEEES---TTS
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHc----------cCeEEEecccHHHHHHHHHHHhcC-----CcccCc---eee
Confidence            44467889999999987554454444333          247999999999999988776533     222221   000


Q ss_pred             chHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcC--hHHHHHHHHHHCCCCCcEEEEec
Q 006737          496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG--FRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       496 ~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g--f~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      ..     ...++.-|-|+|-..+...+.+.    ..+.+.++||+||+|..--..  +...+... ... ..+.+|++||
T Consensus        66 ~~-----~~~g~~~i~vMc~at~~~~~~~p----~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~-~~~-g~~~~i~mTA  134 (148)
T PF07652_consen   66 MR-----THFGSSIIDVMCHATYGHFLLNP----CRLKNYDVIIMDECHFTDPTSIAARGYLREL-AES-GEAKVIFMTA  134 (148)
T ss_dssp             S---------SSSSEEEEEHHHHHHHHHTS----SCTTS-SEEEECTTT--SHHHHHHHHHHHHH-HHT-TS-EEEEEES
T ss_pred             ec-----cccCCCcccccccHHHHHHhcCc----ccccCccEEEEeccccCCHHHHhhheeHHHh-hhc-cCeeEEEEeC
Confidence            00     11233467889999988877664    346789999999999964322  23333332 222 2467999999


Q ss_pred             cCChhh
Q 006737          574 TMPKEL  579 (633)
Q Consensus       574 Tl~~el  579 (633)
                      |-|-..
T Consensus       135 TPPG~~  140 (148)
T PF07652_consen  135 TPPGSE  140 (148)
T ss_dssp             S-TT--
T ss_pred             CCCCCC
Confidence            988653

The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.73  E-value=5.7e-08  Score=113.26  Aligned_cols=131  Identities=23%  Similarity=0.244  Sum_probs=100.8

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..|+++|.-..-.+..|+  |+...||+|||++..+|++...+...           .|-|++||--||.|=++.+..++
T Consensus        79 ~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~G~-----------~v~vvT~neyLA~Rd~e~~~~~~  145 (796)
T PRK12906         79 LRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALTGK-----------GVHVVTVNEYLSSRDATEMGELY  145 (796)
T ss_pred             CCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHcCC-----------CeEEEeccHHHHHhhHHHHHHHH
Confidence            378899988777777776  99999999999999999887665543           38899999999999999999999


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      ..+ ++.|+++.++..........   .|||+++|...| .++|...-.   .......+.+.||||||.+|
T Consensus       146 ~~L-Gl~vg~i~~~~~~~~r~~~y---~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        146 RWL-GLTVGLNLNSMSPDEKRAAY---NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             Hhc-CCeEEEeCCCCCHHHHHHHh---cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            877 89999999886655433333   379999999877 344433210   01224567899999999876

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=98.72  E-value=7.8e-08  Score=110.40  Aligned_cols=130  Identities=21%  Similarity=0.220  Sum_probs=100.5

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.-..-.++.|+  |+.+.||.|||++..+|++...+...           .|.|++|+-.||.+-++.+..++.
T Consensus        78 r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~G~-----------~VhvvT~NdyLA~RDae~m~~ly~  144 (764)
T PRK12326         78 RPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQGR-----------RVHVITVNDYLARRDAEWMGPLYE  144 (764)
T ss_pred             CcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHcCC-----------CeEEEcCCHHHHHHHHHHHHHHHH
Confidence            78999999998888885  78999999999999999986665442           388999999999999999999988


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .+ ++.|+++.++..........   .|||+++|..-| .++|...-.   .......+.+.||||+|.+|
T Consensus       145 ~L-GLsvg~i~~~~~~~err~aY---~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        145 AL-GLTVGWITEESTPEERRAAY---ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             hc-CCEEEEECCCCCHHHHHHHH---cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            76 89999998887655333333   379999998876 233322110   01234668899999999876

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

Probab=98.71  E-value=1.6e-07  Score=105.06  Aligned_cols=156  Identities=21%  Similarity=0.195  Sum_probs=102.8

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhc
Q 006737          402 MTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKN  481 (633)
Q Consensus       402 pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~  481 (633)
                      ..+.-.+.+.++..++-+||.|.||||||.  +||..  |...+...     .+.++=+..|.|-.|..+..++.+-..-
T Consensus       266 Vy~ykdell~av~e~QVLiI~GeTGSGKTT--QiPQy--L~EaGytk-----~gk~IgcTQPRRVAAmSVAaRVA~EMgv  336 (902)
T KOG0923|consen  266 VYPYKDELLKAVKEHQVLIIVGETGSGKTT--QIPQY--LYEAGYTK-----GGKKIGCTQPRRVAAMSVAARVAEEMGV  336 (902)
T ss_pred             chhhHHHHHHHHHhCcEEEEEcCCCCCccc--cccHH--HHhccccc-----CCceEeecCcchHHHHHHHHHHHHHhCc
Confidence            345556777788888899999999999998  88865  55554322     1334668999999998887665444321


Q ss_pred             CCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccC-CcC-hHHHHHHHH
Q 006737          482 HDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL-DLG-FRKDVENIV  559 (633)
Q Consensus       482 ~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll-d~g-f~~~l~~Il  559 (633)
                      ..|-.|+.     ++  ..+.......-|-++|.|.|++-+...    .+|.+.++|||||||.-- .-+ ....+..|.
T Consensus       337 kLG~eVGY-----sI--RFEdcTSekTvlKYMTDGmLlREfL~e----pdLasYSViiiDEAHERTL~TDILfgLvKDIa  405 (902)
T KOG0923|consen  337 KLGHEVGY-----SI--RFEDCTSEKTVLKYMTDGMLLREFLSE----PDLASYSVIIVDEAHERTLHTDILFGLVKDIA  405 (902)
T ss_pred             ccccccce-----EE--EeccccCcceeeeeecchhHHHHHhcc----ccccceeEEEeehhhhhhhhhhHHHHHHHHHH
Confidence            11111111     00  111112233568899999999877665    678999999999999643 221 222333333


Q ss_pred             HHCCCCCcEEEEeccCChh
Q 006737          560 DCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       560 ~~lpk~~Q~IlfSATl~~e  578 (633)
                       ...++..+++.|||+..+
T Consensus       406 -r~RpdLKllIsSAT~DAe  423 (902)
T KOG0923|consen  406 -RFRPDLKLLISSATMDAE  423 (902)
T ss_pred             -hhCCcceEEeeccccCHH
Confidence             344688999999999887

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

Probab=98.66  E-value=2.1e-07  Score=104.26  Aligned_cols=155  Identities=20%  Similarity=0.187  Sum_probs=102.7

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      +-.....+.+.+..|-.++-|||++.||||||.  +||.+  |+..+...     .++ +-+..|.|..|..++..+..-
T Consensus       354 ~LPvf~~R~~ll~~ir~n~vvvivgETGSGKTT--Ql~Qy--L~edGY~~-----~Gm-IGcTQPRRvAAiSVAkrVa~E  423 (1042)
T KOG0924|consen  354 YLPVFACRDQLLSVIRENQVVVIVGETGSGKTT--QLAQY--LYEDGYAD-----NGM-IGCTQPRRVAAISVAKRVAEE  423 (1042)
T ss_pred             hcchHHHHHHHHHHHhhCcEEEEEecCCCCchh--hhHHH--HHhccccc-----CCe-eeecCchHHHHHHHHHHHHHH
Confidence            334456677788888888899999999999998  66654  55554432     222 457889999999988777655


Q ss_pred             HhcCCCceEE--EEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          479 LKNHDGIGVL--TLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       479 ~~~~~~i~v~--~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      .....|-.|+  +-+.+         .......|-++|.|.|+.-.-..    ..|....+||+||||.-.-.  .+.+.
T Consensus       424 M~~~lG~~VGYsIRFEd---------vT~~~T~IkymTDGiLLrEsL~d----~~L~kYSviImDEAHERslN--tDilf  488 (1042)
T KOG0924|consen  424 MGVTLGDTVGYSIRFED---------VTSEDTKIKYMTDGILLRESLKD----RDLDKYSVIIMDEAHERSLN--TDILF  488 (1042)
T ss_pred             hCCccccccceEEEeee---------cCCCceeEEEeccchHHHHHhhh----hhhhheeEEEechhhhcccc--hHHHH
Confidence            4322222221  11111         12233578899999998755433    45889999999999965421  22333


Q ss_pred             HHHH---HCCCCCcEEEEeccCChh
Q 006737          557 NIVD---CLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       557 ~Il~---~lpk~~Q~IlfSATl~~e  578 (633)
                      .|+.   .-..+..+|++|||+...
T Consensus       489 Gllk~~larRrdlKliVtSATm~a~  513 (1042)
T KOG0924|consen  489 GLLKKVLARRRDLKLIVTSATMDAQ  513 (1042)
T ss_pred             HHHHHHHHhhccceEEEeeccccHH
Confidence            3333   223478999999999877

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=98.66  E-value=2.4e-07  Score=108.53  Aligned_cols=66  Identities=24%  Similarity=0.384  Sum_probs=51.4

Q ss_pred             CCCCCcHHHHHHHHHHh---CC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          398 GYIQMTRVQEATLSACL---EG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il---~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      || ++++-|.+.+..|.   ++      +.++|.|+||+|||++|++|++-.....+.          ++||-+.|+.|-
T Consensus        23 ~~-e~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~~k----------~vVIST~T~~LQ   91 (697)
T PRK11747         23 GF-IPRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAEKK----------KLVISTATVALQ   91 (697)
T ss_pred             CC-CcCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHcCC----------eEEEEcCCHHHH
Confidence            44 68899988665544   33      678999999999999999999865443322          599999999999


Q ss_pred             HHHHHH
Q 006737          469 SQIAAE  474 (633)
Q Consensus       469 ~Qi~~~  474 (633)
                      .|+...
T Consensus        92 eQL~~k   97 (697)
T PRK11747         92 EQLVSK   97 (697)
T ss_pred             HHHHhh
Confidence            998643

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

Probab=98.65  E-value=1.1e-07  Score=109.41  Aligned_cols=152  Identities=19%  Similarity=0.176  Sum_probs=101.4

Q ss_pred             CCcHHHHHHHHHH----hCCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSAC----LEGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~i----l~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .++..|..||..+    ..|+ -+|+++.||+|||... +.++..|.+....        -++|+|+-+++|+.|.+..+
T Consensus       165 ~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~~~~--------KRVLFLaDR~~Lv~QA~~af  235 (875)
T COG4096         165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWV--------KRVLFLADRNALVDQAYGAF  235 (875)
T ss_pred             cchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhcchh--------heeeEEechHHHHHHHHHHH
Confidence            5788998888654    4454 5999999999999763 4566667665432        26999999999999999888


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcc-c-CcccccCCeeEEEEecccccCCcChHH
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENK-S-GLSVRLMGLKMLVLDEADHLLDLGFRK  553 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~-~-~~~~~Ls~l~~LVIDEAD~Lld~gf~~  553 (633)
                      ..+.....  .+..+.+. ...        ..++|.|+|-..+...+... . ...+....+++|||||||+=.    ..
T Consensus       236 ~~~~P~~~--~~n~i~~~-~~~--------~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi----~~  300 (875)
T COG4096         236 EDFLPFGT--KMNKIEDK-KGD--------TSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGI----YS  300 (875)
T ss_pred             HHhCCCcc--ceeeeecc-cCC--------cceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhH----Hh
Confidence            87765332  22222221 111        13799999999998877654 1 112334458999999999843    33


Q ss_pred             HHHHHHHHCCCCCcEEEEeccCChh
Q 006737          554 DVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       554 ~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....|+.++..-  +++++||..+.
T Consensus       301 ~~~~I~dYFdA~--~~gLTATP~~~  323 (875)
T COG4096         301 EWSSILDYFDAA--TQGLTATPKET  323 (875)
T ss_pred             hhHHHHHHHHHH--HHhhccCcccc
Confidence            444666655322  33348887764

>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

Probab=98.64  E-value=1.1e-07  Score=98.62  Aligned_cols=151  Identities=17%  Similarity=0.196  Sum_probs=84.0

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      ..+.+|++-..|+|||+..+. ++..+........     .-.+|||+|. .+..|...++..++... .+++..+.|..
T Consensus        24 ~~~g~lL~de~GlGKT~~~i~-~~~~l~~~~~~~~-----~~~~LIv~P~-~l~~~W~~E~~~~~~~~-~~~v~~~~~~~   95 (299)
T PF00176_consen   24 PPRGGLLADEMGLGKTITAIA-LISYLKNEFPQRG-----EKKTLIVVPS-SLLSQWKEEIEKWFDPD-SLRVIIYDGDS   95 (299)
T ss_dssp             TT-EEEE---TTSSHHHHHHH-HHHHHHHCCTTSS------S-EEEEE-T-TTHHHHHHHHHHHSGT--TS-EEEESSSC
T ss_pred             CCCCEEEEECCCCCchhhhhh-hhhhhhhcccccc-----ccceeEeecc-chhhhhhhhhccccccc-ccccccccccc
Confidence            346799999999999987554 3334433322110     0138999999 88899999999887432 45666666665


Q ss_pred             cchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          495 RFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ....... ......+|+|+|...+...........+.-....+|||||+|.+-+.  .......+..+. ....+++|||
T Consensus        96 ~~~~~~~-~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~--~s~~~~~l~~l~-~~~~~lLSgT  171 (299)
T PF00176_consen   96 ERRRLSK-NQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNK--DSKRYKALRKLR-ARYRWLLSGT  171 (299)
T ss_dssp             HHHHTTS-SSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTT--TSHHHHHHHCCC-ECEEEEE-SS
T ss_pred             ccccccc-cccccceeeeccccccccccccccccccccccceeEEEecccccccc--cccccccccccc-cceEEeeccc
Confidence            1111111 11234689999999988111000000111234889999999999432  333334444454 5678899999


Q ss_pred             CCh
Q 006737          575 MPK  577 (633)
Q Consensus       575 l~~  577 (633)
                      .-.
T Consensus       172 P~~  174 (299)
T PF00176_consen  172 PIQ  174 (299)
T ss_dssp             -SS
T ss_pred             ccc
Confidence            543

g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.

>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

Probab=98.61  E-value=4.8e-07  Score=93.98  Aligned_cols=132  Identities=22%  Similarity=0.255  Sum_probs=95.1

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      -..|+++|.-++=.+..|+  |+...||-|||++..+|+.-..+..           ..|=|++..-.||..=++.+..+
T Consensus        75 g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~G-----------~~V~vvT~NdyLA~RD~~~~~~~  141 (266)
T PF07517_consen   75 GLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQG-----------KGVHVVTSNDYLAKRDAEEMRPF  141 (266)
T ss_dssp             S----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTTS-----------S-EEEEESSHHHHHHHHHHHHHH
T ss_pred             CCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHhc-----------CCcEEEeccHHHhhccHHHHHHH
Confidence            3479999999988887776  9999999999999888876554433           23889999999999999999999


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhH-HHHhcccCc---ccccCCeeEEEEecccccC
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLL-DHIENKSGL---SVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl-~lL~~~~~~---~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      +..+ ++.+.+++++...........   ++|+++|...|. ++|...-..   ......+.++||||||.++
T Consensus       142 y~~L-Glsv~~~~~~~~~~~r~~~Y~---~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  142 YEFL-GLSVGIITSDMSSEERREAYA---ADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             HHHT-T--EEEEETTTEHHHHHHHHH---SSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             HHHh-hhccccCccccCHHHHHHHHh---CcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            8876 999999999887544333332   689999999884 445432111   1124678999999999876

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=98.55  E-value=4.3e-07  Score=106.16  Aligned_cols=129  Identities=23%  Similarity=0.237  Sum_probs=97.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.-.--++..|+  |+.+.||-|||+++.+|+.-..+...           .|-||+++-.||..=++.+..+..
T Consensus        85 r~ydVQliGgl~Lh~G~--IAEM~TGEGKTL~atlpaylnAL~Gk-----------gVhVVTvNdYLA~RDae~m~~vy~  151 (939)
T PRK12902         85 RHFDVQLIGGMVLHEGQ--IAEMKTGEGKTLVATLPSYLNALTGK-----------GVHVVTVNDYLARRDAEWMGQVHR  151 (939)
T ss_pred             CcchhHHHhhhhhcCCc--eeeecCCCChhHHHHHHHHHHhhcCC-----------CeEEEeCCHHHHHhHHHHHHHHHH
Confidence            67788877666666664  89999999999999999875544432           388999999999998888888887


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-----HHHHhcccCcccccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-----LDHIENKSGLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-----l~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .+ |+.|+++.++........   ...|||+++|+..|     .+.+..... ......+.+.||||||.+|
T Consensus       152 ~L-GLtvg~i~~~~~~~err~---aY~~DItYgTn~e~gFDYLRDnm~~~~~-~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        152 FL-GLSVGLIQQDMSPEERKK---NYACDITYATNSELGFDYLRDNMATDIS-EVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             Hh-CCeEEEECCCCChHHHHH---hcCCCeEEecCCcccccchhhhhccccc-ccccCccceEEEeccccee
Confidence            76 999999887765443222   23589999999988     454433211 1235778899999999876

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=98.54  E-value=3.7e-07  Score=106.69  Aligned_cols=133  Identities=21%  Similarity=0.179  Sum_probs=96.3

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|. .|+++|.-..=++..  .-|+.+.||.|||+++.+|+.-..+..           ..|-||+++..||.+-++.+.
T Consensus        73 lG~-r~ydvQlig~l~L~~--G~IaEm~TGEGKTL~a~l~ayl~aL~G-----------~~VhVvT~NdyLA~RD~e~m~  138 (870)
T CHL00122         73 LGL-RHFDVQLIGGLVLND--GKIAEMKTGEGKTLVATLPAYLNALTG-----------KGVHIVTVNDYLAKRDQEWMG  138 (870)
T ss_pred             hCC-CCCchHhhhhHhhcC--CccccccCCCCchHHHHHHHHHHHhcC-----------CceEEEeCCHHHHHHHHHHHH
Confidence            354 478888776555544  469999999999999999996433322           238899999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhH-HHHhcccC---cccccCCeeEEEEecccccC
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLL-DHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl-~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .+...+ |+.|+++.++.+........   .|||+++|..-|- ++|...-.   .......+.+.||||||.+|
T Consensus       139 pvy~~L-GLsvg~i~~~~~~~err~aY---~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        139 QIYRFL-GLTVGLIQEGMSSEERKKNY---LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             HHHHHc-CCceeeeCCCCChHHHHHhc---CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            998877 89999988877755433332   3799999997552 33322210   01235678899999999876

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=98.52  E-value=1.3e-06  Score=105.24  Aligned_cols=156  Identities=13%  Similarity=0.190  Sum_probs=103.7

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .+.++|...+..++    +|.+.|++-..|.|||+.. +.++..+......      .+ .+|||||. .+..+..+++.
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~~~------~g-p~LIVvP~-SlL~nW~~Ei~  239 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYRGI------TG-PHMVVAPK-STLGNWMNEIR  239 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhcCC------CC-CEEEEeCh-HHHHHHHHHHH
Confidence            68899999988765    5778999999999999864 3344444332111      11 37999996 66677888888


Q ss_pred             HHHhcCCCceEEEEECCccchHHH--HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQ--RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~--~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                      +++   +.+.+..++|........  ..+.....+|+|+|.+.+......     +.--...+|||||||+|-+.  ...
T Consensus       240 kw~---p~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~-----L~k~~W~~VIvDEAHrIKN~--~Sk  309 (1033)
T PLN03142        240 RFC---PVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTA-----LKRFSWRYIIIDEAHRIKNE--NSL  309 (1033)
T ss_pred             HHC---CCCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHH-----hccCCCCEEEEcCccccCCH--HHH
Confidence            775   467788888765432221  122334579999999888654321     11224679999999998653  334


Q ss_pred             HHHHHHHCCCCCcEEEEeccCC
Q 006737          555 VENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      +..++..+.. ...+++|+|.-
T Consensus       310 lskalr~L~a-~~RLLLTGTPl  330 (1033)
T PLN03142        310 LSKTMRLFST-NYRLLITGTPL  330 (1033)
T ss_pred             HHHHHHHhhc-CcEEEEecCCC
Confidence            4555555543 34678899964

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.50  E-value=2e-06  Score=99.98  Aligned_cols=131  Identities=15%  Similarity=0.099  Sum_probs=92.8

Q ss_pred             cCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH---HH
Q 006737          424 KTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQ  500 (633)
Q Consensus       424 pTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~  500 (633)
                      .+|||||.+|+-. +...+..+.          ++|||+|...|+.|+...++..+.   +..+..++++.+...   .+
T Consensus       168 ~~GSGKTevyl~~-i~~~l~~Gk----------~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~w  233 (665)
T PRK14873        168 LPGEDWARRLAAA-AAATLRAGR----------GALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRRW  233 (665)
T ss_pred             CCCCcHHHHHHHH-HHHHHHcCC----------eEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHHH
Confidence            3599999998754 444444322          599999999999999999998873   256788888876554   33


Q ss_pred             HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC---cC---hHHHHHHHHHHCCCCCcEEEEecc
Q 006737          501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD---LG---FRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       501 ~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld---~g---f~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ..+..+...|||+|-..+          ...+.++.+|||||-|.-.-   .+   +..++-..... ..+..+|+-|||
T Consensus       234 ~~~~~G~~~IViGtRSAv----------FaP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~-~~~~~lvLgSaT  302 (665)
T PRK14873        234 LAVLRGQARVVVGTRSAV----------FAPVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAH-QHGCALLIGGHA  302 (665)
T ss_pred             HHHhCCCCcEEEEcceeE----------EeccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHH-HcCCcEEEECCC
Confidence            455667789999995443          35688999999999996541   11   22233333333 247889999999


Q ss_pred             CChhh
Q 006737          575 MPKEL  579 (633)
Q Consensus       575 l~~el  579 (633)
                      -+-+.
T Consensus       303 PSles  307 (665)
T PRK14873        303 RTAEA  307 (665)
T ss_pred             CCHHH
Confidence            88774

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

Probab=98.47  E-value=3.7e-07  Score=106.22  Aligned_cols=73  Identities=29%  Similarity=0.378  Sum_probs=59.4

Q ss_pred             HcCCCCCcHHHHHHHHHH----hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          396 AAGYIQMTRVQEATLSAC----LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       396 ~~g~~~pt~iQ~~aIp~i----l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      .+....+++.|.+++..+    .+++.+++.||||+|||++|++|++.......          .+++|.++|+.|..|+
T Consensus        10 ~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~----------~~viist~t~~lq~q~   79 (654)
T COG1199          10 AFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG----------KKVIISTRTKALQEQL   79 (654)
T ss_pred             hCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC----------CcEEEECCCHHHHHHH
Confidence            355668999999888553    44667999999999999999999998765543          2599999999999999


Q ss_pred             HHHHHHH
Q 006737          472 AAEAIAL  478 (633)
Q Consensus       472 ~~~l~~l  478 (633)
                      .+....+
T Consensus        80 ~~~~~~~   86 (654)
T COG1199          80 LEEDLPI   86 (654)
T ss_pred             HHhhcch
Confidence            8876654

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.40  E-value=2.9e-06  Score=101.72  Aligned_cols=159  Identities=17%  Similarity=0.136  Sum_probs=94.2

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .|.|+|..++-.++..  .-+|+.-..|.|||.-..+-+-..+.....         -++|||||+ .|+.|...++.+.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g~~---------~rvLIVvP~-sL~~QW~~El~~k  221 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTGRA---------ERVLILVPE-TLQHQWLVEMLRR  221 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcCCC---------CcEEEEcCH-HHHHHHHHHHHHH
Confidence            5899999998776543  368999999999998765544333332211         149999998 8999998888766


Q ss_pred             HhcCCCceEEEEECCccchHHHH--HHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCc-C-hHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQR--RLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G-FRKD  554 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~--~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~-g-f~~~  554 (633)
                      +    ++.+.++.++........  ... ...+++|+|.+.|...-....  .+.-...++|||||||++-.. + -...
T Consensus       222 F----~l~~~i~~~~~~~~~~~~~~~pf-~~~~~vI~S~~~l~~~~~~~~--~l~~~~wdlvIvDEAH~lk~~~~~~s~~  294 (956)
T PRK04914        222 F----NLRFSLFDEERYAEAQHDADNPF-ETEQLVICSLDFLRRNKQRLE--QALAAEWDLLVVDEAHHLVWSEEAPSRE  294 (956)
T ss_pred             h----CCCeEEEcCcchhhhcccccCcc-ccCcEEEEEHHHhhhCHHHHH--HHhhcCCCEEEEechhhhccCCCCcCHH
Confidence            5    344444433321110000  000 125799999876653110000  011236789999999998621 1 1112


Q ss_pred             HHHHHHHCCCCCcEEEEeccCC
Q 006737          555 VENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      +..+.....+...++++|||--
T Consensus       295 y~~v~~La~~~~~~LLLTATP~  316 (956)
T PRK04914        295 YQVVEQLAEVIPGVLLLTATPE  316 (956)
T ss_pred             HHHHHHHhhccCCEEEEEcCcc
Confidence            2222222223456899999964

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

Probab=98.39  E-value=2.7e-06  Score=101.08  Aligned_cols=148  Identities=19%  Similarity=0.274  Sum_probs=87.2

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH-----HHHhc-CCC--ceEE
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI-----ALLKN-HDG--IGVL  488 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~-----~l~~~-~~~--i~v~  488 (633)
                      .++.+.++||+|||.+|+-.++......+         ..+.||+||+.+.-..+.+.+.     ..+.. +.+  +...
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~---------~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~  130 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYG---------LFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELY  130 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcC---------CcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEE
Confidence            47999999999999999877765433322         2369999999998887775554     22221 122  3333


Q ss_pred             EEECCc-------cchHHHHHHhc------CCCcEEEECchhhHHHHh-cc-------cCcccc---cCCe-eEEEEecc
Q 006737          489 TLVGGT-------RFKVDQRRLES------DPCQILVATPGRLLDHIE-NK-------SGLSVR---LMGL-KMLVLDEA  543 (633)
Q Consensus       489 ~l~Gg~-------~~~~~~~~l~~------~~~dILIaTPgrLl~lL~-~~-------~~~~~~---Ls~l-~~LVIDEA  543 (633)
                      .+.++.       .+......+..      +.++|+|+|-+.|..-.. +.       .+....   +... -+|||||.
T Consensus       131 ~~~S~k~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEP  210 (986)
T PRK15483        131 VINAGDKKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEP  210 (986)
T ss_pred             EEecCcccccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECC
Confidence            444332       11223233322      247999999888854211 00       000011   1222 27999999


Q ss_pred             cccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          544 DHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      |++...  ...+..| ..+++.+ ++.||||.+.
T Consensus       211 h~~~~~--~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        211 HRFPRD--NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             CCCCcc--hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            998642  2233444 5555444 6779999987

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

Probab=98.37  E-value=3.7e-06  Score=91.70  Aligned_cols=177  Identities=20%  Similarity=0.152  Sum_probs=109.7

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHH--HHHHhcCCCCCCCCCC
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE--AVLKATSSSTTQLVPP  455 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~--~l~~~~~~~~~~~~~~  455 (633)
                      ...|...+.++.-.+.|++.---.....+.+-+..+.+++-+++++.||||||.  ++|..-  ..+...          
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKtt--QiPq~~~~~~~~~~----------   91 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTT--QIPQFVLEYELSHL----------   91 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCccc--cCcHHHHHHHHhhc----------
Confidence            456888889999888887753323344455666777888999999999999998  555432  221111          


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      ..+....|.|-.|.++..++-.-.    ++..+.-+|-.- .  .+.-.....-+-+||.+.|++-..+.    ..+...
T Consensus        92 ~~v~CTQprrvaamsva~RVadEM----Dv~lG~EVGysI-r--fEdC~~~~T~Lky~tDgmLlrEams~----p~l~~y  160 (699)
T KOG0925|consen   92 TGVACTQPRRVAAMSVAQRVADEM----DVTLGEEVGYSI-R--FEDCTSPNTLLKYCTDGMLLREAMSD----PLLGRY  160 (699)
T ss_pred             cceeecCchHHHHHHHHHHHHHHh----ccccchhccccc-c--ccccCChhHHHHHhcchHHHHHHhhC----cccccc
Confidence            137889999999999877665443    333322222111 0  00000111122356777776655443    458899


Q ss_pred             eEEEEecccccCC-cC-hHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          536 KMLVLDEADHLLD-LG-FRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       536 ~~LVIDEAD~Lld-~g-f~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+||+||||.-.- .+ ..-.+..++..- ++..+|++|||+-..
T Consensus       161 ~viiLDeahERtlATDiLmGllk~v~~~r-pdLk~vvmSatl~a~  204 (699)
T KOG0925|consen  161 GVIILDEAHERTLATDILMGLLKEVVRNR-PDLKLVVMSATLDAE  204 (699)
T ss_pred             cEEEechhhhhhHHHHHHHHHHHHHHhhC-CCceEEEeecccchH
Confidence            9999999996431 11 222333444333 489999999999776

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.28  E-value=3.3e-06  Score=99.38  Aligned_cols=75  Identities=19%  Similarity=0.224  Sum_probs=59.9

Q ss_pred             cCCCCCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      +-|..++|.|.+.+..    +..+.++++.||||+|||++.+.|+|..+.....        .++++|.+.|..-..|+.
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~~--------~~kIiy~sRThsQl~q~i   77 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKPE--------VRKIIYASRTHSQLEQAT   77 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhccc--------cccEEEEcccchHHHHHH
Confidence            3466779999887655    4568899999999999999999999987654321        246899999999999999


Q ss_pred             HHHHHHH
Q 006737          473 AEAIALL  479 (633)
Q Consensus       473 ~~l~~l~  479 (633)
                      ++++++.
T Consensus        78 ~Elk~~~   84 (705)
T TIGR00604        78 EELRKLM   84 (705)
T ss_pred             HHHHhhh
Confidence            9988853

All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.21  E-value=5.2e-06  Score=98.66  Aligned_cols=168  Identities=23%  Similarity=0.190  Sum_probs=101.3

Q ss_pred             CCcHHHHHHHHHHhC--------CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          401 QMTRVQEATLSACLE--------GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~--------grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      .-..+|-.|+..+..        |-=+|-.|.||+|||++=.= |+..+...        ..++|..|-.-.|.|..|.-
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNAR-ImyaLsd~--------~~g~RfsiALGLRTLTLQTG  478 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANAR-AMYALRDD--------KQGARFAIALGLRSLTLQTG  478 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHH-HHHHhCCC--------CCCceEEEEccccceeccch
Confidence            346788888887665        11255669999999997432 22223222        23467778888888888888


Q ss_pred             HHHHHHHhcCCCceEEEEECCccchHHHH----HH---------------------------------------hc----
Q 006737          473 AEAIALLKNHDGIGVLTLVGGTRFKVDQR----RL---------------------------------------ES----  505 (633)
Q Consensus       473 ~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~----~l---------------------------------------~~----  505 (633)
                      ..+++.+.- ..-..++++|+.....-.+    ..                                       ..    
T Consensus       479 da~r~rL~L-~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~  557 (1110)
T TIGR02562       479 HALKTRLNL-SDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKE  557 (1110)
T ss_pred             HHHHHhcCC-CccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhh
Confidence            888776532 2334555666543222110    00                                       00    


Q ss_pred             ---CCCcEEEECchhhHHHHhcc--cCcccccCC--eeEEEEecccccCCcChHHHHHHHHHHCC-CCCcEEEEeccCCh
Q 006737          506 ---DPCQILVATPGRLLDHIENK--SGLSVRLMG--LKMLVLDEADHLLDLGFRKDVENIVDCLP-RRRQSLLFSATMPK  577 (633)
Q Consensus       506 ---~~~dILIaTPgrLl~lL~~~--~~~~~~Ls~--l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSATl~~  577 (633)
                         -...|+|||+..++......  +.....+-.  =+.|||||+|.+-.. ....+..++..+. -...+|++|||+|+
T Consensus       558 ~rll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~-~~~~L~rlL~w~~~lG~~VlLmSATLP~  636 (1110)
T TIGR02562       558 KTLLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPE-DLPALLRLVQLAGLLGSRVLLSSATLPP  636 (1110)
T ss_pred             hhhhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHH-HHHHHHHHHHHHHHcCCCEEEEeCCCCH
Confidence               03579999999998876322  111111111  257999999997643 3334445544322 26889999999999


Q ss_pred             hh
Q 006737          578 EL  579 (633)
Q Consensus       578 el  579 (633)
                      .+
T Consensus       637 ~l  638 (1110)
T TIGR02562       637 AL  638 (1110)
T ss_pred             HH
Confidence            84

The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.

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

Probab=98.05  E-value=2.2e-05  Score=77.80  Aligned_cols=74  Identities=16%  Similarity=0.308  Sum_probs=49.3

Q ss_pred             CCcHHHHHHHHHHhCCCc-EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEGKD-AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grD-vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ++++-|..|+..+++... .+|.||.|||||.+ +..++..+.....  ......+.++||++|+...+.++.+.+.+
T Consensus         1 ~ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~-l~~~i~~~~~~~~--~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    1 KLNESQREAIQSALSSNGITLIQGPPGTGKTTT-LASIIAQLLQRFK--SRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             ---HHHHHHHHHHCTSSE-EEEE-STTSSHHHH-HHHHHHHH---------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcCCCCEEEECCCCCChHHH-HHHHHHHhccchh--hhhhhccccceeecCCchhHHHHHHHHHh
Confidence            367899999999999998 99999999999954 3334444421000  00011234699999999999999988877

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=98.00  E-value=7.3e-06  Score=90.61  Aligned_cols=230  Identities=8%  Similarity=-0.018  Sum_probs=141.5

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          392 KALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       392 ~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      ..+..+.......+|..+|..+..|+++++.-.|.+||.+||.+.....+......         ..+++.||.+++...
T Consensus       277 ~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~~s---------~~~~~~~~~~~~~~~  347 (1034)
T KOG4150|consen  277 SLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCHAT---------NSLLPSEMVEHLRNG  347 (1034)
T ss_pred             HHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCccc---------ceecchhHHHHhhcc
Confidence            34445666778899999999999999999999999999999999887665544321         268999999998765


Q ss_pred             HHHHHHHHhcCCCce--EEEEECCccchHHHHHHhcCCCcEEEECchhhHHHH-hcccCcccccCCeeEEEEecccccCC
Q 006737          472 AAEAIALLKNHDGIG--VLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHI-ENKSGLSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       472 ~~~l~~l~~~~~~i~--v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL-~~~~~~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      .+-+.-.....+..+  ++-.+.+.. ......++..+.++|++.|..+...+ .+...+...+-.+.++++||+|..+.
T Consensus       348 ~~~~~V~~~~I~~~K~A~V~~~D~~s-E~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~  426 (1034)
T KOG4150|consen  348 SKGQVVHVEVIKARKSAYVEMSDKLS-ETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLF  426 (1034)
T ss_pred             CCceEEEEEehhhhhcceeecccCCC-chhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeec
Confidence            432221111111111  111222222 33455566667899999998776543 33333344455678899999998764


Q ss_pred             cC---hHHHHHHHHHHC-----CCCCcEEEEeccCChhhhccccceEee-eccccccccCccceEEEeehh---------
Q 006737          549 LG---FRKDVENIVDCL-----PRRRQSLLFSATMPKELVLKREHTYID-TVGLGSVETPVKVSKYNIYVF---------  610 (633)
Q Consensus       549 ~g---f~~~l~~Il~~l-----pk~~Q~IlfSATl~~el~l~~~~~~i~-~~~~~~~~~~~~V~q~~i~v~---------  610 (633)
                      .-   -..++..++..+     +.+.|++-.|||+-..+.+..+---++ ..-+.....|..-++++++-+         
T Consensus       427 ~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs~~K~~V~WNP~~~P~~~~~  506 (1034)
T KOG4150|consen  427 PTKALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPSSEKLFVLWNPSAPPTSKSE  506 (1034)
T ss_pred             chhhHHHHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCCccceEEEeCCCCCCcchhh
Confidence            31   233444444433     246899999999987754432211111 001112345555666655432         


Q ss_pred             ---------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ---------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ---------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                               -+......++.++|.||+++.
T Consensus       507 ~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~  536 (1034)
T KOG4150|consen  507 KSSKVVEVSHLFAEMVQHGLRCIAFCPSRK  536 (1034)
T ss_pred             hhhHHHHHHHHHHHHHHcCCcEEEeccHHH
Confidence                     222334566779999999753

>COG4889 Predicted helicase [General function prediction only]

Probab=97.99  E-value=1.8e-05  Score=91.16  Aligned_cols=139  Identities=20%  Similarity=0.208  Sum_probs=90.4

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCC-----CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          391 IKALTAAGYIQMTRVQEATLSACLEG-----KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       391 l~~L~~~g~~~pt~iQ~~aIp~il~g-----rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      ..+|.-..-.+|+|+|+.||...+.|     +--| .+..|+|||+.. |-+.+.+..            .++|+|+|+.
T Consensus       151 ~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkL-IMAcGTGKTfTs-LkisEala~------------~~iL~LvPSI  216 (1518)
T COG4889         151 QDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKL-IMACGTGKTFTS-LKISEALAA------------ARILFLVPSI  216 (1518)
T ss_pred             ccccccCCCCCCChhHHHHHHHHHhhcccccCCcE-EEecCCCccchH-HHHHHHHhh------------hheEeecchH
Confidence            33333345568999999999998865     2223 344699999875 445565544            2599999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH------------------------HHHhcCCCcEEEECchhhHHH
Q 006737          466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ------------------------RRLESDPCQILVATPGRLLDH  521 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~------------------------~~l~~~~~dILIaTPgrLl~l  521 (633)
                      .|..|..++...-..  ..++...++++.......                        ..-+..+--||++|...|...
T Consensus       217 sLLsQTlrew~~~~~--l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i  294 (1518)
T COG4889         217 SLLSQTLREWTAQKE--LDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRI  294 (1518)
T ss_pred             HHHHHHHHHHhhccC--ccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHH
Confidence            999998877655421  145555554443322111                        111223456899999888765


Q ss_pred             HhcccCcccccCCeeEEEEecccccCC
Q 006737          522 IENKSGLSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       522 L~~~~~~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      -+..   ..-+..+++||.||||+-..
T Consensus       295 ~eAQ---e~G~~~fDliicDEAHRTtG  318 (1518)
T COG4889         295 KEAQ---EAGLDEFDLIICDEAHRTTG  318 (1518)
T ss_pred             HHHH---HcCCCCccEEEecchhcccc
Confidence            5433   23477899999999998653

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=97.95  E-value=5.9e-05  Score=88.47  Aligned_cols=132  Identities=23%  Similarity=0.236  Sum_probs=94.3

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      |. .|+++|.-.--.+..|+  |+.+.||-|||++..||+.-..+...           .|-||+..--||..=.+.+..
T Consensus        76 G~-r~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~Gk-----------gVhVVTvNdYLA~RDae~mg~  141 (925)
T PRK12903         76 GK-RPYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALTGK-----------GVIVSTVNEYLAERDAEEMGK  141 (925)
T ss_pred             CC-CcCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhcCC-----------ceEEEecchhhhhhhHHHHHH
Confidence            44 78888987776777774  79999999999999999864443332           277888888999877777777


Q ss_pred             HHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      +..++ |+.|+++..+..........   .|||+++|..-| .++|...-.   .......+.+.||||+|.+|
T Consensus       142 vy~fL-GLsvG~i~~~~~~~~rr~aY---~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        142 VFNFL-GLSVGINKANMDPNLKREAY---ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             HHHHh-CCceeeeCCCCChHHHHHhc---cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            77665 89999888766544333322   489999998876 345543210   01225678899999999876

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

Probab=97.93  E-value=7.2e-05  Score=90.61  Aligned_cols=141  Identities=16%  Similarity=0.161  Sum_probs=89.6

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccc
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF  496 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~  496 (633)
                      +.-+|+--||||||+.... +...+... .       ..+.+|+|+-.++|-.|+.+.+..+......  ..   ...+.
T Consensus       274 ~~G~IWHtqGSGKTlTm~~-~A~~l~~~-~-------~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~--~~---~~~s~  339 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFK-LARLLLEL-P-------KNPKVLFVVDRKDLDDQTSDEFQSFGKVAFN--DP---KAEST  339 (962)
T ss_pred             CceEEEeecCCchHHHHHH-HHHHHHhc-c-------CCCeEEEEechHHHHHHHHHHHHHHHHhhhh--cc---cccCH
Confidence            4589999999999997443 22333333 1       2357999999999999999999988653311  11   22333


Q ss_pred             hHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       497 ~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      ..-.+.+....-.|||+|-..|...+.........-.++ +||+||||+--   ++..-..+...++ +...++||.|--
T Consensus       340 ~~Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~i-vvI~DEaHRSQ---~G~~~~~~~~~~~-~a~~~gFTGTPi  414 (962)
T COG0610         340 SELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNV-VVIIDEAHRSQ---YGELAKLLKKALK-KAIFIGFTGTPI  414 (962)
T ss_pred             HHHHHHHhcCCCcEEEEEecccchhhhcccccccCCCcE-EEEEechhhcc---ccHHHHHHHHHhc-cceEEEeeCCcc
Confidence            333445554445899999999988875541111112222 78999999943   2333333344444 377999998863

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=97.90  E-value=1.6e-05  Score=87.07  Aligned_cols=153  Identities=17%  Similarity=0.158  Sum_probs=101.8

Q ss_pred             CCCcHHHHHHHHHHhCC---CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG---KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g---rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ..++|+|..++..++.+   ++-||+.|.|+|||++-+-.+. .+.             -.+|||+.+--.+.|...++.
T Consensus       301 t~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~-tik-------------K~clvLcts~VSVeQWkqQfk  366 (776)
T KOG1123|consen  301 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAAC-TIK-------------KSCLVLCTSAVSVEQWKQQFK  366 (776)
T ss_pred             cccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeee-eec-------------ccEEEEecCccCHHHHHHHHH
Confidence            46899999999998853   5889999999999997554332 111             148999999999999998888


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-----cccccCCeeEEEEecccccCCcCh
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-----LSVRLMGLKMLVLDEADHLLDLGF  551 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-----~~~~Ls~l~~LVIDEAD~Lld~gf  551 (633)
                      .+..-. .-.++.++.+...      ....++.|+|+|...+..--++...     ..+.-....++|+||+|.+...-|
T Consensus       367 ~wsti~-d~~i~rFTsd~Ke------~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MF  439 (776)
T KOG1123|consen  367 QWSTIQ-DDQICRFTSDAKE------RFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMF  439 (776)
T ss_pred             hhcccC-ccceEEeeccccc------cCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHH
Confidence            776422 3445555554332      2234589999997665321111000     001123467899999999987656


Q ss_pred             HHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          552 RKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       552 ~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +..+.-+-..+     -+.++||+-.+
T Consensus       440 RRVlsiv~aHc-----KLGLTATLvRE  461 (776)
T KOG1123|consen  440 RRVLSIVQAHC-----KLGLTATLVRE  461 (776)
T ss_pred             HHHHHHHHHHh-----hccceeEEeec
Confidence            65555444444     56889998655

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

Probab=97.89  E-value=2.4e-06  Score=99.97  Aligned_cols=164  Identities=19%  Similarity=0.216  Sum_probs=112.1

Q ss_pred             CCCCcHHHHHHHHHHhC-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLE-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      +..+.|+|.+.+-.+.. ..++++.+|||+|||++|-+.++..+....         ..+|+|++|..+|+..-.+....
T Consensus       925 ~~~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p---------~~kvvyIap~kalvker~~Dw~~  995 (1230)
T KOG0952|consen  925 YKYFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYP---------GSKVVYIAPDKALVKERSDDWSK  995 (1230)
T ss_pred             hcccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCC---------CccEEEEcCCchhhcccccchhh
Confidence            33566677766654433 457899999999999999998876554332         34799999999999988888777


Q ss_pred             HHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHH
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN  557 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~  557 (633)
                      ... .+++++.-+.|......  ....  .++|+|+||++.-.+..+.. ....+.++..+|+||.|++.+. ..+.++.
T Consensus       996 r~~-~~g~k~ie~tgd~~pd~--~~v~--~~~~~ittpek~dgi~Rsw~-~r~~v~~v~~iv~de~hllg~~-rgPVle~ 1068 (1230)
T KOG0952|consen  996 RDE-LPGIKVIELTGDVTPDV--KAVR--EADIVITTPEKWDGISRSWQ-TRKYVQSVSLIVLDEIHLLGED-RGPVLEV 1068 (1230)
T ss_pred             hcc-cCCceeEeccCccCCCh--hhee--cCceEEcccccccCcccccc-chhhhccccceeecccccccCC-CcceEEE
Confidence            654 34888999888876542  2222  36999999999877665332 2345789999999999998753 3333333


Q ss_pred             HHH-------HCCCCCcEEEEeccCChh
Q 006737          558 IVD-------CLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       558 Il~-------~lpk~~Q~IlfSATl~~e  578 (633)
                      +..       .+++..|.+.+|--+.+.
T Consensus      1069 ivsr~n~~s~~t~~~vr~~glsta~~na 1096 (1230)
T KOG0952|consen 1069 IVSRMNYISSQTEEPVRYLGLSTALANA 1096 (1230)
T ss_pred             EeeccccCccccCcchhhhhHhhhhhcc
Confidence            322       233345666665544443

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

Probab=97.88  E-value=4e-05  Score=76.24  Aligned_cols=123  Identities=21%  Similarity=0.270  Sum_probs=71.3

Q ss_pred             CCcHHHHHHHHHHhCCC--cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEGK--DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~gr--DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ++++-|.+++..++...  -++++++.|+|||.+ +-.+...+...          +.++++++||...+..+.+.+   
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~-l~~~~~~~~~~----------g~~v~~~apT~~Aa~~L~~~~---   66 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTL-LKALAEALEAA----------GKRVIGLAPTNKAAKELREKT---   66 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHH-HHHHHHHHHHT----------T--EEEEESSHHHHHHHHHHH---
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHH-HHHHHHHHHhC----------CCeEEEECCcHHHHHHHHHhh---
Confidence            36889999999997654  477889999999974 23344443332          135999999999988755442   


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCc----ccccCCeeEEEEecccccCCcChHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGL----SVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~----~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                           ++.+.                         |   +..++......    ...+....+||||||-.+..    ..
T Consensus        67 -----~~~a~-------------------------T---i~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~~----~~  109 (196)
T PF13604_consen   67 -----GIEAQ-------------------------T---IHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVDS----RQ  109 (196)
T ss_dssp             -----TS-EE-------------------------E---HHHHTTEECCEECCSSCC-TSTSEEEESSGGG-BH----HH
T ss_pred             -----Ccchh-------------------------h---HHHHHhcCCcccccccccCCcccEEEEecccccCH----HH
Confidence                 11111                         1   11111111000    01144567999999988763    47


Q ss_pred             HHHHHHHCCC-CCcEEEEecc
Q 006737          555 VENIVDCLPR-RRQSLLFSAT  574 (633)
Q Consensus       555 l~~Il~~lpk-~~Q~IlfSAT  574 (633)
                      +..++..++. ..++|++-=+
T Consensus       110 ~~~ll~~~~~~~~klilvGD~  130 (196)
T PF13604_consen  110 LARLLRLAKKSGAKLILVGDP  130 (196)
T ss_dssp             HHHHHHHS-T-T-EEEEEE-T
T ss_pred             HHHHHHHHHhcCCEEEEECCc
Confidence            7788888776 5666666543

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=97.87  E-value=0.00017  Score=82.73  Aligned_cols=155  Identities=14%  Similarity=0.249  Sum_probs=100.9

Q ss_pred             CCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .++++|.+-+.-    ..+|-+.|+.-.-|-|||+- .|.+|..+.....      .++| -|||+|.--|.+= ++++.
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQ-tIs~l~yl~~~~~------~~GP-fLVi~P~StL~NW-~~Ef~  237 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQ-TISLLGYLKGRKG------IPGP-FLVIAPKSTLDNW-MNEFK  237 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHH-HHHHHHHHHHhcC------CCCC-eEEEeeHhhHHHH-HHHHH
Confidence            678888776544    44677999999999999985 3344444433221      2234 4799998887653 34555


Q ss_pred             HHHhcCCCceEEEEECCccchHH--HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVD--QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~--~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                      ++   ++++.+.+++|+......  ...+..+..+|+|+|.+..+.--.     .+.--.-+||||||||+|-+.  ...
T Consensus       238 rf---~P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk~-----~lk~~~W~ylvIDEaHRiKN~--~s~  307 (971)
T KOG0385|consen  238 RF---TPSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDKS-----FLKKFNWRYLVIDEAHRIKNE--KSK  307 (971)
T ss_pred             Hh---CCCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhHH-----HHhcCCceEEEechhhhhcch--hhH
Confidence            54   678999999998653332  223344578999999887764311     112225689999999999764  445


Q ss_pred             HHHHHHHCCCCCcEEEEeccC
Q 006737          555 VENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      +..++..+.-.. .+++|.|-
T Consensus       308 L~~~lr~f~~~n-rLLlTGTP  327 (971)
T KOG0385|consen  308 LSKILREFKTDN-RLLLTGTP  327 (971)
T ss_pred             HHHHHHHhcccc-eeEeeCCc
Confidence            556777665444 44556664

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

Probab=97.84  E-value=0.00038  Score=80.18  Aligned_cols=165  Identities=15%  Similarity=0.157  Sum_probs=97.2

Q ss_pred             cCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          384 CGISPLTIKALTAAGYIQMTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       384 l~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      +.++..|..        .+.++|+..+.-+.    ++.--|+.-.-|-|||.-- +..|..|.....      ..+ .||
T Consensus       196 ~~vPg~I~~--------~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQi-isFLaaL~~S~k------~~~-paL  259 (923)
T KOG0387|consen  196 FKVPGFIWS--------KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQI-ISFLAALHHSGK------LTK-PAL  259 (923)
T ss_pred             ccccHHHHH--------HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhH-HHHHHHHhhccc------ccC-ceE
Confidence            556666644        45678998877654    3445677778899999631 222222322211      111 399


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH------------HHHHHhcCCCcEEEECchhhHHHHhcccC
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV------------DQRRLESDPCQILVATPGRLLDHIENKSG  527 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~------------~~~~l~~~~~dILIaTPgrLl~lL~~~~~  527 (633)
                      ||||. .++.|.++++..+.   +.++|.++++......            ..........+|+|+|...|.-+ . .  
T Consensus       260 IVCP~-Tii~qW~~E~~~w~---p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~-~-d--  331 (923)
T KOG0387|consen  260 IVCPA-TIIHQWMKEFQTWW---PPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ-G-D--  331 (923)
T ss_pred             EEccH-HHHHHHHHHHHHhC---cceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc-C-c--
Confidence            99996 46677777777775   4788989888765211            01111122347999997776432 1 1  


Q ss_pred             cccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          528 LSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       528 ~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                       .+.-..-+|+|+||.|+|-+..  ..+......++ ..+.|++|.|.=
T Consensus       332 -~l~~~~W~y~ILDEGH~IrNpn--s~islackki~-T~~RiILSGTPi  376 (923)
T KOG0387|consen  332 -DLLGILWDYVILDEGHRIRNPN--SKISLACKKIR-TVHRIILSGTPI  376 (923)
T ss_pred             -ccccccccEEEecCcccccCCc--cHHHHHHHhcc-ccceEEeeCccc
Confidence             1222345799999999997652  23333333333 455677787753

>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 []

Probab=97.83  E-value=6.7e-05  Score=75.24  Aligned_cols=140  Identities=19%  Similarity=0.231  Sum_probs=73.0

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      +...|.-|..++.++++..-+++.||.|||||+..+..+++.+......         +.+|+-|+.+....+       
T Consensus         2 I~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~---------kiii~Rp~v~~~~~l-------   65 (205)
T PF02562_consen    2 IKPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEGEYD---------KIIITRPPVEAGEDL-------   65 (205)
T ss_dssp             ----SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-S---------EEEEEE-S--TT----------
T ss_pred             ccCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCc---------EEEEEecCCCCcccc-------
Confidence            3456889999999999888899999999999999888888887664322         577887876542221       


Q ss_pred             HhcCCCc---eE-----------EEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          479 LKNHDGI---GV-----------LTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       479 ~~~~~~i---~v-----------~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                       .+.++-   +.           ..+.+..    ....+... ..|-+..+.-+.     +    ..+.+ .+||||||.
T Consensus        66 -GflpG~~~eK~~p~~~p~~d~l~~~~~~~----~~~~~~~~-~~Ie~~~~~~iR-----G----rt~~~-~~iIvDEaQ  129 (205)
T PF02562_consen   66 -GFLPGDLEEKMEPYLRPIYDALEELFGKE----KLEELIQN-GKIEIEPLAFIR-----G----RTFDN-AFIIVDEAQ  129 (205)
T ss_dssp             --SS---------TTTHHHHHHHTTTS-TT----CHHHHHHT-TSEEEEEGGGGT-----T------B-S-EEEEE-SGG
T ss_pred             -ccCCCCHHHHHHHHHHHHHHHHHHHhChH----hHHHHhhc-CeEEEEehhhhc-----C----ccccc-eEEEEeccc
Confidence             111100   00           0000111    11111111 245555433321     1    22332 789999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      .+.    ..++..++..+..++++|++--.
T Consensus       130 N~t----~~~~k~ilTR~g~~skii~~GD~  155 (205)
T PF02562_consen  130 NLT----PEELKMILTRIGEGSKIIITGDP  155 (205)
T ss_dssp             G------HHHHHHHHTTB-TT-EEEEEE--
T ss_pred             CCC----HHHHHHHHcccCCCcEEEEecCc
Confidence            876    55888999999988988887543

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK10536 hypothetical protein; Provisional

Probab=97.66  E-value=0.00066  Score=70.32  Aligned_cols=148  Identities=14%  Similarity=0.133  Sum_probs=83.2

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHH------
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQ------  470 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Q------  470 (633)
                      .++...+..|...+..+.++..+++.|++|||||+..+..+++.+.....         -+++|.-|+.+....      
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~---------~kIiI~RP~v~~ge~LGfLPG  125 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHKDV---------DRIIVTRPVLQADEDLGFLPG  125 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcCCe---------eEEEEeCCCCCchhhhCcCCC
Confidence            45667889999999999998889999999999999776666655544221         246666666543221      


Q ss_pred             -HHHHHHHHHhcC-CCceEEEEECCccchHHHHHHh-cCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccC
Q 006737          471 -IAAEAIALLKNH-DGIGVLTLVGGTRFKVDQRRLE-SDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       471 -i~~~l~~l~~~~-~~i~v~~l~Gg~~~~~~~~~l~-~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                       +.+.+..++... ..+.  .+.|..    ....+. ...-.|-|.. -   .++..     ..| +-.+||||||+.+.
T Consensus       126 ~~~eK~~p~~~pi~D~L~--~~~~~~----~~~~~~~~~~~~Iei~~-l---~ymRG-----rtl-~~~~vIvDEaqn~~  189 (262)
T PRK10536        126 DIAEKFAPYFRPVYDVLV--RRLGAS----FMQYCLRPEIGKVEIAP-F---AYMRG-----RTF-ENAVVILDEAQNVT  189 (262)
T ss_pred             CHHHHHHHHHHHHHHHHH--HHhChH----HHHHHHHhccCcEEEec-H---HHhcC-----Ccc-cCCEEEEechhcCC
Confidence             111111111100 0000  001111    111111 1111344443 2   22221     123 23789999999876


Q ss_pred             CcChHHHHHHHHHHCCCCCcEEEEec
Q 006737          548 DLGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       548 d~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      -    .++..++..+..+.++|++--
T Consensus       190 ~----~~~k~~ltR~g~~sk~v~~GD  211 (262)
T PRK10536        190 A----AQMKMFLTRLGENVTVIVNGD  211 (262)
T ss_pred             H----HHHHHHHhhcCCCCEEEEeCC
Confidence            3    688889999998888777543

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=97.65  E-value=0.00013  Score=86.66  Aligned_cols=130  Identities=21%  Similarity=0.249  Sum_probs=89.4

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.-.--.+..|+  |+.+.||-||||+..||+.-..+....           |-||+-.--||.-=.+.+..++.
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~G~g-----------VHvVTvNDYLA~RDaewm~p~y~  204 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALTGRG-----------VHVVTVNDYLAQRDKEWMNPVFE  204 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHcCCC-----------cEEEeechHhhhhhHHHHHHHHH
Confidence            46677766555566665  889999999999999999755554422           66777778888876667777776


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      ++ |+.|.|+..+.......   ....|||.++|..-| .++|...-.   .......+.+.||||+|.+|
T Consensus       205 fl-GLtVg~i~~~~~~~~Rr---~aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        205 FH-GLSVGVILNTMRPEERR---EQYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             Hh-CCeeeeeCCCCCHHHHH---HhCCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            66 99999987655544322   233589999998766 333322210   01224678899999999876

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=97.53  E-value=0.0013  Score=77.07  Aligned_cols=164  Identities=17%  Similarity=0.207  Sum_probs=104.1

Q ss_pred             CCcHHHHHHHHHHhC---CC-------cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHH
Q 006737          401 QMTRVQEATLSACLE---GK-------DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQ  470 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~---gr-------DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Q  470 (633)
                      .+.|+|++.+.-+..   |.       -+|+.-..|+|||+. +|+.+..+++..+....   .--++|||+|. .|+.-
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq-~IsflwtlLrq~P~~~~---~~~k~lVV~P~-sLv~n  312 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQ-CISFIWTLLRQFPQAKP---LINKPLVVAPS-SLVNN  312 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHH-HHHHHHHHHHhCcCccc---cccccEEEccH-HHHHH
Confidence            568999999877543   22       355555679999986 45566666665332100   11358999994 68888


Q ss_pred             HHHHHHHHHhcCCCceEEEEECCccc-hHHHHH-H----hcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          471 IAAEAIALLKNHDGIGVLTLVGGTRF-KVDQRR-L----ESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       471 i~~~l~~l~~~~~~i~v~~l~Gg~~~-~~~~~~-l----~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      ..++|.++.... .+....++|.... ...... +    .....-|+|.+.+.+.+++..     +.+..+.+||+||.|
T Consensus       313 WkkEF~KWl~~~-~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~-----il~~~~glLVcDEGH  386 (776)
T KOG0390|consen  313 WKKEFGKWLGNH-RINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK-----ILLIRPGLLVCDEGH  386 (776)
T ss_pred             HHHHHHHhcccc-ccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH-----HhcCCCCeEEECCCC
Confidence            889998887642 5667777777663 000010 1    111235777888888766543     456789999999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ++=+.  ...+...+..+. -..-|++|.|+=..
T Consensus       387 rlkN~--~s~~~kaL~~l~-t~rRVLLSGTp~QN  417 (776)
T KOG0390|consen  387 RLKNS--DSLTLKALSSLK-TPRRVLLTGTPIQN  417 (776)
T ss_pred             Cccch--hhHHHHHHHhcC-CCceEEeeCCcccc
Confidence            98653  344555555554 34467789997544

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

Probab=97.46  E-value=0.00037  Score=75.39  Aligned_cols=108  Identities=16%  Similarity=0.252  Sum_probs=65.7

Q ss_pred             cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccch
Q 006737          418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK  497 (633)
Q Consensus       418 DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~  497 (633)
                      -++|.|..|||||++. +-++..+....        .+..++++++...|...+...+......                
T Consensus         3 v~~I~G~aGTGKTvla-~~l~~~l~~~~--------~~~~~~~l~~n~~l~~~l~~~l~~~~~~----------------   57 (352)
T PF09848_consen    3 VILITGGAGTGKTVLA-LNLAKELQNSE--------EGKKVLYLCGNHPLRNKLREQLAKKYNP----------------   57 (352)
T ss_pred             EEEEEecCCcCHHHHH-HHHHHHhhccc--------cCCceEEEEecchHHHHHHHHHhhhccc----------------
Confidence            4789999999999863 33343331111        1235899999999998877666544200                


Q ss_pred             HHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcC-------hHHHHHHHHHH
Q 006737          498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG-------FRKDVENIVDC  561 (633)
Q Consensus       498 ~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g-------f~~~l~~Il~~  561 (633)
                              ......+..|..+...+...   .......++|||||||+|...+       ...++..|+..
T Consensus        58 --------~~~~~~~~~~~~~i~~~~~~---~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   58 --------KLKKSDFRKPTSFINNYSES---DKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             --------chhhhhhhhhHHHHhhcccc---cccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence                    00123344444444433211   1335688999999999998732       34667777665

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=97.46  E-value=0.00032  Score=83.65  Aligned_cols=131  Identities=19%  Similarity=0.195  Sum_probs=86.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .++++|.-.--.+..|  -|+.+.||-||||+..||+.-..+....           |-||+..--||.-=.+.+..+..
T Consensus       169 ~~yDVQliGgivLh~G--~IAEM~TGEGKTLvAtlp~yLnAL~Gkg-----------VHvVTVNDYLA~RDaewmgply~  235 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQG--KIAEMATGEGKTLVATLPVYLNALTGNG-----------VHVVTVNDYLAKRDSEWMGPLYE  235 (1112)
T ss_pred             cccchHHhhhhhhcCC--ceeeecCCCCchhHHHHHHHHHHHcCCC-----------cEEEEechhhhhccHHHHHHHHH
Confidence            3566665554445555  4899999999999999999766554432           66778888888766666666666


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      ++ |+.|+|+..........+.  ...|||.++|..-| .++|...-.   .......+.+.||||+|.+|
T Consensus       236 fL-GLsvg~i~~~~~~~~~rr~--aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        236 FH-GLSVDCIDKHQPNSEARRK--AYNADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             Hh-CCceeecCCCCCCHHHHHH--hCCCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            55 8999988653222222222  23489999998766 333322210   01235668899999999876

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

Probab=97.44  E-value=0.00055  Score=77.14  Aligned_cols=65  Identities=23%  Similarity=0.347  Sum_probs=50.6

Q ss_pred             CCCcHHHHHHHHHHhCCCc-EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKD-AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grD-vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      +.+.+-|..|+....+.++ .+++||+|+|||.....-+.+.+ ..+.          ++||..||.+.+..|.+.+
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlv-k~~k----------~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLV-KQKK----------RVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHH-HcCC----------eEEEEcCchHHHHHHHHHh
Confidence            3578889999999988865 57889999999987655444444 4332          6999999999999888753

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

Probab=97.42  E-value=0.00071  Score=76.68  Aligned_cols=84  Identities=17%  Similarity=0.269  Sum_probs=64.9

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          393 ALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       393 ~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      .+...++.+++.-|..|+.++|+..=.||++|+|+|||+.-.- |+-++.+...         ..+||.+|+.-.+.|+.
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~-IVyhl~~~~~---------~~VLvcApSNiAVDqLa  471 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSAT-IVYHLARQHA---------GPVLVCAPSNIAVDQLA  471 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHH-HHHHHHHhcC---------CceEEEcccchhHHHHH
Confidence            4455678889999999999999999999999999999987543 3444444322         14999999999999998


Q ss_pred             HHHHHHHhcCCCceEEEEE
Q 006737          473 AEAIALLKNHDGIGVLTLV  491 (633)
Q Consensus       473 ~~l~~l~~~~~~i~v~~l~  491 (633)
                      +.+.+.     +++|.-++
T Consensus       472 eKIh~t-----gLKVvRl~  485 (935)
T KOG1802|consen  472 EKIHKT-----GLKVVRLC  485 (935)
T ss_pred             HHHHhc-----CceEeeee
Confidence            887765     56665443

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=97.42  E-value=0.00099  Score=76.86  Aligned_cols=157  Identities=15%  Similarity=0.228  Sum_probs=95.2

Q ss_pred             CcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       402 pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      +-++|.--+..+.    .+-+.|+.-.-|-|||.- ++..|..|...+.       ++| -|||||.--|-+    -+++
T Consensus       400 LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQ-vIaFlayLkq~g~-------~gp-HLVVvPsSTleN----WlrE  466 (941)
T KOG0389|consen  400 LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQ-VIAFLAYLKQIGN-------PGP-HLVVVPSSTLEN----WLRE  466 (941)
T ss_pred             ccchhhhhHHHHHHHHHccccceehhhccCcchhH-HHHHHHHHHHcCC-------CCC-cEEEecchhHHH----HHHH
Confidence            6778877665532    234678888899999953 3444444443332       222 489999866644    5566


Q ss_pred             HHhcCCCceEEEEECCccchHHHH-HHhc--CCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHH
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQR-RLES--DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~-~l~~--~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                      +.++++.++|..++|........+ .+..  .+.+||++|......--...  ..+.-.++.++|+||+|.|-+.. ...
T Consensus       467 f~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDR--sflk~~~~n~viyDEgHmLKN~~-SeR  543 (941)
T KOG0389|consen  467 FAKWCPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDR--SFLKNQKFNYVIYDEGHMLKNRT-SER  543 (941)
T ss_pred             HHHhCCceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHH--HHHHhccccEEEecchhhhhccc-hHH
Confidence            666678999999999875554433 2233  26899999975543110000  01223467899999999987653 222


Q ss_pred             HHHHHHHCCCCCcEEEEeccCC
Q 006737          555 VENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      +..++. ++ ..+.|+++.|--
T Consensus       544 y~~LM~-I~-An~RlLLTGTPL  563 (941)
T KOG0389|consen  544 YKHLMS-IN-ANFRLLLTGTPL  563 (941)
T ss_pred             HHHhcc-cc-ccceEEeeCCcc
Confidence            333322 22 345677788753

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=97.39  E-value=0.00048  Score=80.44  Aligned_cols=137  Identities=19%  Similarity=0.243  Sum_probs=84.8

Q ss_pred             cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccch
Q 006737          418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK  497 (633)
Q Consensus       418 DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~  497 (633)
                      -.+|.||.|||||.+..-+ |...+..         +..++|+|+-.+.|+.++...++...-  .++....-..+..  
T Consensus        51 V~vVRSpMGTGKTtaLi~w-Lk~~l~~---------~~~~VLvVShRrSL~~sL~~rf~~~~l--~gFv~Y~d~~~~~--  116 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRW-LKDALKN---------PDKSVLVVSHRRSLTKSLAERFKKAGL--SGFVNYLDSDDYI--  116 (824)
T ss_pred             eEEEECCCCCCcHHHHHHH-HHHhccC---------CCCeEEEEEhHHHHHHHHHHHHhhcCC--Ccceeeecccccc--
Confidence            4688899999999865443 3332211         123699999999999999888875421  1222111111111  


Q ss_pred             HHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH------H-HHHHCCCCCcEEE
Q 006737          498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE------N-IVDCLPRRRQSLL  570 (633)
Q Consensus       498 ~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~------~-Il~~lpk~~Q~Il  570 (633)
                           +.....+-+++..+.|.++..      ..+.+.++|||||+..++..-|...+.      . +...+.....+|+
T Consensus       117 -----i~~~~~~rLivqIdSL~R~~~------~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~  185 (824)
T PF02399_consen  117 -----IDGRPYDRLIVQIDSLHRLDG------SLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIV  185 (824)
T ss_pred             -----ccccccCeEEEEehhhhhccc------ccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEE
Confidence                 111124677777777766532      236678999999999877543322222      2 2334556678999


Q ss_pred             EeccCChhh
Q 006737          571 FSATMPKEL  579 (633)
Q Consensus       571 fSATl~~el  579 (633)
                      +-||++...
T Consensus       186 ~DA~ln~~t  194 (824)
T PF02399_consen  186 MDADLNDQT  194 (824)
T ss_pred             ecCCCCHHH
Confidence            999999883

It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication

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

Probab=97.39  E-value=0.0014  Score=78.10  Aligned_cols=154  Identities=16%  Similarity=0.252  Sum_probs=97.1

Q ss_pred             CcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       402 pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ++.+|..-+..+.    ++-|-|+.-.-|-|||.- .|.+|.|+.-.+.. .     || -||||||-.+.+= .-+|++
T Consensus       616 LReYQkiGLdWLatLYeknlNGILADEmGLGKTIQ-tISllAhLACeegn-W-----GP-HLIVVpTsviLnW-EMElKR  686 (1958)
T KOG0391|consen  616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQ-TISLLAHLACEEGN-W-----GP-HLIVVPTSVILNW-EMELKR  686 (1958)
T ss_pred             HHHHHHhhHHHHHHHHHhcccceehhhhcccchhH-HHHHHHHHHhcccC-C-----CC-ceEEeechhhhhh-hHHHhh
Confidence            4567777665543    234778888999999974 45667776554321 1     12 5899999766542 235555


Q ss_pred             HHhcCCCceEEEEECCccchHHH--HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHH
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQ--RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV  555 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~--~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l  555 (633)
                      +   ++++++..++|........  ...+.+..||.|++...+..-+..     +.-.+.+|+||||||.+-++ -...+
T Consensus       687 w---cPglKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~A-----FkrkrWqyLvLDEaqnIKnf-ksqrW  757 (1958)
T KOG0391|consen  687 W---CPGLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLTA-----FKRKRWQYLVLDEAQNIKNF-KSQRW  757 (1958)
T ss_pred             h---CCcceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHHH-----HHhhccceeehhhhhhhcch-hHHHH
Confidence            5   5699999999986543322  223345678999887776654432     23457889999999999765 23344


Q ss_pred             HHHHHHCCCCCcEEEEeccC
Q 006737          556 ENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       556 ~~Il~~lpk~~Q~IlfSATl  575 (633)
                      ..+++. +. .|.++++.|-
T Consensus       758 QAllnf-ns-qrRLLLtgTP  775 (1958)
T KOG0391|consen  758 QALLNF-NS-QRRLLLTGTP  775 (1958)
T ss_pred             HHHhcc-ch-hheeeecCCc
Confidence            455443 32 3455666663

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.37  E-value=0.0015  Score=77.15  Aligned_cols=129  Identities=19%  Similarity=0.243  Sum_probs=77.7

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+++-|++|+..+..++-+++.++.|+|||.+. -.++..+.....        ...+++++||-..|..+.+..    
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~~--------~~~v~l~ApTg~AA~~L~e~~----  388 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELGG--------LLPVGLAAPTGRAAKRLGEVT----  388 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcCC--------CceEEEEeCchHHHHHHHHhc----
Confidence            4799999999999999999999999999999742 223333322210        124788999998887543221    


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHH
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV  559 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il  559 (633)
                          +....          ....+...       .|+......      .......++||||||+++...    .+..++
T Consensus       389 ----g~~a~----------Tih~lL~~-------~~~~~~~~~------~~~~~~~~llIvDEaSMvd~~----~~~~Ll  437 (720)
T TIGR01448       389 ----GLTAS----------TIHRLLGY-------GPDTFRHNH------LEDPIDCDLLIVDESSMMDTW----LALSLL  437 (720)
T ss_pred             ----CCccc----------cHHHHhhc-------cCCccchhh------hhccccCCEEEEeccccCCHH----HHHHHH
Confidence                11100          11111110       111110000      011235679999999998643    567777


Q ss_pred             HHCCCCCcEEEEe
Q 006737          560 DCLPRRRQSLLFS  572 (633)
Q Consensus       560 ~~lpk~~Q~IlfS  572 (633)
                      ..++...++|++-
T Consensus       438 ~~~~~~~rlilvG  450 (720)
T TIGR01448       438 AALPDHARLLLVG  450 (720)
T ss_pred             HhCCCCCEEEEEC
Confidence            7888888887764

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

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

Probab=97.36  E-value=0.0012  Score=67.07  Aligned_cols=154  Identities=20%  Similarity=0.254  Sum_probs=94.9

Q ss_pred             ccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhC---CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLE---GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       381 F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~---grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      |+-+.-+..++=.+.. ++ -+++.|.++...+.+   |.|.+.+.-.|.|||.+ ++|++..++.++..         .
T Consensus         5 w~p~~~P~wLl~E~e~-~i-liR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~~---------L   72 (229)
T PF12340_consen    5 WDPMEYPDWLLFEIES-NI-LIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGSR---------L   72 (229)
T ss_pred             CCchhChHHHHHHHHc-Cc-eeeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCCc---------E
Confidence            4444445555544432 22 578999999988876   57999999999999976 78998887765432         3


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEE--CCccchH----HH----HHHhcCCCcEEEECchhhHHHHhccc-
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLV--GGTRFKV----DQ----RRLESDPCQILVATPGRLLDHIENKS-  526 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~--Gg~~~~~----~~----~~l~~~~~dILIaTPgrLl~lL~~~~-  526 (633)
                      |.+++| ++|..|..+.+...+...-+-.+..+.  -.+....    ..    +..... -.|+++||+.++.+.-..- 
T Consensus        73 vrviVp-k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~-~gill~~PEhilSf~L~~le  150 (229)
T PF12340_consen   73 VRVIVP-KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRS-GGILLATPEHILSFKLKGLE  150 (229)
T ss_pred             EEEEcC-HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHc-CCEEEeChHHHHHHHHHHHH
Confidence            667777 569999998888777654444443332  1222111    11    112222 2699999998864321110 


Q ss_pred             -----C---------cccccCCeeEEEEecccccCC
Q 006737          527 -----G---------LSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       527 -----~---------~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                           .         ....+.....=|+||+|.++.
T Consensus       151 ~l~~~~~~~~~~l~~~q~~l~~~~rdilDEsDe~L~  186 (229)
T PF12340_consen  151 RLQDGKPEEARELLKIQKWLDEHSRDILDESDEILS  186 (229)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhcCCeEeECchhccC
Confidence                 0         000133444578999998875

There are two conserved sequence motifs: LLE and NMG.

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.30  E-value=0.0016  Score=75.08  Aligned_cols=143  Identities=19%  Similarity=0.245  Sum_probs=83.4

Q ss_pred             HHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCC
Q 006737          404 RVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHD  483 (633)
Q Consensus       404 ~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~  483 (633)
                      ..|+.++..++.++-+++.|+.|||||.+. ..++..+.......     ..+++++++||--.|..+.+.+....... 
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~~~~-----~~~~I~l~APTGkAA~rL~e~~~~~~~~l-  220 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTV-ARLLLALVKQSPKQ-----GKLRIALAAPTGKAAARLAESLRKAVKNL-  220 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhcccc-----CCCcEEEECCcHHHHHHHHHHHHhhhccc-
Confidence            799999999999999999999999999853 22333333221110     12468999999999988776665433211 


Q ss_pred             CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCc---ccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          484 GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGL---SVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       484 ~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~---~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                        ..       . .....     ...+-..|-.+|+........+   ..+...+++||||||=++.    ...+..++.
T Consensus       221 --~~-------~-~~~~~-----~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMvd----~~l~~~ll~  281 (586)
T TIGR01447       221 --AA-------A-EALIA-----ALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMVD----LPLMAKLLK  281 (586)
T ss_pred             --cc-------c-hhhhh-----ccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccCC----HHHHHHHHH
Confidence              00       0 00000     0011123333333221110000   0122357899999997764    336777888


Q ss_pred             HCCCCCcEEEEe
Q 006737          561 CLPRRRQSLLFS  572 (633)
Q Consensus       561 ~lpk~~Q~IlfS  572 (633)
                      .++...++|++-
T Consensus       282 al~~~~rlIlvG  293 (586)
T TIGR01447       282 ALPPNTKLILLG  293 (586)
T ss_pred             hcCCCCEEEEEC
Confidence            888888777764

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

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

Probab=97.30  E-value=0.0031  Score=69.53  Aligned_cols=131  Identities=20%  Similarity=0.246  Sum_probs=83.1

Q ss_pred             CCcHHHHHHHHHHhCCC-----cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEGK-----DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~gr-----DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .+-|+|.+-+--+....     --|+.-.-|.|||.-.+.-+|    ....        +-.+|||+|+.+|. |..+++
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLll----ae~~--------ra~tLVvaP~VAlm-QW~nEI  250 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLL----AEVD--------RAPTLVVAPTVALM-QWKNEI  250 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHH----hccc--------cCCeeEEccHHHHH-HHHHHH
Confidence            45678887765544332     235566779999975433222    2211        12389999999985 566777


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhc-ccC---------cccccCCee--EEEEecc
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIEN-KSG---------LSVRLMGLK--MLVLDEA  543 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~-~~~---------~~~~Ls~l~--~LVIDEA  543 (633)
                      .....  ..+++.+++|..... ..+.+.+  .|++.+|...+...... ..+         ....|.+++  -||+|||
T Consensus       251 ~~~T~--gslkv~~YhG~~R~~-nikel~~--YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEA  325 (791)
T KOG1002|consen  251 ERHTS--GSLKVYIYHGAKRDK-NIKELMN--YDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEA  325 (791)
T ss_pred             HHhcc--CceEEEEEecccccC-CHHHhhc--CcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhh
Confidence            77765  367888888765533 3444443  69999999888776644 221         111255555  5899999


Q ss_pred             cccCCc
Q 006737          544 DHLLDL  549 (633)
Q Consensus       544 D~Lld~  549 (633)
                      |.+-+.
T Consensus       326 H~IK~R  331 (791)
T KOG1002|consen  326 HNIKDR  331 (791)
T ss_pred             cccccc
Confidence            998753

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

Probab=97.29  E-value=0.0024  Score=67.37  Aligned_cols=175  Identities=18%  Similarity=0.170  Sum_probs=106.8

Q ss_pred             ccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhC----------CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCC
Q 006737          383 ECGISPLTIKALTAAGYIQMTRVQEATLSACLE----------GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQL  452 (633)
Q Consensus       383 el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~----------grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~  452 (633)
                      .+.|++.++.    .|  .++..|.+++-....          ..-.++--.||.||.-.-.--|+.+.+...       
T Consensus        25 ~~~lp~~~~~----~g--~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~Gr-------   91 (303)
T PF13872_consen   25 RLHLPEEVID----SG--LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRGR-------   91 (303)
T ss_pred             ccCCCHHHHh----cc--cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcCC-------
Confidence            3456665432    22  568888888755432          345778888999987654444555555442       


Q ss_pred             CCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          453 VPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       453 ~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                         .++|+|+.+-.|-.+..+.+..+...  .+.+..+.. .... ....+   .-.||++|.-.|...-.........|
T Consensus        92 ---~r~vwvS~s~dL~~Da~RDl~DIG~~--~i~v~~l~~-~~~~-~~~~~---~~GvlF~TYs~L~~~~~~~~~~~sRl  161 (303)
T PF13872_consen   92 ---KRAVWVSVSNDLKYDAERDLRDIGAD--NIPVHPLNK-FKYG-DIIRL---KEGVLFSTYSTLISESQSGGKYRSRL  161 (303)
T ss_pred             ---CceEEEECChhhhhHHHHHHHHhCCC--cccceechh-hccC-cCCCC---CCCccchhHHHHHhHHhccCCccchH
Confidence               25899999999999999999988654  233322211 0000 00111   23699999888766543211111111


Q ss_pred             C--------C-eeEEEEecccccCCcC--------hHHHHHHHHHHCCCCCcEEEEeccCChhhhc
Q 006737          533 M--------G-LKMLVLDEADHLLDLG--------FRKDVENIVDCLPRRRQSLLFSATMPKELVL  581 (633)
Q Consensus       533 s--------~-l~~LVIDEAD~Lld~g--------f~~~l~~Il~~lpk~~Q~IlfSATl~~el~l  581 (633)
                      .        + =.+||+||+|..-+..        -...+..+.+.+|+ .++|.+|||-..+...
T Consensus       162 ~ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~LP~-ARvvY~SATgasep~N  226 (303)
T PF13872_consen  162 DQLVDWCGEDFDGVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRLPN-ARVVYASATGASEPRN  226 (303)
T ss_pred             HHHHHHHhcCCCceEEeccchhcCCCCccCccccHHHHHHHHHHHhCCC-CcEEEecccccCCCce
Confidence            1        1 1379999999987542        23456666777865 4599999999877543

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=97.26  E-value=0.0013  Score=76.19  Aligned_cols=143  Identities=19%  Similarity=0.261  Sum_probs=83.9

Q ss_pred             cHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcC
Q 006737          403 TRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH  482 (633)
Q Consensus       403 t~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~  482 (633)
                      .+.|+.|+-..+..+-++|.|++|+|||.+. .-++..+.....      ....++++++||...|..+.+.+.......
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~~------~~~~~i~l~APTgkAA~rL~e~~~~~~~~~  226 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQLAD------GERCRIRLAAPTGKAAARLTESLGKALRQL  226 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhcC------CCCcEEEEECCcHHHHHHHHHHHHhhhhcc
Confidence            5899999999999999999999999999753 223333332211      012468899999999998877665443211


Q ss_pred             CCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCc---ccccCCeeEEEEecccccCCcChHHHHHHHH
Q 006737          483 DGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGL---SVRLMGLKMLVLDEADHLLDLGFRKDVENIV  559 (633)
Q Consensus       483 ~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~---~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il  559 (633)
                      . +           .......    ...-..|-.+|+........+   ..+.-.+++||||||-++-    ...+..++
T Consensus       227 ~-~-----------~~~~~~~----~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMvd----~~lm~~ll  286 (615)
T PRK10875        227 P-L-----------TDEQKKR----IPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMVD----LPMMARLI  286 (615)
T ss_pred             c-c-----------chhhhhc----CCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhccc----HHHHHHHH
Confidence            0 0           0000000    001112222222211100000   0122346899999997764    44677788


Q ss_pred             HHCCCCCcEEEEe
Q 006737          560 DCLPRRRQSLLFS  572 (633)
Q Consensus       560 ~~lpk~~Q~IlfS  572 (633)
                      ..+++..++|++-
T Consensus       287 ~al~~~~rlIlvG  299 (615)
T PRK10875        287 DALPPHARVIFLG  299 (615)
T ss_pred             HhcccCCEEEEec
Confidence            8888888887774

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

Probab=97.16  E-value=0.00087  Score=76.41  Aligned_cols=142  Identities=19%  Similarity=0.315  Sum_probs=88.5

Q ss_pred             CCcHHHHHHHHHHhC-----CCcEEEEccCCCCchhhhHHHHHHHHHHh-cCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLE-----GKDAVVKAKTGTGKSIAFLLPAIEAVLKA-TSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~-----grDvLv~ApTGSGKTlaylLPiL~~l~~~-~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      .+-|+|..++..++-     ..--|+..--|-|||+..+--++..-... ........ .. .+|||||- .|+.|.+.+
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~-a~-~TLII~Pa-Sli~qW~~E  401 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGES-AS-KTLIICPA-SLIHQWEAE  401 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccc-cC-CeEEeCcH-HHHHHHHHH
Confidence            367899999887763     23456677778999996544444322211 11111111 11 48999995 677888888


Q ss_pred             HHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHH----HHhcccCcccccCCe--eEEEEecccccCC
Q 006737          475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLD----HIENKSGLSVRLMGL--KMLVLDEADHLLD  548 (633)
Q Consensus       475 l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~----lL~~~~~~~~~Ls~l--~~LVIDEAD~Lld  548 (633)
                      +....... .+.|.+++|........+.+..  +||||+|..-+..    -+..... ...|-.|  ..||+||||.+-+
T Consensus       402 v~~rl~~n-~LsV~~~HG~n~r~i~~~~L~~--YDvViTTY~lva~~~~~e~~~~~~-~spL~~I~W~RVILDEAH~IrN  477 (901)
T KOG4439|consen  402 VARRLEQN-ALSVYLYHGPNKREISAKELRK--YDVVITTYNLVANKPDDELEEGKN-SSPLARIAWSRVILDEAHNIRN  477 (901)
T ss_pred             HHHHHhhc-ceEEEEecCCccccCCHHHHhh--cceEEEeeeccccCCchhhhcccC-ccHHHHhhHHHhhhhhhhhhcc
Confidence            87776543 7899999998764444555554  6999999766544    1111111 1123333  4699999999865


Q ss_pred             c
Q 006737          549 L  549 (633)
Q Consensus       549 ~  549 (633)
                      .
T Consensus       478 ~  478 (901)
T KOG4439|consen  478 S  478 (901)
T ss_pred             c
Confidence            4

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=97.12  E-value=0.0024  Score=74.45  Aligned_cols=148  Identities=18%  Similarity=0.219  Sum_probs=79.2

Q ss_pred             cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhc-----CCCceEEEEEC
Q 006737          418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKN-----HDGIGVLTLVG  492 (633)
Q Consensus       418 DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~-----~~~i~v~~l~G  492 (633)
                      ++=|.+.||+|||.||+=.+++.-...+         -.+-||||||.+.-.-++........+     +.+.+.-.++-
T Consensus        76 NiDI~METGTGKTy~YlrtmfeLhk~YG---------~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~  146 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFELHKKYG---------LFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIY  146 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHHHHHHhC---------ceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEee
Confidence            7888999999999999876664322222         136799999998765544333332222     22333333322


Q ss_pred             CccchHHHHHHhcCCCcEEEECchhhHH------HHhccc----Cc----ccc---cCCe-eEEEEecccccCCcChHHH
Q 006737          493 GTRFKVDQRRLESDPCQILVATPGRLLD------HIENKS----GL----SVR---LMGL-KMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       493 g~~~~~~~~~l~~~~~dILIaTPgrLl~------lL~~~~----~~----~~~---Ls~l-~~LVIDEAD~Lld~gf~~~  554 (633)
                      ..... ....-.++.+.||+.|-..+..      ++....    +.    ...   +..+ -+|||||=|+|...  -..
T Consensus       147 ~~~~~-~~~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~--~k~  223 (985)
T COG3587         147 DEDIE-KFKFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGD--DKT  223 (985)
T ss_pred             chHHH-HHhhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccc--hHH
Confidence            21111 1122233456788777555432      121110    00    000   1112 27999999999853  223


Q ss_pred             HHHHHHHCCCCCcEEEEeccCChhh
Q 006737          555 VENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +..|....|  .-++=|+||.+.+.
T Consensus       224 ~~~i~~l~p--l~ilRfgATfkd~y  246 (985)
T COG3587         224 YGAIKQLNP--LLILRFGATFKDEY  246 (985)
T ss_pred             HHHHHhhCc--eEEEEecccchhhh
Confidence            333333322  23677899999884

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.11  E-value=0.00071  Score=69.89  Aligned_cols=86  Identities=24%  Similarity=0.296  Sum_probs=65.6

Q ss_pred             CCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECC-ccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          454 PPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGG-TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       454 ~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg-~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      +.|.+|||+..--=|.++.+.++.+-..  +..|+-++.. ....++...+....++|.||||+||..++.++   .+.+
T Consensus       125 gsP~~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~---~L~l  199 (252)
T PF14617_consen  125 GSPHVLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENG---ALSL  199 (252)
T ss_pred             CCCEEEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcC---CCCc
Confidence            3567999999887788888777766311  2334444444 36677888888888999999999999999877   5789


Q ss_pred             CCeeEEEEeccc
Q 006737          533 MGLKMLVLDEAD  544 (633)
Q Consensus       533 s~l~~LVIDEAD  544 (633)
                      +++.+||||--|
T Consensus       200 ~~l~~ivlD~s~  211 (252)
T PF14617_consen  200 SNLKRIVLDWSY  211 (252)
T ss_pred             ccCeEEEEcCCc
Confidence            999999999754

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.08  E-value=0.0024  Score=58.01  Aligned_cols=19  Identities=21%  Similarity=0.389  Sum_probs=12.5

Q ss_pred             CCCcEEEEccCCCCchhhh
Q 006737          415 EGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlay  433 (633)
                      .++.+++.|++|+|||.+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~   21 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLI   21 (131)
T ss_dssp             ----EEEEE-TTSSHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHH
Confidence            3457899999999999853

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

Probab=97.02  E-value=0.0034  Score=73.44  Aligned_cols=79  Identities=19%  Similarity=0.147  Sum_probs=53.4

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCC-----------------CC--------CC
Q 006737          401 QMTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSS-----------------ST--------TQ  451 (633)
Q Consensus       401 ~pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~-----------------~~--------~~  451 (633)
                      +|++.|...+..++    ...+.++.+|||+|||++.+...|.........                 ..        ..
T Consensus        21 qpY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~~s~e~  100 (945)
T KOG1132|consen   21 QPYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGEKSEEA  100 (945)
T ss_pred             CcchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCCchhhh
Confidence            67899987766655    467899999999999998776666544332100                 00        00


Q ss_pred             C------CCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          452 L------VPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       452 ~------~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      .      ..-|++.|-+-|..-..|+++++++..
T Consensus       101 ~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen  101 GEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             cCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence            0      125677777788888888888887663

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

Probab=96.82  E-value=0.0033  Score=68.54  Aligned_cols=60  Identities=32%  Similarity=0.389  Sum_probs=44.4

Q ss_pred             CCcHHHHHHHHHH------hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          401 QMTRVQEATLSAC------LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       401 ~pt~iQ~~aIp~i------l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      ++++-|+.++..+      ..+..+++.|+-|+|||.  ++-++...+...         +..+++++||-..|..+
T Consensus         1 ~Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~--l~~~i~~~~~~~---------~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    1 KLNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSF--LIKAIIDYLRSR---------GKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhH--HHHHHHHHhccc---------cceEEEecchHHHHHhc
Confidence            3677899998887      678899999999999997  444444443331         23589999998887765

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.79  E-value=0.015  Score=69.15  Aligned_cols=62  Identities=23%  Similarity=0.214  Sum_probs=45.1

Q ss_pred             CCCcHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      ..+++-|..|+..++.+ +-+++.++.|+|||..  +-.+..++...         +..+++++||--.|..+.
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtl--l~~i~~~~~~~---------g~~V~~~ApTg~Aa~~L~  413 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTM--LKAAREAWEAA---------GYRVIGAALSGKAAEGLQ  413 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHH--HHHHHHHHHhC---------CCeEEEEeCcHHHHHHHH
Confidence            36899999999999874 5678999999999974  33333333321         235889999987776543

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>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

Probab=96.78  E-value=0.0034  Score=65.30  Aligned_cols=71  Identities=24%  Similarity=0.332  Sum_probs=51.7

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhc
Q 006737          402 MTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKN  481 (633)
Q Consensus       402 pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~  481 (633)
                      +|+-|.+++..  ....++|.|..|||||.+.+--++..+....       ..+-++|+|++|+..|.++...+...+..
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~-------~~~~~Il~lTft~~aa~e~~~ri~~~l~~   71 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG-------VPPERILVLTFTNAAAQEMRERIRELLEE   71 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS-------STGGGEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhcccc-------CChHHheecccCHHHHHHHHHHHHHhcCc
Confidence            57889999987  6678999999999999975544444343332       12235999999999999999999887653

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>PF13245 AAA_19: Part of AAA domain

Probab=96.76  E-value=0.0043  Score=52.46  Aligned_cols=53  Identities=30%  Similarity=0.412  Sum_probs=35.5

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      +.-++|.+|.|||||... +.++..+.......      +-++||++||+..+..+.+.+
T Consensus        10 ~~~~vv~g~pGtGKT~~~-~~~i~~l~~~~~~~------~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTL-AARIAELLAARADP------GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHHhcCC------CCeEEEECCCHHHHHHHHHHH
Confidence            334556999999999653 34444444321100      125999999999999988777

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

Probab=96.71  E-value=0.0072  Score=71.44  Aligned_cols=137  Identities=21%  Similarity=0.224  Sum_probs=84.3

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCc-EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          385 GISPLTIKALTAAGYIQMTRVQEATLSACLEGKD-AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       385 ~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grD-vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      .+.|.+.+.    -+..++.-|++|+-.++..+| .+|.|-+|+|||...  ..+-+++-...         -+||+.+=
T Consensus       657 ~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI--~~LIkiL~~~g---------kkVLLtsy  721 (1100)
T KOG1805|consen  657 VLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTI--SLLIKILVALG---------KKVLLTSY  721 (1100)
T ss_pred             ccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhH--HHHHHHHHHcC---------CeEEEEeh
Confidence            345555543    245788999999999998886 588899999999853  33333333221         25888888


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHH----------------hcCCCcEEEECchhhHHHHhcccC
Q 006737          464 TRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRL----------------ESDPCQILVATPGRLLDHIENKSG  527 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l----------------~~~~~dILIaTPgrLl~lL~~~~~  527 (633)
                      |...+..|.-.+...     ++.+.-+-.+.....+.+.+                .-+.+.|+.+|-..+.+.|-.   
T Consensus       722 ThsAVDNILiKL~~~-----~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf~---  793 (1100)
T KOG1805|consen  722 THSAVDNILIKLKGF-----GIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLFV---  793 (1100)
T ss_pred             hhHHHHHHHHHHhcc-----CcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhhh---
Confidence            887777665544433     22221111111111111111                113468999998888765533   


Q ss_pred             cccccCCeeEEEEecccccCC
Q 006737          528 LSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       528 ~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                          .+.++|+|||||-.++.
T Consensus       794 ----~R~FD~cIiDEASQI~l  810 (1100)
T KOG1805|consen  794 ----NRQFDYCIIDEASQILL  810 (1100)
T ss_pred             ----ccccCEEEEcccccccc
Confidence                34689999999998764

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.65  E-value=0.012  Score=71.62  Aligned_cols=60  Identities=25%  Similarity=0.246  Sum_probs=44.6

Q ss_pred             CCcHHHHHHHHHHhCCCc-EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          401 QMTRVQEATLSACLEGKD-AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grD-vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      .+++-|..++..++.+++ +++.+..|+|||..  +-.+..+....         +.+++.++||--.|..+
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~--l~~~~~~~e~~---------G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM--LGVAREAWEAA---------GYEVRGAALSGIAAENL  406 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH--HHHHHHHHHHc---------CCeEEEecCcHHHHHHH
Confidence            699999999999998765 68899999999984  33333333321         23689999998777554

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=96.64  E-value=0.0044  Score=72.48  Aligned_cols=154  Identities=23%  Similarity=0.255  Sum_probs=96.5

Q ss_pred             HHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCce
Q 006737          407 EATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIG  486 (633)
Q Consensus       407 ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~  486 (633)
                      ...+.++....-++|.+.||+|||.-+.--+|+.+.......      ..-+.+-.|+|-.+.-+.+.+.+--...    
T Consensus       384 ~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~------~~na~v~qprrisaisiaerva~er~e~----  453 (1282)
T KOG0921|consen  384 SEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGA------SFNAVVSQPRRISAISLAERVANERGEE----  453 (1282)
T ss_pred             HHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccc------cccceeccccccchHHHHHHHHHhhHHh----
Confidence            344555556677889999999999988888888877654322      1237788899988877776654332111    


Q ss_pred             EEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC-cChHHHHHHHHHHCCCC
Q 006737          487 VLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRR  565 (633)
Q Consensus       487 v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~  565 (633)
                      ++-.+| .........-... --|++||-+-|+.++.+.      +..+.++|+||.|...- ..|...+.+-+..+-++
T Consensus       454 ~g~tvg-y~vRf~Sa~prpy-g~i~fctvgvllr~~e~g------lrg~sh~i~deiherdv~~dfll~~lr~m~~ty~d  525 (1282)
T KOG0921|consen  454 VGETCG-YNVRFDSATPRPY-GSIMFCTVGVLLRMMENG------LRGISHVIIDEIHERDVDTDFVLIVLREMISTYRD  525 (1282)
T ss_pred             hccccc-ccccccccccccc-cceeeeccchhhhhhhhc------ccccccccchhhhhhccchHHHHHHHHhhhccchh
Confidence            111111 1111110001111 269999999999999876      56888999999997653 33555444444344446


Q ss_pred             CcEEEEeccCChh
Q 006737          566 RQSLLFSATMPKE  578 (633)
Q Consensus       566 ~Q~IlfSATl~~e  578 (633)
                      ..++++|||+.-.
T Consensus       526 l~v~lmsatIdTd  538 (1282)
T KOG0921|consen  526 LRVVLMSATIDTD  538 (1282)
T ss_pred             hhhhhhhcccchh
Confidence            6677777777655

>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

Probab=96.59  E-value=0.027  Score=50.63  Aligned_cols=17  Identities=29%  Similarity=0.446  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      ++.+++.|++|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            67899999999999963

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

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

Probab=96.54  E-value=0.016  Score=64.27  Aligned_cols=158  Identities=20%  Similarity=0.250  Sum_probs=95.9

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHh-CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEccc
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACL-EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT  464 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il-~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPT  464 (633)
                      +++.|+..|        -|+|.+-+...+ .|.-+++.-.-|-|||+-.+  ++...+...-         | .|||||.
T Consensus       191 ~d~kLvs~L--------lPFQreGv~faL~RgGR~llADeMGLGKTiQAl--aIA~yyraEw---------p-lliVcPA  250 (689)
T KOG1000|consen  191 MDPKLVSRL--------LPFQREGVIFALERGGRILLADEMGLGKTIQAL--AIARYYRAEW---------P-LLIVCPA  250 (689)
T ss_pred             cCHHHHHhh--------CchhhhhHHHHHhcCCeEEEecccccchHHHHH--HHHHHHhhcC---------c-EEEEecH
Confidence            346665544        588999887755 46678888999999998543  3334444432         1 6899996


Q ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       465 ReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      - +-....+.+..++.....  +.++.++.+.....-   . ...|.|.+.+.|..+-..     +.-....+||+||.|
T Consensus       251 s-vrftWa~al~r~lps~~p--i~vv~~~~D~~~~~~---t-~~~v~ivSye~ls~l~~~-----l~~~~~~vvI~DEsH  318 (689)
T KOG1000|consen  251 S-VRFTWAKALNRFLPSIHP--IFVVDKSSDPLPDVC---T-SNTVAIVSYEQLSLLHDI-----LKKEKYRVVIFDESH  318 (689)
T ss_pred             H-HhHHHHHHHHHhcccccc--eEEEecccCCccccc---c-CCeEEEEEHHHHHHHHHH-----HhcccceEEEEechh
Confidence            4 334455666666644322  344444433221110   1 136888887776543221     222347899999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      .|-+.. ...+..++..+..-..+|++|.|-.
T Consensus       319 ~Lk~sk-tkr~Ka~~dllk~akhvILLSGTPa  349 (689)
T KOG1000|consen  319 MLKDSK-TKRTKAATDLLKVAKHVILLSGTPA  349 (689)
T ss_pred             hhhccc-hhhhhhhhhHHHHhhheEEecCCcc
Confidence            987542 3335555555555677999999963

>PRK06921 hypothetical protein; Provisional

Probab=96.42  E-value=0.037  Score=57.83  Aligned_cols=27  Identities=15%  Similarity=0.320  Sum_probs=18.8

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVL  442 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~  442 (633)
                      .+..+++.|++|+|||... ..+.+.+.
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~  142 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELM  142 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHh
Confidence            3578999999999999632 23344443

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

Probab=96.39  E-value=0.0056  Score=68.53  Aligned_cols=99  Identities=26%  Similarity=0.234  Sum_probs=67.4

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccc
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF  496 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~  496 (633)
                      +-++-++||.||||.    .+|+++...+.           +++--|.|-||.+|++.+.+.     ++.+-+++|....
T Consensus       192 kIi~H~GPTNSGKTy----~ALqrl~~aks-----------GvycGPLrLLA~EV~~r~na~-----gipCdL~TGeE~~  251 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTY----RALQRLKSAKS-----------GVYCGPLRLLAHEVYDRLNAL-----GIPCDLLTGEERR  251 (700)
T ss_pred             eEEEEeCCCCCchhH----HHHHHHhhhcc-----------ceecchHHHHHHHHHHHhhhc-----CCCccccccceee
Confidence            346778999999996    57788776643           689999999999999999887     6666677775432


Q ss_pred             hHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCc
Q 006737          497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL  549 (633)
Q Consensus       497 ~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~  549 (633)
                      ...-   ..+.++.+=||-+.+.           --..+++.||||+..|-+.
T Consensus       252 ~~~~---~~~~a~hvScTVEM~s-----------v~~~yeVAViDEIQmm~Dp  290 (700)
T KOG0953|consen  252 FVLD---NGNPAQHVSCTVEMVS-----------VNTPYEVAVIDEIQMMRDP  290 (700)
T ss_pred             ecCC---CCCcccceEEEEEEee-----------cCCceEEEEehhHHhhcCc
Confidence            2211   1223566667755431           1134667777777777653

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

Probab=96.34  E-value=0.026  Score=60.85  Aligned_cols=150  Identities=18%  Similarity=0.162  Sum_probs=85.6

Q ss_pred             cCCCCCcHHHHHHHHHHhCCC--cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGK--DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~gr--DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      .|+..-+..|.-|+.+++.-.  =|.+.++.|||||+..+...+...+..+.-        -++||.=|+..+-.+|   
T Consensus       224 wGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y--------~KiiVtRp~vpvG~dI---  292 (436)
T COG1875         224 WGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRY--------RKIIVTRPTVPVGEDI---  292 (436)
T ss_pred             hccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhhh--------ceEEEecCCcCccccc---
Confidence            577778888999999988764  356779999999999888888887766532        2467766776554332   


Q ss_pred             HHHHHhcCCCceE---EEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe-------eEEEEeccc
Q 006737          475 AIALLKNHDGIGV---LTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL-------KMLVLDEAD  544 (633)
Q Consensus       475 l~~l~~~~~~i~v---~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l-------~~LVIDEAD  544 (633)
                           .+.+|..-   .-..+  ......+.+.+..    =++-+.|...+....-....+..|       .+||||||.
T Consensus       293 -----GfLPG~eEeKm~PWmq--~i~DnLE~L~~~~----~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQ  361 (436)
T COG1875         293 -----GFLPGTEEEKMGPWMQ--AIFDNLEVLFSPN----EPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQ  361 (436)
T ss_pred             -----CcCCCchhhhccchHH--HHHhHHHHHhccc----ccchHHHHHHHhccceeeeeeeeecccccccceEEEehhh
Confidence                 11111000   00000  0000111111110    012233333333221100111111       489999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      .|-    ..++..|+........+|++.
T Consensus       362 NLT----pheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         362 NLT----PHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             ccC----HHHHHHHHHhccCCCEEEEcC
Confidence            886    458999999999888888754

>PRK08181 transposase; Validated

Probab=96.31  E-value=0.039  Score=57.77  Aligned_cols=47  Identities=17%  Similarity=0.140  Sum_probs=28.6

Q ss_pred             cCCeeEEEEecccccCCcC-hHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLG-FRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +..+++|||||++.+.... -...+..|++..-....+|+.|-.-+.+
T Consensus       165 l~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~~~~  212 (269)
T PRK08181        165 LDKFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQPFGE  212 (269)
T ss_pred             HhcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCCHHH
Confidence            3467799999999875432 3345667766543345565555544444

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=96.24  E-value=0.051  Score=66.70  Aligned_cols=138  Identities=18%  Similarity=0.182  Sum_probs=81.1

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          385 GISPLTIKALTAAGYIQMTRVQEATLSACLE-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       385 ~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      ++++..+......+ ..+++-|..++..+.. ++-++++|+.|+|||.+  +-.+..+....         +.+++.++|
T Consensus       366 ~v~~~~l~a~~~~~-~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~--l~~~~~~~e~~---------G~~V~g~Ap  433 (1102)
T PRK13826        366 GVREAVLAATFARH-ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTM--MKAAREAWEAA---------GYRVVGGAL  433 (1102)
T ss_pred             CCCHHHHHHHHhcC-CCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHH--HHHHHHHHHHc---------CCeEEEEcC
Confidence            34555555544433 4799999999998865 45688999999999974  33333333321         236889999


Q ss_pred             cHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecc
Q 006737          464 TRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEA  543 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEA  543 (633)
                      |--.|..+.+.    .    ++...                         |-.+++......   ...+..-.+||||||
T Consensus       434 TgkAA~~L~e~----~----Gi~a~-------------------------TIas~ll~~~~~---~~~l~~~~vlVIDEA  477 (1102)
T PRK13826        434 AGKAAEGLEKE----A----GIQSR-------------------------TLSSWELRWNQG---RDQLDNKTVFVLDEA  477 (1102)
T ss_pred             cHHHHHHHHHh----h----CCCee-------------------------eHHHHHhhhccC---ccCCCCCcEEEEECc
Confidence            98777654321    1    22211                         111111000011   123556678999999


Q ss_pred             cccCCcChHHHHHHHHHHCC-CCCcEEEEecc
Q 006737          544 DHLLDLGFRKDVENIVDCLP-RRRQSLLFSAT  574 (633)
Q Consensus       544 D~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSAT  574 (633)
                      -++...    ++..++...+ ...++|++.=+
T Consensus       478 sMv~~~----~m~~Ll~~~~~~garvVLVGD~  505 (1102)
T PRK13826        478 GMVASR----QMALFVEAVTRAGAKLVLVGDP  505 (1102)
T ss_pred             ccCCHH----HHHHHHHHHHhcCCEEEEECCH
Confidence            877533    5555666554 45677776533

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

Probab=96.14  E-value=0.029  Score=63.41  Aligned_cols=150  Identities=14%  Similarity=0.169  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHhC-----C----CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          404 RVQEATLSACLE-----G----KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       404 ~iQ~~aIp~il~-----g----rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      |+|+-++-.++.     |    +.+++.-+-+.|||.....-++-.+.-..       ..+..+++++++++-|..+++.
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~g-------~~~~~i~~~A~~~~QA~~~f~~   73 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLDG-------EPGAEIYCAANTRDQAKIVFDE   73 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcCC-------ccCceEEEEeCCHHHHHHHHHH
Confidence            577777777663     2    46888889999999854443343333221       1235699999999999999999


Q ss_pred             HHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHH
Q 006737          475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKD  554 (633)
Q Consensus       475 l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~  554 (633)
                      +..+....+.+....         .........-.|.+-..+.+...+..... ..+=.+..++|+||+|.+-+......
T Consensus        74 ~~~~i~~~~~l~~~~---------~~~~~~~~~~~i~~~~~~s~~~~~s~~~~-~~dG~~~~~~i~DE~h~~~~~~~~~~  143 (477)
T PF03354_consen   74 AKKMIEASPELRKRK---------KPKIIKSNKKEIEFPKTGSFFKALSSDAD-SLDGLNPSLAIFDELHAHKDDELYDA  143 (477)
T ss_pred             HHHHHHhChhhccch---------hhhhhhhhceEEEEcCCCcEEEEEecCCC-CccCCCCceEEEeCCCCCCCHHHHHH
Confidence            999987544322100         00000111123444333444333332221 12223578999999999876544444


Q ss_pred             HHHHHHHCCCCCcEEEE
Q 006737          555 VENIVDCLPRRRQSLLF  571 (633)
Q Consensus       555 l~~Il~~lpk~~Q~Ilf  571 (633)
                      +..-.... ++.+++++
T Consensus       144 l~~g~~~r-~~pl~~~I  159 (477)
T PF03354_consen  144 LESGMGAR-PNPLIIII  159 (477)
T ss_pred             HHhhhccC-CCceEEEE
Confidence            44443332 34555555

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=96.12  E-value=0.028  Score=67.98  Aligned_cols=159  Identities=19%  Similarity=0.253  Sum_probs=96.8

Q ss_pred             CcHHHHHHHHHH--h-CCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSAC--L-EGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       402 pt~iQ~~aIp~i--l-~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ++.+|++-+.-+  + .++ +-|+|---|-|||+-.+.-+....++...+  ......+-.|||||. .|+-....++.+
T Consensus       976 LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~--~~e~~~~PSLIVCPs-TLtGHW~~E~~k 1052 (1549)
T KOG0392|consen  976 LRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSE--SSEFNRLPSLIVCPS-TLTGHWKSEVKK 1052 (1549)
T ss_pred             HHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhccc--chhhccCCeEEECCc-hhhhHHHHHHHH
Confidence            456787766542  2 233 779999999999996544333333333211  112222338999995 688888888887


Q ss_pred             HHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHH
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN  557 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~  557 (633)
                      ++.   .++|..++|+...+...+.-. ...+|||++...+.+-+..-     .-...-|+|+||-|.|-+.  ...+.+
T Consensus      1053 f~p---fL~v~~yvg~p~~r~~lR~q~-~~~~iiVtSYDv~RnD~d~l-----~~~~wNYcVLDEGHVikN~--ktkl~k 1121 (1549)
T KOG0392|consen 1053 FFP---FLKVLQYVGPPAERRELRDQY-KNANIIVTSYDVVRNDVDYL-----IKIDWNYCVLDEGHVIKNS--KTKLTK 1121 (1549)
T ss_pred             hcc---hhhhhhhcCChHHHHHHHhhc-cccceEEeeHHHHHHHHHHH-----HhcccceEEecCcceecch--HHHHHH
Confidence            764   467777777655443322222 23699999988886433211     1124568999999998764  444445


Q ss_pred             HHHHCCCCCcEEEEeccC
Q 006737          558 IVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       558 Il~~lpk~~Q~IlfSATl  575 (633)
                      .++.+..+. .+++|.|-
T Consensus      1122 avkqL~a~h-RLILSGTP 1138 (1549)
T KOG0392|consen 1122 AVKQLRANH-RLILSGTP 1138 (1549)
T ss_pred             HHHHHhhcc-eEEeeCCC
Confidence            555555444 44557774

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

Probab=96.11  E-value=0.018  Score=67.97  Aligned_cols=126  Identities=23%  Similarity=0.285  Sum_probs=87.0

Q ss_pred             HHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCce
Q 006737          407 EATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIG  486 (633)
Q Consensus       407 ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~  486 (633)
                      .+.+-.+.....-++.+.||-||||+..+|+.-..+..+           .+.+|+-.--||.--.+.+..+..+. ++.
T Consensus        84 VQliG~i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~gk-----------gVhvVTvNdYLA~RDae~m~~l~~~L-Gls  151 (822)
T COG0653          84 VQLLGGIVLHLGDIAEMRTGEGKTLVATLPAYLNALAGK-----------GVHVVTVNDYLARRDAEWMGPLYEFL-GLS  151 (822)
T ss_pred             HHHhhhhhhcCCceeeeecCCchHHHHHHHHHHHhcCCC-----------CcEEeeehHHhhhhCHHHHHHHHHHc-CCc
Confidence            344444444455689999999999999999864433322           27788888899988888888888766 899


Q ss_pred             EEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcc---cCcccccCCeeEEEEecccccC
Q 006737          487 VLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENK---SGLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       487 v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~---~~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      |++...+..........   .|||.++|-..| .++|...   .........+.+.||||+|-++
T Consensus       152 vG~~~~~m~~~ek~~aY---~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         152 VGVILAGMSPEEKRAAY---ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             eeeccCCCChHHHHHHH---hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            99988887655444433   379999998776 2222111   0001234568899999999776

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

Probab=96.03  E-value=0.01  Score=66.38  Aligned_cols=68  Identities=24%  Similarity=0.354  Sum_probs=48.1

Q ss_pred             CCcHHHHHHHHHHhCC-----CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG-----KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g-----rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .|+.=|-+||..+..|     +.-++.|.||||||+... -++..+   ..          -+||++|.+-||.|++.++
T Consensus        12 ~PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~A-nVI~~~---~r----------PtLV~AhNKTLAaQLy~Ef   77 (663)
T COG0556          12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTMA-NVIAKV---QR----------PTLVLAHNKTLAAQLYSEF   77 (663)
T ss_pred             CCCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHHH-HHHHHh---CC----------CeEEEecchhHHHHHHHHH
Confidence            3555566666555443     577889999999998532 222222   11          1899999999999999999


Q ss_pred             HHHHhcC
Q 006737          476 IALLKNH  482 (633)
Q Consensus       476 ~~l~~~~  482 (633)
                      +.++...
T Consensus        78 k~fFP~N   84 (663)
T COG0556          78 KEFFPEN   84 (663)
T ss_pred             HHhCcCc
Confidence            9998543

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.00  E-value=0.11  Score=57.04  Aligned_cols=56  Identities=20%  Similarity=0.285  Sum_probs=33.9

Q ss_pred             cCccccCCCHHHHHHHHHc---C--CCCCcHHH---HHHH----HHH-------hCCCcEEEEccCCCCchhhhH
Q 006737          379 KRFDECGISPLTIKALTAA---G--YIQMTRVQ---EATL----SAC-------LEGKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~---g--~~~pt~iQ---~~aI----p~i-------l~grDvLv~ApTGSGKTlayl  434 (633)
                      ..+..+|+++.+.+.|...   +  ...+...+   ...+    +.+       ..|..+++++|||+|||....
T Consensus        81 ~~L~~~g~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~g~ii~lvGptGvGKTTtia  155 (374)
T PRK14722         81 KYLFAAGFSAQLVRMIVDNLPEGEGYDTLDAAADWAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTA  155 (374)
T ss_pred             HHHHHCCCCHHHHHHHHHhhhhhcccCCHHHHHHHHHHHHHhcchhhcCCCccccCCcEEEEECCCCCCHHHHHH
Confidence            4467788999888887552   1  11222222   2222    111       235689999999999998644

>PRK07952 DNA replication protein DnaC; Validated

Probab=95.97  E-value=0.085  Score=54.50  Aligned_cols=48  Identities=23%  Similarity=0.369  Sum_probs=30.3

Q ss_pred             cCCeeEEEEecccccCCcChHH-HHHHHHHH-CCCCCcEEEEeccCChhh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRK-DVENIVDC-LPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~-~l~~Il~~-lpk~~Q~IlfSATl~~el  579 (633)
                      +..+++|||||++......+.. .+..|++. ......+|+.|---+.++
T Consensus       160 l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l  209 (244)
T PRK07952        160 LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEM  209 (244)
T ss_pred             hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHH
Confidence            3467899999999876544443 45556664 334566777665544443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=95.94  E-value=0.026  Score=50.07  Aligned_cols=17  Identities=24%  Similarity=0.489  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      +..+++.+|+|+|||..
T Consensus         2 ~~~~~l~G~~G~GKTtl   18 (148)
T smart00382        2 GEVILIVGPPGSGKTTL   18 (148)
T ss_pred             CCEEEEECCCCCcHHHH
Confidence            45789999999999984

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>PRK04296 thymidine kinase; Provisional

Probab=95.93  E-value=0.007  Score=59.83  Aligned_cols=39  Identities=15%  Similarity=0.207  Sum_probs=24.5

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      .++++||||||+.+..    .++..++..+.+.-..+++++-.
T Consensus        77 ~~~dvviIDEaq~l~~----~~v~~l~~~l~~~g~~vi~tgl~  115 (190)
T PRK04296         77 EKIDCVLIDEAQFLDK----EQVVQLAEVLDDLGIPVICYGLD  115 (190)
T ss_pred             CCCCEEEEEccccCCH----HHHHHHHHHHHHcCCeEEEEecC
Confidence            3678999999976532    34666666644444455665544

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

Probab=95.86  E-value=0.034  Score=67.29  Aligned_cols=153  Identities=16%  Similarity=0.244  Sum_probs=92.6

Q ss_pred             CCCcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .+++.+|..-+.-++    ++.++|+.-.-|-|||+- .+..|..|.....      ..|| .|||+|.--+.. ..+.+
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvq-ti~fl~~l~~~~~------~~gp-flvvvplst~~~-W~~ef  439 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQ-TITFLSYLFHSLQ------IHGP-FLVVVPLSTITA-WEREF  439 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchH-HHHHHHHHHHhhh------ccCC-eEEEeehhhhHH-HHHHH
Confidence            457888887766554    578999999999999964 2233333333221      1223 578889765543 23455


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHH---hcC-----CCcEEEECchhhHHHHhcccCcccccCCe--eEEEEecccc
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRL---ESD-----PCQILVATPGRLLDHIENKSGLSVRLMGL--KMLVLDEADH  545 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l---~~~-----~~dILIaTPgrLl~lL~~~~~~~~~Ls~l--~~LVIDEAD~  545 (633)
                      ....    .+++.+++|.......++..   ...     ..++||+|.+.++.-       +..|+.|  .+++|||||+
T Consensus       440 ~~w~----~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkD-------k~~L~~i~w~~~~vDeahr  508 (1373)
T KOG0384|consen  440 ETWT----DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKD-------KAELSKIPWRYLLVDEAHR  508 (1373)
T ss_pred             HHHh----hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhcc-------HhhhccCCcceeeecHHhh
Confidence            5553    67889999987655433222   222     478999998877542       1334444  6899999999


Q ss_pred             cCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          546 LLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       546 Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      |-+.  ...+...+..+.-+.+ ++++.|-
T Consensus       509 LkN~--~~~l~~~l~~f~~~~r-llitgTP  535 (1373)
T KOG0384|consen  509 LKND--ESKLYESLNQFKMNHR-LLITGTP  535 (1373)
T ss_pred             cCch--HHHHHHHHHHhcccce-eeecCCC
Confidence            9754  2233333444433333 4455554

>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

Probab=95.83  E-value=0.052  Score=52.44  Aligned_cols=48  Identities=19%  Similarity=0.154  Sum_probs=29.4

Q ss_pred             EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          419 AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       419 vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      +++.|++|+|||...+--+...+ +.+          -.|+|++ +.+...++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~-~~g----------~~v~~~s-~e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGL-ARG----------EPGLYVT-LEESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH-HCC----------CcEEEEE-CCCCHHHHHHHHHHc
Confidence            68999999999975332222222 221          2376664 456677776666655

A related protein is found in archaea.

>PRK06526 transposase; Provisional

Probab=95.80  E-value=0.043  Score=57.00  Aligned_cols=46  Identities=13%  Similarity=-0.020  Sum_probs=27.6

Q ss_pred             CCeeEEEEecccccCCcC-hHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLG-FRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...++|||||+|.+.... -...+..++........+|+.|..-+..
T Consensus       158 ~~~dlLIIDD~g~~~~~~~~~~~L~~li~~r~~~~s~IitSn~~~~~  204 (254)
T PRK06526        158 GRYPLLIVDEVGYIPFEPEAANLFFQLVSSRYERASLIVTSNKPFGR  204 (254)
T ss_pred             ccCCEEEEcccccCCCCHHHHHHHHHHHHHHHhcCCEEEEcCCCHHH
Confidence            456899999999875322 2334556665432334566666665554

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=95.66  E-value=0.098  Score=48.46  Aligned_cols=46  Identities=15%  Similarity=0.383  Sum_probs=30.6

Q ss_pred             CCeeEEEEecccccCCcC----------hHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLG----------FRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g----------f~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+|||||++.+.+..          ....+..+...+.....++++....++.
T Consensus        84 ~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~  139 (165)
T cd01120          84 GGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSG  139 (165)
T ss_pred             CCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCc
Confidence            467899999999875432          3456666666666555566666666554

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PRK08727 hypothetical protein; Validated

Probab=95.65  E-value=0.063  Score=54.80  Aligned_cols=45  Identities=11%  Similarity=0.090  Sum_probs=25.8

Q ss_pred             CCeeEEEEecccccCCcC-hHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLG-FRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      .+..+|||||+|.+.... ....+..+++.+.. ..++ ++|+..++.
T Consensus        92 ~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~v-I~ts~~~p~  138 (233)
T PRK08727         92 EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITL-LYTARQMPD  138 (233)
T ss_pred             hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeE-EEECCCChh
Confidence            355689999999987543 33445555554432 3344 455544443

>TIGR00376 DNA helicase, putative

Probab=95.64  E-value=0.033  Score=65.19  Aligned_cols=67  Identities=18%  Similarity=0.291  Sum_probs=52.0

Q ss_pred             CCCcHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ..+++.|..|+..++.. ..++|.||+|+|||.+. .-++.++....          .++|+++||...+.++.+.+..
T Consensus       156 ~~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~-~~ii~~~~~~g----------~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       156 PNLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTL-VELIRQLVKRG----------LRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHHcC----------CCEEEEcCcHHHHHHHHHHHHh
Confidence            46799999999998876 57889999999999753 33344443321          2599999999999998888765

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.61  E-value=0.12  Score=56.99  Aligned_cols=47  Identities=11%  Similarity=0.096  Sum_probs=31.8

Q ss_pred             cCCeeEEEEecccccCCcC-hHHHHHHHHHHCCCC-CcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLG-FRKDVENIVDCLPRR-RQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lpk~-~Q~IlfSATl~~e  578 (633)
                      +.+.++||||++.++.... ....+..++...... --++++|||....
T Consensus       252 ~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~  300 (388)
T PRK12723        252 SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTS  300 (388)
T ss_pred             hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHH
Confidence            3578899999999876321 334555666655433 3568889999765

>PRK12377 putative replication protein; Provisional

Probab=95.59  E-value=0.17  Score=52.38  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=26.5

Q ss_pred             cCCeeEEEEecccccCCcC-hHHHHHHHHHH-CCCCCcEEEEecc
Q 006737          532 LMGLKMLVLDEADHLLDLG-FRKDVENIVDC-LPRRRQSLLFSAT  574 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~g-f~~~l~~Il~~-lpk~~Q~IlfSAT  574 (633)
                      +.++++|||||++...... -...+..|++. ......+|+.|--
T Consensus       161 l~~~dLLiIDDlg~~~~s~~~~~~l~~ii~~R~~~~~ptiitSNl  205 (248)
T PRK12377        161 LCKVDLLVLDEIGIQRETKNEQVVLNQIIDRRTASMRSVGMLTNL  205 (248)
T ss_pred             hcCCCEEEEcCCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEcCC
Confidence            4578899999996543222 34455566654 3345677776553

>PRK05642 DNA replication initiation factor; Validated

Probab=95.55  E-value=0.077  Score=54.23  Aligned_cols=46  Identities=15%  Similarity=0.284  Sum_probs=30.5

Q ss_pred             CCeeEEEEecccccCCc-ChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDL-GFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .++++||||++|.+... .....+..+++.+......+++++|.++.
T Consensus        96 ~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~  142 (234)
T PRK05642         96 EQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPR  142 (234)
T ss_pred             hhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHH
Confidence            35578999999988643 34566778887665443456666665443

>PHA02533 17 large terminase protein; Provisional

Probab=95.55  E-value=0.15  Score=58.57  Aligned_cols=149  Identities=15%  Similarity=0.098  Sum_probs=86.1

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|.|.|...+..+..++=.++..+-..|||.+...-++.......         +..+++++|++..|..+++.++.+..
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~~---------~~~v~i~A~~~~QA~~vF~~ik~~ie  129 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFNK---------DKNVGILAHKASMAAEVLDRTKQAIE  129 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhCC---------CCEEEEEeCCHHHHHHHHHHHHHHHH
Confidence            578999999988766665677788889999876544443333221         23699999999999999999887765


Q ss_pred             cCCCc-eEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHH
Q 006737          481 NHDGI-GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV  559 (633)
Q Consensus       481 ~~~~i-~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il  559 (633)
                      ..+.+ ...+.. ..   .....+ .+++.|.+.|-..  +        ...=.++.++||||+|.+-+  +...+..+.
T Consensus       130 ~~P~l~~~~i~~-~~---~~~I~l-~NGS~I~~lss~~--~--------t~rG~~~~~liiDE~a~~~~--~~e~~~ai~  192 (534)
T PHA02533        130 LLPDFLQPGIVE-WN---KGSIEL-ENGSKIGAYASSP--D--------AVRGNSFAMIYIDECAFIPN--FIDFWLAIQ  192 (534)
T ss_pred             hCHHHhhcceee-cC---ccEEEe-CCCCEEEEEeCCC--C--------ccCCCCCceEEEeccccCCC--HHHHHHHHH
Confidence            44322 111100 00   001111 2334554443211  0        11122567899999998754  333444444


Q ss_pred             HHCCC--CCcEEEEeccC
Q 006737          560 DCLPR--RRQSLLFSATM  575 (633)
Q Consensus       560 ~~lpk--~~Q~IlfSATl  575 (633)
                      ..+..  ..+++++|..-
T Consensus       193 p~lasg~~~r~iiiSTp~  210 (534)
T PHA02533        193 PVISSGRSSKIIITSTPN  210 (534)
T ss_pred             HHHHcCCCceEEEEECCC
Confidence            43332  23566666654

>PRK14974 cell division protein FtsY; Provisional

Probab=95.53  E-value=0.11  Score=56.27  Aligned_cols=46  Identities=15%  Similarity=0.262  Sum_probs=36.6

Q ss_pred             CCeeEEEEecccccC-CcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLL-DLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Ll-d~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...++||||.|.++. +..+...+..+...+.++.-+++++||..+.
T Consensus       221 ~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d  267 (336)
T PRK14974        221 RGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGND  267 (336)
T ss_pred             CCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchh
Confidence            356799999999886 3456778888888787787789999988765

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=95.53  E-value=0.11  Score=51.97  Aligned_cols=43  Identities=9%  Similarity=0.244  Sum_probs=25.2

Q ss_pred             eeEEEEecccccCCc-ChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          535 LKMLVLDEADHLLDL-GFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       535 l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ..+|||||+|.+... .....+..++..+......+++|++.+.
T Consensus        91 ~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~  134 (226)
T TIGR03420        91 ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAP  134 (226)
T ss_pred             CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCCh
Confidence            357999999998643 2355566666543322224555665443

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK06893 DNA replication initiation factor; Validated

Probab=95.51  E-value=0.036  Score=56.41  Aligned_cols=46  Identities=13%  Similarity=0.239  Sum_probs=31.3

Q ss_pred             CCeeEEEEecccccCCc-ChHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDL-GFRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      .+.++|||||+|.+... .+...+..+++.+.. ..++|++|++.++.
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            45678999999998633 244456666665543 45677888887655

>PRK08116 hypothetical protein; Validated

Probab=95.42  E-value=0.17  Score=52.89  Aligned_cols=47  Identities=23%  Similarity=0.335  Sum_probs=28.6

Q ss_pred             cCCeeEEEEecccc--cCCcChHHHHHHHHHHC-CCCCcEEEEeccCChhh
Q 006737          532 LMGLKMLVLDEADH--LLDLGFRKDVENIVDCL-PRRRQSLLFSATMPKEL  579 (633)
Q Consensus       532 Ls~l~~LVIDEAD~--Lld~gf~~~l~~Il~~l-pk~~Q~IlfSATl~~el  579 (633)
                      +.+.++||||+++.  ..+| ....+..|++.. ....++|+.|-.-+.++
T Consensus       176 l~~~dlLviDDlg~e~~t~~-~~~~l~~iin~r~~~~~~~IiTsN~~~~eL  225 (268)
T PRK08116        176 LVNADLLILDDLGAERDTEW-AREKVYNIIDSRYRKGLPTIVTTNLSLEEL  225 (268)
T ss_pred             hcCCCEEEEecccCCCCCHH-HHHHHHHHHHHHHHCCCCEEEECCCCHHHH
Confidence            34677899999964  3333 345566666643 34466777666555554

>PRK06835 DNA replication protein DnaC; Validated

Probab=95.31  E-value=0.22  Score=53.79  Aligned_cols=46  Identities=15%  Similarity=0.303  Sum_probs=27.8

Q ss_pred             cCCeeEEEEecccccCCcC-hHHHHHHHHHHCC-CCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLG-FRKDVENIVDCLP-RRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lp-k~~Q~IlfSATl~~e  578 (633)
                      +.++++||||+.+...... ....+..|++..- ...++|+ |..++..
T Consensus       244 l~~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIi-TSNl~~~  291 (329)
T PRK06835        244 LINCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMII-STNLSLE  291 (329)
T ss_pred             hccCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEE-ECCCCHH
Confidence            3467899999998765333 3456667766442 3455555 5554443

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.23  E-value=0.021  Score=64.69  Aligned_cols=73  Identities=27%  Similarity=0.322  Sum_probs=44.0

Q ss_pred             CCCcEEEECchhhHHHHhcccCcccc---cCCeeE-EEEecccccCCcC---------hHHHHH---HHHHHCCCCCcEE
Q 006737          506 DPCQILVATPGRLLDHIENKSGLSVR---LMGLKM-LVLDEADHLLDLG---------FRKDVE---NIVDCLPRRRQSL  569 (633)
Q Consensus       506 ~~~dILIaTPgrLl~lL~~~~~~~~~---Ls~l~~-LVIDEAD~Lld~g---------f~~~l~---~Il~~lpk~~Q~I  569 (633)
                      ....|.++|-..|...+.+...-.+.   |.+..+ ++-||||+|-...         -...+.   .+.-.-+++--++
T Consensus        80 d~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nkd~~~l  159 (812)
T COG3421          80 DAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNKDNLLL  159 (812)
T ss_pred             CceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCCCceee
Confidence            45789999999997776544322232   444444 4679999986321         111122   2222334556678


Q ss_pred             EEeccCChh
Q 006737          570 LFSATMPKE  578 (633)
Q Consensus       570 lfSATl~~e  578 (633)
                      .||||++++
T Consensus       160 ef~at~~k~  168 (812)
T COG3421         160 EFSATIPKE  168 (812)
T ss_pred             hhhhcCCcc
Confidence            899999976

>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 [, ]

Probab=95.23  E-value=0.14  Score=50.98  Aligned_cols=46  Identities=22%  Similarity=0.385  Sum_probs=33.0

Q ss_pred             CCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ++.++|+||=+-+... ......+..++..+.+..-.+++|||...+
T Consensus        82 ~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~  128 (196)
T PF00448_consen   82 KGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQE  128 (196)
T ss_dssp             TTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGH
T ss_pred             cCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChH
Confidence            4577899998876553 235667777777776666788889999877

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>TIGR01075 uvrD DNA helicase II

Probab=95.13  E-value=0.043  Score=65.09  Aligned_cols=71  Identities=21%  Similarity=0.237  Sum_probs=52.8

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+++-|.+++.+.  ...++|.|..|||||.+. ..-+.++.....      .++-++|+|+-|+..|.++.+.+.+++
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~L-~~Ria~Li~~~~------v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         3 DGLNDKQREAVAAP--PGNLLVLAGAGSGKTRVL-THRIAWLLSVEN------ASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             cccCHHHHHHHcCC--CCCEEEEecCCCCHHHHH-HHHHHHHHHcCC------CCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            46899999998753  458999999999999873 333344443211      123369999999999999999988875

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.12  E-value=0.3  Score=54.49  Aligned_cols=59  Identities=19%  Similarity=0.255  Sum_probs=33.6

Q ss_pred             ECchhhHHHHhcccCcccccCCeeEEEEecccccCC-cChHHHHHHHHHHC-CCCCcEEEEeccCChh
Q 006737          513 ATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCL-PRRRQSLLFSATMPKE  578 (633)
Q Consensus       513 aTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~l-pk~~Q~IlfSATl~~e  578 (633)
                      .++..+...+..       +...++||||-+-+... ......+..++... .+..-.+++|||....
T Consensus       285 ~~~~~l~~~l~~-------~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~~  345 (424)
T PRK05703        285 YDPKELAKALEQ-------LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKYE  345 (424)
T ss_pred             CCHHhHHHHHHH-------hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCHH
Confidence            445555555532       23578899998865432 22344555555522 2234477889987754

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.06  E-value=0.21  Score=55.11  Aligned_cols=63  Identities=11%  Similarity=0.093  Sum_probs=36.6

Q ss_pred             EECchhhHHHHhcccCcccccCCeeEEEEecccccCCc-ChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          512 VATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-GFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       512 IaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +.+|..|.+.+..-    ....+.++|+||-+=+.... .....+..++....+..-++++|||....
T Consensus       302 ~~d~~~L~~aL~~l----k~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~  365 (436)
T PRK11889        302 VRDEAAMTRALTYF----KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSK  365 (436)
T ss_pred             cCCHHHHHHHHHHH----HhccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChH
Confidence            44677776666432    11125788999988765532 23445555555444444467789886654

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

Probab=94.93  E-value=0.05  Score=64.74  Aligned_cols=131  Identities=15%  Similarity=0.231  Sum_probs=82.7

Q ss_pred             CCCcHHHHHHHHHHhC---C-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLE---G-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~---g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .++.++|...+..+.+   + -+-|+.-.+|-|||.. .+.++..++..+.      ..+| -|||||+--|.+=. .+|
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQ-tIsLitYLmE~K~------~~GP-~LvivPlstL~NW~-~Ef  463 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQ-TISLITYLMEHKQ------MQGP-FLIIVPLSTLVNWS-SEF  463 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHH-HHHHHHHHHHHcc------cCCC-eEEeccccccCCch-hhc
Confidence            4688888888766543   3 3778888999999976 3445555555443      2234 47999998887643 233


Q ss_pred             HHHHhcCCCceEEEEECCccchH-HHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe--eEEEEecccccCCc
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKV-DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL--KMLVLDEADHLLDL  549 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~-~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l--~~LVIDEAD~Lld~  549 (633)
                      .   ...+.+....+.|...... -...+..+..+||++|.+.+..    .   ...|+.|  .++||||.|+|-+.
T Consensus       464 ~---kWaPSv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik----d---k~lLsKI~W~yMIIDEGHRmKNa  530 (1157)
T KOG0386|consen  464 P---KWAPSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK----D---KALLSKISWKYMIIDEGHRMKNA  530 (1157)
T ss_pred             c---ccccceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC----C---HHHHhccCCcceeecccccccch
Confidence            3   3344566655555433222 1223334678999999776643    2   2334544  58999999999753

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=94.90  E-value=0.13  Score=57.54  Aligned_cols=44  Identities=16%  Similarity=0.305  Sum_probs=26.4

Q ss_pred             CCeeEEEEecccccCCcC-hHHHHHHHHHHCC-CCCcEEEEeccCCh
Q 006737          533 MGLKMLVLDEADHLLDLG-FRKDVENIVDCLP-RRRQSLLFSATMPK  577 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lp-k~~Q~IlfSATl~~  577 (633)
                      .++++|||||+|.+.... ....+..+++.+. ...++|+ +++.++
T Consensus       210 ~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iii-ts~~~p  255 (450)
T PRK00149        210 RSVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVL-TSDRPP  255 (450)
T ss_pred             hcCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEE-ECCCCH
Confidence            356789999999986432 2345555555443 3455544 555544

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=94.76  E-value=0.12  Score=54.74  Aligned_cols=117  Identities=15%  Similarity=0.232  Sum_probs=62.6

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCC-CCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCcc
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTT-QLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR  495 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~-~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~  495 (633)
                      .+++++|+|+.|||.     ++++.........+ ....-|.++|-+|...-....|..+-..+.-.    +    ....
T Consensus        62 p~lLivG~snnGKT~-----Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~lgaP----~----~~~~  128 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTM-----IIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEALGAP----Y----RPRD  128 (302)
T ss_pred             CceEEecCCCCcHHH-----HHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHhCcc----c----CCCC
Confidence            489999999999998     33444443221111 11223556777788777666666655443210    0    0000


Q ss_pred             chHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcCh--HHHHHHHHHHCCCCCcE
Q 006737          496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF--RKDVENIVDCLPRRRQS  568 (633)
Q Consensus       496 ~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf--~~~l~~Il~~lpk~~Q~  568 (633)
                      ......              .....+|.        --.+++|||||+|.++....  ...+...++.+.+..++
T Consensus       129 ~~~~~~--------------~~~~~llr--------~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~i  181 (302)
T PF05621_consen  129 RVAKLE--------------QQVLRLLR--------RLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQI  181 (302)
T ss_pred             CHHHHH--------------HHHHHHHH--------HcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCC
Confidence            000000              01123332        23788999999999986553  23344555565554443

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=94.73  E-value=0.18  Score=52.40  Aligned_cols=48  Identities=25%  Similarity=0.389  Sum_probs=32.5

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      .+.++++.|++|+|||.... .+.+.+...+          . -++++++-+|+.++...
T Consensus       104 ~~~nl~l~G~~G~GKThLa~-Ai~~~l~~~g----------~-sv~f~~~~el~~~Lk~~  151 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAI-AIGNELLKAG----------I-SVLFITAPDLLSKLKAA  151 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHHcC----------C-eEEEEEHHHHHHHHHHH
Confidence            67799999999999997543 3344444322          2 35667888888776543

>PRK08084 DNA replication initiation factor; Provisional

Probab=94.72  E-value=0.21  Score=51.04  Aligned_cols=44  Identities=14%  Similarity=0.286  Sum_probs=26.9

Q ss_pred             eeEEEEecccccCCc-ChHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          535 LKMLVLDEADHLLDL-GFRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       535 l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      +++|||||+|.+... .....+..+++.+.. ....+++|++.++.
T Consensus        98 ~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~  143 (235)
T PRK08084         98 LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPR  143 (235)
T ss_pred             CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChH
Confidence            468999999998643 345556666665432 23245556665544

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

Probab=94.68  E-value=0.9  Score=54.35  Aligned_cols=149  Identities=15%  Similarity=0.211  Sum_probs=71.5

Q ss_pred             cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCC---CceEEEEECCc
Q 006737          418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHD---GIGVLTLVGGT  494 (633)
Q Consensus       418 DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~---~i~v~~l~Gg~  494 (633)
                      -+|+.---|-||||-. +..|+.++.....      .--+||||+|..-+. ..+++|.++.....   .+.|..+..-.
T Consensus       698 GcILAHcMGLGKTlQV-vtflhTvL~c~kl------g~ktaLvV~PlNt~~-NW~~EFekWm~~~e~~~~leV~eL~~vk  769 (1567)
T KOG1015|consen  698 GCILAHCMGLGKTLQV-VTFLHTVLLCDKL------GFKTALVVCPLNTAL-NWMNEFEKWMEGLEDDEKLEVSELATVK  769 (1567)
T ss_pred             chHHHHhhcccceehh-hHHHHHHHHhhcc------CCceEEEEcchHHHH-HHHHHHHHhcccccccccceeehhhhcc
Confidence            3444444588999853 2333333332211      112599999976554 45677777765321   34444332222


Q ss_pred             cchHHHH---HHhcCCCcEEEECchhhHHHHhcccCcc-----------cccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          495 RFKVDQR---RLESDPCQILVATPGRLLDHIENKSGLS-----------VRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       495 ~~~~~~~---~l~~~~~dILIaTPgrLl~lL~~~~~~~-----------~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                      .......   .....+ -|.|.-...+..+- ......           +.-..-++||.||+|.|-+.  ...+...+.
T Consensus       770 r~e~R~~~L~~W~~~g-gVmIiGYdmyRnLa-~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNe--ksa~Skam~  845 (1567)
T KOG1015|consen  770 RPEERSYMLQRWQEDG-GVMIIGYDMYRNLA-QGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNE--KSAVSKAMN  845 (1567)
T ss_pred             ChHHHHHHHHHHHhcC-CEEEEehHHHHHHh-cccchhhhHHHHHHHHhccCCCCCeEEecchhhhccc--hHHHHHHHH
Confidence            2122221   112222 34443333332222 111100           11224579999999998754  345555555


Q ss_pred             HCCCCCcEEEEeccCChh
Q 006737          561 CLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl~~e  578 (633)
                      .+.-.++|++....|-+.
T Consensus       846 ~irtkRRI~LTGTPLQNN  863 (1567)
T KOG1015|consen  846 SIRTKRRIILTGTPLQNN  863 (1567)
T ss_pred             HHHhheeEEeecCchhhh
Confidence            554455555544444444

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

Probab=94.53  E-value=0.08  Score=53.33  Aligned_cols=129  Identities=18%  Similarity=0.220  Sum_probs=68.9

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      .|..+++.+++|+|||...+--+.+.+.....          +|++++ +.+-..++.+.+..+.-              
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge----------~vlyvs-~ee~~~~l~~~~~s~g~--------------   72 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNFGE----------KVLYVS-FEEPPEELIENMKSFGW--------------   72 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHHT------------EEEEE-SSS-HHHHHHHHHTTTS--------------
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCC----------cEEEEE-ecCCHHHHHHHHHHcCC--------------
Confidence            45789999999999997543334444444121          376766 45555666666654421              


Q ss_pred             cchHHHHHHhcCCCcEEEEC----------chhhHHHHhcccCcccccCCeeEEEEecccccCC----cChHHHHHHHHH
Q 006737          495 RFKVDQRRLESDPCQILVAT----------PGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD----LGFRKDVENIVD  560 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaT----------PgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld----~gf~~~l~~Il~  560 (633)
                      +..   .....+...++=+.          +..+...+...    +.-...+.||||-...+..    ..++..+..+..
T Consensus        73 d~~---~~~~~g~l~~~d~~~~~~~~~~~~~~~l~~~i~~~----i~~~~~~~vVIDsls~l~~~~~~~~~r~~l~~l~~  145 (226)
T PF06745_consen   73 DLE---EYEDSGKLKIIDAFPERIGWSPNDLEELLSKIREA----IEELKPDRVVIDSLSALLLYDDPEELRRFLRALIK  145 (226)
T ss_dssp             -HH---HHHHTTSEEEEESSGGGST-TSCCHHHHHHHHHHH----HHHHTSSEEEEETHHHHTTSSSGGGHHHHHHHHHH
T ss_pred             cHH---HHhhcCCEEEEecccccccccccCHHHHHHHHHHH----HHhcCCCEEEEECHHHHhhcCCHHHHHHHHHHHHH
Confidence            001   01111111222122          22333333222    1112347999999998832    225667777777


Q ss_pred             HCCCCCcEEEEeccC
Q 006737          561 CLPRRRQSLLFSATM  575 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl  575 (633)
                      .+.....+++|++..
T Consensus       146 ~l~~~~~t~llt~~~  160 (226)
T PF06745_consen  146 FLKSRGVTTLLTSEM  160 (226)
T ss_dssp             HHHHTTEEEEEEEEE
T ss_pred             HHHHCCCEEEEEEcc
Confidence            776666677777774

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

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

Probab=94.50  E-value=0.2  Score=57.86  Aligned_cols=152  Identities=15%  Similarity=0.247  Sum_probs=96.3

Q ss_pred             CcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       402 pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      +..+|..-+.-+.    .|=|-|+.-.-|-|||+- .+.+|.|+.....      .-|| -|||+|.--|-    +-..+
T Consensus       568 LKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQ-sisvlAhLaE~~n------IwGP-FLVVtpaStL~----NWaqE  635 (1185)
T KOG0388|consen  568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQ-SISVLAHLAETHN------IWGP-FLVVTPASTLH----NWAQE  635 (1185)
T ss_pred             hHHHhhccHHHHHHHHHccccceehhhhccchhHH-HHHHHHHHHHhcc------CCCc-eEEeehHHHHh----HHHHH
Confidence            3455655554443    466788888999999975 4567788877643      2234 47888866554    34455


Q ss_pred             HHhcCCCceEEEEECCccchHHHHHH--------hcCCCcEEEECchhhHH---HHhcccCcccccCCeeEEEEeccccc
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQRRL--------ESDPCQILVATPGRLLD---HIENKSGLSVRLMGLKMLVLDEADHL  546 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~~l--------~~~~~dILIaTPgrLl~---lL~~~~~~~~~Ls~l~~LVIDEAD~L  546 (633)
                      +..+++.++++-+.|+.......+.+        ...+.||+|+|...+..   ++..        -.-.|.|+|||..+
T Consensus       636 isrFlP~~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qk--------vKWQYMILDEAQAI  707 (1185)
T KOG0388|consen  636 ISRFLPSFKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQK--------VKWQYMILDEAQAI  707 (1185)
T ss_pred             HHHhCccceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHHh--------hhhhheehhHHHHh
Confidence            55667789999899987644333221        23468999998766532   2221        24568999999988


Q ss_pred             CCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          547 LDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       547 ld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      -.. ....+..++..-.  +-.++++.|--
T Consensus       708 KSS-sS~RWKtLLsF~c--RNRLLLTGTPI  734 (1185)
T KOG0388|consen  708 KSS-SSSRWKTLLSFKC--RNRLLLTGTPI  734 (1185)
T ss_pred             hhh-hhhHHHHHhhhhc--cceeeecCCcc
Confidence            532 4455566655432  33567777753

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=94.49  E-value=0.27  Score=55.26  Aligned_cols=47  Identities=15%  Similarity=0.154  Sum_probs=28.6

Q ss_pred             cCCeeEEEEecccccCCc-ChHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDL-GFRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      +.++++|||||+|.+... .....+..+++.+.. ..|+|+.|-..|..
T Consensus       204 ~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~  252 (450)
T PRK14087        204 ICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPEL  252 (450)
T ss_pred             hccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHH
Confidence            346789999999988643 244566666665433 44555544444434

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=94.41  E-value=0.2  Score=55.32  Aligned_cols=43  Identities=16%  Similarity=0.346  Sum_probs=25.7

Q ss_pred             CeeEEEEecccccCCcC-hHHHHHHHHHHC-CCCCcEEEEeccCCh
Q 006737          534 GLKMLVLDEADHLLDLG-FRKDVENIVDCL-PRRRQSLLFSATMPK  577 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g-f~~~l~~Il~~l-pk~~Q~IlfSATl~~  577 (633)
                      .+++|||||+|.+.... ....+..+++.+ ....++|+ +++.++
T Consensus       199 ~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iii-ts~~~p  243 (405)
T TIGR00362       199 SVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVL-TSDRPP  243 (405)
T ss_pred             hCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEE-ecCCCH
Confidence            46789999999886542 234455555543 23456555 555443

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=94.35  E-value=0.085  Score=55.85  Aligned_cols=46  Identities=15%  Similarity=0.299  Sum_probs=35.3

Q ss_pred             ccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          531 RLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       531 ~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      .....++|||||||.|... -...+.+.++..++...+|+.+..++.
T Consensus       126 ~~~~fKiiIlDEcdsmtsd-aq~aLrr~mE~~s~~trFiLIcnylsr  171 (346)
T KOG0989|consen  126 PCPPFKIIILDECDSMTSD-AQAALRRTMEDFSRTTRFILICNYLSR  171 (346)
T ss_pred             CCCcceEEEEechhhhhHH-HHHHHHHHHhccccceEEEEEcCChhh
Confidence            3556789999999998743 566778888887778888888776544

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=94.30  E-value=0.087  Score=62.13  Aligned_cols=71  Identities=14%  Similarity=0.166  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .+++-|.+++.+.  ...++|.|..|||||.+..- -+.+++....      .++-++|+|+.|+..|.++.+++..++.
T Consensus         2 ~Ln~~Q~~av~~~--~g~~lV~AgpGSGKT~vL~~-Ria~Li~~~~------v~p~~IL~lTFT~kAA~em~~Rl~~~l~   72 (672)
T PRK10919          2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITN-KIAHLIRGCG------YQARHIAAVTFTNKAAREMKERVAQTLG   72 (672)
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCCHHHHHHH-HHHHHHHhcC------CCHHHeeeEechHHHHHHHHHHHHHHhC
Confidence            4789999998753  45789999999999987433 3344443211      1223599999999999999999987764

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=94.30  E-value=0.3  Score=63.92  Aligned_cols=134  Identities=16%  Similarity=0.185  Sum_probs=79.5

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .+++-|..++..++..  +=+++.++.|+|||.+  +-.+..+....         +.++++++||-..+..+.+.....
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~--l~~l~~~~~~~---------G~~V~~lAPTgrAA~~L~e~~g~~  497 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI--AQLLLHLASEQ---------GYEIQIITAGSLSAQELRQKIPRL  497 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH--HHHHHHHHHhc---------CCeEEEEeCCHHHHHHHHHHhcch
Confidence            5889999999999876  4678999999999974  33333343321         236999999998877665442211


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                      ..              ........+..   ..-..|..+|+   . .   ...+..-++||||||-++...    .+..+
T Consensus       498 A~--------------Ti~~~l~~l~~---~~~~~tv~~fl---~-~---~~~l~~~~vlIVDEAsMl~~~----~~~~L  549 (1960)
T TIGR02760       498 AS--------------TFITWVKNLFN---DDQDHTVQGLL---D-K---SSPFSNKDIFVVDEANKLSNN----ELLKL  549 (1960)
T ss_pred             hh--------------hHHHHHHhhcc---cccchhHHHhh---c-c---cCCCCCCCEEEEECCCCCCHH----HHHHH
Confidence            00              00000111111   11112222232   1 1   123556789999999887643    66667


Q ss_pred             HHHC-CCCCcEEEEec
Q 006737          559 VDCL-PRRRQSLLFSA  573 (633)
Q Consensus       559 l~~l-pk~~Q~IlfSA  573 (633)
                      +... +.+.++|++-=
T Consensus       550 l~~a~~~garvVlvGD  565 (1960)
T TIGR02760       550 IDKAEQHNSKLILLND  565 (1960)
T ss_pred             HHHHhhcCCEEEEEcC
Confidence            6655 35678887754

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

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

Probab=94.27  E-value=0.61  Score=52.53  Aligned_cols=42  Identities=19%  Similarity=0.214  Sum_probs=28.6

Q ss_pred             CCCCCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHH
Q 006737          398 GYIQMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIE  439 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~  439 (633)
                      -|...+|-|-.-+-.    +-++.++++.+|+|+|||.+.+--++.
T Consensus        13 PY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~a   58 (755)
T KOG1131|consen   13 PYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIA   58 (755)
T ss_pred             CCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHH
Confidence            455667777554433    334668999999999999875544443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=94.16  E-value=0.73  Score=54.69  Aligned_cols=44  Identities=18%  Similarity=0.292  Sum_probs=28.3

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+++||||+|.|.... .+.+.++++.-+....+|+ ++|-+..
T Consensus       118 gr~KVIIIDEah~LT~~A-~NALLKtLEEPP~~v~FIL-aTtd~~K  161 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHA-FNAMLKTLEEPPPHVKFIL-ATTDPQK  161 (830)
T ss_pred             CCceEEEEeChhhCCHHH-HHHHHHHHHhcCCCeEEEE-EECChhh
Confidence            357899999999987543 3455566666665554444 4454444

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=94.09  E-value=0.23  Score=57.57  Aligned_cols=47  Identities=23%  Similarity=0.349  Sum_probs=30.5

Q ss_pred             CCeeEEEEecccccCCcC-hHHHHHHHHHHCCC-CCcEEEEeccCChhh
Q 006737          533 MGLKMLVLDEADHLLDLG-FRKDVENIVDCLPR-RRQSLLFSATMPKEL  579 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lpk-~~Q~IlfSATl~~el  579 (633)
                      .++++||||++|.+.... ....+..+++.+.. +.++|+.|-..|.++
T Consensus       376 ~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL  424 (617)
T PRK14086        376 REMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQL  424 (617)
T ss_pred             hcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhh
Confidence            457889999999986543 34556667665543 567776555544443

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.05  E-value=0.36  Score=56.37  Aligned_cols=39  Identities=18%  Similarity=0.298  Sum_probs=26.1

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+++||||+|.|....+ +.+.++++.-+.++.+|+.|
T Consensus       123 gr~KViIIDEah~Ls~~Aa-NALLKTLEEPP~~v~FILaT  161 (700)
T PRK12323        123 GRFKVYMIDEVHMLTNHAF-NAMLKTLEEPPEHVKFILAT  161 (700)
T ss_pred             CCceEEEEEChHhcCHHHH-HHHHHhhccCCCCceEEEEe
Confidence            4678999999999975433 44555566555566555554

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=94.02  E-value=0.35  Score=51.34  Aligned_cols=42  Identities=19%  Similarity=0.358  Sum_probs=27.5

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      ...++|||||+|.+... ....+..+++..+...++|+ +++-+
T Consensus       124 ~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il-~~~~~  165 (337)
T PRK12402        124 ADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFII-ATRQP  165 (337)
T ss_pred             CCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEE-EeCCh
Confidence            45678999999988642 44566677776666666555 44433

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=94.01  E-value=0.48  Score=56.90  Aligned_cols=41  Identities=20%  Similarity=0.292  Sum_probs=23.8

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCC-CCCcEEEEecc
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLP-RRRQSLLFSAT  574 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSAT  574 (633)
                      ..+.+|||||+|.|... ....+..++.... ...+++++..+
T Consensus       868 r~v~IIILDEID~L~kK-~QDVLYnLFR~~~~s~SKLiLIGIS  909 (1164)
T PTZ00112        868 RNVSILIIDEIDYLITK-TQKVLFTLFDWPTKINSKLVLIAIS  909 (1164)
T ss_pred             ccceEEEeehHhhhCcc-HHHHHHHHHHHhhccCCeEEEEEec
Confidence            34678999999999864 2344445554322 24455544433

>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

Probab=93.97  E-value=0.018  Score=56.68  Aligned_cols=126  Identities=24%  Similarity=0.238  Sum_probs=53.6

Q ss_pred             EEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH
Q 006737          420 VVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD  499 (633)
Q Consensus       420 Lv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~  499 (633)
                      |+.|+-|-|||.+.-+.+...+..          ...+++|.+|+.+-+..+++.+..-+... +++.    ........
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~----------~~~~I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~----~~~~~~~~   65 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQK----------GKIRILVTAPSPENVQTLFEFAEKGLKAL-GYKE----EKKKRIGQ   65 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS---------------EEEE-SS--S-HHHHHCC------------------------
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHh----------cCceEEEecCCHHHHHHHHHHHHhhcccc-cccc----cccccccc
Confidence            578999999998654432211111          11359999999999888877665443321 1111    00000000


Q ss_pred             HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       500 ~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+......|-+..|..+...          ....++||||||=.+-    .+.+..++..    ...++||.|+.--
T Consensus        66 ~~~~~~~~~~i~f~~Pd~l~~~----------~~~~DlliVDEAAaIp----~p~L~~ll~~----~~~vv~stTi~GY  126 (177)
T PF05127_consen   66 IIKLRFNKQRIEFVAPDELLAE----------KPQADLLIVDEAAAIP----LPLLKQLLRR----FPRVVFSTTIHGY  126 (177)
T ss_dssp             -------CCC--B--HHHHCCT--------------SCEEECTGGGS-----HHHHHHHHCC----SSEEEEEEEBSST
T ss_pred             ccccccccceEEEECCHHHHhC----------cCCCCEEEEechhcCC----HHHHHHHHhh----CCEEEEEeecccc
Confidence            0111112346666777655321          1235789999997764    3455555433    3477888888653

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=93.95  E-value=0.27  Score=59.16  Aligned_cols=45  Identities=20%  Similarity=0.239  Sum_probs=31.1

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||||.|... -.+.+.++++..+..+.+|+.+ |-+..
T Consensus       118 ~~~~KV~IIDEad~lt~~-a~NaLLK~LEEpP~~~~fIl~t-t~~~k  162 (824)
T PRK07764        118 ESRYKIFIIDEAHMVTPQ-GFNALLKIVEEPPEHLKFIFAT-TEPDK  162 (824)
T ss_pred             cCCceEEEEechhhcCHH-HHHHHHHHHhCCCCCeEEEEEe-CChhh
Confidence            356789999999999754 4456667777777666666654 54444

>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

Probab=93.94  E-value=0.26  Score=49.89  Aligned_cols=49  Identities=22%  Similarity=0.333  Sum_probs=33.3

Q ss_pred             cCCeeEEEEecccccCCcC-hHHHHHHHHHHCC-CCCcEEEEeccCChhhh
Q 006737          532 LMGLKMLVLDEADHLLDLG-FRKDVENIVDCLP-RRRQSLLFSATMPKELV  580 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lp-k~~Q~IlfSATl~~el~  580 (633)
                      +..+++||||.+|.+.... ....+..+++.+. ...|+|+.|...|.++.
T Consensus        95 ~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~  145 (219)
T PF00308_consen   95 LRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELS  145 (219)
T ss_dssp             HCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTT
T ss_pred             hhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCcccc
Confidence            4578899999999987542 4556666666543 35677777777777653

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=93.89  E-value=0.61  Score=54.38  Aligned_cols=139  Identities=19%  Similarity=0.227  Sum_probs=84.6

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcC-CCceEEEEEC
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH-DGIGVLTLVG  492 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~-~~i~v~~l~G  492 (633)
                      ...+-.++..|--.|||.... +++..++...        .+.+++|++|.+..+..+++++...+... +...+..+.|
T Consensus       252 fkqk~tVflVPRR~GKTwivv-~iI~~ll~s~--------~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG  322 (738)
T PHA03368        252 FRQRATVFLVPRRHGKTWFLV-PLIALALATF--------RGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG  322 (738)
T ss_pred             hhccceEEEecccCCchhhHH-HHHHHHHHhC--------CCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC
Confidence            455678888999999998644 6665554432        24679999999999999999998876532 1111222222


Q ss_pred             CccchHHHHHHhcCC-CcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC-CCCcEEE
Q 006737          493 GTRFKVDQRRLESDP-CQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP-RRRQSLL  570 (633)
Q Consensus       493 g~~~~~~~~~l~~~~-~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~Il  570 (633)
                       ...   ...+.++. ..|.++|-       .+..  ...=..+++||||||+.+-+.    .+..|+-.+. .+.++|+
T Consensus       323 -e~I---~i~f~nG~kstI~FaSa-------rntN--siRGqtfDLLIVDEAqFIk~~----al~~ilp~l~~~n~k~I~  385 (738)
T PHA03368        323 -ETI---SFSFPDGSRSTIVFASS-------HNTN--GIRGQDFNLLFVDEANFIRPD----AVQTIMGFLNQTNCKIIF  385 (738)
T ss_pred             -cEE---EEEecCCCccEEEEEec-------cCCC--CccCCcccEEEEechhhCCHH----HHHHHHHHHhccCccEEE
Confidence             111   00111111 24555532       1110  122236889999999998764    4444443332 3799999


Q ss_pred             EeccCChh
Q 006737          571 FSATMPKE  578 (633)
Q Consensus       571 fSATl~~e  578 (633)
                      +|.|.+..
T Consensus       386 ISS~Ns~~  393 (738)
T PHA03368        386 VSSTNTGK  393 (738)
T ss_pred             EecCCCCc
Confidence            99998765

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=93.78  E-value=0.29  Score=62.33  Aligned_cols=63  Identities=25%  Similarity=0.352  Sum_probs=45.2

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhh--HHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAF--LLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlay--lLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      .+++-|..++..++..  +-++|++..|+|||...  ++-++..+...         .+..++.++||-..+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e~---------~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPES---------ERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhhc---------cCceEEEEechHHHHHHHH
Confidence            6899999999999965  67899999999999853  22222222111         1245888999988887653

>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]

Probab=93.77  E-value=0.0075  Score=66.67  Aligned_cols=104  Identities=13%  Similarity=0.008  Sum_probs=89.1

Q ss_pred             eeeeeccCCCCccCCCCcchhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCc---CCCCCCCCch
Q 006737           21 RVFARPMGGGPRTFPGGLNKWQWKRMHEKKAKEKEKRLLEQEKQLYQARVRSQIRTKLFDKADPDSE---TNQHKPMSPD   97 (633)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~   97 (633)
                      -++++.++|+++||+..+..|+|..+...+.|..-.+++....+-|.+++.+|.++.+...+...-.   ..+..+..++
T Consensus       121 Dvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~  200 (543)
T KOG0342|consen  121 DVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEAD  200 (543)
T ss_pred             cceeeeccCCCceeeehhHHHHHHHhcccCCCCCeeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHH
Confidence            4678899999999999999999999999999999999999999999999999999999776443221   2245556778


Q ss_pred             HHHHHHHHhhcccCcccccCCCCCCCc
Q 006737           98 EHVKALADRFMKEGAEDLWNEDDGPVK  124 (633)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (633)
                      ...|.....+.+||....|-+|.++..
T Consensus       201 kl~k~~niliATPGRLlDHlqNt~~f~  227 (543)
T KOG0342|consen  201 KLVKGCNILIATPGRLLDHLQNTSGFL  227 (543)
T ss_pred             HhhccccEEEeCCchHHhHhhcCCcch
Confidence            888889999999999999999998844

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=93.74  E-value=0.3  Score=56.84  Aligned_cols=40  Identities=13%  Similarity=0.139  Sum_probs=27.6

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....++|||||+|.|... -.+.+.+.++..+..+.+|+.+
T Consensus       130 ~a~~KVvIIDEad~Ls~~-a~naLLKtLEePp~~~~fIl~t  169 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTA-AFNALLKTLEEPPPHVKFIFAT  169 (598)
T ss_pred             cCCcEEEEEEChHhCCHH-HHHHHHHHHHhCCCCeEEEEEe
Confidence            457789999999999753 3445555666666666666654

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=93.66  E-value=0.32  Score=49.02  Aligned_cols=43  Identities=16%  Similarity=0.248  Sum_probs=26.8

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCc-EEEEeccCCh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQ-SLLFSATMPK  577 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q-~IlfSATl~~  577 (633)
                      ..++|||||+|.+... -...+..+++.+..... +++++++.++
T Consensus        90 ~~~~liiDdi~~l~~~-~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDDA-QQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCch-HHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            3457999999987543 34445555554433333 5777777654

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=93.62  E-value=0.32  Score=53.37  Aligned_cols=135  Identities=14%  Similarity=0.201  Sum_probs=73.5

Q ss_pred             EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHH-HHHHHHHHHHHHHhcCCCceEEEEECCccch
Q 006737          419 AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRE-LASQIAAEAIALLKNHDGIGVLTLVGGTRFK  497 (633)
Q Consensus       419 vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTRe-La~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~  497 (633)
                      .++.+..|||||.+.++-++..++...        ++.++||+-|+.. |..-++..+...+... ++....-.....+ 
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~~--------~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~-g~~~~~~~~~~~~-   73 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAINK--------KQQNILAARKVQNSIRDSVFKDIENLLSIE-GINYEFKKSKSSM-   73 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhcC--------CCcEEEEEehhhhHHHHHHHHHHHHHHHHc-CChhheeecCCcc-
Confidence            578899999999998887777776641        1246899999987 6666677777665433 2221111111100 


Q ss_pred             HHHHHHhcCCCcEEEECc-hhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC--CCCcEEEEecc
Q 006737          498 VDQRRLESDPCQILVATP-GRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP--RRRQSLLFSAT  574 (633)
Q Consensus       498 ~~~~~l~~~~~dILIaTP-grLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp--k~~Q~IlfSAT  574 (633)
                        ...+...+..|++..- ..... +       .....+.+++||||..+...    .+..++..+.  ...+.|++|.|
T Consensus        74 --~i~~~~~g~~i~f~g~~d~~~~-i-------k~~~~~~~~~idEa~~~~~~----~~~~l~~rlr~~~~~~~i~~t~N  139 (396)
T TIGR01547        74 --EIKILNTGKKFIFKGLNDKPNK-L-------KSGAGIAIIWFEEASQLTFE----DIKELIPRLRETGGKKFIIFSSN  139 (396)
T ss_pred             --EEEecCCCeEEEeecccCChhH-h-------hCcceeeeehhhhhhhcCHH----HHHHHHHHhhccCCccEEEEEcC
Confidence              0011111234555432 11111 1       12334689999999998543    3333333332  22224666766


Q ss_pred             CCh
Q 006737          575 MPK  577 (633)
Q Consensus       575 l~~  577 (633)
                      -..
T Consensus       140 P~~  142 (396)
T TIGR01547       140 PES  142 (396)
T ss_pred             cCC
Confidence            543

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=93.60  E-value=0.43  Score=53.54  Aligned_cols=45  Identities=16%  Similarity=0.332  Sum_probs=26.1

Q ss_pred             CeeEEEEecccccCCcC-hHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLG-FRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      .+++|||||+|.+.+.. ....+..+++.+.. ..|+|+.|-.-|..
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~  240 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQK  240 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHH
Confidence            46789999999887542 33445555554433 34555544444444

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=93.59  E-value=0.55  Score=49.62  Aligned_cols=39  Identities=15%  Similarity=0.307  Sum_probs=27.4

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ..++|||||+|.+........+..+++..+..+++|+.+
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEc
Confidence            456899999999844335566677777777777666544

>PRK11054 helD DNA helicase IV; Provisional

Probab=93.57  E-value=0.26  Score=58.18  Aligned_cols=73  Identities=18%  Similarity=0.212  Sum_probs=52.5

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      -..+++-|+.++-.  ...+++|.|..|||||.+.+ .-+..++....      ..+-++|+|+.|+..|..+.+++...
T Consensus       194 ~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~-~r~ayLl~~~~------~~~~~IL~ltft~~AA~em~eRL~~~  264 (684)
T PRK11054        194 SSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLV-ARAGWLLARGQ------AQPEQILLLAFGRQAAEEMDERIRER  264 (684)
T ss_pred             CCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHH-HHHHHHHHhCC------CCHHHeEEEeccHHHHHHHHHHHHHh
Confidence            35799999999864  33578999999999998643 33333443221      11236999999999999999988776


Q ss_pred             Hh
Q 006737          479 LK  480 (633)
Q Consensus       479 ~~  480 (633)
                      +.
T Consensus       265 lg  266 (684)
T PRK11054        265 LG  266 (684)
T ss_pred             cC
Confidence            54

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=93.47  E-value=1.5  Score=51.51  Aligned_cols=153  Identities=8%  Similarity=0.111  Sum_probs=83.5

Q ss_pred             CcHHHHHHHHHH---hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          402 MTRVQEATLSAC---LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       402 pt~iQ~~aIp~i---l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      |+|.=.+-|..+   +..+-.++.+|-|.|||.+..+.++ .+...         .+.+++|++|...-+.++++.+...
T Consensus       170 ~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~-~La~f---------~Gi~IlvTAH~~~ts~evF~rv~~~  239 (752)
T PHA03333        170 PSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILA-AMISF---------LEIDIVVQAQRKTMCLTLYNRVETV  239 (752)
T ss_pred             CChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHH-HHHHh---------cCCeEEEECCChhhHHHHHHHHHHH
Confidence            344433334333   3456678889999999987544433 22221         1246999999999999999988888


Q ss_pred             HhcCC------C-ceEEEEECCcc-chHHH-HHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCc
Q 006737          479 LKNHD------G-IGVLTLVGGTR-FKVDQ-RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL  549 (633)
Q Consensus       479 ~~~~~------~-i~v~~l~Gg~~-~~~~~-~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~  549 (633)
                      +....      . -.+..+.|+.. ..... ...+.++..|.+++-.       .+   ...-...++||||||..+-. 
T Consensus       240 le~lg~~~~fp~~~~iv~vkgg~E~I~f~~p~gak~G~sti~F~Ars-------~~---s~RG~~~DLLIVDEAAfI~~-  308 (752)
T PHA03333        240 VHAYQHKPWFPEEFKIVTLKGTDENLEYISDPAAKEGKTTAHFLASS-------PN---AARGQNPDLVIVDEAAFVNP-  308 (752)
T ss_pred             HHHhccccccCCCceEEEeeCCeeEEEEecCcccccCcceeEEeccc-------CC---CcCCCCCCEEEEECcccCCH-
Confidence            75321      1 11222222211 00000 0000011223332211       01   11223568999999999875 


Q ss_pred             ChHHHHHHHHHHCC-CCCcEEEEeccCChh
Q 006737          550 GFRKDVENIVDCLP-RRRQSLLFSATMPKE  578 (633)
Q Consensus       550 gf~~~l~~Il~~lp-k~~Q~IlfSATl~~e  578 (633)
                         ..+..|+-.+. ...+++++|.+.+..
T Consensus       309 ---~~l~aIlP~l~~~~~k~IiISS~~~~~  335 (752)
T PHA03333        309 ---GALLSVLPLMAVKGTKQIHISSPVDAD  335 (752)
T ss_pred             ---HHHHHHHHHHccCCCceEEEeCCCCcc
Confidence               35555555444 467888889887554

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.45  E-value=1.3  Score=51.56  Aligned_cols=45  Identities=18%  Similarity=0.225  Sum_probs=29.5

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||||.|... -.+.+.++++..+...-+|+.+ |-++.
T Consensus       116 ~~~~KVvIIDEah~Lt~~-A~NALLK~LEEpp~~~~fIL~t-te~~k  160 (584)
T PRK14952        116 QSRYRIFIVDEAHMVTTA-GFNALLKIVEEPPEHLIFIFAT-TEPEK  160 (584)
T ss_pred             cCCceEEEEECCCcCCHH-HHHHHHHHHhcCCCCeEEEEEe-CChHh
Confidence            456789999999999754 3445566666666555555544 55444

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=93.42  E-value=0.36  Score=54.22  Aligned_cols=47  Identities=13%  Similarity=0.287  Sum_probs=28.8

Q ss_pred             CCeeEEEEecccccCCcC-hHHHHHHHHHHCC-CCCcEEEEeccCChhh
Q 006737          533 MGLKMLVLDEADHLLDLG-FRKDVENIVDCLP-RRRQSLLFSATMPKEL  579 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g-f~~~l~~Il~~lp-k~~Q~IlfSATl~~el  579 (633)
                      .++++|||||+|.+.... ....+..+++.+. ...|+|+.|-+.|.++
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l  249 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDL  249 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHH
Confidence            467799999999987532 3455556655432 3456655554445543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=93.37  E-value=0.47  Score=51.73  Aligned_cols=16  Identities=25%  Similarity=0.488  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      .+++++||+|+|||.+
T Consensus        56 ~~~lI~G~~GtGKT~l   71 (394)
T PRK00411         56 LNVLIYGPPGTGKTTT   71 (394)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            5799999999999985

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=93.32  E-value=0.29  Score=50.30  Aligned_cols=33  Identities=9%  Similarity=0.180  Sum_probs=21.9

Q ss_pred             CCcHHHHHHHHHHh----CCC-cEEEEccCCCCchhhh
Q 006737          401 QMTRVQEATLSACL----EGK-DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       401 ~pt~iQ~~aIp~il----~gr-DvLv~ApTGSGKTlay  433 (633)
                      .+++.+..++..+.    .+. .++++|++|+|||...
T Consensus        23 ~~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        23 YPSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            34555555555443    223 6889999999999743

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

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

Probab=93.32  E-value=0.52  Score=50.03  Aligned_cols=51  Identities=24%  Similarity=0.346  Sum_probs=35.0

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcC
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATS  446 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~  446 (633)
                      .+.+|++|++++-+.+.+..                  ...=++|.+|||||||.. +..++.++.+...
T Consensus       104 ~i~~~e~LglP~i~~~~~~~------------------~~GLILVTGpTGSGKSTT-lAamId~iN~~~~  154 (353)
T COG2805         104 KIPTLEELGLPPIVRELAES------------------PRGLILVTGPTGSGKSTT-LAAMIDYINKHKA  154 (353)
T ss_pred             cCCCHHHcCCCHHHHHHHhC------------------CCceEEEeCCCCCcHHHH-HHHHHHHHhccCC
Confidence            34568888888877663322                  112488999999999976 4567777766543

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.19  E-value=0.63  Score=47.51  Aligned_cols=53  Identities=17%  Similarity=0.073  Sum_probs=34.3

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      .|..+++.|++|+|||...+--+.+.+...           -.+||++ +.+-..|+.+.+..+.
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~g-----------e~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMG-----------EPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHcC-----------CcEEEEE-eeCCHHHHHHHHHHhC
Confidence            467899999999999974332233333211           1377776 5667777777776653

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=93.18  E-value=0.41  Score=56.32  Aligned_cols=66  Identities=23%  Similarity=0.328  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHHHHhCC-----CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG-----KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g-----rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .|++.|..++..+.++     +..++.+.||||||+... .++..+   .          ..+|||+|+..+|.|+++.+
T Consensus        12 ~~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~---~----------r~vLIVt~~~~~A~~l~~dL   77 (652)
T PRK05298         12 KPAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL---Q----------RPTLVLAHNKTLAAQLYSEF   77 (652)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh---C----------CCEEEEECCHHHHHHHHHHH
Confidence            6899999999887543     257799999999998532 222211   1          13899999999999999999


Q ss_pred             HHHHh
Q 006737          476 IALLK  480 (633)
Q Consensus       476 ~~l~~  480 (633)
                      ..++.
T Consensus        78 ~~~~~   82 (652)
T PRK05298         78 KEFFP   82 (652)
T ss_pred             HHhcC
Confidence            88864

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=93.14  E-value=0.94  Score=53.63  Aligned_cols=151  Identities=19%  Similarity=0.176  Sum_probs=86.7

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhCCC--cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          394 LTAAGYIQMTRVQEATLSACLEGK--DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       394 L~~~g~~~pt~iQ~~aIp~il~gr--DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      |.....+....-|.+.+..++..+  -+++.|.-|-|||.+.-|.+.. +.....        +..++|++|+.+-+..+
T Consensus       207 l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~-~~~~~~--------~~~iiVTAP~~~nv~~L  277 (758)
T COG1444         207 LYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAA-AARLAG--------SVRIIVTAPTPANVQTL  277 (758)
T ss_pred             HhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHH-HHHhcC--------CceEEEeCCCHHHHHHH
Confidence            444445555555666666666654  5888999999999987665532 222111        24699999999999988


Q ss_pred             HHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcCh
Q 006737          472 AAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF  551 (633)
Q Consensus       472 ~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf  551 (633)
                      +..+.+-+... +.+-.+......   ...........|=+-+|....            . .-++||||||=.|-    
T Consensus       278 f~fa~~~l~~l-g~~~~v~~d~~g---~~~~~~~~~~~i~y~~P~~a~------------~-~~DllvVDEAAaIp----  336 (758)
T COG1444         278 FEFAGKGLEFL-GYKRKVAPDALG---EIREVSGDGFRIEYVPPDDAQ------------E-EADLLVVDEAAAIP----  336 (758)
T ss_pred             HHHHHHhHHHh-CCcccccccccc---ceeeecCCceeEEeeCcchhc------------c-cCCEEEEehhhcCC----
Confidence            87776655433 222111111000   000011111234445553321            1 15689999997764    


Q ss_pred             HHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          552 RKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       552 ~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+.+.+++...    +.++||.|+.--
T Consensus       337 lplL~~l~~~~----~rv~~sTTIhGY  359 (758)
T COG1444         337 LPLLHKLLRRF----PRVLFSTTIHGY  359 (758)
T ss_pred             hHHHHHHHhhc----CceEEEeeeccc
Confidence            45666666554    478888888543

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

Probab=93.14  E-value=0.32  Score=58.18  Aligned_cols=160  Identities=16%  Similarity=0.158  Sum_probs=89.8

Q ss_pred             CCCcHHHHHHHHHHh-----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACL-----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE  474 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il-----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~  474 (633)
                      ..+.++|...+..+.     .+.+.++...-|.|||+..+.-+.. +.......      ...+||++|+- ++.+..++
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~-~~~~~~~~------~~~~liv~p~s-~~~nw~~e  408 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLS-LLESIKVY------LGPALIVVPAS-LLSNWKRE  408 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHh-hhhcccCC------CCCeEEEecHH-HHHHHHHH
Confidence            456677887776644     2557788899999999764433322 22221110      12488999974 44555666


Q ss_pred             HHHHHhcCCCce-EEEEECCccc----hHHHHHHhcCC----CcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc
Q 006737          475 AIALLKNHDGIG-VLTLVGGTRF----KVDQRRLESDP----CQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH  545 (633)
Q Consensus       475 l~~l~~~~~~i~-v~~l~Gg~~~----~~~~~~l~~~~----~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~  545 (633)
                      +.++.   +.++ +...+|....    ......+....    .+|+++|-+.|...+....  .+.-....++|+||||.
T Consensus       409 ~~k~~---~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~--~l~~~~~~~~v~DEa~~  483 (866)
T COG0553         409 FEKFA---PDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHG--GLKKIEWDRVVLDEAHR  483 (866)
T ss_pred             HhhhC---ccccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHH--HHhhceeeeeehhhHHH
Confidence            65554   3555 6777776541    22222222211    5899999888877321110  12234567999999999


Q ss_pred             cCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          546 LLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       546 Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      +-+.. ......+. .++.... +++|.|.
T Consensus       484 ikn~~-s~~~~~l~-~~~~~~~-~~LtgTP  510 (866)
T COG0553         484 IKNDQ-SSEGKALQ-FLKALNR-LDLTGTP  510 (866)
T ss_pred             Hhhhh-hHHHHHHH-HHhhcce-eeCCCCh
Confidence            76432 22222222 3332232 6667765

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=93.12  E-value=0.31  Score=57.21  Aligned_cols=70  Identities=14%  Similarity=0.147  Sum_probs=51.4

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          402 MTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       402 pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      +++-|.+++.+  ....++|.|..|||||.+.+- -+.+++....      ..+-++|+|+.|+..|.++.+.+.+.+.
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~-ri~~ll~~~~------~~p~~IL~vTFt~~Aa~em~~Rl~~~l~   71 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITN-KIAYLIQNCG------YKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHH-HHHHHHHhcC------CCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            68899998865  346899999999999986443 3334443211      1123589999999999999999987764

Designed to identify rep members of the uvrD/rep subfamily.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=93.11  E-value=0.51  Score=60.77  Aligned_cols=65  Identities=23%  Similarity=0.263  Sum_probs=44.7

Q ss_pred             CCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      ..+++.|..++..++.+  +-++|++..|+|||..  +-.+..++.....     ..+..++.++||--.|..+
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~--l~~v~~~~~~l~~-----~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQ--FRAVMSAVNTLPE-----SERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHH--HHHHHHHHHHhhc-----ccCceEEEECCcHHHHHHH
Confidence            36899999999999985  4688999999999975  2222222221100     0124588899998888654

>PRK09183 transposase/IS protein; Provisional

Probab=93.08  E-value=0.48  Score=49.27  Aligned_cols=21  Identities=19%  Similarity=0.259  Sum_probs=17.7

Q ss_pred             HhCCCcEEEEccCCCCchhhh
Q 006737          413 CLEGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       413 il~grDvLv~ApTGSGKTlay  433 (633)
                      +..+.++++.||+|+|||...
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa  119 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLA  119 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHH
Confidence            456889999999999999743

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=93.02  E-value=0.18  Score=59.94  Aligned_cols=72  Identities=18%  Similarity=0.242  Sum_probs=53.1

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+++-|.+++.+.  ...++|.|..|||||.+-. .-+.++.....      .++-++|+|+-|+..|.++.+++.++.
T Consensus         8 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~vl~-~Ria~Li~~~~------v~p~~IL~lTFT~kAA~Em~~Rl~~~~   78 (721)
T PRK11773          8 DSLNDKQREAVAAP--LGNMLVLAGAGSGKTRVLV-HRIAWLMQVEN------ASPYSIMAVTFTNKAAAEMRHRIEQLL   78 (721)
T ss_pred             HhcCHHHHHHHhCC--CCCEEEEecCCCCHHHHHH-HHHHHHHHcCC------CChhHeEeeeccHHHHHHHHHHHHHHh
Confidence            35899999998753  4589999999999998643 33334443211      122359999999999999999998886


Q ss_pred             h
Q 006737          480 K  480 (633)
Q Consensus       480 ~  480 (633)
                      .
T Consensus        79 ~   79 (721)
T PRK11773         79 G   79 (721)
T ss_pred             c
Confidence            4

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=92.95  E-value=0.28  Score=50.69  Aligned_cols=22  Identities=27%  Similarity=0.407  Sum_probs=17.7

Q ss_pred             HHhCCCcEEEEccCCCCchhhh
Q 006737          412 ACLEGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       412 ~il~grDvLv~ApTGSGKTlay  433 (633)
                      -+..|.-+++.|++|+|||...
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~   47 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFL   47 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHH
Confidence            3456778999999999999743

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>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

Probab=92.95  E-value=0.5  Score=42.42  Aligned_cols=14  Identities=29%  Similarity=0.525  Sum_probs=12.5

Q ss_pred             EEEEccCCCCchhh
Q 006737          419 AVVKAKTGTGKSIA  432 (633)
Q Consensus       419 vLv~ApTGSGKTla  432 (633)
                      +++.||+|+|||..
T Consensus         1 ill~G~~G~GKT~l   14 (132)
T PF00004_consen    1 ILLHGPPGTGKTTL   14 (132)
T ss_dssp             EEEESSTTSSHHHH
T ss_pred             CEEECcCCCCeeHH
Confidence            68999999999974

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=92.78  E-value=0.92  Score=53.44  Aligned_cols=44  Identities=18%  Similarity=0.190  Sum_probs=28.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      +...++|||||+|.|... -...+.++++..+..+.+|+.+ |-+.
T Consensus       117 ~gk~KVIIIDEad~Ls~~-A~NALLKtLEEPp~~v~fILaT-td~~  160 (709)
T PRK08691        117 AGKYKVYIIDEVHMLSKS-AFNAMLKTLEEPPEHVKFILAT-TDPH  160 (709)
T ss_pred             hCCcEEEEEECccccCHH-HHHHHHHHHHhCCCCcEEEEEe-CCcc
Confidence            456789999999987643 3345666666666666565544 4333

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

Probab=92.67  E-value=0.33  Score=53.16  Aligned_cols=34  Identities=21%  Similarity=0.260  Sum_probs=21.9

Q ss_pred             HHHHHhCCC--cEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          409 TLSACLEGK--DAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       409 aIp~il~gr--DvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      ..|.+.++.  |+++.|+||+|||++.. -++..+..
T Consensus        33 l~~~~~~~~p~n~~iyG~~GTGKT~~~~-~v~~~l~~   68 (366)
T COG1474          33 LAPALRGERPSNIIIYGPTGTGKTATVK-FVMEELEE   68 (366)
T ss_pred             HHHHhcCCCCccEEEECCCCCCHhHHHH-HHHHHHHh
Confidence            344444443  79999999999998633 24444433

>PRK05973 replicative DNA helicase; Provisional

Probab=92.67  E-value=0.58  Score=48.23  Aligned_cols=82  Identities=20%  Similarity=0.197  Sum_probs=47.3

Q ss_pred             cCCCHHHHHHHHHcCCCC----------CcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCC
Q 006737          384 CGISPLTIKALTAAGYIQ----------MTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLV  453 (633)
Q Consensus       384 l~L~~~Ll~~L~~~g~~~----------pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~  453 (633)
                      +.+++.+-+...+.||..          +||... +..-+..|.-++|.|++|+|||...+--+.+.+ ..+        
T Consensus        23 ~~~~~~~~~~a~~~g~~~w~~~~~~~~~~~p~~~-l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a-~~G--------   92 (237)
T PRK05973         23 IPLHEALDRIAAEEGFSSWSLLAAKAAATTPAEE-LFSQLKPGDLVLLGARPGHGKTLLGLELAVEAM-KSG--------   92 (237)
T ss_pred             CcHHHHHHHHHHHhccchHHHHHHhccCCCCHHH-hcCCCCCCCEEEEEeCCCCCHHHHHHHHHHHHH-hcC--------
Confidence            345555555555666654          455222 344455677889999999999974333233322 221        


Q ss_pred             CCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          454 PPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       454 ~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                        -.++|++ .-+-..|+.+.+..+
T Consensus        93 --e~vlyfS-lEes~~~i~~R~~s~  114 (237)
T PRK05973         93 --RTGVFFT-LEYTEQDVRDRLRAL  114 (237)
T ss_pred             --CeEEEEE-EeCCHHHHHHHHHHc
Confidence              1366664 344456777776655

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=92.56  E-value=0.91  Score=46.34  Aligned_cols=53  Identities=19%  Similarity=0.197  Sum_probs=31.5

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ..|.-+++.+++|+|||...+ -++..+.+..          -++++++ +-+-..++.+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~-~~~~~~~~~g----------~~~~yi~-~e~~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQ-RLAYGFLQNG----------YSVSYVS-TQLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHH-HHHHHHHhCC----------CcEEEEe-CCCCHHHHHHHHHHh
Confidence            457789999999999997522 2233333221          2477777 444445555555444

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=92.52  E-value=0.29  Score=57.60  Aligned_cols=66  Identities=24%  Similarity=0.336  Sum_probs=49.4

Q ss_pred             CCcHHHHHHHHHHhCC-----CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEG-----KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g-----rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .|+-.|..+|..+.++     +..++.|.||||||+...- +++.+   ..          .+|||+|+..+|.|++..+
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a~-~~~~~---~~----------p~Lvi~~n~~~A~ql~~el   74 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMAN-VIAQV---NR----------PTLVIAHNKTLAAQLYNEF   74 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHHH-HHHHh---CC----------CEEEEECCHHHHHHHHHHH
Confidence            5788888888877543     3667999999999985321 22221   11          2899999999999999999


Q ss_pred             HHHHh
Q 006737          476 IALLK  480 (633)
Q Consensus       476 ~~l~~  480 (633)
                      +.++.
T Consensus        75 ~~f~p   79 (655)
T TIGR00631        75 KEFFP   79 (655)
T ss_pred             HHhCC
Confidence            99864

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)

>PF13173 AAA_14: AAA domain

Probab=92.48  E-value=0.81  Score=41.94  Aligned_cols=39  Identities=23%  Similarity=0.322  Sum_probs=27.3

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      .-.+|||||+|.+-+  +...+..+.... ++.++++.+...
T Consensus        61 ~~~~i~iDEiq~~~~--~~~~lk~l~d~~-~~~~ii~tgS~~   99 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPD--WEDALKFLVDNG-PNIKIILTGSSS   99 (128)
T ss_pred             CCcEEEEehhhhhcc--HHHHHHHHHHhc-cCceEEEEccch
Confidence            445799999999864  577777777755 456676654443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=92.45  E-value=0.82  Score=50.04  Aligned_cols=42  Identities=21%  Similarity=0.315  Sum_probs=27.9

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ....++|||||||.|.. .-.+.+.++++..+....+|++|..
T Consensus       139 ~~~~kVviIDead~m~~-~aanaLLK~LEepp~~~~~IL~t~~  180 (365)
T PRK07471        139 EGGWRVVIVDTADEMNA-NAANALLKVLEEPPARSLFLLVSHA  180 (365)
T ss_pred             cCCCEEEEEechHhcCH-HHHHHHHHHHhcCCCCeEEEEEECC
Confidence            45678999999999863 3455666666665555555554443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.45  E-value=2.2  Score=48.58  Aligned_cols=45  Identities=16%  Similarity=0.166  Sum_probs=27.9

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||+|.|.... .+.+.+.++.-|....+|+ .+|-...
T Consensus       114 ~~~~KVvIIDEah~Ls~~A-~NaLLK~LEePp~~v~fIl-atte~~K  158 (491)
T PRK14964        114 SSKFKVYIIDEVHMLSNSA-FNALLKTLEEPAPHVKFIL-ATTEVKK  158 (491)
T ss_pred             cCCceEEEEeChHhCCHHH-HHHHHHHHhCCCCCeEEEE-EeCChHH
Confidence            4578899999999987542 3445555555555554444 4454443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=92.29  E-value=1.2  Score=48.02  Aligned_cols=41  Identities=17%  Similarity=0.101  Sum_probs=30.2

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEec
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      ....+++|||+||.|... -.+.+.++++.-|.++.+|++|.
T Consensus       111 ~g~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~~~fiL~~~  151 (319)
T PRK08769        111 YGIAQVVIVDPADAINRA-ACNALLKTLEEPSPGRYLWLISA  151 (319)
T ss_pred             cCCcEEEEeccHhhhCHH-HHHHHHHHhhCCCCCCeEEEEEC
Confidence            456789999999999643 45666777777676776666654

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=92.24  E-value=1.5  Score=46.16  Aligned_cols=62  Identities=10%  Similarity=0.072  Sum_probs=36.1

Q ss_pred             ECchhhHHHHhcccCcccccCCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          513 ATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       513 aTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+|..|...+..-    ......++||||-+=+... ......+..++....+..-++++|||....
T Consensus       137 ~~~~~l~~~l~~l----~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~  199 (270)
T PRK06731        137 RDEAAMTRALTYF----KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSK  199 (270)
T ss_pred             CCHHHHHHHHHHH----HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHH
Confidence            3555555554321    1123578899999877642 224445555555555554467789987654

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

Probab=92.22  E-value=0.38  Score=55.57  Aligned_cols=126  Identities=15%  Similarity=0.135  Sum_probs=73.0

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH-HHHHH
Q 006737          401 QMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA-AEAIA  477 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~-~~l~~  477 (633)
                      ..+|+|.+.+..+...  +.|+++.++-+|||.+.+. ++-.......         .-+|++.||.++|.... ..+..
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n-~~g~~i~~~P---------~~~l~v~Pt~~~a~~~~~~rl~P   85 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLN-WIGYSIDQDP---------GPMLYVQPTDDAAKDFSKERLDP   85 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHh-hceEEEEeCC---------CCEEEEEEcHHHHHHHHHHHHHH
Confidence            5688899888887764  5899999999999984333 2222222211         23899999999999876 56777


Q ss_pred             HHhcCCCceEEEEE---CCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccC
Q 006737          478 LLKNHDGIGVLTLV---GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       478 l~~~~~~i~v~~l~---Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      ++...+.++-.+.-   .........+.+. + ..|.++.-..         ...+.-..+++|++||+|.+.
T Consensus        86 mi~~sp~l~~~~~~~~~~~~~~t~~~k~f~-g-g~l~~~ga~S---------~~~l~s~~~r~~~~DEvD~~p  147 (557)
T PF05876_consen   86 MIRASPVLRRKLSPSKSRDSGNTILYKRFP-G-GFLYLVGANS---------PSNLRSRPARYLLLDEVDRYP  147 (557)
T ss_pred             HHHhCHHHHHHhCchhhcccCCchhheecC-C-CEEEEEeCCC---------CcccccCCcCEEEEechhhcc
Confidence            76655443311111   0011111111111 2 2333332111         112334578999999999985

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=92.22  E-value=0.51  Score=48.83  Aligned_cols=17  Identities=29%  Similarity=0.452  Sum_probs=14.8

Q ss_pred             CcEEEEccCCCCchhhh
Q 006737          417 KDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       417 rDvLv~ApTGSGKTlay  433 (633)
                      .++++.||+|+|||...
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            47999999999999754

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=92.13  E-value=0.36  Score=51.90  Aligned_cols=68  Identities=25%  Similarity=0.350  Sum_probs=42.9

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          390 TIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       390 Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      .+..|.+.|+  +++.|...+.. +..+++++++|+||||||.. +-.++..+....        +..++++|-.+.||.
T Consensus       123 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~~--------~~~rivtIEd~~El~  191 (319)
T PRK13894        123 TLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQD--------PTERVFIIEDTGEIQ  191 (319)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhcC--------CCceEEEEcCCCccc
Confidence            3455555564  56777777765 45677999999999999963 333443332111        123577777777763

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.13  E-value=0.6  Score=52.44  Aligned_cols=52  Identities=31%  Similarity=0.287  Sum_probs=32.2

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .|.-+++.+++|+|||...+- ++..+...          +-++||+. +.+...|+...+..+
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq-~a~~~a~~----------g~~vlYvs-~Ees~~qi~~ra~rl  130 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQ-VAARLAAA----------GGKVLYVS-GEESASQIKLRAERL  130 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHH-HHHHHHhc----------CCeEEEEE-ccccHHHHHHHHHHc
Confidence            466789999999999974322 22222221          12477876 455666776666554

>PRK04195 replication factor C large subunit; Provisional

Probab=92.09  E-value=1.2  Score=50.58  Aligned_cols=42  Identities=17%  Similarity=0.190  Sum_probs=27.0

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhC---CCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE---GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~---grDvLv~ApTGSGKTla  432 (633)
                      ++|+++-..+..++.|...            +.....   .+.+++.||+|+|||.+
T Consensus        11 ~~l~dlvg~~~~~~~l~~~------------l~~~~~g~~~~~lLL~GppG~GKTtl   55 (482)
T PRK04195         11 KTLSDVVGNEKAKEQLREW------------IESWLKGKPKKALLLYGPPGVGKTSL   55 (482)
T ss_pred             CCHHHhcCCHHHHHHHHHH------------HHHHhcCCCCCeEEEECCCCCCHHHH
Confidence            3466766666666655442            011112   46799999999999974

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=92.03  E-value=2  Score=50.41  Aligned_cols=44  Identities=20%  Similarity=0.217  Sum_probs=27.8

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+++||||||+|... -.+.+.++++.-|....+|+. .|-+..
T Consensus       118 g~~KV~IIDEah~Ls~~-a~NALLKtLEEPp~~v~FIL~-Tt~~~k  161 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLA-TTDPQK  161 (647)
T ss_pred             CCCEEEEEechHhCCHH-HHHHHHHHHHcCCCCeEEEEe-cCCccc
Confidence            46789999999998754 344555566665555545443 444443

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=91.94  E-value=0.43  Score=51.40  Aligned_cols=66  Identities=20%  Similarity=0.302  Sum_probs=40.4

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHh-CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          392 KALTAAGYIQMTRVQEATLSACL-EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       392 ~~L~~~g~~~pt~iQ~~aIp~il-~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      ..+.+.|.  +++.|...|..+. .+.+++|+|+||||||.. +-.++..+.....        .-+++++-.+.||.
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTl-l~aL~~~i~~~~~--------~~rivtiEd~~El~  187 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTL-ANAVIAEIVASAP--------EDRLVILEDTAEIQ  187 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHHHhcCCC--------CceEEEecCCcccc
Confidence            34445554  6677777766544 466999999999999973 2233333322111        12567777777763

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=91.94  E-value=1.5  Score=48.28  Aligned_cols=18  Identities=22%  Similarity=0.368  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      ++-+++++|||+|||...
T Consensus       206 ~~ii~lvGptGvGKTTt~  223 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTL  223 (407)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            567889999999999754

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=91.90  E-value=0.55  Score=52.66  Aligned_cols=32  Identities=19%  Similarity=0.247  Sum_probs=25.6

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEccCCCCchhhh
Q 006737          402 MTRVQEATLSACLEGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       402 pt~iQ~~aIp~il~grDvLv~ApTGSGKTlay  433 (633)
                      +-.....++..+..++++++++++|+|||...
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            44455666777778999999999999999754

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=91.85  E-value=0.26  Score=50.46  Aligned_cols=43  Identities=19%  Similarity=0.274  Sum_probs=30.6

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      ..-++||+||||.|-+ |-...+.+.++...+.+++.+.+-+..
T Consensus       112 grhKIiILDEADSMT~-gAQQAlRRtMEiyS~ttRFalaCN~s~  154 (333)
T KOG0991|consen  112 GRHKIIILDEADSMTA-GAQQALRRTMEIYSNTTRFALACNQSE  154 (333)
T ss_pred             CceeEEEeeccchhhh-HHHHHHHHHHHHHcccchhhhhhcchh
Confidence            4567899999999974 456677777777766666666555543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.82  E-value=1.2  Score=50.86  Aligned_cols=39  Identities=15%  Similarity=0.184  Sum_probs=27.3

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+++||||||.|.... .+.+.++++..|..+.+|+.+
T Consensus       118 ~~~kV~iIDE~~~ls~~a-~naLLk~LEepp~~~~fIlat  156 (509)
T PRK14958        118 GRFKVYLIDEVHMLSGHS-FNALLKTLEEPPSHVKFILAT  156 (509)
T ss_pred             CCcEEEEEEChHhcCHHH-HHHHHHHHhccCCCeEEEEEE
Confidence            356899999999987543 345666777766666666544

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=91.78  E-value=2  Score=49.08  Aligned_cols=45  Identities=16%  Similarity=0.168  Sum_probs=25.2

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||+|.|... -...+.+.++..+... +++|.+|-...
T Consensus       126 ~~~~KVvIIDEa~~Ls~~-a~naLLk~LEepp~~~-vfI~aTte~~k  170 (507)
T PRK06645        126 QGKHKIFIIDEVHMLSKG-AFNALLKTLEEPPPHI-IFIFATTEVQK  170 (507)
T ss_pred             cCCcEEEEEEChhhcCHH-HHHHHHHHHhhcCCCE-EEEEEeCChHH
Confidence            456789999999998643 2333444444433333 44444444333

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=91.67  E-value=0.74  Score=60.45  Aligned_cols=63  Identities=17%  Similarity=0.292  Sum_probs=44.0

Q ss_pred             CCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhH--HHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFL--LPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlayl--LPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      ..+++.|..++..++.+  +-++|++..|+|||....  +-.+..+...         .+..++.++||-..+..+
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~---------~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES---------EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh---------cCCeEEEEeChHHHHHHH
Confidence            46899999999999876  456788999999997531  1222222221         124688899998877665

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=91.63  E-value=0.34  Score=57.70  Aligned_cols=72  Identities=17%  Similarity=0.246  Sum_probs=52.7

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+++-|.+++.+.  ...++|.|..|||||.+..-=+ .+++....      ..+-++|+|+-|+..|..+.+.+..++
T Consensus         3 ~~Ln~~Q~~av~~~--~g~~lV~AgaGSGKT~~l~~ri-a~Li~~~~------i~P~~IL~lTFT~kAA~em~~Rl~~~~   73 (726)
T TIGR01073         3 AHLNPEQREAVKTT--EGPLLIMAGAGSGKTRVLTHRI-AHLIAEKN------VAPWNILAITFTNKAAREMKERVEKLL   73 (726)
T ss_pred             cccCHHHHHHHhCC--CCCEEEEeCCCCCHHHHHHHHH-HHHHHcCC------CCHHHeeeeeccHHHHHHHHHHHHHHh
Confidence            46899999999753  4579999999999998644333 33433211      112358999999999999999988776


Q ss_pred             h
Q 006737          480 K  480 (633)
Q Consensus       480 ~  480 (633)
                      .
T Consensus        74 ~   74 (726)
T TIGR01073        74 G   74 (726)
T ss_pred             c
Confidence            4

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.62  E-value=1.4  Score=53.15  Aligned_cols=44  Identities=20%  Similarity=0.215  Sum_probs=28.6

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+++||||||.|... -.+.+.++++.-+..+.+|+. .|-+..
T Consensus       118 gk~KViIIDEAh~LT~e-AqNALLKtLEEPP~~vrFILa-TTe~~k  161 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRS-SFNALLKTLEEPPEHVKFLLA-TTDPQK  161 (944)
T ss_pred             CCcEEEEEechHhcCHH-HHHHHHHHHhccCCCeEEEEE-CCCchh
Confidence            35789999999999633 345556666665656655554 454444

>PRK08939 primosomal protein DnaI; Reviewed

Probab=91.60  E-value=0.87  Score=48.65  Aligned_cols=48  Identities=15%  Similarity=0.086  Sum_probs=26.8

Q ss_pred             cCCeeEEEEecccccC--CcChHHHHHHHHHH-CCCCCcEEEEeccCChhh
Q 006737          532 LMGLKMLVLDEADHLL--DLGFRKDVENIVDC-LPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Ll--d~gf~~~l~~Il~~-lpk~~Q~IlfSATl~~el  579 (633)
                      +.++++|||||+..-.  +|.....+..|++. +.....+|+.|---..++
T Consensus       215 l~~~dlLiIDDiG~e~~s~~~~~~ll~~Il~~R~~~~~~ti~TSNl~~~el  265 (306)
T PRK08939        215 VKEAPVLMLDDIGAEQMSSWVRDEVLGVILQYRMQEELPTFFTSNFDFDEL  265 (306)
T ss_pred             hcCCCEEEEecCCCccccHHHHHHHHHHHHHHHHHCCCeEEEECCCCHHHH
Confidence            4578899999997543  33222334455553 234555666554444443

>PLN03025 replication factor C subunit; Provisional

Probab=91.58  E-value=1.4  Score=46.93  Aligned_cols=41  Identities=17%  Similarity=0.276  Sum_probs=26.7

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      ..++|||||||.|... -...+..+++..+....+|+ +++..
T Consensus        99 ~~kviiiDE~d~lt~~-aq~aL~~~lE~~~~~t~~il-~~n~~  139 (319)
T PLN03025         99 RHKIVILDEADSMTSG-AQQALRRTMEIYSNTTRFAL-ACNTS  139 (319)
T ss_pred             CeEEEEEechhhcCHH-HHHHHHHHHhcccCCceEEE-EeCCc
Confidence            4678999999998743 34556666666665555544 44433

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

Probab=91.44  E-value=2.3  Score=48.60  Aligned_cols=98  Identities=21%  Similarity=0.212  Sum_probs=73.3

Q ss_pred             CCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchH---HHH
Q 006737          425 TGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQR  501 (633)
Q Consensus       425 TGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~---~~~  501 (633)
                      .++|++..-++.+.+.+....         .|-+||.+-+.+-|.|++.++.    .+.++++.+++|......   ...
T Consensus       366 vF~gse~~K~lA~rq~v~~g~---------~PP~lIfVQs~eRak~L~~~L~----~~~~i~v~vIh~e~~~~qrde~~~  432 (593)
T KOG0344|consen  366 VFCGSEKGKLLALRQLVASGF---------KPPVLIFVQSKERAKQLFEELE----IYDNINVDVIHGERSQKQRDETME  432 (593)
T ss_pred             eeeecchhHHHHHHHHHhccC---------CCCeEEEEecHHHHHHHHHHhh----hccCcceeeEecccchhHHHHHHH
Confidence            477888777777666654431         1348999999999999988876    245899999999865443   345


Q ss_pred             HHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          502 RLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       502 ~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      .+..+...|+|||     ++|.++    +++.++.+||.+..-
T Consensus       433 ~FR~g~IwvLicT-----dll~RG----iDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  433 RFRIGKIWVLICT-----DLLARG----IDFKGVNLVINYDFP  466 (593)
T ss_pred             HHhccCeeEEEeh-----hhhhcc----ccccCcceEEecCCC
Confidence            6667788999999     566665    789999999997654

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=91.38  E-value=0.45  Score=59.98  Aligned_cols=126  Identities=16%  Similarity=0.164  Sum_probs=76.1

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      ++|+-|.++|.  ..+++++|.|..|||||.+.+--++..+... .       ..-++|+|+=|+..|.++.+++...+.
T Consensus         1 ~~t~~Q~~ai~--~~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-~-------~~~~il~~tFt~~aa~e~~~ri~~~l~   70 (1232)
T TIGR02785         1 QWTDEQWQAIY--TRGQNILVSASAGSGKTAVLVERIIKKILRG-V-------DIDRLLVVTFTNAAAREMKERIEEALQ   70 (1232)
T ss_pred             CCCHHHHHHHh--CCCCCEEEEecCCCcHHHHHHHHHHHHHhcC-C-------CHhhEEEEeccHHHHHHHHHHHHHHHH
Confidence            36899999997  3688999999999999987655555555432 1       112489999999999999888877654


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH  545 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~  545 (633)
                      ....-..    .......+...+    ...-|+|-..+...+-+.....+.+ +-.+=|.||...
T Consensus        71 ~~~~~~p----~~~~L~~q~~~~----~~~~i~Tihsf~~~~~~~~~~~l~l-dP~F~i~de~e~  126 (1232)
T TIGR02785        71 KALQQEP----NSKHLRRQLALL----NTANISTLHSFCLKVIRKHYYLLDL-DPSFRILTDTEQ  126 (1232)
T ss_pred             HHHhcCc----hhHHHHHHHhhc----cCCeEeeHHHHHHHHHHHhhhhcCC-CCCceeCCHHHH
Confidence            2110000    001111111111    2566888888865443332222222 113456887775

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>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

Probab=91.26  E-value=2.2  Score=41.11  Aligned_cols=43  Identities=19%  Similarity=0.261  Sum_probs=30.5

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      -...+++|||+||.|... -.+.+.++++.-|.+..+|++|...
T Consensus       100 ~~~~KviiI~~ad~l~~~-a~NaLLK~LEepp~~~~fiL~t~~~  142 (162)
T PF13177_consen  100 EGKYKVIIIDEADKLTEE-AQNALLKTLEEPPENTYFILITNNP  142 (162)
T ss_dssp             TSSSEEEEEETGGGS-HH-HHHHHHHHHHSTTTTEEEEEEES-G
T ss_pred             cCCceEEEeehHhhhhHH-HHHHHHHHhcCCCCCEEEEEEECCh
Confidence            356889999999998743 5677778888877777666655443

...

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=91.20  E-value=0.32  Score=52.44  Aligned_cols=62  Identities=24%  Similarity=0.232  Sum_probs=44.7

Q ss_pred             CCCCCcHHHHHHHHHHhCCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      .|..+++-|...+-.+..++ |+|+++.||||||.  +|-++   ...-..       .=++|.+--|.||..+.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTT--lLNal---~~~i~~-------~eRvItiEDtaELql~~  216 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTT--LLNAL---SGFIDS-------DERVITIEDTAELQLAH  216 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHH--HHHHH---HhcCCC-------cccEEEEeehhhhccCC
Confidence            46789999999999888877 99999999999997  33333   221111       11588888888876553

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.13  E-value=1.1  Score=52.22  Aligned_cols=44  Identities=18%  Similarity=0.273  Sum_probs=26.7

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+++||||+|.|.... .+.+.++++..|....+|+ .+|-+..
T Consensus       123 g~~KV~IIDEvh~Ls~~a-~NaLLKtLEEPP~~~~fIL-~Ttd~~k  166 (618)
T PRK14951        123 GRFKVFMIDEVHMLTNTA-FNAMLKTLEEPPEYLKFVL-ATTDPQK  166 (618)
T ss_pred             CCceEEEEEChhhCCHHH-HHHHHHhcccCCCCeEEEE-EECCchh
Confidence            467899999999987543 3334455555444454544 4455444

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=91.12  E-value=2.4  Score=50.67  Aligned_cols=20  Identities=25%  Similarity=0.275  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCchhhhHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLL  435 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylL  435 (633)
                      ++-+.+++|||+|||.+...
T Consensus       185 g~Vi~lVGpnGvGKTTTiaK  204 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAK  204 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            44578999999999986543

>PRK10689 transcription-repair coupling factor; Provisional

Probab=91.10  E-value=0.65  Score=57.96  Aligned_cols=78  Identities=19%  Similarity=0.229  Sum_probs=61.6

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      +++|++|+++-+..+++.+.+++   +++.+.+++|+.+.....   ..+..+..+|||||     +.+..+    +++.
T Consensus       811 qv~vf~n~i~~ie~la~~L~~~~---p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaT-----dIierG----IDIP  878 (1147)
T PRK10689        811 QVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCT-----TIIETG----IDIP  878 (1147)
T ss_pred             eEEEEECCHHHHHHHHHHHHHhC---CCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEEC-----chhhcc----cccc
Confidence            69999999999988888887764   367899999998765432   44566789999999     344544    7889


Q ss_pred             CeeEEEEeccccc
Q 006737          534 GLKMLVLDEADHL  546 (633)
Q Consensus       534 ~l~~LVIDEAD~L  546 (633)
                      ++.+|||+.||++
T Consensus       879 ~v~~VIi~~ad~f  891 (1147)
T PRK10689        879 TANTIIIERADHF  891 (1147)
T ss_pred             cCCEEEEecCCCC
Confidence            9999999999874

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=91.10  E-value=0.83  Score=49.20  Aligned_cols=24  Identities=25%  Similarity=0.385  Sum_probs=17.5

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAV  441 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l  441 (633)
                      .+++++||+|+|||.+. -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            58999999999999753 2334444

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.04  E-value=1.9  Score=47.09  Aligned_cols=39  Identities=18%  Similarity=0.296  Sum_probs=24.6

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+++||||||.|....+ +.+.+.++..+....+|+.+
T Consensus       118 ~~~kviIIDEa~~l~~~a~-naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        118 SRFKVYLIDEVHMLSRHSF-NALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             CCceEEEEEChhhcCHHHH-HHHHHHHhcCCCCeEEEEEc
Confidence            4567999999999875322 33455555555555555543

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.02  E-value=3.5  Score=47.88  Aligned_cols=45  Identities=16%  Similarity=0.218  Sum_probs=28.9

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||+|.|... -.+.+.++++..+....+|+ .+|-+..
T Consensus       117 ~~~~KVvIIdev~~Lt~~-a~naLLk~LEepp~~~~fIl-~t~~~~k  161 (576)
T PRK14965        117 RSRYKIFIIDEVHMLSTN-AFNALLKTLEEPPPHVKFIF-ATTEPHK  161 (576)
T ss_pred             cCCceEEEEEChhhCCHH-HHHHHHHHHHcCCCCeEEEE-EeCChhh
Confidence            456789999999988743 34556666666555554544 4454444

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

Probab=91.02  E-value=0.3  Score=54.72  Aligned_cols=49  Identities=22%  Similarity=0.363  Sum_probs=37.7

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .++++.||||||||..|++|.+-   ....          -+||+-|--||........++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll---~~~~----------s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLL---NYPG----------SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHH---hccC----------CEEEEECCCcHHHHHHHHHHHC
Confidence            47999999999999999999762   2211          1789999999988776655554

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>PF05729 NACHT: NACHT domain

Probab=90.68  E-value=1.7  Score=40.37  Aligned_cols=41  Identities=20%  Similarity=0.263  Sum_probs=27.1

Q ss_pred             EEEEecccccCCcC-------hHHHHHHHHHH-CCCCCcEEEEeccCCh
Q 006737          537 MLVLDEADHLLDLG-------FRKDVENIVDC-LPRRRQSLLFSATMPK  577 (633)
Q Consensus       537 ~LVIDEAD~Lld~g-------f~~~l~~Il~~-lpk~~Q~IlfSATl~~  577 (633)
                      +||||-+|.+....       +...+..++.. ++++.++++.|.+-+.
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~  132 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAF  132 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChH
Confidence            49999999988632       33445555554 5567777777766544

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=90.68  E-value=1.9  Score=43.39  Aligned_cols=19  Identities=37%  Similarity=0.457  Sum_probs=16.0

Q ss_pred             CCCcEEEEccCCCCchhhh
Q 006737          415 EGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlay  433 (633)
                      .|..+++.+++|+|||...
T Consensus        19 ~G~~~~i~G~~G~GKT~l~   37 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFC   37 (229)
T ss_pred             CCeEEEEECCCCCChHHHH
Confidence            4678999999999999743

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=90.55  E-value=2.2  Score=46.10  Aligned_cols=32  Identities=13%  Similarity=0.091  Sum_probs=25.0

Q ss_pred             CcHHHHHHHHHHhCCC----cEEEEccCCCCchhhh
Q 006737          402 MTRVQEATLSACLEGK----DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       402 pt~iQ~~aIp~il~gr----DvLv~ApTGSGKTlay  433 (633)
                      ++|+|...+..+....    -++++||.|.|||...
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A   39 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALA   39 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHH
Confidence            4688888888877542    5889999999999753

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=90.52  E-value=1.3  Score=48.71  Aligned_cols=52  Identities=27%  Similarity=0.258  Sum_probs=30.8

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .|.-+++.+++|+|||...+ -+...+....          -+++|+.-. +...|+...+..+
T Consensus        81 ~GslvLI~G~pG~GKStLll-q~a~~~a~~g----------~~VlYvs~E-Es~~qi~~Ra~rl  132 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLL-QVAARLAKRG----------GKVLYVSGE-ESPEQIKLRADRL  132 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHH-HHHHHHHhcC----------CeEEEEECC-cCHHHHHHHHHHc
Confidence            45678999999999997433 2223332221          247777643 4456665555444

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=90.50  E-value=0.87  Score=48.47  Aligned_cols=68  Identities=32%  Similarity=0.411  Sum_probs=40.6

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          390 TIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       390 Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      -+..|.+.|.  +++.|...+.. +..+++++++|+||||||... -.++..+....        +.-+++++--+.|+.
T Consensus       107 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~~--------~~~ri~tiEd~~El~  175 (299)
T TIGR02782       107 TLDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKND--------PTDRVVIIEDTRELQ  175 (299)
T ss_pred             CHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhccC--------CCceEEEECCchhhc
Confidence            3445555553  55556666555 445679999999999999742 22333332211        113577777777764

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=90.49  E-value=1.2  Score=49.49  Aligned_cols=47  Identities=26%  Similarity=0.357  Sum_probs=35.0

Q ss_pred             CeeEEEEecccccCCc-ChHHHHHHHHHHCCC-CCcEEEEeccCChhhh
Q 006737          534 GLKMLVLDEADHLLDL-GFRKDVENIVDCLPR-RRQSLLFSATMPKELV  580 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~-gf~~~l~~Il~~lpk-~~Q~IlfSATl~~el~  580 (633)
                      ++++|+||.++.+... .....+..+++.+.. ..|+|+.|...|.++.
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence            7889999999998765 356777777776654 3477777777777753

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=90.46  E-value=0.76  Score=56.15  Aligned_cols=79  Identities=16%  Similarity=0.177  Sum_probs=62.6

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      -+++|++|+++-+..+++.++++.   +++++..++|+.......   ..+..+..+|||||.     .+..+    +++
T Consensus       661 ~qv~if~n~i~~~e~l~~~L~~~~---p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~-----iie~G----IDI  728 (926)
T TIGR00580       661 GQVFYVHNRIESIEKLATQLRELV---PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT-----IIETG----IDI  728 (926)
T ss_pred             CeEEEEECCcHHHHHHHHHHHHhC---CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhhcc----ccc
Confidence            369999999999998888887764   478899999998755433   355667899999994     45554    788


Q ss_pred             CCeeEEEEeccccc
Q 006737          533 MGLKMLVLDEADHL  546 (633)
Q Consensus       533 s~l~~LVIDEAD~L  546 (633)
                      .++.+||++.++..
T Consensus       729 p~v~~VIi~~a~~~  742 (926)
T TIGR00580       729 PNANTIIIERADKF  742 (926)
T ss_pred             ccCCEEEEecCCCC
Confidence            89999999999874

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=90.39  E-value=1.6  Score=44.22  Aligned_cols=52  Identities=15%  Similarity=0.127  Sum_probs=29.6

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .|.-+++.+++|+|||...+--+...+ ...          -+++|+.= .+-..++.+.+..+
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~~-~~g----------~~~~y~~~-e~~~~~~~~~~~~~   75 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGAL-KQG----------KKVYVITT-ENTSKSYLKQMESV   75 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHHH-hCC----------CEEEEEEc-CCCHHHHHHHHHHC
Confidence            356789999999999974333223222 211          13656553 34445555555554

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=90.34  E-value=5.6  Score=45.75  Aligned_cols=55  Identities=16%  Similarity=0.202  Sum_probs=33.0

Q ss_pred             cCccccCCCHHHHHHHHHcCC--CCCcHHHHHHHHH------------HhCCCcEEEEccCCCCchhhh
Q 006737          379 KRFDECGISPLTIKALTAAGY--IQMTRVQEATLSA------------CLEGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~--~~pt~iQ~~aIp~------------il~grDvLv~ApTGSGKTlay  433 (633)
                      ..+..+|+++.+.+.|...--  .........++..            +..|+.++++||||+|||...
T Consensus       299 ~~L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTta  367 (559)
T PRK12727        299 ELMDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTI  367 (559)
T ss_pred             HHHHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHH
Confidence            345677888888888865311  1111112222211            234678889999999999854

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=90.30  E-value=1.1  Score=49.32  Aligned_cols=19  Identities=21%  Similarity=0.389  Sum_probs=16.4

Q ss_pred             CCCcEEEEccCCCCchhhh
Q 006737          415 EGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlay  433 (633)
                      .++-+.++||||.|||..-
T Consensus       202 ~~~vi~LVGPTGVGKTTTl  220 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTL  220 (407)
T ss_pred             cCcEEEEECCCCCcHHHHH
Confidence            3788999999999999853

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=90.29  E-value=0.23  Score=54.40  Aligned_cols=48  Identities=27%  Similarity=0.332  Sum_probs=36.3

Q ss_pred             cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       418 DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      +++++|+||||||.++++|.+-.   ..          -.+||+-|--|+........+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~---~~----------~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT---WP----------GSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc---CC----------CCEEEEccchhHHHHHHHHHHHc
Confidence            47899999999999999987632   11          13889999999998766555443

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.17  E-value=1.4  Score=50.41  Aligned_cols=17  Identities=18%  Similarity=0.249  Sum_probs=14.2

Q ss_pred             cEEEEccCCCCchhhhH
Q 006737          418 DAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       418 DvLv~ApTGSGKTlayl  434 (633)
                      -+|++||.|+|||.+..
T Consensus        38 a~Lf~GppGtGKTTlA~   54 (504)
T PRK14963         38 AYLFSGPRGVGKTTTAR   54 (504)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            35999999999998643

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=90.14  E-value=1.6  Score=44.20  Aligned_cols=19  Identities=21%  Similarity=0.338  Sum_probs=15.8

Q ss_pred             hCCCcEEEEccCCCCchhh
Q 006737          414 LEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTla  432 (633)
                      ..|.-+++.|++|+|||..
T Consensus        11 ~~G~l~lI~G~~G~GKT~~   29 (242)
T cd00984          11 QPGDLIIIAARPSMGKTAF   29 (242)
T ss_pred             CCCeEEEEEeCCCCCHHHH
Confidence            4567789999999999964

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>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 []

Probab=90.08  E-value=2.8  Score=44.17  Aligned_cols=132  Identities=17%  Similarity=0.169  Sum_probs=55.4

Q ss_pred             EEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH-HH---HHHHHHhcCCCceEEEEECCcc
Q 006737          420 VVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI-AA---EAIALLKNHDGIGVLTLVGGTR  495 (633)
Q Consensus       420 Lv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi-~~---~l~~l~~~~~~i~v~~l~Gg~~  495 (633)
                      ++.++.|+|||.+.++.++..+.....        ...++++ ||...+..+ ..   .+..+......+........ .
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~--------~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~   70 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP--------GRRVIIA-STYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDR-K   70 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS----------EEEEE-ESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SS-E
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC--------CcEEEEe-cCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCC-c
Confidence            567899999999877777766654432        1245454 666555543 32   22222222111111100010 0


Q ss_pred             chHHHHHHhcCCCcEEEECchh--hHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEec
Q 006737          496 FKVDQRRLESDPCQILVATPGR--LLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       496 ~~~~~~~l~~~~~dILIaTPgr--Ll~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      .     .+ .+++.|.+.+-..  -..-+.        =..+.+|||||+-.+.+..+...+...+.... ....+++|-
T Consensus        71 ~-----~~-~nG~~i~~~~~~~~~~~~~~~--------G~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~-~~~~~~~s~  135 (384)
T PF03237_consen   71 I-----IL-PNGSRIQFRGADSPDSGDNIR--------GFEYDLIIIDEAAKVPDDAFSELIRRLRATWG-GSIRMYIST  135 (384)
T ss_dssp             E-----EE-TTS-EEEEES-----SHHHHH--------TS--SEEEEESGGGSTTHHHHHHHHHHHHCST-T--EEEEEE
T ss_pred             E-----Ee-cCceEEEEecccccccccccc--------ccccceeeeeecccCchHHHHHHHHhhhhccc-CcceEEeec
Confidence            0     01 2344565555221  111111        13677899999988876544444444433332 222225555


Q ss_pred             cCC
Q 006737          574 TMP  576 (633)
Q Consensus       574 Tl~  576 (633)
                      |..
T Consensus       136 p~~  138 (384)
T PF03237_consen  136 PPN  138 (384)
T ss_dssp             ---
T ss_pred             CCC
Confidence            443

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=90.06  E-value=4.7  Score=46.74  Aligned_cols=45  Identities=16%  Similarity=0.220  Sum_probs=26.2

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||+|.|.... ...+.++++..|... +++|.+|-+..
T Consensus       117 ~~~~kViIIDE~~~Lt~~a-~naLLKtLEepp~~~-ifIlatt~~~k  161 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTGA-FNALLKTLEEPPAHV-IFILATTEPHK  161 (559)
T ss_pred             cCCeEEEEEECcccCCHHH-HHHHHHHhcCCCCCe-EEEEEeCChhh
Confidence            4567899999999987532 334444455444343 44444554443

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=89.94  E-value=0.44  Score=57.21  Aligned_cols=66  Identities=11%  Similarity=0.018  Sum_probs=54.7

Q ss_pred             cEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          509 QILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       509 dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      .|+++||..|..-|-.+   .+.+..|..|||||||++.+..-...+.++...-++..=+.+|||....
T Consensus         9 gi~~~T~rIl~~DlL~~---ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596         9 GIFSITSRILVVDLLTG---IIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             CEEEEechhhHhHHhcC---CCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcc
Confidence            79999999986544444   3789999999999999998777777888888887777889999998764

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=89.92  E-value=1  Score=51.03  Aligned_cols=127  Identities=16%  Similarity=0.164  Sum_probs=66.6

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      .|.-+++.+++|+|||+..+- .+....+..          -+++|++ +-|-..|+...+..+.-..            
T Consensus       262 ~gs~~li~G~~G~GKt~l~~~-f~~~~~~~g----------e~~~y~s-~eEs~~~i~~~~~~lg~~~------------  317 (484)
T TIGR02655       262 KDSIILATGATGTGKTLLVSK-FLENACANK----------ERAILFA-YEESRAQLLRNAYSWGIDF------------  317 (484)
T ss_pred             CCcEEEEECCCCCCHHHHHHH-HHHHHHHCC----------CeEEEEE-eeCCHHHHHHHHHHcCCCh------------
Confidence            456899999999999974332 222222221          2477765 7788888888887663110            


Q ss_pred             cchHHHHHHhcCCCcEEEE-----CchhhHHHHhcccCcccccCCeeEEEEecccccCC----cChHHHHHHHHHHCCCC
Q 006737          495 RFKVDQRRLESDPCQILVA-----TPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD----LGFRKDVENIVDCLPRR  565 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIa-----TPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld----~gf~~~l~~Il~~lpk~  565 (633)
                        .   .....+...|+-.     .|+.++..+...    +.-.+.+.||||=.-.+..    ......+..+...+...
T Consensus       318 --~---~~~~~g~l~~~~~~p~~~~~~~~~~~i~~~----i~~~~~~~vvIDsi~~~~~~~~~~~~r~~~~~l~~~lk~~  388 (484)
T TIGR02655       318 --E---EMEQQGLLKIICAYPESAGLEDHLQIIKSE----IADFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQE  388 (484)
T ss_pred             --H---HHhhCCcEEEEEcccccCChHHHHHHHHHH----HHHcCCCEEEEcCHHHHHHhcCHHHHHHHHHHHHHHHhhC
Confidence              1   1111111222221     234444444322    2223567899998876532    11333444555665544


Q ss_pred             CcEEEEecc
Q 006737          566 RQSLLFSAT  574 (633)
Q Consensus       566 ~Q~IlfSAT  574 (633)
                      --+++|+..
T Consensus       389 ~it~~~t~~  397 (484)
T TIGR02655       389 EITGFFTNT  397 (484)
T ss_pred             CCeEEEeec
Confidence            344444433

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

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

Probab=89.90  E-value=2.4  Score=48.36  Aligned_cols=150  Identities=15%  Similarity=0.104  Sum_probs=85.5

Q ss_pred             CCcHHHHHHHHHHhC----------CCcEEEEccCCCCchhhhH-HHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHH
Q 006737          401 QMTRVQEATLSACLE----------GKDAVVKAKTGTGKSIAFL-LPAIEAVLKATSSSTTQLVPPIYVLILCPTRELAS  469 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~----------grDvLv~ApTGSGKTlayl-LPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~  469 (633)
                      .+-|+|.-++-.|+.          -+..+|..|-+-|||.... |.....+.....        +-...|++|+.+-+.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~--------~~~~~i~A~s~~qa~  132 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRS--------GAGIYILAPSVEQAA  132 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhhhc--------CCcEEEEeccHHHHH
Confidence            567899998888873          1468899999999996433 222222333211        124889999999999


Q ss_pred             HHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCc
Q 006737          470 QIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL  549 (633)
Q Consensus       470 Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~  549 (633)
                      +.+..++.+....+.+..            ..........|.+.--...+..+..... ..+-.+..+.||||.|...+.
T Consensus       133 ~~F~~ar~mv~~~~~l~~------------~~~~q~~s~~i~~~~~~s~ik~~aa~~~-~~Dg~~~~~~I~DEih~f~~~  199 (546)
T COG4626         133 NSFNPARDMVKRDDDLRD------------LCNVQTHSRTITHRKTDSTIKAVAADPN-TVDGLNSVGAIIDELHLFGKQ  199 (546)
T ss_pred             HhhHHHHHHHHhCcchhh------------hhccccceeEEEecccceeeeeeccCCC-cccCCCcceEEEehhhhhcCH
Confidence            999999888764431111            1111111112333222233333333321 123335568999999998765


Q ss_pred             ChHHHHHHHHHHC--CCCCcEEEEec
Q 006737          550 GFRKDVENIVDCL--PRRRQSLLFSA  573 (633)
Q Consensus       550 gf~~~l~~Il~~l--pk~~Q~IlfSA  573 (633)
                      +  ..+..+..-+  .++.+++..|-
T Consensus       200 ~--~~~~~~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         200 E--DMYSEAKGGLGARPEGLVVYITT  223 (546)
T ss_pred             H--HHHHHHHhhhccCcCceEEEEec
Confidence            2  4444444433  23555665553

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=89.87  E-value=2.6  Score=44.39  Aligned_cols=18  Identities=28%  Similarity=0.451  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      ++.+++++|||+|||...
T Consensus       194 ~~vi~~vGptGvGKTTt~  211 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTL  211 (282)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            457889999999999754

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=89.74  E-value=0.89  Score=47.77  Aligned_cols=45  Identities=22%  Similarity=0.403  Sum_probs=29.5

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....++|||||||.|.. +-...+..+++.-+.+..+|+.+- -+..
T Consensus       107 ~~~~kviiidead~mt~-~A~nallk~lEep~~~~~~il~~n-~~~~  151 (325)
T COG0470         107 EGGYKVVIIDEADKLTE-DAANALLKTLEEPPKNTRFILITN-DPSK  151 (325)
T ss_pred             CCCceEEEeCcHHHHhH-HHHHHHHHHhccCCCCeEEEEEcC-Chhh
Confidence            35788999999999875 345566666666555565555443 4443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.56  E-value=1.6  Score=49.44  Aligned_cols=43  Identities=16%  Similarity=0.211  Sum_probs=24.2

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ..+++||||||.|... ..+.+..+++.-+... ++++.+|-+..
T Consensus       121 ~~KV~IIDEah~Ls~~-A~NALLKtLEEPp~~v-iFILaTte~~k  163 (484)
T PRK14956        121 KYKVYIIDEVHMLTDQ-SFNALLKTLEEPPAHI-VFILATTEFHK  163 (484)
T ss_pred             CCEEEEEechhhcCHH-HHHHHHHHhhcCCCce-EEEeecCChhh
Confidence            5679999999998753 3344444444433222 33344454433

>PRK04328 hypothetical protein; Provisional

Probab=89.50  E-value=2.2  Score=44.00  Aligned_cols=53  Identities=17%  Similarity=0.057  Sum_probs=32.1

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      .|..+++.+++|+|||...+--+.+.+...           -.++|++ +.+-..++.+.+..+.
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~g-----------e~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQMG-----------EPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhcC-----------CcEEEEE-eeCCHHHHHHHHHHcC
Confidence            467889999999999864322233333221           1366665 5566666666666553

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=89.41  E-value=3.4  Score=46.18  Aligned_cols=45  Identities=18%  Similarity=0.316  Sum_probs=25.1

Q ss_pred             CeeEEEEecccccC-CcChHHHHHHHHHHCC---CCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLL-DLGFRKDVENIVDCLP---RRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Ll-d~gf~~~l~~Il~~lp---k~~Q~IlfSATl~~e  578 (633)
                      ..++||||=+-+.. +......+..++....   +.--++++|||....
T Consensus       299 ~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~  347 (432)
T PRK12724        299 GSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYH  347 (432)
T ss_pred             CCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHH
Confidence            56678888665542 2223344444444432   223467778888774

>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

Probab=89.39  E-value=0.8  Score=45.10  Aligned_cols=40  Identities=23%  Similarity=0.399  Sum_probs=24.8

Q ss_pred             eEEEEecccccC-C----cChHHHHHHHHHHCCC-CCcEEEEeccC
Q 006737          536 KMLVLDEADHLL-D----LGFRKDVENIVDCLPR-RRQSLLFSATM  575 (633)
Q Consensus       536 ~~LVIDEAD~Ll-d----~gf~~~l~~Il~~lpk-~~Q~IlfSATl  575 (633)
                      -+|||||+|.+. .    ..+...+..++..+.. ....++++++-
T Consensus       120 ~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  120 VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            589999999998 2    2366677777766332 33445555554

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=89.35  E-value=2  Score=49.77  Aligned_cols=74  Identities=22%  Similarity=0.277  Sum_probs=56.4

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.|+|+..|.++++.+...     ++.+..++|+.......   ..+..+..+|||||     +.+..+    +++
T Consensus       258 ~k~LVF~nt~~~ae~l~~~L~~~-----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaT-----dv~arG----IDi  323 (572)
T PRK04537        258 ARTMVFVNTKAFVERVARTLERH-----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVAT-----DVAARG----LHI  323 (572)
T ss_pred             CcEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEe-----hhhhcC----CCc
Confidence            35999999999999998877654     67899999987765433   45556778999999     345544    778


Q ss_pred             CCeeEEEEecc
Q 006737          533 MGLKMLVLDEA  543 (633)
Q Consensus       533 s~l~~LVIDEA  543 (633)
                      .++++||.-+.
T Consensus       324 p~V~~VInyd~  334 (572)
T PRK04537        324 DGVKYVYNYDL  334 (572)
T ss_pred             cCCCEEEEcCC
Confidence            88988886544

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=89.22  E-value=2.2  Score=48.45  Aligned_cols=20  Identities=25%  Similarity=0.262  Sum_probs=16.1

Q ss_pred             CCcEEEEccCCCCchhhhHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLL  435 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylL  435 (633)
                      |+-++++||||+|||.+...
T Consensus       256 g~Vi~LvGpnGvGKTTTiaK  275 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAK  275 (484)
T ss_pred             CcEEEEECCCCccHHHHHHH
Confidence            55688999999999986443

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=89.20  E-value=2.4  Score=47.08  Aligned_cols=26  Identities=27%  Similarity=0.371  Sum_probs=18.3

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEA  440 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~  440 (633)
                      ..|.=+++.|+||+|||.. ++-+..+
T Consensus       192 ~~g~liviag~pg~GKT~~-al~ia~~  217 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKTTL-ALNIAEN  217 (421)
T ss_pred             CCCceEEEEeCCCCCHHHH-HHHHHHH
Confidence            3566788899999999964 4444433

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>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

Probab=89.11  E-value=1.2  Score=45.89  Aligned_cols=141  Identities=18%  Similarity=0.169  Sum_probs=67.7

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCcc
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR  495 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~  495 (633)
                      |.=+++.|.||.|||.. ++-+..++.....         ..|+|++.- .-..++..++.....   ++....+..+.-
T Consensus        19 g~L~vi~a~pg~GKT~~-~l~ia~~~a~~~~---------~~vly~SlE-m~~~~l~~R~la~~s---~v~~~~i~~g~l   84 (259)
T PF03796_consen   19 GELTVIAARPGVGKTAF-ALQIALNAALNGG---------YPVLYFSLE-MSEEELAARLLARLS---GVPYNKIRSGDL   84 (259)
T ss_dssp             T-EEEEEESTTSSHHHH-HHHHHHHHHHTTS---------SEEEEEESS-S-HHHHHHHHHHHHH---TSTHHHHHCCGC
T ss_pred             CcEEEEEecccCCchHH-HHHHHHHHHHhcC---------CeEEEEcCC-CCHHHHHHHHHHHhh---cchhhhhhcccc
Confidence            44578889999999964 4455555444321         247777642 222333333333322   221111111111


Q ss_pred             chHHH-------HHHhcCCCcEE-EECch----hhHHHHhcccCcccccCCeeEEEEecccccCCc----ChHHHHHHHH
Q 006737          496 FKVDQ-------RRLESDPCQIL-VATPG----RLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL----GFRKDVENIV  559 (633)
Q Consensus       496 ~~~~~-------~~l~~~~~dIL-IaTPg----rLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~----gf~~~l~~Il  559 (633)
                      ...+.       ..+...  .+. ..+|.    .|...+..-   ......+.+||||=+|.|-..    .....+..+.
T Consensus        85 ~~~e~~~~~~~~~~l~~~--~l~i~~~~~~~~~~i~~~i~~~---~~~~~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~  159 (259)
T PF03796_consen   85 SDEEFERLQAAAEKLSDL--PLYIEDTPSLTIDDIESKIRRL---KREGKKVDVVFIDYLQLLKSEDSSDNRRQEIGEIS  159 (259)
T ss_dssp             HHHHHHHHHHHHHHHHTS--EEEEEESSS-BHHHHHHHHHHH---HHHSTTEEEEEEEEGGGSBTSCSSSCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHhhC--cEEEECCCCCCHHHHHHHHHHH---HhhccCCCEEEechHHHhcCCCCCCCHHHHHHHHH
Confidence            11111       122222  344 34443    444444322   122368899999999998753    2344444443


Q ss_pred             HHCC-----CCCcEEEEeccC
Q 006737          560 DCLP-----RRRQSLLFSATM  575 (633)
Q Consensus       560 ~~lp-----k~~Q~IlfSATl  575 (633)
                      ..|.     .++.+|++|..-
T Consensus       160 ~~Lk~lA~~~~i~vi~~sQln  180 (259)
T PF03796_consen  160 RELKALAKELNIPVIALSQLN  180 (259)
T ss_dssp             HHHHHHHHHHTSEEEEEEEBS
T ss_pred             HHHHHHHHHcCCeEEEccccC
Confidence            3332     156677766643

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.07  E-value=2.9  Score=48.28  Aligned_cols=40  Identities=15%  Similarity=0.114  Sum_probs=27.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....+++||||||.|... -.+.+.++++..|....+|+.+
T Consensus       117 ~g~~kViIIDEa~~ls~~-a~naLLK~LEepp~~v~fIL~T  156 (546)
T PRK14957        117 QGRYKVYLIDEVHMLSKQ-SFNALLKTLEEPPEYVKFILAT  156 (546)
T ss_pred             cCCcEEEEEechhhccHH-HHHHHHHHHhcCCCCceEEEEE
Confidence            346689999999998753 3455666666666666566544

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.01  E-value=2.6  Score=49.19  Aligned_cols=44  Identities=20%  Similarity=0.305  Sum_probs=24.9

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...++|||||||.|... -...+.++++..+ ..-+++|.+|-+..
T Consensus       118 g~~kVIIIDEad~Lt~~-a~naLLk~LEEP~-~~~ifILaTt~~~k  161 (624)
T PRK14959        118 GRYKVFIIDEAHMLTRE-AFNALLKTLEEPP-ARVTFVLATTEPHK  161 (624)
T ss_pred             CCceEEEEEChHhCCHH-HHHHHHHHhhccC-CCEEEEEecCChhh
Confidence            45689999999998633 2233344444332 23345555555444

>TIGR03689 pup_AAA proteasome ATPase

Probab=89.01  E-value=1.1  Score=51.23  Aligned_cols=17  Identities=24%  Similarity=0.446  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      .+.+|+.+|+|+|||+.
T Consensus       216 p~GILLyGPPGTGKT~L  232 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLI  232 (512)
T ss_pred             CcceEEECCCCCcHHHH
Confidence            46799999999999984

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=88.85  E-value=1.3  Score=44.44  Aligned_cols=131  Identities=18%  Similarity=0.189  Sum_probs=62.9

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      .|.-+++.+++|+|||...+--+.+.+. ..          -.++|++ +.+-..++.+.+..+...             
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~-~g----------~~~~y~s-~e~~~~~l~~~~~~~~~~-------------   69 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLK-NG----------EKAMYIS-LEEREERILGYAKSKGWD-------------   69 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh-CC----------CeEEEEE-CCCCHHHHHHHHHHcCCC-------------
Confidence            3567899999999998632222333222 21          1366664 445567776666555211             


Q ss_pred             cchHHHHHHhcCCCcEEEECchhhHH---HHhcccCcccccCCeeEEEEecccccC----C-cChHHHHHHHHHHCCCCC
Q 006737          495 RFKVDQRRLESDPCQILVATPGRLLD---HIENKSGLSVRLMGLKMLVLDEADHLL----D-LGFRKDVENIVDCLPRRR  566 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaTPgrLl~---lL~~~~~~~~~Ls~l~~LVIDEAD~Ll----d-~gf~~~l~~Il~~lpk~~  566 (633)
                       ...   .+.. ...|+-.+|..+..   .+...-...+.-..++.||||=...+.    + ..+...+..++..+....
T Consensus        70 -~~~---~~~~-~l~~~~~~~~~~~~~~~~l~~~~~~~i~~~~~~~vVIDsls~l~~~~~~~~~~r~~l~~l~~~lk~~~  144 (224)
T TIGR03880        70 -LED---YIDK-SLYIVRLDPSDFKTSLNRIKNELPILIKELGASRVVIDPISLLETLFDDDAERRTELFRFYSSLRETG  144 (224)
T ss_pred             -hHH---HHhC-CeEEEecCHHHHHhhHHHHHHHHHHHHHHhCCCEEEEcChHHHhhhcCCHHHHHHHHHHHHHHHHhCC
Confidence             010   0111 12222223332211   111000000111246789999877551    1 113455666777666555


Q ss_pred             cEEEEeccC
Q 006737          567 QSLLFSATM  575 (633)
Q Consensus       567 Q~IlfSATl  575 (633)
                      .++++++..
T Consensus       145 ~tvll~s~~  153 (224)
T TIGR03880       145 VTTILTSEA  153 (224)
T ss_pred             CEEEEEEcc
Confidence            566766654

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=88.77  E-value=2.4  Score=44.01  Aligned_cols=18  Identities=22%  Similarity=0.195  Sum_probs=15.5

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .|.-++|.+++|+|||..
T Consensus        35 ~gs~~lI~G~pGtGKT~l   52 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLM   52 (259)
T ss_pred             CCcEEEEEcCCCCCHHHH
Confidence            467789999999999974

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=88.67  E-value=3.4  Score=46.38  Aligned_cols=17  Identities=18%  Similarity=0.352  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCchhhh
Q 006737          417 KDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       417 rDvLv~ApTGSGKTlay  433 (633)
                      ..+++++++|+|||.+.
T Consensus        96 ~vI~lvG~~GsGKTTta  112 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTA  112 (437)
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            46889999999999864

>CHL00181 cbbX CbbX; Provisional

Probab=88.44  E-value=2  Score=45.41  Aligned_cols=19  Identities=32%  Similarity=0.452  Sum_probs=15.9

Q ss_pred             CCcEEEEccCCCCchhhhH
Q 006737          416 GKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       416 grDvLv~ApTGSGKTlayl  434 (633)
                      +.++++.||+|+|||.+..
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4579999999999998644

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=88.40  E-value=2.9  Score=45.60  Aligned_cols=43  Identities=16%  Similarity=0.226  Sum_probs=28.8

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ...++|||||||.|... -.+.+.++++..+....+|++| +-+.
T Consensus       140 g~~rVviIDeAd~l~~~-aanaLLk~LEEpp~~~~fiLit-~~~~  182 (351)
T PRK09112        140 GNWRIVIIDPADDMNRN-AANAILKTLEEPPARALFILIS-HSSG  182 (351)
T ss_pred             CCceEEEEEchhhcCHH-HHHHHHHHHhcCCCCceEEEEE-CChh
Confidence            46789999999998643 3455777777755556555554 4343

>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

Probab=88.20  E-value=6  Score=43.36  Aligned_cols=46  Identities=20%  Similarity=0.238  Sum_probs=31.5

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHC-CCCCcEEEEeccCChhh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCL-PRRRQSLLFSATMPKEL  579 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~l-pk~~Q~IlfSATl~~el  579 (633)
                      ....+|.+||.|.- |.+-.-.+..++..+ ....-+|+.|-+.|+++
T Consensus       126 ~~~~lLcfDEF~V~-DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  126 KESRLLCFDEFQVT-DIADAMILKRLFEALFKRGVVLVATSNRPPEDL  172 (362)
T ss_pred             hcCCEEEEeeeecc-chhHHHHHHHHHHHHHHCCCEEEecCCCChHHH
Confidence            35668999999863 444455666676644 44677777788888774

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=88.19  E-value=0.55  Score=54.67  Aligned_cols=49  Identities=20%  Similarity=0.205  Sum_probs=38.5

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .++++.||||||||..|++|.+-..  ..           -+||+-|--|+........+++
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~--~~-----------S~VV~DpKGEl~~~Ta~~R~~~  207 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW--ED-----------SVVVHDIKLENYELTSGWREKQ  207 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC--CC-----------CEEEEeCcHHHHHHHHHHHHHC
Confidence            4799999999999999999987432  11           2889999999998777555543

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=88.19  E-value=2.2  Score=50.97  Aligned_cols=52  Identities=12%  Similarity=0.132  Sum_probs=29.9

Q ss_pred             ccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++++-....++.+.++   .+..+.-.+...   +..++.++++||+|+|||+.
T Consensus       174 ~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~g---i~~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLG---IEPPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC---CCCCceEEEECCCCCChHHH
Confidence            35688886555555555442   111111111111   23457899999999999974

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.14  E-value=2.1  Score=49.15  Aligned_cols=40  Identities=15%  Similarity=0.178  Sum_probs=26.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....+++||||||.|.... .+.+.+.++..|....+|+.+
T Consensus       117 ~~~~kVvIIDEad~ls~~a-~naLLK~LEepp~~~~fIL~t  156 (527)
T PRK14969        117 RGRFKVYIIDEVHMLSKSA-FNAMLKTLEEPPEHVKFILAT  156 (527)
T ss_pred             cCCceEEEEcCcccCCHHH-HHHHHHHHhCCCCCEEEEEEe
Confidence            3467899999999987542 344555666655566555544

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=88.14  E-value=6.7  Score=39.17  Aligned_cols=50  Identities=22%  Similarity=0.405  Sum_probs=37.6

Q ss_pred             CCeeEEEEecccccCCcCh--HHHHHHHHHHCCCCCcEEEEeccCChhhhcc
Q 006737          533 MGLKMLVLDEADHLLDLGF--RKDVENIVDCLPRRRQSLLFSATMPKELVLK  582 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf--~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~  582 (633)
                      ...++||+||+-..++.++  ...+..++..-|...-+|+.--..|+++.-.
T Consensus       114 ~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~  165 (191)
T PRK05986        114 ESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEA  165 (191)
T ss_pred             CCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHh
Confidence            4688999999998888874  5678888888777766666666677765433

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

Probab=88.09  E-value=1.6  Score=49.73  Aligned_cols=86  Identities=17%  Similarity=0.279  Sum_probs=60.3

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHH---HhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRR---LESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~---l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.|-|+.-|.++...+...     ++.+.+++|+.+..+....   +..+.+.|||||-     ...+    .+++
T Consensus       342 ~KvIIFc~tkr~~~~l~~~l~~~-----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd-----VAaR----GLDi  407 (519)
T KOG0331|consen  342 GKVIIFCETKRTCDELARNLRRK-----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD-----VAAR----GLDV  407 (519)
T ss_pred             CcEEEEecchhhHHHHHHHHHhc-----CcceeeecccccHHHHHHHHHhcccCCcceEEEcc-----cccc----cCCC
Confidence            47999999999999988877765     5778999999887765444   4467899999993     2222    3677


Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCC
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLP  563 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp  563 (633)
                      .+|++||-        .+|-..++..++.+.
T Consensus       408 ~dV~lVIn--------ydfP~~vEdYVHRiG  430 (519)
T KOG0331|consen  408 PDVDLVIN--------YDFPNNVEDYVHRIG  430 (519)
T ss_pred             ccccEEEe--------CCCCCCHHHHHhhcC
Confidence            77777763        334444554554443

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.95  E-value=3.8  Score=48.18  Aligned_cols=44  Identities=18%  Similarity=0.230  Sum_probs=28.1

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+++||||||+|... -...+.++++..+....+|+ .+|-+..
T Consensus       117 gk~KV~IIDEVh~LS~~-A~NALLKtLEEPP~~v~FIL-aTtd~~k  160 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTH-SFNALLKTLEEPPEHVKFLF-ATTDPQK  160 (702)
T ss_pred             CCcEEEEEechHhcCHH-HHHHHHHHHhcCCCCcEEEE-EECChHh
Confidence            45689999999988754 34456666666665554544 4454433

>PRK06904 replicative DNA helicase; Validated

Probab=87.74  E-value=4.6  Score=45.82  Aligned_cols=142  Identities=18%  Similarity=0.212  Sum_probs=67.9

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEE-EC
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL-VG  492 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l-~G  492 (633)
                      ..|.=+++.|.||.|||. |.+-+..++....         +..|+|++ .-.-..|+..++.....   ++....+ .|
T Consensus       219 ~~G~LiiIaarPg~GKTa-falnia~~~a~~~---------g~~Vl~fS-lEMs~~ql~~Rlla~~s---~v~~~~i~~g  284 (472)
T PRK06904        219 QPSDLIIVAARPSMGKTT-FAMNLCENAAMAS---------EKPVLVFS-LEMPAEQIMMRMLASLS---RVDQTKIRTG  284 (472)
T ss_pred             CCCcEEEEEeCCCCChHH-HHHHHHHHHHHhc---------CCeEEEEe-ccCCHHHHHHHHHHhhC---CCCHHHhccC
Confidence            345556778999999997 4444444443221         11255554 34555666655544432   2222212 22


Q ss_pred             CccchHHHH-------HHhcCCCcEEEE-----CchhhHHHHhcccCcccccCCeeEEEEecccccCCcC----hHHHHH
Q 006737          493 GTRFKVDQR-------RLESDPCQILVA-----TPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG----FRKDVE  556 (633)
Q Consensus       493 g~~~~~~~~-------~l~~~~~dILIa-----TPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g----f~~~l~  556 (633)
                      ..-...++.       .+.. ...+.|-     |+..+...+...   ......+++||||=.+.|...+    ....+.
T Consensus       285 ~~l~~~e~~~~~~a~~~l~~-~~~l~I~d~~~~t~~~i~~~~r~~---~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~  360 (472)
T PRK06904        285 QNLDQQDWAKISSTVGMFKQ-KPNLYIDDSSGLTPTELRSRARRV---YRENGGLSLIMVDYLQLMRAPGFEDNRTLEIA  360 (472)
T ss_pred             CCCCHHHHHHHHHHHHHHhc-CCCEEEECCCCCCHHHHHHHHHHH---HHhCCCCCEEEEecHHhcCCCCCCCcHHHHHH
Confidence            111111221       2211 2345553     333333322221   0111258899999999885332    233444


Q ss_pred             HHHHHC---CC--CCcEEEEec
Q 006737          557 NIVDCL---PR--RRQSLLFSA  573 (633)
Q Consensus       557 ~Il~~l---pk--~~Q~IlfSA  573 (633)
                      .|...|   -+  ++.+|++|-
T Consensus       361 ~isr~LK~lAkel~ipVi~lsQ  382 (472)
T PRK06904        361 EISRSLKALAKELKVPVVALSQ  382 (472)
T ss_pred             HHHHHHHHHHHHhCCeEEEEEe
Confidence            443333   22  677888773

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=87.69  E-value=4.3  Score=42.53  Aligned_cols=38  Identities=21%  Similarity=0.346  Sum_probs=25.3

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ..++|||||+|.+... ....+..+++..+....+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~-~~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSD-AQQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHH-HHHHHHHHHhcCCCCCeEEEEe
Confidence            4578999999998643 3445666666666666555544

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=87.66  E-value=0.54  Score=53.55  Aligned_cols=40  Identities=20%  Similarity=0.269  Sum_probs=29.5

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEE
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLF  571 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~Ilf  571 (633)
                      +++-+++|+||+-.-+|......+.+.+..+.+++-+|+.
T Consensus       486 l~~~~iliLDE~TSaLD~~te~~I~~~l~~~~~~~TvIiI  525 (529)
T TIGR02868       486 LADAPILLLDEPTEHLDAGTESELLEDLLAALSGKTVVVI  525 (529)
T ss_pred             hcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEE
Confidence            6677899999999988887777787777766545434443

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK13342 recombination factor protein RarA; Reviewed

Probab=87.58  E-value=2.2  Score=47.31  Aligned_cols=38  Identities=16%  Similarity=0.209  Sum_probs=23.0

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      .-.+|||||+|++...    ....++..+.. ..++++.+|-.
T Consensus        92 ~~~vL~IDEi~~l~~~----~q~~LL~~le~-~~iilI~att~  129 (413)
T PRK13342         92 RRTILFIDEIHRFNKA----QQDALLPHVED-GTITLIGATTE  129 (413)
T ss_pred             CceEEEEechhhhCHH----HHHHHHHHhhc-CcEEEEEeCCC
Confidence            3457999999998632    33344444433 45666666543

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.57  E-value=3.2  Score=48.63  Aligned_cols=41  Identities=10%  Similarity=0.114  Sum_probs=24.8

Q ss_pred             ccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          531 RLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       531 ~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....-++|||||+|.|.... .+.+.+.++..+...-+|+++
T Consensus       124 ~~~~~KVvIIdEad~Lt~~a-~naLLK~LEePp~~tv~IL~t  164 (620)
T PRK14954        124 QKGRYRVYIIDEVHMLSTAA-FNAFLKTLEEPPPHAIFIFAT  164 (620)
T ss_pred             hcCCCEEEEEeChhhcCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            34567899999999997532 334444555544444444433

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=87.53  E-value=1.9  Score=51.47  Aligned_cols=40  Identities=15%  Similarity=0.215  Sum_probs=24.6

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+|||||+|.+...    ....++..+. +.++++++||-.+.
T Consensus       109 ~~~IL~IDEIh~Ln~~----qQdaLL~~lE-~g~IiLI~aTTenp  148 (725)
T PRK13341        109 KRTILFIDEVHRFNKA----QQDALLPWVE-NGTITLIGATTENP  148 (725)
T ss_pred             CceEEEEeChhhCCHH----HHHHHHHHhc-CceEEEEEecCCCh
Confidence            3457999999998632    2223333333 35677878875543

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=87.47  E-value=4  Score=39.51  Aligned_cols=53  Identities=23%  Similarity=0.354  Sum_probs=40.5

Q ss_pred             cCCeeEEEEecccccCCcC--hHHHHHHHHHHCCCCCcEEEEeccCChhhhcccc
Q 006737          532 LMGLKMLVLDEADHLLDLG--FRKDVENIVDCLPRRRQSLLFSATMPKELVLKRE  584 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~g--f~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~~~  584 (633)
                      ....++|||||+=..+..+  -...+..+++..|...-+|+.+-..|+++.-..+
T Consensus        93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            4578999999999887776  4677888888888777777777777877654433

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.43  E-value=2.2  Score=48.43  Aligned_cols=17  Identities=24%  Similarity=0.303  Sum_probs=14.2

Q ss_pred             cEEEEccCCCCchhhhH
Q 006737          418 DAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       418 DvLv~ApTGSGKTlayl  434 (633)
                      .+|++||+|+|||.+..
T Consensus        38 ~~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         38 AYIFAGPRGTGKTTVAR   54 (472)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37999999999998543

>PRK08506 replicative DNA helicase; Provisional

Probab=87.37  E-value=2.7  Score=47.57  Aligned_cols=139  Identities=15%  Similarity=0.169  Sum_probs=66.7

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEE-ECC
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL-VGG  493 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l-~Gg  493 (633)
                      .|.=+++.|.||.|||.. ++-+..++...+          ..|+|++ .-.-+.|+..++.....   ++....+ .|.
T Consensus       191 ~G~LivIaarpg~GKT~f-al~ia~~~~~~g----------~~V~~fS-lEMs~~ql~~Rlla~~s---~v~~~~i~~~~  255 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTL-CLNMALKALNQD----------KGVAFFS-LEMPAEQLMLRMLSAKT---SIPLQNLRTGD  255 (472)
T ss_pred             CCceEEEEcCCCCChHHH-HHHHHHHHHhcC----------CcEEEEe-CcCCHHHHHHHHHHHhc---CCCHHHHhcCC
Confidence            455678899999999964 444444443321          1255553 34555666555544322   2222111 122


Q ss_pred             ccchHHH-------HHHhcCCCcEEEE-C----chhhHHHHhcccCcccccCCeeEEEEecccccCCcC----hHHHHHH
Q 006737          494 TRFKVDQ-------RRLESDPCQILVA-T----PGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG----FRKDVEN  557 (633)
Q Consensus       494 ~~~~~~~-------~~l~~~~~dILIa-T----PgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g----f~~~l~~  557 (633)
                      .. ..++       ..+...  .+.|- +    +..|...+..-   ......+++||||=.+.|...+    ....+..
T Consensus       256 l~-~~e~~~~~~a~~~l~~~--~l~I~d~~~~ti~~I~~~~r~l---~~~~~~~~lvvIDyLql~~~~~~~~~r~~ev~~  329 (472)
T PRK08506        256 LD-DDEWERLSDACDELSKK--KLFVYDSGYVNIHQVRAQLRKL---KSQHPEIGLAVIDYLQLMSGSGNFKDRHLQISE  329 (472)
T ss_pred             CC-HHHHHHHHHHHHHHHcC--CeEEECCCCCCHHHHHHHHHHH---HHhCCCCCEEEEcChhhccCCCCCCCHHHHHHH
Confidence            11 1111       122222  34443 3    33333333221   1112358899999999875322    2333444


Q ss_pred             HHHHC---CC--CCcEEEEecc
Q 006737          558 IVDCL---PR--RRQSLLFSAT  574 (633)
Q Consensus       558 Il~~l---pk--~~Q~IlfSAT  574 (633)
                      |...|   -+  ++.+|++|-.
T Consensus       330 isr~LK~lAkel~ipVi~lsQL  351 (472)
T PRK08506        330 ISRGLKLLARELDIPIIALSQL  351 (472)
T ss_pred             HHHHHHHHHHHhCCcEEEEeec
Confidence            43332   22  6778887743

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=87.28  E-value=1.3  Score=52.64  Aligned_cols=45  Identities=20%  Similarity=0.290  Sum_probs=39.9

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +--+||||.-|.+.+...-..+..+++..|.+.+.|+.|=+-|.-
T Consensus       129 ~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP~l  173 (894)
T COG2909         129 GPLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRPQL  173 (894)
T ss_pred             CceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCCCC
Confidence            445899999999999888999999999999999999988887764

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.23  E-value=6.7  Score=46.07  Aligned_cols=41  Identities=20%  Similarity=0.182  Sum_probs=23.8

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ....++|||||||.|... -...+.+.++.-+....+ +|.++
T Consensus       119 ~~~~KViIIDEad~Lt~~-a~naLLK~LEePp~~tvf-IL~t~  159 (620)
T PRK14948        119 QARWKVYVIDECHMLSTA-AFNALLKTLEEPPPRVVF-VLATT  159 (620)
T ss_pred             cCCceEEEEECccccCHH-HHHHHHHHHhcCCcCeEE-EEEeC
Confidence            346689999999998643 234445555544434333 33344

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=87.21  E-value=6.7  Score=45.56  Aligned_cols=137  Identities=17%  Similarity=0.204  Sum_probs=85.0

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhc-CCCceEEEEEC
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKN-HDGIGVLTLVG  492 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~-~~~i~v~~l~G  492 (633)
                      +..+-.++--|--.|||+ |+.|++..++..-        .++++.|++.-+..++-+++++...+.. ++.-.+...  
T Consensus       200 FKQkaTVFLVPRRHGKTW-f~VpiIsllL~s~--------~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~--  268 (668)
T PHA03372        200 FKQKATVFLVPRRHGKTW-FIIPIISFLLKNI--------IGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIEN--  268 (668)
T ss_pred             hhccceEEEecccCCcee-hHHHHHHHHHHhh--------cCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeee--
Confidence            445667777899999997 6888888887742        3578999999999888888777655432 221111111  


Q ss_pred             CccchHHHHHHhcCCCcEEEECchhhHHH--HhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC-CCCcEE
Q 006737          493 GTRFKVDQRRLESDPCQILVATPGRLLDH--IENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP-RRRQSL  569 (633)
Q Consensus       493 g~~~~~~~~~l~~~~~dILIaTPgrLl~l--L~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~I  569 (633)
                                  . +-.|.+.-|+.=...  +.....-.+.=.+..+|+|||||-+-.    ..+..|+-.+. +++.+|
T Consensus       269 ------------k-~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~~----~a~~tilgfm~q~~~KiI  331 (668)
T PHA03372        269 ------------K-DNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIKK----DAFNTILGFLAQNTTKII  331 (668)
T ss_pred             ------------c-CcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccCH----HHHHHhhhhhcccCceEE
Confidence                        1 114555544332100  110000013344678999999998763    36666776554 578999


Q ss_pred             EEeccCChh
Q 006737          570 LFSATMPKE  578 (633)
Q Consensus       570 lfSATl~~e  578 (633)
                      ..|.|.+..
T Consensus       332 fISS~Nsg~  340 (668)
T PHA03372        332 FISSTNTTN  340 (668)
T ss_pred             EEeCCCCCC
Confidence            999997544

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=87.21  E-value=3.5  Score=46.09  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=16.0

Q ss_pred             CCCcEEEEccCCCCchhhhH
Q 006737          415 EGKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlayl  434 (633)
                      .|.-+.++||||+|||....
T Consensus       190 ~g~vi~lvGpnG~GKTTtla  209 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTA  209 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHH
Confidence            35568899999999998543

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=87.16  E-value=0.7  Score=53.62  Aligned_cols=43  Identities=28%  Similarity=0.383  Sum_probs=34.8

Q ss_pred             CCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          401 QMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       401 ~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      +|+.||...+..    |-.|+--|+.+|||+|||+..+..+|..|..
T Consensus        15 ~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~   61 (821)
T KOG1133|consen   15 TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRD   61 (821)
T ss_pred             CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHH
Confidence            688999877655    4468988999999999999988877776653

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=87.13  E-value=7  Score=42.16  Aligned_cols=44  Identities=11%  Similarity=0.224  Sum_probs=29.8

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ....+++|||++|.|.. .....+.++++..+.... ++++++-+.
T Consensus       111 ~~~~kV~iiEp~~~Ld~-~a~naLLk~LEep~~~~~-~Ilvth~~~  154 (325)
T PRK08699        111 RGGLRVILIHPAESMNL-QAANSLLKVLEEPPPQVV-FLLVSHAAD  154 (325)
T ss_pred             cCCceEEEEechhhCCH-HHHHHHHHHHHhCcCCCE-EEEEeCChH
Confidence            45678999999999864 466777778877765544 444444433

>PRK09087 hypothetical protein; Validated

Probab=87.10  E-value=1.8  Score=44.10  Aligned_cols=40  Identities=13%  Similarity=0.200  Sum_probs=24.6

Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc-CChh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT-MPKE  578 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT-l~~e  578 (633)
                      +|+||++|.+.  .-...+..+++.+......++++++ -|+.
T Consensus        90 ~l~iDDi~~~~--~~~~~lf~l~n~~~~~g~~ilits~~~p~~  130 (226)
T PRK09087         90 PVLIEDIDAGG--FDETGLFHLINSVRQAGTSLLMTSRLWPSS  130 (226)
T ss_pred             eEEEECCCCCC--CCHHHHHHHHHHHHhCCCeEEEECCCChHH
Confidence            69999999873  2345677777766543334555554 4444

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=87.05  E-value=3.9  Score=44.12  Aligned_cols=40  Identities=15%  Similarity=0.111  Sum_probs=28.0

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....+++|||+||.|... -.+.+.++++.-|.+.-+|+.|
T Consensus       105 ~g~~KV~iI~~a~~m~~~-AaNaLLKtLEEPp~~~~fiL~t  144 (325)
T PRK06871        105 QGGNKVVYIQGAERLTEA-AANALLKTLEEPRPNTYFLLQA  144 (325)
T ss_pred             cCCceEEEEechhhhCHH-HHHHHHHHhcCCCCCeEEEEEE
Confidence            456789999999999743 4566667777656566555544

>TIGR00665 DnaB replicative DNA helicase

Probab=87.04  E-value=3  Score=46.40  Aligned_cols=139  Identities=19%  Similarity=0.210  Sum_probs=66.2

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEE-EC
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL-VG  492 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l-~G  492 (633)
                      ..|.=+++.|+||+|||. |++-++.++....         +..+++++ .-.-..|+..++.....   ++....+ .|
T Consensus       193 ~~G~l~vi~g~pg~GKT~-~~l~~a~~~a~~~---------g~~vl~~S-lEm~~~~i~~R~~~~~~---~v~~~~~~~g  258 (434)
T TIGR00665       193 QPSDLIILAARPSMGKTA-FALNIAENAAIKE---------GKPVAFFS-LEMSAEQLAMRMLSSES---RVDSQKLRTG  258 (434)
T ss_pred             CCCeEEEEEeCCCCChHH-HHHHHHHHHHHhC---------CCeEEEEe-CcCCHHHHHHHHHHHhc---CCCHHHhccC
Confidence            346667889999999996 4444444433211         11255553 34445555555544432   2221111 12


Q ss_pred             CccchHHH-------HHHhcCCCcEEE-ECc----hhhHHHHhcccCcccccCCeeEEEEecccccCCcC----hHHHHH
Q 006737          493 GTRFKVDQ-------RRLESDPCQILV-ATP----GRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG----FRKDVE  556 (633)
Q Consensus       493 g~~~~~~~-------~~l~~~~~dILI-aTP----grLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g----f~~~l~  556 (633)
                      .... .+.       ..+..  ..+.| .+|    ..|...+..-    ..-..+++||||=.+.|...+    ....+.
T Consensus       259 ~l~~-~~~~~~~~a~~~l~~--~~l~i~d~~~~~~~~i~~~i~~~----~~~~~~~~vvID~l~~i~~~~~~~~r~~~i~  331 (434)
T TIGR00665       259 KLSD-EDWEKLTSAAGKLSE--APLYIDDTPGLTITELRAKARRL----KREHGLGLIVIDYLQLMSGSGRSENRQQEVS  331 (434)
T ss_pred             CCCH-HHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHHH----HHhcCCCEEEEcchHhcCCCCCCCCHHHHHH
Confidence            2111 111       12222  23444 333    3343333221    111358899999998875321    223344


Q ss_pred             HHHHHCC-----CCCcEEEEec
Q 006737          557 NIVDCLP-----RRRQSLLFSA  573 (633)
Q Consensus       557 ~Il~~lp-----k~~Q~IlfSA  573 (633)
                      .|...|.     .++.+|++|-
T Consensus       332 ~i~~~Lk~lA~e~~i~vi~lsq  353 (434)
T TIGR00665       332 EISRSLKALAKELNVPVIALSQ  353 (434)
T ss_pred             HHHHHHHHHHHHhCCeEEEEec
Confidence            4444332     2577777774

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=87.04  E-value=1.6  Score=50.70  Aligned_cols=41  Identities=17%  Similarity=0.250  Sum_probs=24.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      +...++|||||+|.|... -.+.+.++++..+... +++|.+|
T Consensus       118 ~~~~kVvIIDEa~~L~~~-a~naLLk~LEepp~~t-v~Il~t~  158 (585)
T PRK14950        118 LARYKVYIIDEVHMLSTA-AFNALLKTLEEPPPHA-IFILATT  158 (585)
T ss_pred             cCCeEEEEEeChHhCCHH-HHHHHHHHHhcCCCCe-EEEEEeC
Confidence            456789999999998753 2334444455544343 4444444

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=86.91  E-value=4.6  Score=44.62  Aligned_cols=42  Identities=14%  Similarity=0.199  Sum_probs=24.5

Q ss_pred             ccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          531 RLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       531 ~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      .....++|||||||.|.... ...+...++..+... +++|.++
T Consensus       124 ~~~~~kvvIIdea~~l~~~~-~~~LLk~LEep~~~t-~~Il~t~  165 (397)
T PRK14955        124 QKGRYRVYIIDEVHMLSIAA-FNAFLKTLEEPPPHA-IFIFATT  165 (397)
T ss_pred             hcCCeEEEEEeChhhCCHHH-HHHHHHHHhcCCCCe-EEEEEeC
Confidence            35677899999999997532 233444444444444 3344444

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=86.89  E-value=1.6  Score=43.28  Aligned_cols=20  Identities=20%  Similarity=0.355  Sum_probs=16.1

Q ss_pred             CCCcEEEEccCCCCchhhhH
Q 006737          415 EGKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlayl  434 (633)
                      .|.-+.+.+++|+|||...+
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~   30 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICM   30 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            35678999999999997543

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=86.86  E-value=5.7  Score=41.68  Aligned_cols=19  Identities=16%  Similarity=0.225  Sum_probs=14.8

Q ss_pred             CCcEEEEccCCCCchhhhH
Q 006737          416 GKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       416 grDvLv~ApTGSGKTlayl  434 (633)
                      .+-+++++++|+|||....
T Consensus        72 ~~vi~l~G~~G~GKTTt~a   90 (272)
T TIGR00064        72 PNVILFVGVNGVGKTTTIA   90 (272)
T ss_pred             CeEEEEECCCCCcHHHHHH
Confidence            3467788999999998543

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

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

Probab=86.85  E-value=3.1  Score=47.61  Aligned_cols=69  Identities=17%  Similarity=0.279  Sum_probs=52.1

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.+.|+..|..+...+...     ++++..++|+.......   ..++.+..+|+|||-     ...++    +++.
T Consensus       275 ~~IVF~~tk~~~~~l~~~l~~~-----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTD-----vaaRG----iDi~  340 (513)
T COG0513         275 RVIVFVRTKRLVEELAESLRKR-----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATD-----VAARG----LDIP  340 (513)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHC-----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEec-----hhhcc----CCcc
Confidence            5999999999999987766655     78999999998866543   455667899999994     22333    5666


Q ss_pred             CeeEEE
Q 006737          534 GLKMLV  539 (633)
Q Consensus       534 ~l~~LV  539 (633)
                      ++.+||
T Consensus       341 ~v~~Vi  346 (513)
T COG0513         341 DVSHVI  346 (513)
T ss_pred             ccceeE
Confidence            666664

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=86.85  E-value=2.9  Score=46.40  Aligned_cols=70  Identities=20%  Similarity=0.227  Sum_probs=53.5

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.+++++-|..++..+...     ++.+..++|+.......   ..+..+..+|||||-     .+..+    +++.
T Consensus       247 ~~lVF~~s~~~~~~l~~~L~~~-----~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd-----~~~~G----iDip  312 (434)
T PRK11192        247 RSIVFVRTRERVHELAGWLRKA-----GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATD-----VAARG----IDID  312 (434)
T ss_pred             eEEEEeCChHHHHHHHHHHHhC-----CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEcc-----ccccC----ccCC
Confidence            6999999999999988887653     78889999987765443   455667889999993     33333    6778


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      ++.+||.
T Consensus       313 ~v~~VI~  319 (434)
T PRK11192        313 DVSHVIN  319 (434)
T ss_pred             CCCEEEE
Confidence            8888774

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=86.82  E-value=3  Score=46.19  Aligned_cols=45  Identities=22%  Similarity=0.361  Sum_probs=28.7

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||||.|... ..+.+.++++.-+... ++++.||-+..
T Consensus       115 ~~~~kViiIDead~m~~~-aanaLLk~LEep~~~~-~fIL~a~~~~~  159 (394)
T PRK07940        115 TGRWRIVVIEDADRLTER-AANALLKAVEEPPPRT-VWLLCAPSPED  159 (394)
T ss_pred             cCCcEEEEEechhhcCHH-HHHHHHHHhhcCCCCC-eEEEEECChHH
Confidence            346789999999999754 3455666666544454 45555555544

>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 [, ]

Probab=86.81  E-value=1.4  Score=45.62  Aligned_cols=45  Identities=16%  Similarity=0.227  Sum_probs=27.2

Q ss_pred             HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          413 CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       413 il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      +..+.+++++|+||||||... -.++..+...          .-+++++--+.|+-
T Consensus       124 v~~~~~ili~G~tGSGKTT~l-~all~~i~~~----------~~~iv~iEd~~E~~  168 (270)
T PF00437_consen  124 VRGRGNILISGPTGSGKTTLL-NALLEEIPPE----------DERIVTIEDPPELR  168 (270)
T ss_dssp             HHTTEEEEEEESTTSSHHHHH-HHHHHHCHTT----------TSEEEEEESSS-S-
T ss_pred             cccceEEEEECCCccccchHH-HHHhhhcccc----------ccceEEecccccee
Confidence            345779999999999999843 3334433222          12466666665553

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=86.72  E-value=0.76  Score=49.93  Aligned_cols=45  Identities=20%  Similarity=0.201  Sum_probs=28.6

Q ss_pred             HHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          412 ACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       412 ~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      ++..+++++|+|+||||||.. +-.++..+..           .-+++.+-.+.||.
T Consensus       158 ~v~~~~nilI~G~tGSGKTTl-l~aLl~~i~~-----------~~rivtiEd~~El~  202 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTM-SKTLISAIPP-----------QERLITIEDTLELV  202 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHH-HHHHHcccCC-----------CCCEEEECCCcccc
Confidence            355678999999999999973 2222222211           12466777777764

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=86.63  E-value=5.4  Score=43.38  Aligned_cols=40  Identities=23%  Similarity=0.157  Sum_probs=26.9

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....+++|||+||.|... -.+.+.++++.-|.+.-+|++|
T Consensus       130 ~~~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t  169 (342)
T PRK06964        130 RGGARVVVLYPAEALNVA-AANALLKTLEEPPPGTVFLLVS  169 (342)
T ss_pred             cCCceEEEEechhhcCHH-HHHHHHHHhcCCCcCcEEEEEE
Confidence            456789999999999743 4556666666655555444444

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=86.57  E-value=1.7  Score=48.09  Aligned_cols=72  Identities=21%  Similarity=0.186  Sum_probs=54.6

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|+++..|..+++.+...     ++.+..++|+.......   ..+..+.++|||||     +.+..+    +++.
T Consensus       257 ~~lVF~~t~~~~~~l~~~L~~~-----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaT-----dv~~rG----iDip  322 (423)
T PRK04837        257 RAIIFANTKHRCEEIWGHLAAD-----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVAT-----DVAARG----LHIP  322 (423)
T ss_pred             eEEEEECCHHHHHHHHHHHHhC-----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEe-----chhhcC----CCcc
Confidence            6999999999999888777643     78899999987655433   44566789999999     344444    7788


Q ss_pred             CeeEEEEec
Q 006737          534 GLKMLVLDE  542 (633)
Q Consensus       534 ~l~~LVIDE  542 (633)
                      ++++||.-+
T Consensus       323 ~v~~VI~~d  331 (423)
T PRK04837        323 AVTHVFNYD  331 (423)
T ss_pred             ccCEEEEeC
Confidence            888877544

>PRK07004 replicative DNA helicase; Provisional

Probab=86.54  E-value=2.9  Score=47.26  Aligned_cols=40  Identities=13%  Similarity=0.181  Sum_probs=25.2

Q ss_pred             CeeEEEEecccccCCcC----hHHHHHHHHHHCC-----CCCcEEEEec
Q 006737          534 GLKMLVLDEADHLLDLG----FRKDVENIVDCLP-----RRRQSLLFSA  573 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g----f~~~l~~Il~~lp-----k~~Q~IlfSA  573 (633)
                      .+++||||=.+.|...+    ....+..|...+.     .++.+|++|-
T Consensus       324 ~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQ  372 (460)
T PRK07004        324 KLGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELDVPVIALSQ  372 (460)
T ss_pred             CCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEec
Confidence            58899999999886321    3334455544332     2577777775

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=86.44  E-value=2.5  Score=46.63  Aligned_cols=16  Identities=31%  Similarity=0.561  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      +.++++||+|+|||+.
T Consensus       166 ~gvLL~GppGtGKT~l  181 (389)
T PRK03992        166 KGVLLYGPPGTGKTLL  181 (389)
T ss_pred             CceEEECCCCCChHHH
Confidence            5799999999999974

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

Probab=86.41  E-value=3.3  Score=45.68  Aligned_cols=17  Identities=24%  Similarity=0.302  Sum_probs=14.9

Q ss_pred             cEEEEccCCCCchhhhH
Q 006737          418 DAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       418 DvLv~ApTGSGKTlayl  434 (633)
                      ++|+.+|+|+|||....
T Consensus        50 SmIl~GPPG~GKTTlA~   66 (436)
T COG2256          50 SMILWGPPGTGKTTLAR   66 (436)
T ss_pred             eeEEECCCCCCHHHHHH
Confidence            89999999999998544

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

Probab=86.29  E-value=1.3  Score=43.54  Aligned_cols=47  Identities=17%  Similarity=0.317  Sum_probs=27.7

Q ss_pred             HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          413 CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       413 il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      +-.++++++.|++|+|||.... .+...+...+          ..|++ +.+.+|...+
T Consensus        44 ~~~~~~l~l~G~~G~GKThLa~-ai~~~~~~~g----------~~v~f-~~~~~L~~~l   90 (178)
T PF01695_consen   44 IENGENLILYGPPGTGKTHLAV-AIANEAIRKG----------YSVLF-ITASDLLDEL   90 (178)
T ss_dssp             -SC--EEEEEESTTSSHHHHHH-HHHHHHHHTT------------EEE-EEHHHHHHHH
T ss_pred             cccCeEEEEEhhHhHHHHHHHH-HHHHHhccCC----------cceeE-eecCceeccc
Confidence            3467899999999999997543 3444454432          23544 5566666554

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=86.27  E-value=2.7  Score=44.30  Aligned_cols=18  Identities=22%  Similarity=0.274  Sum_probs=15.5

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      +.++++.||+|+|||.+.
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            458999999999999754

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=85.90  E-value=4.2  Score=48.79  Aligned_cols=43  Identities=21%  Similarity=0.339  Sum_probs=26.6

Q ss_pred             eEEEEecccccCCcCh----HHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          536 KMLVLDEADHLLDLGF----RKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf----~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+|+|||+|.+...+-    ...+..++..+-...++.++.||-+++
T Consensus       280 ~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~~g~i~vIgATt~~E  326 (758)
T PRK11034        280 SILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQE  326 (758)
T ss_pred             CEEEeccHHHHhccCCCCCcHHHHHHHHHHHHhCCCeEEEecCChHH
Confidence            4799999999975431    233444444332345577777777665

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=85.89  E-value=3.1  Score=45.00  Aligned_cols=41  Identities=22%  Similarity=0.198  Sum_probs=27.5

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEec
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      ....+++|||+||.|... -.+.+.++++.=|...-+|++|.
T Consensus       106 ~g~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t~  146 (334)
T PRK07993        106 LGGAKVVWLPDAALLTDA-AANALLKTLEEPPENTWFFLACR  146 (334)
T ss_pred             cCCceEEEEcchHhhCHH-HHHHHHHHhcCCCCCeEEEEEEC
Confidence            457889999999999753 45566666666555554444443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=85.82  E-value=1.6  Score=51.86  Aligned_cols=45  Identities=13%  Similarity=0.186  Sum_probs=27.0

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ....+++||||||.|... -...+...++..|... +++|.+|-+..
T Consensus       116 ~g~~KV~IIDEa~~LT~~-A~NALLKtLEEPP~~t-ifILaTte~~K  160 (725)
T PRK07133        116 QSKYKIYIIDEVHMLSKS-AFNALLKTLEEPPKHV-IFILATTEVHK  160 (725)
T ss_pred             cCCCEEEEEEChhhCCHH-HHHHHHHHhhcCCCce-EEEEEcCChhh
Confidence            456789999999998643 3344555555544444 33444454444

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=85.82  E-value=5.8  Score=46.28  Aligned_cols=44  Identities=18%  Similarity=0.279  Sum_probs=26.2

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...+++||||||.|... -...+..+++..|... +++|.+|-+..
T Consensus       118 ~~~KVIIIDEad~Lt~~-A~NaLLKtLEEPp~~t-vfIL~Tt~~~K  161 (605)
T PRK05896        118 FKYKVYIIDEAHMLSTS-AWNALLKTLEEPPKHV-VFIFATTEFQK  161 (605)
T ss_pred             CCcEEEEEechHhCCHH-HHHHHHHHHHhCCCcE-EEEEECCChHh
Confidence            45678999999998643 3345555555555444 44444454443

>PRK05748 replicative DNA helicase; Provisional

Probab=85.80  E-value=3.9  Score=45.87  Aligned_cols=142  Identities=19%  Similarity=0.220  Sum_probs=67.6

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEE-EC
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL-VG  492 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l-~G  492 (633)
                      ..|.-++|.|+||.|||. |.+-++.++.....         -.|+|+ ..-.-..|+..++.....   ++....+ .|
T Consensus       201 ~~G~livIaarpg~GKT~-~al~ia~~~a~~~g---------~~v~~f-SlEms~~~l~~R~l~~~~---~v~~~~i~~~  266 (448)
T PRK05748        201 QPNDLIIVAARPSVGKTA-FALNIAQNVATKTD---------KNVAIF-SLEMGAESLVMRMLCAEG---NIDAQRLRTG  266 (448)
T ss_pred             CCCceEEEEeCCCCCchH-HHHHHHHHHHHhCC---------CeEEEE-eCCCCHHHHHHHHHHHhc---CCCHHHhhcC
Confidence            345668889999999996 44445444332111         125554 444455566555543322   2221111 12


Q ss_pred             CccchHHHH-------HHhcCCCcEEEE-Cc----hhhHHHHhcccCcccccCCeeEEEEecccccCCcC-----hHHHH
Q 006737          493 GTRFKVDQR-------RLESDPCQILVA-TP----GRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG-----FRKDV  555 (633)
Q Consensus       493 g~~~~~~~~-------~l~~~~~dILIa-TP----grLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g-----f~~~l  555 (633)
                      ... ..+..       .+..  ..+.|. +|    ..+...+..-   ......+++||||=.+.|-..+     ....+
T Consensus       267 ~l~-~~e~~~~~~a~~~l~~--~~~~i~d~~~~ti~~i~~~~r~~---~~~~~~~~~vvIDyL~li~~~~~~~~~r~~~i  340 (448)
T PRK05748        267 QLT-DDDWPKLTIAMGSLSD--APIYIDDTPGIKVTEIRARCRRL---AQEHGGLGLILIDYLQLIQGSGRSGENRQQEV  340 (448)
T ss_pred             CCC-HHHHHHHHHHHHHHhc--CCEEEECCCCCCHHHHHHHHHHH---HHhcCCCCEEEEccchhcCCCCCCCcCHHHHH
Confidence            222 11221       2222  245553 44    3333333221   0111268899999999884221     22334


Q ss_pred             HHHHHHCC-----CCCcEEEEeccC
Q 006737          556 ENIVDCLP-----RRRQSLLFSATM  575 (633)
Q Consensus       556 ~~Il~~lp-----k~~Q~IlfSATl  575 (633)
                      ..|...+.     .++.+|++|-.-
T Consensus       341 ~~i~~~LK~lAke~~i~vi~lsQln  365 (448)
T PRK05748        341 SEISRSLKALAKELKVPVIALSQLS  365 (448)
T ss_pred             HHHHHHHHHHHHHhCCeEEEecccC
Confidence            44444332     257777777644

>PRK08760 replicative DNA helicase; Provisional

Probab=85.77  E-value=3.3  Score=47.03  Aligned_cols=139  Identities=20%  Similarity=0.208  Sum_probs=65.2

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEE-EC
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL-VG  492 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l-~G  492 (633)
                      ..|.=++|.|.||.|||.. ++-+...+.....         ..|+|++ .-.-..|+..++......   +....+ .|
T Consensus       227 ~~G~LivIaarPg~GKTaf-al~iA~~~a~~~g---------~~V~~fS-lEMs~~ql~~Rl~a~~s~---i~~~~i~~g  292 (476)
T PRK08760        227 QPTDLIILAARPAMGKTTF-ALNIAEYAAIKSK---------KGVAVFS-MEMSASQLAMRLISSNGR---INAQRLRTG  292 (476)
T ss_pred             CCCceEEEEeCCCCChhHH-HHHHHHHHHHhcC---------CceEEEe-ccCCHHHHHHHHHHhhCC---CcHHHHhcC
Confidence            3455678889999999964 4444444432111         1255553 333345555555444321   211111 12


Q ss_pred             CccchHHH-------HHHhcCCCcEEEE-C----chhhHHHHhcccCcccccCCeeEEEEecccccCCcC----hHHHHH
Q 006737          493 GTRFKVDQ-------RRLESDPCQILVA-T----PGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG----FRKDVE  556 (633)
Q Consensus       493 g~~~~~~~-------~~l~~~~~dILIa-T----PgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g----f~~~l~  556 (633)
                      ... ..++       ..+..  ..|.|. +    +..+...+..-    ..-..+++||||=.+.|...+    ....+.
T Consensus       293 ~l~-~~e~~~~~~a~~~l~~--~~l~I~d~~~~t~~~I~~~~r~l----~~~~~~~lVvIDyLql~~~~~~~~~r~~ei~  365 (476)
T PRK08760        293 ALE-DEDWARVTGAIKMLKE--TKIFIDDTPGVSPEVLRSKCRRL----KREHDLGLIVIDYLQLMSVPGNSENRATEIS  365 (476)
T ss_pred             CCC-HHHHHHHHHHHHHHhc--CCEEEeCCCCCCHHHHHHHHHHH----HHhcCCCEEEEecHHhcCCCCCCcccHHHHH
Confidence            211 1111       12222  345554 2    33333333221    112358899999999875221    223344


Q ss_pred             HHHHHC---CC--CCcEEEEec
Q 006737          557 NIVDCL---PR--RRQSLLFSA  573 (633)
Q Consensus       557 ~Il~~l---pk--~~Q~IlfSA  573 (633)
                      .|...|   -+  ++.+|++|-
T Consensus       366 ~Isr~LK~lAkel~ipVi~lsQ  387 (476)
T PRK08760        366 EISRSLKGLAKELNVPVIALSQ  387 (476)
T ss_pred             HHHHHHHHHHHHhCCEEEEeec
Confidence            443333   22  566777663

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=85.71  E-value=2.7  Score=47.21  Aligned_cols=70  Identities=23%  Similarity=0.241  Sum_probs=53.1

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++.-|..+++.+...     ++.+..++|+......   ...+..+..+|||||     +.+..+    +++.
T Consensus       247 ~~lVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaT-----dv~~rG----iDip  312 (456)
T PRK10590        247 QVLVFTRTKHGANHLAEQLNKD-----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVAT-----DIAARG----LDIE  312 (456)
T ss_pred             cEEEEcCcHHHHHHHHHHHHHC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEc-----cHHhcC----CCcc
Confidence            5899999999999988777654     6788999998776543   345566788999999     344444    7778


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      +|++||.
T Consensus       313 ~v~~VI~  319 (456)
T PRK10590        313 ELPHVVN  319 (456)
T ss_pred             cCCEEEE
Confidence            8888774

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=85.54  E-value=1.9  Score=46.65  Aligned_cols=20  Identities=30%  Similarity=0.513  Sum_probs=17.3

Q ss_pred             HHhCCCcEEEEccCCCCchh
Q 006737          412 ACLEGKDAVVKAKTGTGKSI  431 (633)
Q Consensus       412 ~il~grDvLv~ApTGSGKTl  431 (633)
                      ++..+++++|+|+||||||.
T Consensus       156 ~v~~~~nili~G~tgSGKTT  175 (332)
T PRK13900        156 AVISKKNIIISGGTSTGKTT  175 (332)
T ss_pred             HHHcCCcEEEECCCCCCHHH
Confidence            34567899999999999997

>PTZ00110 helicase; Provisional

Probab=85.29  E-value=2.9  Score=48.23  Aligned_cols=72  Identities=17%  Similarity=0.187  Sum_probs=54.2

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.|+|+.-|..+...+...     ++.+.+++|+.......   ..++.+...|||||.     .+..+    +++
T Consensus       378 ~k~LIF~~t~~~a~~l~~~L~~~-----g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTd-----v~~rG----IDi  443 (545)
T PTZ00110        378 DKILIFVETKKGADFLTKELRLD-----GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATD-----VASRG----LDV  443 (545)
T ss_pred             CeEEEEecChHHHHHHHHHHHHc-----CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcc-----hhhcC----CCc
Confidence            47999999999999988777643     67788999987765433   455667789999993     44443    778


Q ss_pred             CCeeEEEEe
Q 006737          533 MGLKMLVLD  541 (633)
Q Consensus       533 s~l~~LVID  541 (633)
                      .+|.+||.=
T Consensus       444 ~~v~~VI~~  452 (545)
T PTZ00110        444 KDVKYVINF  452 (545)
T ss_pred             ccCCEEEEe
Confidence            888888863

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=85.28  E-value=0.92  Score=53.49  Aligned_cols=48  Identities=23%  Similarity=0.288  Sum_probs=36.6

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      .+++++||||||||..|++|-+-..   ..          .+||+-|--|+........++
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~---~g----------S~VV~DpKGE~~~~Ta~~R~~  187 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF---KG----------SVIALDVKGELFELTSRARKA  187 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC---CC----------CEEEEeCCchHHHHHHHHHHh
Confidence            4899999999999999999986431   11          288999999988776544443

>PRK09165 replicative DNA helicase; Provisional

Probab=85.22  E-value=3.9  Score=46.70  Aligned_cols=26  Identities=8%  Similarity=0.046  Sum_probs=17.5

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAV  441 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l  441 (633)
                      .|.=+++.|+||.|||.. .+-+...+
T Consensus       216 ~g~livIaarpg~GKT~~-al~ia~~~  241 (497)
T PRK09165        216 PSDLIILAGRPSMGKTAL-ATNIAFNA  241 (497)
T ss_pred             CCceEEEEeCCCCChHHH-HHHHHHHH
Confidence            455678899999999964 33333333

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=85.19  E-value=3.1  Score=41.73  Aligned_cols=20  Identities=25%  Similarity=0.375  Sum_probs=16.0

Q ss_pred             CCCcEEEEccCCCCchhhhH
Q 006737          415 EGKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlayl  434 (633)
                      .|.-+++.+++|+|||...+
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~   41 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICL   41 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHH
Confidence            35678999999999997543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=85.14  E-value=3.9  Score=45.78  Aligned_cols=73  Identities=22%  Similarity=0.366  Sum_probs=54.5

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|+|+.-|..+++.+...     ++.+..++|+.......   ..+..+..+|||||-     .+..+    +++.
T Consensus       244 ~~lVF~~t~~~~~~l~~~L~~~-----~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTd-----v~~rG----iDi~  309 (460)
T PRK11776        244 SCVVFCNTKKECQEVADALNAQ-----GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATD-----VAARG----LDIK  309 (460)
T ss_pred             ceEEEECCHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEec-----ccccc----cchh
Confidence            5899999999999998887654     67889999988765433   345567789999993     33333    6677


Q ss_pred             CeeEEEEecc
Q 006737          534 GLKMLVLDEA  543 (633)
Q Consensus       534 ~l~~LVIDEA  543 (633)
                      ++.+||.-+.
T Consensus       310 ~v~~VI~~d~  319 (460)
T PRK11776        310 ALEAVINYEL  319 (460)
T ss_pred             cCCeEEEecC
Confidence            8888776544

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=84.95  E-value=7.6  Score=40.78  Aligned_cols=16  Identities=13%  Similarity=0.254  Sum_probs=14.4

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      +++++.+|||+|||..
T Consensus       112 ~~~~i~g~~g~GKttl  127 (270)
T TIGR02858       112 LNTLIISPPQCGKTTL  127 (270)
T ss_pred             eEEEEEcCCCCCHHHH
Confidence            5889999999999983

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

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

Probab=84.92  E-value=0.73  Score=54.12  Aligned_cols=160  Identities=20%  Similarity=0.258  Sum_probs=92.0

Q ss_pred             CCCcHHHHHHHHHHhCCC----------cEEEEccC--CCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHH
Q 006737          400 IQMTRVQEATLSACLEGK----------DAVVKAKT--GTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTREL  467 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~gr----------DvLv~ApT--GSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReL  467 (633)
                      ..++.+|.+++-..+...          -.||--..  |-|.|.|-+  |++..++..          -++|+++=+..|
T Consensus       263 g~lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgi--IfeNyLkGR----------KrAlW~SVSsDL  330 (1300)
T KOG1513|consen  263 GHLSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGI--IFENYLKGR----------KRALWFSVSSDL  330 (1300)
T ss_pred             cchhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEE--Eehhhhccc----------ceeEEEEecccc
Confidence            356777877776554422          24444333  456666544  344444432          369999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEEEE----CCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-ccccc--------CC
Q 006737          468 ASQIAAEAIALLKNHDGIGVLTLV----GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-LSVRL--------MG  534 (633)
Q Consensus       468 a~Qi~~~l~~l~~~~~~i~v~~l~----Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-~~~~L--------s~  534 (633)
                      -.+..+.+..+...  +|.|..+.    +..+.+ .....+   --||+||.-.|+---....+ ....+        .+
T Consensus       331 KfDAERDL~DigA~--~I~V~alnK~KYakIss~-en~n~k---rGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~  404 (1300)
T KOG1513|consen  331 KFDAERDLRDIGAT--GIAVHALNKFKYAKISSK-ENTNTK---RGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGED  404 (1300)
T ss_pred             ccchhhchhhcCCC--Cccceehhhccccccccc-ccCCcc---ceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhc
Confidence            88888888777542  45554332    111111 111112   25999998766432221110 00001        11


Q ss_pred             e-eEEEEecccccCCc---------ChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          535 L-KMLVLDEADHLLDL---------GFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       535 l-~~LVIDEAD~Lld~---------gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      + .+||+||+|.--+.         -....+..+-+.|| +.++|.-|||=..+
T Consensus       405 feGvIvfDECHkAKNL~p~~~~k~TKtG~tVLdLQk~LP-~ARVVYASATGAsE  457 (1300)
T KOG1513|consen  405 FEGVIVFDECHKAKNLVPTAGAKSTKTGKTVLDLQKKLP-NARVVYASATGASE  457 (1300)
T ss_pred             cceeEEehhhhhhcccccccCCCcCcccHhHHHHHHhCC-CceEEEeeccCCCC
Confidence            1 37999999976441         16677888888887 56689999997655

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=84.90  E-value=3.8  Score=47.31  Aligned_cols=60  Identities=27%  Similarity=0.280  Sum_probs=41.1

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      ++-+||+|..|||||.+.+ +=+..++-.-.+   +...+ .+||+.|.+-+..-|.+++-.++.
T Consensus       226 ~~ilVVQGaAGSGKTtiAL-HRvAyLlY~~R~---~l~~k-~vlvl~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         226 NKILVVQGAAGSGKTTIAL-HRVAYLLYGYRG---PLQAK-PVLVLGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             CCeEEEecCCCCCchhHHH-HHHHHHHhcccc---ccccC-ceEEEcCcHHHHHHHHHhchhhcc
Confidence            4568999999999998743 333333322111   11112 299999999999999999888864

>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

Probab=84.86  E-value=1.2  Score=45.70  Aligned_cols=15  Identities=20%  Similarity=0.319  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCchhh
Q 006737          418 DAVVKAKTGTGKSIA  432 (633)
Q Consensus       418 DvLv~ApTGSGKTla  432 (633)
                      ++|++||+|+|||..
T Consensus        52 h~lf~GPPG~GKTTL   66 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTL   66 (233)
T ss_dssp             EEEEESSTTSSHHHH
T ss_pred             eEEEECCCccchhHH
Confidence            699999999999973

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=84.72  E-value=11  Score=36.64  Aligned_cols=41  Identities=7%  Similarity=0.258  Sum_probs=25.1

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ....++|||||+|.|... ....+...++..++..- ++|.++
T Consensus        94 ~~~~kviiide~~~l~~~-~~~~Ll~~le~~~~~~~-~il~~~  134 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEA-AANALLKTLEEPPPNTL-FILITP  134 (188)
T ss_pred             cCCeEEEEEechhhhCHH-HHHHHHHHhcCCCCCeE-EEEEEC
Confidence            456789999999998743 33445555555444444 444444

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=84.50  E-value=7.6  Score=46.97  Aligned_cols=43  Identities=14%  Similarity=0.253  Sum_probs=35.5

Q ss_pred             eeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      --+||||++|.+.+......+..++..++....+|+.|-+.++
T Consensus       122 ~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~~  164 (903)
T PRK04841        122 PLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLPP  164 (903)
T ss_pred             CEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCCC
Confidence            3479999999997666777888999999988999888877544

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=84.49  E-value=7.9  Score=41.63  Aligned_cols=18  Identities=22%  Similarity=0.244  Sum_probs=14.8

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      +.-+++++|+|+|||...
T Consensus       114 ~~vi~lvGpnGsGKTTt~  131 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTI  131 (318)
T ss_pred             CeEEEEECCCCCcHHHHH
Confidence            456788999999999753

>PRK08840 replicative DNA helicase; Provisional

Probab=84.45  E-value=6.7  Score=44.40  Aligned_cols=40  Identities=18%  Similarity=0.200  Sum_probs=24.5

Q ss_pred             CeeEEEEecccccCCcC----hHHHHHHHHHHCC-----CCCcEEEEec
Q 006737          534 GLKMLVLDEADHLLDLG----FRKDVENIVDCLP-----RRRQSLLFSA  573 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g----f~~~l~~Il~~lp-----k~~Q~IlfSA  573 (633)
                      .+++||||=.+.|...+    ....+..|...|.     -++.+|++|-
T Consensus       329 ~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~LsQ  377 (464)
T PRK08840        329 GLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLKALAKELNVPVVALSQ  377 (464)
T ss_pred             CCCEEEEccHHhcCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEEEe
Confidence            58899999999885222    2233444443332     2577888773

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=84.41  E-value=3.7  Score=49.10  Aligned_cols=52  Identities=17%  Similarity=0.167  Sum_probs=30.2

Q ss_pred             ccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++++-.+.+.+.|...   .+..+.-++..-   +...+.+++.||+|+|||+.
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g---~~~~~giLL~GppGtGKT~l  503 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMG---IRPPKGVLLFGPPGTGKTLL  503 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEECCCCCCHHHH
Confidence            34678887777777666553   111111111110   11235699999999999983

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>cd01394 radB RadB

Probab=84.28  E-value=4.9  Score=40.06  Aligned_cols=18  Identities=33%  Similarity=0.348  Sum_probs=15.0

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      |.-+++.+++|+|||...
T Consensus        19 g~i~~i~G~~GsGKT~l~   36 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIA   36 (218)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456889999999999743

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

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

Probab=84.27  E-value=1.3  Score=50.06  Aligned_cols=41  Identities=27%  Similarity=0.303  Sum_probs=29.3

Q ss_pred             cHHHHHHHHHHhCCC--cEEEEccCCCCchhhhHHHHHHHHHHh
Q 006737          403 TRVQEATLSACLEGK--DAVVKAKTGTGKSIAFLLPAIEAVLKA  444 (633)
Q Consensus       403 t~iQ~~aIp~il~gr--DvLv~ApTGSGKTlaylLPiL~~l~~~  444 (633)
                      ++.|...+-.+++..  =+|+.||||||||.. +..+++.+...
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~~  285 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNTP  285 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcCC
Confidence            567777777766644  478999999999975 45566666543

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=84.26  E-value=8.6  Score=43.12  Aligned_cols=16  Identities=19%  Similarity=0.279  Sum_probs=13.4

Q ss_pred             cEEEEccCCCCchhhh
Q 006737          418 DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       418 DvLv~ApTGSGKTlay  433 (633)
                      -+++++++|+|||.+.
T Consensus       102 vi~lvG~~GvGKTTta  117 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTC  117 (429)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999753

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK10436 hypothetical protein; Provisional

Probab=84.03  E-value=1.3  Score=49.97  Aligned_cols=25  Identities=24%  Similarity=0.476  Sum_probs=18.3

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAV  441 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l  441 (633)
                      +.-+|+++|||||||... ..++..+
T Consensus       218 ~GliLvtGpTGSGKTTtL-~a~l~~~  242 (462)
T PRK10436        218 QGLILVTGPTGSGKTVTL-YSALQTL  242 (462)
T ss_pred             CCeEEEECCCCCChHHHH-HHHHHhh
Confidence            446899999999999852 3455554

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=84.03  E-value=10  Score=41.05  Aligned_cols=17  Identities=18%  Similarity=0.282  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCCchhhh
Q 006737          417 KDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       417 rDvLv~ApTGSGKTlay  433 (633)
                      +.++++||.|+|||...
T Consensus        40 ~~~L~~G~~G~GKt~~a   56 (367)
T PRK14970         40 QALLFCGPRGVGKTTCA   56 (367)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            36889999999999743

>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

Probab=84.00  E-value=1.4  Score=41.53  Aligned_cols=47  Identities=19%  Similarity=0.304  Sum_probs=32.9

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      ...+++|+||...=+|......+..++..+....++++++.--...+
T Consensus        97 ~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~  143 (157)
T cd00267          97 LNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPELA  143 (157)
T ss_pred             cCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHH
Confidence            45678999999998887777788777776544334666665554443

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=83.77  E-value=8.8  Score=45.36  Aligned_cols=109  Identities=16%  Similarity=0.183  Sum_probs=71.2

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      -++||+++|+..|..+.+.+...     ++.+..++|+......   ...+..+..+|+|||     ..+..+    +++
T Consensus       443 ~~vLIf~~tk~~ae~L~~~L~~~-----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t-----~~L~rG----fDi  508 (655)
T TIGR00631       443 ERVLVTTLTKKMAEDLTDYLKEL-----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGI-----NLLREG----LDL  508 (655)
T ss_pred             CEEEEEECCHHHHHHHHHHHhhh-----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEc-----ChhcCC----eee
Confidence            46999999999999988887765     6778888887654332   234556778999998     344444    778


Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCC--CCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLP--RRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp--k~~Q~IlfSATl~~e  578 (633)
                      ..+++||+=+++...-......+.+++....  ....++++--..+..
T Consensus       509 P~v~lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~  556 (655)
T TIGR00631       509 PEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDS  556 (655)
T ss_pred             CCCcEEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHH
Confidence            8999999888887532222233333332221  234466665566554

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)

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

Probab=83.76  E-value=3.1  Score=39.97  Aligned_cols=48  Identities=21%  Similarity=0.245  Sum_probs=35.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      +.+-+++++||--.-+|......+..++..+... .+|+++..-...+.
T Consensus       112 ~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~-~tii~~sh~~~~~~  159 (171)
T cd03228         112 LRDPPILILDEATSALDPETEALILEALRALAKG-KTVIVIAHRLSTIR  159 (171)
T ss_pred             hcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCC-CEEEEEecCHHHHH
Confidence            4567899999999988888888888888877554 56666655444443

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=83.74  E-value=4.2  Score=46.33  Aligned_cols=52  Identities=25%  Similarity=0.220  Sum_probs=31.4

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .|.-+++.+++|+|||...+--+.+. ....          -+++|++ +-+...++.+.+..+
T Consensus       272 ~g~~~li~G~~G~GKT~l~~~~~~~~-~~~g----------~~~~yis-~e~~~~~i~~~~~~~  323 (509)
T PRK09302        272 RGSIILVSGATGTGKTLLASKFAEAA-CRRG----------ERCLLFA-FEESRAQLIRNARSW  323 (509)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH-HhCC----------CcEEEEE-ecCCHHHHHHHHHHc
Confidence            35678899999999997433223222 2221          1377775 445566776666554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=83.66  E-value=6.7  Score=44.23  Aligned_cols=73  Identities=21%  Similarity=0.342  Sum_probs=54.2

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      .+||.++|+..|.+++..+...     ++.+..++++.......   ..+..+.++|||||.     .+..+    +++.
T Consensus       228 ~~IIF~~s~~~~e~la~~L~~~-----g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~-----~~~~G----ID~p  293 (470)
T TIGR00614       228 SGIIYCPSRKKSEQVTASLQNL-----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATV-----AFGMG----INKP  293 (470)
T ss_pred             ceEEEECcHHHHHHHHHHHHhc-----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEec-----hhhcc----CCcc
Confidence            4799999999999998887754     78889999987765433   345567889999993     23333    6677


Q ss_pred             CeeEEEEecc
Q 006737          534 GLKMLVLDEA  543 (633)
Q Consensus       534 ~l~~LVIDEA  543 (633)
                      ++++||.-..
T Consensus       294 ~V~~VI~~~~  303 (470)
T TIGR00614       294 DVRFVIHYSL  303 (470)
T ss_pred             cceEEEEeCC
Confidence            8888776544

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=83.58  E-value=4.7  Score=38.96  Aligned_cols=48  Identities=15%  Similarity=0.182  Sum_probs=34.3

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      +.+-+++|+||.-.-+|......+..++..+.+. .+|+++..-...+.
T Consensus       114 ~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~-~tii~~sh~~~~~~  161 (178)
T cd03247         114 LQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKD-KTLIWITHHLTGIE  161 (178)
T ss_pred             hcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCC-CEEEEEecCHHHHH
Confidence            5667899999999988887777887887766543 45666555444443

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=83.52  E-value=6.6  Score=43.59  Aligned_cols=51  Identities=12%  Similarity=0.145  Sum_probs=29.7

Q ss_pred             cCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      .+|++++--+...+.|...   -+..|.-++..-   +...+.+++.||+|+|||+.
T Consensus       142 v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G---l~~pkgvLL~GppGTGKT~L  195 (398)
T PTZ00454        142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG---IDPPRGVLLYGPPGTGKTML  195 (398)
T ss_pred             CCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC---CCCCceEEEECCCCCCHHHH
Confidence            3577876555555555442   222222222111   12357899999999999984

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=83.50  E-value=2  Score=45.19  Aligned_cols=16  Identities=19%  Similarity=0.335  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      ..++++||+|+|||..
T Consensus        31 ~~~ll~Gp~G~GKT~l   46 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTL   46 (305)
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999973

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=83.47  E-value=2.5  Score=48.06  Aligned_cols=55  Identities=16%  Similarity=0.230  Sum_probs=30.5

Q ss_pred             cccccCccccC---CCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          375 ILSQKRFDECG---ISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       375 ~~~~~~F~el~---L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      +.+.-.|++||   |+.+.-..+...   -...|.-+.+--+++   =+-+|+.+|+|+||||.
T Consensus       212 i~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~H---VKGiLLyGPPGTGKTLi  272 (744)
T KOG0741|consen  212 INPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKH---VKGILLYGPPGTGKTLI  272 (744)
T ss_pred             cCCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccc---eeeEEEECCCCCChhHH
Confidence            33445688886   455444333322   111222233333332   25789999999999984

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=83.40  E-value=3.9  Score=40.19  Aligned_cols=51  Identities=20%  Similarity=0.359  Sum_probs=38.9

Q ss_pred             CCeeEEEEecccccCCcCh--HHHHHHHHHHCCCCCcEEEEeccCChhhhccc
Q 006737          533 MGLKMLVLDEADHLLDLGF--RKDVENIVDCLPRRRQSLLFSATMPKELVLKR  583 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf--~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~~  583 (633)
                      ..+++||+||+-..++.++  ...+..+++.-|...-+|+..-..|+++.-..
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~A  148 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELA  148 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhC
Confidence            4689999999998887773  56778888888877777777777777764433

Alternate name: corrinoid adenosyltransferase.

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=83.37  E-value=3.5  Score=46.46  Aligned_cols=71  Identities=17%  Similarity=0.257  Sum_probs=53.7

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|++++-|..+++.+...     ++.+..++|+.......   ..+..+...|||||     +.+..+    +++.
T Consensus       337 ~~IVF~~s~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT-----~~l~~G----IDi~  402 (475)
T PRK01297        337 RVMVFANRKDEVRRIEERLVKD-----GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVAT-----DVAGRG----IHID  402 (475)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEc-----cccccC----Cccc
Confidence            6999999999999888777544     67788889987765543   44556778999999     344444    7788


Q ss_pred             CeeEEEEe
Q 006737          534 GLKMLVLD  541 (633)
Q Consensus       534 ~l~~LVID  541 (633)
                      ++++||.-
T Consensus       403 ~v~~VI~~  410 (475)
T PRK01297        403 GISHVINF  410 (475)
T ss_pred             CCCEEEEe
Confidence            89888864

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=83.30  E-value=4.4  Score=46.05  Aligned_cols=53  Identities=13%  Similarity=0.132  Sum_probs=29.7

Q ss_pred             cccCccccCCCHHHHHHHHHcC--CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          377 SQKRFDECGISPLTIKALTAAG--YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g--~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      +..+|+++.-.+.+...+...-  +..+..++..-   ....+.+++.+|+|+|||+.
T Consensus        50 ~~~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g---~~~~~giLL~GppGtGKT~l  104 (495)
T TIGR01241        50 PKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLG---AKIPKGVLLVGPPGTGKTLL  104 (495)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcC---CCCCCcEEEECCCCCCHHHH
Confidence            3456888866666555544320  12222221111   11235799999999999984

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>TIGR00416 sms DNA repair protein RadA

Probab=83.06  E-value=5.2  Score=45.15  Aligned_cols=52  Identities=29%  Similarity=0.326  Sum_probs=31.8

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .|.-+++.+++|+|||...+- ++..+....          -++||+.- .+-..|+...+..+
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq-~a~~~a~~g----------~kvlYvs~-EEs~~qi~~ra~rl  144 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQ-VACQLAKNQ----------MKVLYVSG-EESLQQIKMRAIRL  144 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHH-HHHHHHhcC----------CcEEEEEC-cCCHHHHHHHHHHc
Confidence            466789999999999975332 333332221          14788765 35556766555544

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=83.01  E-value=5.9  Score=45.20  Aligned_cols=50  Identities=18%  Similarity=0.244  Sum_probs=32.0

Q ss_pred             ccCCCHHHHHHHHHcCCCCCcHHHHHHHHH-------HhC-----CCcEEEEccCCCCchhh
Q 006737          383 ECGISPLTIKALTAAGYIQMTRVQEATLSA-------CLE-----GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       383 el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-------il~-----grDvLv~ApTGSGKTla  432 (633)
                      .+|++++.++.....|.-...+.-...+..       +.+     -..|++.+|.|||||..
T Consensus       493 AFG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaL  554 (744)
T KOG0741|consen  493 AFGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTAL  554 (744)
T ss_pred             ccCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHH
Confidence            467888888887777655444433333321       111     13799999999999963

>PRK13822 conjugal transfer coupling protein TraG; Provisional

Probab=82.93  E-value=1.7  Score=51.06  Aligned_cols=46  Identities=22%  Similarity=0.312  Sum_probs=35.2

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .++++.||||+|||..+++|-+-   ....          -+||+-|--|+...+....
T Consensus       225 ~H~Lv~ApTgsGKt~g~VIPnLL---~~~g----------S~VV~DpKgEl~~~Ta~~R  270 (641)
T PRK13822        225 THGLVFAGSGGFKTTSVVVPTAL---KWGG----------PLVVLDPSTEVAPMVSEHR  270 (641)
T ss_pred             ceEEEEeCCCCCccceEehhhhh---cCCC----------CEEEEeCcHHHHHHHHHHH
Confidence            48999999999999999999752   2111          2788889999887665544

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=82.93  E-value=7.6  Score=44.76  Aligned_cols=40  Identities=15%  Similarity=0.221  Sum_probs=28.8

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....+++||||||.|... -...+.++++..|....+|+.+
T Consensus       115 ~~~~KVvIIDEad~Lt~~-A~NALLK~LEEpp~~t~FIL~t  154 (535)
T PRK08451        115 MARFKIFIIDEVHMLTKE-AFNALLKTLEEPPSYVKFILAT  154 (535)
T ss_pred             cCCeEEEEEECcccCCHH-HHHHHHHHHhhcCCceEEEEEE
Confidence            456789999999998743 3456667777767777666655

>PF12846 AAA_10: AAA-like domain

Probab=82.92  E-value=1.6  Score=44.83  Aligned_cols=26  Identities=23%  Similarity=0.492  Sum_probs=19.5

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      .+++|+|+||+|||.+.. .++..+..
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~   27 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR   27 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH
Confidence            579999999999998765 44444443

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

Probab=82.74  E-value=1.2  Score=52.18  Aligned_cols=41  Identities=32%  Similarity=0.362  Sum_probs=33.0

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEec
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      +++-.+||+|||---||..-...+...+..+.++ ++++.=|
T Consensus       620 lr~P~VLILDEATSALDaeSE~lVq~aL~~~~~~-rTVlvIA  660 (716)
T KOG0058|consen  620 LRNPRVLILDEATSALDAESEYLVQEALDRLMQG-RTVLVIA  660 (716)
T ss_pred             hcCCCEEEEechhhhcchhhHHHHHHHHHHhhcC-CeEEEEe
Confidence            5677899999999999988888888888877666 5666544

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=82.65  E-value=5.8  Score=45.07  Aligned_cols=54  Identities=17%  Similarity=0.212  Sum_probs=34.4

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      .|+-+++.+++|+|||+..+--+.+.+.+...          .+||++= -|-..++.+.+..+.
T Consensus        20 ~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge----------~~lyvs~-eE~~~~l~~~~~~~G   73 (484)
T TIGR02655        20 IGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDE----------PGVFVTF-EESPQDIIKNARSFG   73 (484)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCC----------CEEEEEE-ecCHHHHHHHHHHcC
Confidence            46789999999999997543333333333111          2677763 466677777766664

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=82.57  E-value=47  Score=35.75  Aligned_cols=47  Identities=21%  Similarity=0.257  Sum_probs=27.9

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC-----cEEEEccCCCCchh
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGK-----DAVVKAKTGTGKSI  431 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~gr-----DvLv~ApTGSGKTl  431 (633)
                      ..|++.-=-+...++|++.=+   -||   -+|+++.|+     -+|+.+|+|+||+.
T Consensus       130 VkWsDVAGLE~AKeALKEAVI---LPI---KFPqlFtGkR~PwrgiLLyGPPGTGKSY  181 (439)
T KOG0739|consen  130 VKWSDVAGLEGAKEALKEAVI---LPI---KFPQLFTGKRKPWRGILLYGPPGTGKSY  181 (439)
T ss_pred             CchhhhccchhHHHHHHhhee---ecc---cchhhhcCCCCcceeEEEeCCCCCcHHH
Confidence            446665333444555554211   111   136777764     58999999999985

>PRK08006 replicative DNA helicase; Provisional

Probab=82.57  E-value=10  Score=43.12  Aligned_cols=140  Identities=18%  Similarity=0.175  Sum_probs=66.1

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEE-CC
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV-GG  493 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~-Gg  493 (633)
                      .|.=+++.|.+|.|||. |++-+..++....         +..|+|++. -.-..|+..++.....   ++....+. |.
T Consensus       223 ~G~LiiIaarPgmGKTa-falnia~~~a~~~---------g~~V~~fSl-EM~~~ql~~Rlla~~~---~v~~~~i~~~~  288 (471)
T PRK08006        223 PSDLIIVAARPSMGKTT-FAMNLCENAAMLQ---------DKPVLIFSL-EMPGEQIMMRMLASLS---RVDQTRIRTGQ  288 (471)
T ss_pred             CCcEEEEEeCCCCCHHH-HHHHHHHHHHHhc---------CCeEEEEec-cCCHHHHHHHHHHHhc---CCCHHHhhcCC
Confidence            45557788999999996 4444444433211         112555543 3444555555443322   22222121 22


Q ss_pred             ccchHHHHH-------HhcCCCcEEEE-----CchhhHHHHhcccCcccccCCeeEEEEecccccCCc----ChHHHHHH
Q 006737          494 TRFKVDQRR-------LESDPCQILVA-----TPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL----GFRKDVEN  557 (633)
Q Consensus       494 ~~~~~~~~~-------l~~~~~dILIa-----TPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~----gf~~~l~~  557 (633)
                      .. ..++..       +.. ...+.|-     |+..+...+..-   ......+++||||=.+.|-..    .....+..
T Consensus       289 l~-~~e~~~~~~a~~~~~~-~~~l~I~d~~~~t~~~i~~~~r~~---~~~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~  363 (471)
T PRK08006        289 LD-DEDWARISGTMGILLE-KRNMYIDDSSGLTPTEVRSRARRI---FREHGGLSLIMIDYLQLMRVPSLSDNRTLEIAE  363 (471)
T ss_pred             CC-HHHHHHHHHHHHHHHh-cCCEEEECCCCCCHHHHHHHHHHH---HHhcCCCCEEEEccHHHccCCCCCCCcHHHHHH
Confidence            22 122211       211 2345553     233333322211   111236899999999987522    12334555


Q ss_pred             HHHHCC-----CCCcEEEEec
Q 006737          558 IVDCLP-----RRRQSLLFSA  573 (633)
Q Consensus       558 Il~~lp-----k~~Q~IlfSA  573 (633)
                      |...|.     -++.+|++|-
T Consensus       364 isr~LK~lAkel~ipVi~LsQ  384 (471)
T PRK08006        364 ISRSLKALAKELQVPVVALSQ  384 (471)
T ss_pred             HHHHHHHHHHHhCCeEEEEEe
Confidence            544332     2577888873

>PRK05636 replicative DNA helicase; Provisional

Probab=82.52  E-value=3.7  Score=47.00  Aligned_cols=41  Identities=17%  Similarity=0.194  Sum_probs=24.8

Q ss_pred             CCeeEEEEecccccCCcC----hHHHHHHHHHHC---CC--CCcEEEEec
Q 006737          533 MGLKMLVLDEADHLLDLG----FRKDVENIVDCL---PR--RRQSLLFSA  573 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g----f~~~l~~Il~~l---pk--~~Q~IlfSA  573 (633)
                      ..+++||||=.+.|....    ....+..|...|   -+  ++.+|++|-
T Consensus       374 ~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK~lAkel~ipVi~lsQ  423 (505)
T PRK05636        374 HDLKLIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIAISQ  423 (505)
T ss_pred             cCCCEEEEcchHhcCCCCCCCcHHHHHHHHHHHHHHHHHHhCCeEEEEee
Confidence            458999999999886321    223344443333   22  577777774

>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

Probab=82.51  E-value=3.5  Score=39.69  Aligned_cols=48  Identities=23%  Similarity=0.332  Sum_probs=34.2

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +.+-+++|+||--.-+|......+..++..+.....+++++..-...+
T Consensus       112 ~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~~~~  159 (173)
T cd03246         112 YGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRPETL  159 (173)
T ss_pred             hcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHH
Confidence            567789999999999998888888888876644334555555444444

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PRK13880 conjugal transfer coupling protein TraG; Provisional

Probab=82.45  E-value=1.7  Score=51.13  Aligned_cols=44  Identities=20%  Similarity=0.237  Sum_probs=34.3

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAA  473 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~  473 (633)
                      .+++++||||||||..+++|.|-.   ...          .+||+-|--|+......
T Consensus       176 ~HvlviapTgSGKgvg~ViPnLL~---~~~----------S~VV~D~KGE~~~~Tag  219 (636)
T PRK13880        176 EHVLTYAPTRSGKGVGLVVPTLLS---WGH----------SSVITDLKGELWALTAG  219 (636)
T ss_pred             ceEEEEecCCCCCceEEEccchhh---CCC----------CEEEEeCcHHHHHHHHH
Confidence            589999999999999999998732   111          28899999999765543

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

Probab=82.44  E-value=1.1  Score=51.28  Aligned_cols=47  Identities=13%  Similarity=0.092  Sum_probs=32.4

Q ss_pred             ECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC
Q 006737          513 ATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP  563 (633)
Q Consensus       513 aTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp  563 (633)
                      -+||-..++--..    +....-++.|+||+-.-++.+....+-++++...
T Consensus       571 LS~GEqQRLa~AR----Lfy~kPk~AiLDE~TSAv~~dvE~~~Yr~~r~~g  617 (659)
T KOG0060|consen  571 LSPGEQQRLAFAR----LFYHKPKFAILDECTSAVTEDVEGALYRKCREMG  617 (659)
T ss_pred             cCHHHHHHHHHHH----HHhcCCceEEeechhhhccHHHHHHHHHHHHHcC
Confidence            3566554443322    4567788999999998888777777777776653

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

Probab=82.38  E-value=0.6  Score=53.73  Aligned_cols=44  Identities=25%  Similarity=0.373  Sum_probs=32.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      +++-.++|+|||..-+|..-...+...+..+.+++.+++.+-=+
T Consensus       481 l~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~~rT~iiIaHRl  524 (567)
T COG1132         481 LRNPPILILDEATSALDTETEALIQDALKKLLKGRTTLIIAHRL  524 (567)
T ss_pred             hcCCCEEEEeccccccCHHhHHHHHHHHHHHhcCCEEEEEeccH
Confidence            56668999999999999888888888877665665455544333

>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

Probab=82.29  E-value=3.4  Score=38.79  Aligned_cols=44  Identities=23%  Similarity=0.292  Sum_probs=30.8

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      +.+-+++|+||.-.-+|......+..++..+.   .+++++.--...
T Consensus        86 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~---~til~~th~~~~  129 (144)
T cd03221          86 LENPNLLLLDEPTNHLDLESIEALEEALKEYP---GTVILVSHDRYF  129 (144)
T ss_pred             hcCCCEEEEeCCccCCCHHHHHHHHHHHHHcC---CEEEEEECCHHH
Confidence            44667899999998888877788887777662   355555443333

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=82.24  E-value=2.4  Score=41.53  Aligned_cols=32  Identities=25%  Similarity=0.388  Sum_probs=24.9

Q ss_pred             CCcHHHHHHHHHHh-CCCcEEEEccCCCCchhh
Q 006737          401 QMTRVQEATLSACL-EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       401 ~pt~iQ~~aIp~il-~grDvLv~ApTGSGKTla  432 (633)
                      .+++-|...+.... .|..++++++||||||..
T Consensus         9 ~~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130           9 TFSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            45666777776644 577999999999999984

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=82.06  E-value=1.7  Score=50.33  Aligned_cols=44  Identities=20%  Similarity=0.403  Sum_probs=28.0

Q ss_pred             HHHcCCCCCcHHHHHHHHHHhC--CCcEEEEccCCCCchhhhHHHHHHHH
Q 006737          394 LTAAGYIQMTRVQEATLSACLE--GKDAVVKAKTGTGKSIAFLLPAIEAV  441 (633)
Q Consensus       394 L~~~g~~~pt~iQ~~aIp~il~--grDvLv~ApTGSGKTlaylLPiL~~l  441 (633)
                      |.+.||   .+-|.+.+..++.  +.-++++||||||||... ..++..+
T Consensus       295 l~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       295 IDKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             HHHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            445554   4555556555444  346889999999999753 3455554

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=82.05  E-value=8.6  Score=41.13  Aligned_cols=16  Identities=25%  Similarity=0.308  Sum_probs=13.6

Q ss_pred             cEEEEccCCCCchhhh
Q 006737          418 DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       418 DvLv~ApTGSGKTlay  433 (633)
                      .++++||.|+|||.+.
T Consensus        38 ~~Ll~G~~G~GKt~~a   53 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIA   53 (355)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5789999999999743

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=81.89  E-value=10  Score=41.67  Aligned_cols=48  Identities=23%  Similarity=0.275  Sum_probs=39.0

Q ss_pred             CeeEEEEecccccCCcC--hHHHHHHHHHHCCCCCcEEEEeccCChhhhc
Q 006737          534 GLKMLVLDEADHLLDLG--FRKDVENIVDCLPRRRQSLLFSATMPKELVL  581 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g--f~~~l~~Il~~lpk~~Q~IlfSATl~~el~l  581 (633)
                      .--+||+|-||.+-|++  ..+.+.++-..++...-.|+||++..+....
T Consensus       115 ~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~~y~  164 (438)
T KOG2543|consen  115 QKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEKQYL  164 (438)
T ss_pred             ceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHHHhh
Confidence            45589999999998876  6677778878888777789999999888544

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=81.62  E-value=1.1  Score=48.10  Aligned_cols=27  Identities=19%  Similarity=0.402  Sum_probs=19.6

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      ...|+++.+|||||||+...  .|.+++.
T Consensus        96 ~KSNILLiGPTGsGKTlLAq--TLAk~Ln  122 (408)
T COG1219          96 SKSNILLIGPTGSGKTLLAQ--TLAKILN  122 (408)
T ss_pred             eeccEEEECCCCCcHHHHHH--HHHHHhC
Confidence            34589999999999998443  4445544

>TIGR00959 ffh signal recognition particle protein

Probab=81.57  E-value=7.1  Score=43.75  Aligned_cols=16  Identities=19%  Similarity=0.314  Sum_probs=13.9

Q ss_pred             cEEEEccCCCCchhhh
Q 006737          418 DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       418 DvLv~ApTGSGKTlay  433 (633)
                      -+++++++|+|||.+.
T Consensus       101 vi~~vG~~GsGKTTta  116 (428)
T TIGR00959       101 VILMVGLQGSGKTTTC  116 (428)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            5789999999999864

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>TIGR00763 lon ATP-dependent protease La

Probab=81.47  E-value=6.4  Score=47.44  Aligned_cols=17  Identities=24%  Similarity=0.315  Sum_probs=14.8

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      +..+++++|+|+|||..
T Consensus       347 ~~~lll~GppG~GKT~l  363 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSL  363 (775)
T ss_pred             CceEEEECCCCCCHHHH
Confidence            45799999999999974

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=81.46  E-value=3.9  Score=48.02  Aligned_cols=70  Identities=20%  Similarity=0.256  Sum_probs=52.3

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|+|+.-+.++++.+...     ++.+..++|+......   ...+..+..+|||||     +.+..+    +++.
T Consensus       247 ~~IVF~~tk~~a~~l~~~L~~~-----g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVAT-----dv~arG----IDip  312 (629)
T PRK11634        247 AAIIFVRTKNATLEVAEALERN-----GYNSAALNGDMNQALREQTLERLKDGRLDILIAT-----DVAARG----LDVE  312 (629)
T ss_pred             CEEEEeccHHHHHHHHHHHHhC-----CCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEc-----chHhcC----CCcc
Confidence            5899999999999988877654     6788899998765543   345566788999999     344443    6677


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      +|.+||.
T Consensus       313 ~V~~VI~  319 (629)
T PRK11634        313 RISLVVN  319 (629)
T ss_pred             cCCEEEE
Confidence            7777764

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=81.37  E-value=1.5  Score=50.83  Aligned_cols=47  Identities=19%  Similarity=0.268  Sum_probs=34.3

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +.+-+++|+||+-.-+|......+...+..+.++ .++++.+--...+
T Consensus       491 l~~~~ililDE~ts~lD~~t~~~i~~~l~~~~~~-~tviiitHr~~~~  537 (574)
T PRK11160        491 LHDAPLLLLDEPTEGLDAETERQILELLAEHAQN-KTVLMITHRLTGL  537 (574)
T ss_pred             hcCCCEEEEeCCcccCCHHHHHHHHHHHHHHcCC-CEEEEEecChhHH
Confidence            5677899999999999887888888887776544 4555555544444

>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

Probab=81.36  E-value=2.3  Score=41.63  Aligned_cols=42  Identities=24%  Similarity=0.343  Sum_probs=30.0

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCC-CCcEEEEecc
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPR-RRQSLLFSAT  574 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk-~~Q~IlfSAT  574 (633)
                      .+-+++|+||...-++......+..++..+.. ..++|+.|--
T Consensus       115 ~~p~llilDEp~~~LD~~~~~~i~~~L~~~~~~g~tiIiiSH~  157 (178)
T cd03239         115 KPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITLK  157 (178)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEECC
Confidence            46688999999999988777777777665533 3566665543

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>PRK10867 signal recognition particle protein; Provisional

Probab=81.14  E-value=15  Score=41.23  Aligned_cols=16  Identities=19%  Similarity=0.260  Sum_probs=13.7

Q ss_pred             cEEEEccCCCCchhhh
Q 006737          418 DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       418 DvLv~ApTGSGKTlay  433 (633)
                      -+++++++|+|||.+.
T Consensus       102 vI~~vG~~GsGKTTta  117 (433)
T PRK10867        102 VIMMVGLQGAGKTTTA  117 (433)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            5789999999999754

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=81.01  E-value=4.4  Score=46.91  Aligned_cols=55  Identities=15%  Similarity=0.142  Sum_probs=32.8

Q ss_pred             cccccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          375 ILSQKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       375 ~~~~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+..+|++.|--..+...|.-.   -+++|.-+  +++-.-. -.-+|+|+|.|+||||.
T Consensus       504 tVPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~--k~lGi~~-PsGvLL~GPPGCGKTLl  561 (802)
T KOG0733|consen  504 TVPDVTWDDIGALEEVRLELNMAILAPIKRPDLF--KALGIDA-PSGVLLCGPPGCGKTLL  561 (802)
T ss_pred             ecCCCChhhcccHHHHHHHHHHHHhhhccCHHHH--HHhCCCC-CCceEEeCCCCccHHHH
Confidence            34567799998666666555431   23333222  2222211 23699999999999983

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

Probab=80.96  E-value=13  Score=46.06  Aligned_cols=144  Identities=14%  Similarity=0.135  Sum_probs=96.8

Q ss_pred             HHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHH--HhcCCCCCC--------------------CCCCeEEEEEc
Q 006737          405 VQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVL--KATSSSTTQ--------------------LVPPIYVLILC  462 (633)
Q Consensus       405 iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~--~~~~~~~~~--------------------~~~~~~vLILv  462 (633)
                      -|++.|..+...-|||--+.|=-=.||-..+.-+..+.  ...+..+..                    ...+-++.||.
T Consensus       731 k~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~  810 (1139)
T COG1197         731 KHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRLPVKTFVSEYDDLLIREAILRELLRGGQVFYVH  810 (1139)
T ss_pred             cHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCcceEEEEecCChHHHHHHHHHHHhcCCEEEEEe
Confidence            36777777777777777777766667643333222111  111100000                    01255899999


Q ss_pred             ccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          463 PTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       463 PTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      |..+-..++...++.+.   +..++++.+|......-   ...+..+..||||||.     +++++    +++.+...||
T Consensus       811 NrV~~Ie~~~~~L~~LV---PEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TT-----IIEtG----IDIPnANTiI  878 (1139)
T COG1197         811 NRVESIEKKAERLRELV---PEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTT-----IIETG----IDIPNANTII  878 (1139)
T ss_pred             cchhhHHHHHHHHHHhC---CceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEee-----eeecC----cCCCCCceEE
Confidence            99999999999999986   47889999998765432   3455667899999994     44554    7788999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCC
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPR  564 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk  564 (633)
                      |+-||++.    ..++.++.....+
T Consensus       879 Ie~AD~fG----LsQLyQLRGRVGR  899 (1139)
T COG1197         879 IERADKFG----LAQLYQLRGRVGR  899 (1139)
T ss_pred             Eecccccc----HHHHHHhccccCC
Confidence            99999976    3466666655544

>TIGR02012 tigrfam_recA protein RecA

Probab=80.90  E-value=8.6  Score=41.47  Aligned_cols=43  Identities=21%  Similarity=0.180  Sum_probs=26.6

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELA  468 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa  468 (633)
                      .|+-+.|.+|+|+|||... +.++.......          -.|++|..-..+.
T Consensus        54 ~G~iteI~G~~GsGKTtLa-L~~~~~~~~~g----------~~v~yId~E~~~~   96 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLA-LHAIAEAQKAG----------GTAAFIDAEHALD   96 (321)
T ss_pred             CCeEEEEECCCCCCHHHHH-HHHHHHHHHcC----------CcEEEEcccchhH
Confidence            4677899999999999753 44444433321          2377775544333

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]

Probab=80.81  E-value=6.1  Score=44.91  Aligned_cols=86  Identities=20%  Similarity=0.276  Sum_probs=61.5

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      +.+||.+.+..-|.-+.+.+.++     +++++.++|+.+.....   ..++.+..+|+|||.     ...+    .+++
T Consensus       518 ppiIIFvN~kk~~d~lAk~LeK~-----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD-----vAgR----GIDI  583 (673)
T KOG0333|consen  518 PPIIIFVNTKKGADALAKILEKA-----GYKVTTLHGGKSQEQRENALADFREGTGDILVATD-----VAGR----GIDI  583 (673)
T ss_pred             CCEEEEEechhhHHHHHHHHhhc-----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec-----cccc----CCCC
Confidence            34899999999999888888776     78999999998876543   344555679999994     2222    3667


Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCC
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLP  563 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp  563 (633)
                      .+|.+||        +.+|...+...++.+.
T Consensus       584 pnVSlVi--------nydmaksieDYtHRIG  606 (673)
T KOG0333|consen  584 PNVSLVI--------NYDMAKSIEDYTHRIG  606 (673)
T ss_pred             Cccceee--------ecchhhhHHHHHHHhc
Confidence            7777665        4456666666666554

>TIGR00767 rho transcription termination factor Rho

Probab=80.77  E-value=2.3  Score=47.18  Aligned_cols=20  Identities=20%  Similarity=0.365  Sum_probs=17.1

Q ss_pred             HhCCCcEEEEccCCCCchhh
Q 006737          413 CLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       413 il~grDvLv~ApTGSGKTla  432 (633)
                      +-.|+-+++.+|+|+|||..
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL  184 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVL  184 (415)
T ss_pred             eCCCCEEEEECCCCCChhHH
Confidence            34688999999999999974

Members of this family differ in the specificity of RNA binding.

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

Probab=80.73  E-value=2.9  Score=49.33  Aligned_cols=115  Identities=21%  Similarity=0.323  Sum_probs=61.2

Q ss_pred             EEEEccCCCCchhhhHHHHHH-HHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccch
Q 006737          419 AVVKAKTGTGKSIAFLLPAIE-AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK  497 (633)
Q Consensus       419 vLv~ApTGSGKTlaylLPiL~-~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~  497 (633)
                      .|+.---|-|||..-+.-++. ......   ........-.|||+|+- +..|...++.+. .....+.+.+++|  ...
T Consensus       155 gIladd~glgkt~~ti~l~l~~~~~~~~---~~~~~~~kttLivcp~s-~~~qW~~elek~-~~~~~l~v~v~~g--r~k  227 (674)
T KOG1001|consen  155 GILADDMGLGKTVKTIALILKQKLKSKE---EDRQKEFKTTLIVCPTS-LLTQWKTELEKV-TEEDKLSIYVYHG--RTK  227 (674)
T ss_pred             ceEeeccccchHHHHHHHHHhcccCCcc---hhhccccCceeEecchH-HHHHHHHHHhcc-CCccceEEEEecc--ccc
Confidence            455556688999864333322 111110   00001122378888864 445555555333 2233566777777  111


Q ss_pred             HHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcC
Q 006737          498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG  550 (633)
Q Consensus       498 ~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~g  550 (633)
                       +...+  .+.+|+++|++.+..    ..   ...-.--.||+||||.+.+..
T Consensus       228 -d~~el--~~~dVVltTy~il~~----~~---l~~i~w~Riildea~~ikn~~  270 (674)
T KOG1001|consen  228 -DKSEL--NSYDVVLTTYDILKN----SP---LVKIKWLRIVLDEAHTIKNKD  270 (674)
T ss_pred             -ccchh--cCCceEEeeHHHhhc----cc---ccceeEEEEEeccccccCCcc
Confidence             22222  236899999988863    10   111233469999999998753

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=80.70  E-value=3  Score=45.21  Aligned_cols=40  Identities=23%  Similarity=0.296  Sum_probs=28.4

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHh-CCCcEEEEccCCCCchhh
Q 006737          391 IKALTAAGYIQMTRVQEATLSACL-EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       391 l~~L~~~g~~~pt~iQ~~aIp~il-~grDvLv~ApTGSGKTla  432 (633)
                      +..|.+.|+  +++.+...+..+. .+.+++++++||||||..
T Consensus       154 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl  194 (340)
T TIGR03819       154 LDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL  194 (340)
T ss_pred             HHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH
Confidence            455555554  4566666666554 466999999999999973

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=80.56  E-value=2.2  Score=46.93  Aligned_cols=27  Identities=19%  Similarity=0.183  Sum_probs=19.1

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      +..++|++|||||||.. +-.++.++..
T Consensus       149 ~GlilI~G~TGSGKTT~-l~al~~~i~~  175 (372)
T TIGR02525       149 AGLGLICGETGSGKSTL-AASIYQHCGE  175 (372)
T ss_pred             CCEEEEECCCCCCHHHH-HHHHHHHHHh
Confidence            34789999999999974 3344555543

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=80.40  E-value=2.4  Score=49.69  Aligned_cols=46  Identities=22%  Similarity=0.314  Sum_probs=35.1

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .++++.||||||||..+++|-+   +....          -+||+-|--|+.......-
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnL---L~~~g----------S~VV~DpKgE~~~~Ta~~R  257 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTA---LKYGG----------PLVCLDPSTEVAPMVCEHR  257 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhh---hcCCC----------CEEEEEChHHHHHHHHHHH
Confidence            4899999999999999999974   22211          1889999999977665433

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional

Probab=80.38  E-value=5  Score=45.94  Aligned_cols=73  Identities=16%  Similarity=0.273  Sum_probs=54.2

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      +++||.++++.-|..+.+.+...    .++.+..++|+.......   ..+..+..+|||||.     .+..+    +++
T Consensus       368 ~~~iVFv~s~~~a~~l~~~L~~~----~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTd-----vl~rG----iDi  434 (518)
T PLN00206        368 PPAVVFVSSRLGADLLANAITVV----TGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATG-----VLGRG----VDL  434 (518)
T ss_pred             CCEEEEcCCchhHHHHHHHHhhc----cCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEec-----Hhhcc----CCc
Confidence            35899999999998877666543    267888999987765433   455667889999994     44444    778


Q ss_pred             CCeeEEEEe
Q 006737          533 MGLKMLVLD  541 (633)
Q Consensus       533 s~l~~LVID  541 (633)
                      .++++||.=
T Consensus       435 p~v~~VI~~  443 (518)
T PLN00206        435 LRVRQVIIF  443 (518)
T ss_pred             ccCCEEEEe
Confidence            899988863

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=80.36  E-value=2  Score=46.89  Aligned_cols=18  Identities=28%  Similarity=0.377  Sum_probs=15.6

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .+.-++|++|||||||..
T Consensus       133 ~~glilI~GpTGSGKTTt  150 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTL  150 (358)
T ss_pred             cCCEEEEECCCCCCHHHH
Confidence            456899999999999984

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=80.30  E-value=2.5  Score=45.53  Aligned_cols=41  Identities=17%  Similarity=0.240  Sum_probs=27.9

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEec
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      ....+++|||+||.|... -.+.+.++++.-|.+.-+|+.|.
T Consensus       106 ~~~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t~  146 (319)
T PRK06090        106 LNGYRLFVIEPADAMNES-ASNALLKTLEEPAPNCLFLLVTH  146 (319)
T ss_pred             cCCceEEEecchhhhCHH-HHHHHHHHhcCCCCCeEEEEEEC
Confidence            456789999999999743 45666677776555554444443

>PHA00729 NTP-binding motif containing protein

Probab=80.25  E-value=12  Score=38.25  Aligned_cols=68  Identities=16%  Similarity=0.263  Sum_probs=34.0

Q ss_pred             cEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCc-ChH----HHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          509 QILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-GFR----KDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       509 dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~-gf~----~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      ..++.+...|+..|....   .....+.+||||++=.-+.. .+.    .....+...+...++++.|...-+.++
T Consensus        60 ~~~fid~~~Ll~~L~~a~---~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL  132 (226)
T PHA00729         60 NSYFFELPDALEKIQDAI---DNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDL  132 (226)
T ss_pred             cEEEEEHHHHHHHHHHHH---hcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHH
Confidence            455555566666554321   11234578999994321111 011    222334444444567777777755553

>PTZ00424 helicase 45; Provisional

Probab=80.19  E-value=4.7  Score=43.90  Aligned_cols=72  Identities=15%  Similarity=0.270  Sum_probs=53.4

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++|+.-|..+.+.+...     ++.+..++|+.......   ..+..+..+|||||.     .+..+    +++.
T Consensus       269 ~~ivF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~-----~l~~G----iDip  334 (401)
T PTZ00424        269 QAIIYCNTRRKVDYLTKKMHER-----DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTD-----LLARG----IDVQ  334 (401)
T ss_pred             eEEEEecCcHHHHHHHHHHHHC-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcc-----cccCC----cCcc
Confidence            5899999999998887766543     67889999997755433   345567889999993     33333    7788


Q ss_pred             CeeEEEEec
Q 006737          534 GLKMLVLDE  542 (633)
Q Consensus       534 ~l~~LVIDE  542 (633)
                      ++.+||.-.
T Consensus       335 ~v~~VI~~~  343 (401)
T PTZ00424        335 QVSLVINYD  343 (401)
T ss_pred             cCCEEEEEC
Confidence            888888643

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=80.13  E-value=5.6  Score=47.16  Aligned_cols=78  Identities=23%  Similarity=0.296  Sum_probs=54.0

Q ss_pred             EEEEEcccHH--------HHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcc
Q 006737          457 YVLILCPTRE--------LASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENK  525 (633)
Q Consensus       457 ~vLILvPTRe--------La~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~  525 (633)
                      +++|++|+.+        -+.++++.+...   .+++.+..++|+.......   ..+..+..+|||||.     .+..+
T Consensus       473 q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~---~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~-----vie~G  544 (681)
T PRK10917        473 QAYVVCPLIEESEKLDLQSAEETYEELQEA---FPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATT-----VIEVG  544 (681)
T ss_pred             cEEEEEcccccccchhHHHHHHHHHHHHHH---CCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc-----ceeeC
Confidence            5999999754        233444444433   3357899999997655433   345567789999994     33333


Q ss_pred             cCcccccCCeeEEEEeccccc
Q 006737          526 SGLSVRLMGLKMLVLDEADHL  546 (633)
Q Consensus       526 ~~~~~~Ls~l~~LVIDEAD~L  546 (633)
                          +++.++.+||+..+++.
T Consensus       545 ----iDip~v~~VIi~~~~r~  561 (681)
T PRK10917        545 ----VDVPNATVMVIENAERF  561 (681)
T ss_pred             ----cccCCCcEEEEeCCCCC
Confidence                77889999999998874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	633
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-33
3ly5_A	262	Ddx18 Dead-Domain Length = 262		8e-33
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		7e-30
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		7e-26
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-25
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-25
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		2e-25
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		3e-25
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		4e-25
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		7e-25
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-24
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		3e-24
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		6e-24
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-23
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-23
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		3e-23
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		4e-23
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		5e-23
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		6e-23
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		6e-23
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-22
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-22
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		2e-22
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		2e-22
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		2e-22
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		2e-22
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		2e-22
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-22
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		5e-22
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-21
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		1e-21
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		4e-21
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		5e-21
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-20
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		1e-18
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		3e-18
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-17
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-17
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		9e-14
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-13
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-13
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-13
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-13
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		1e-12
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		1e-12
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-12
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-12
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		1e-11
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		7e-09

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  140 bits (353), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 84/200 (42%), Positives = 122/200 (61%), Gaps = 9/200 (4%)
Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
           RF +  +S  T+K L  A Y  +T +Q+ T+   L+GKD +  AKTG+GK++AFL+P +E
Sbjct: 26  RFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLE 85
Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
           A+ +   +ST  L     VLI+ PTRELA Q       + KNHD    L ++GG   K +
Sbjct: 86  ALYRLQWTSTDGL----GVLIISPTRELAYQTFEVLRKVGKNHDFSAGL-IIGGKDLKHE 140
Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
             R+ +    ILV TPGRLL H++    +S     L+MLVLDEAD +LD+GF   +  ++
Sbjct: 141 AERINN--INILVCTPGRLLQHMDET--VSFHATDLQMLVLDEADRILDMGFADTMNAVI 196
Query: 560 DCLPRRRQSLLFSATMPKEL 579
           + LP++RQ+LLFSAT  K +
Sbjct: 197 ENLPKKRQTLLFSATQTKSV 216

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score =  138 bits (348), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 81/207 (39%), Positives = 127/207 (61%), Gaps = 18/207 (8%)
Query: 390 TIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST 449
           T+KA+   G+  MT +Q  ++   LEG+D +  AKTG+GK++AFL+PA+E ++K      
Sbjct: 65  TLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKL----- 119
Query: 450 TQLVP--PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDP 507
            + +P     VLIL PTRELA Q       L+ +H     L ++GG+    + ++L  + 
Sbjct: 120 -RFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGL-IMGGSNRSAEAQKL-GNG 176
Query: 508 CQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQ 567
             I+VATPGRLLDH++N  G   +   L+ LV+DEAD +LD+GF ++++ I+  LP RRQ
Sbjct: 177 INIIVATPGRLLDHMQNTPGFMYK--NLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQ 234
Query: 568 SLLFSATMPKE------LVLKREHTYI 588
           ++LFSAT  ++      + LK+E  Y+
Sbjct: 235 TMLFSATQTRKVEDLARISLKKEPLYV 261

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  129 bits (323), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 76/209 (36%), Positives = 122/209 (58%), Gaps = 15/209 (7%)
Query: 374 PILSQ---KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKS 430
           PI+ +   K F + G++ +  +A    G+ + T++Q   +   L+G+D +  A+TG+GK+
Sbjct: 35  PIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKT 94
Query: 431 IAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL 490
            AF LP + A+L+            ++ L+L PTRELA QI+ E    L +  G+    +
Sbjct: 95  GAFALPILNALLETPQR--------LFALVLTPTRELAFQIS-EQFEALGSSIGVQSAVI 145
Query: 491 VGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG 550
           VGG         L   P  I++ATPGRL+DH+EN  G ++R   LK LV+DEAD +L++ 
Sbjct: 146 VGGIDSMSQSLALAKKP-HIIIATPGRLIDHLENTKGFNLR--ALKYLVMDEADRILNMD 202
Query: 551 FRKDVENIVDCLPRRRQSLLFSATMPKEL 579
           F  +V+ I+  +PR R++ LFSATM K++
Sbjct: 203 FETEVDKILKVIPRDRKTFLFSATMTKKV 231

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  115 bits (288), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 129/254 (50%), Gaps = 32/254 (12%)
Query: 392 KALTAAGYIQMTRVQEATLSACL--EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST 449
           KA+T   +  +T VQ+ T+   L  E  D + +AKTGTGK+ AFL+P  + ++     S 
Sbjct: 34  KAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ 93
Query: 450 TQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI---GVLTLVGGTRFKVDQRRLESD 506
                 +  +I+ PTR+LA QI AE   +   + G+     ++LVGGT F+    ++   
Sbjct: 94  YM----VKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKL 149
Query: 507 PCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRR 566
              I++ATPGRL+D +E  S    R +  K  VLDEAD LL++GFR D+E I   L  + 
Sbjct: 150 RPNIVIATPGRLIDVLEKYSNKFFRFVDYK--VLDEADRLLEIGFRDDLETISGILNEKN 207
Query: 567 -------QSLLFSAT-------MPKELVLKREHTYIDTVGLGSVETPVKV-------SKY 605
                  ++LLFSAT       +   ++ K+E  ++DTV     E   ++        K+
Sbjct: 208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 267
Query: 606 NIYVFVLVLSIKIQ 619
              +F  V  IK Q
Sbjct: 268 ANSIFAAVEHIKKQ 281

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 84/254 (33%), Positives = 129/254 (50%), Gaps = 32/254 (12%)
Query: 392 KALTAAGYIQMTRVQEATLSACL--EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST 449
           KA+T   +  +T VQ+ T+   L  E  D + +AKTGTGK+ AFL+P  + ++     S 
Sbjct: 85  KAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ 144
Query: 450 TQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI---GVLTLVGGTRFKVDQRRLESD 506
                 +  +I+ PTR+LA QI AE   +   + G+     ++LVGGT F+    ++   
Sbjct: 145 YM----VKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKL 200
Query: 507 PCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRR 566
              I++ATPGRL+D +E  S    R +  K  VLDEAD LL++GFR D+E I   L  + 
Sbjct: 201 RPNIVIATPGRLIDVLEKYSNKFFRFVDYK--VLDEADRLLEIGFRDDLETISGILNEKN 258
Query: 567 -------QSLLFSAT-------MPKELVLKREHTYIDTVGLGSVETPVKV-------SKY 605
                  ++LLFSAT       +   ++ K+E  ++DTV     E   ++        K+
Sbjct: 259 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKF 318
Query: 606 NIYVFVLVLSIKIQ 619
              +F  V  IK Q
Sbjct: 319 ANSIFAAVEHIKKQ 332

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 69/203 (33%), Positives = 114/203 (56%), Gaps = 18/203 (8%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF---LLPA 437
           FD+  +S   ++ + A G+ + + +Q+  +  C++G D + +A++GTGK+  F   +L  
Sbjct: 42  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 101
Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           IE  LKAT +           L+L PTRELA QI    +A L ++ G      +GGT  +
Sbjct: 102 IELDLKATQA-----------LVLAPTRELAQQIQKVVMA-LGDYMGASCHACIGGTNVR 149
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            + ++L+ +   I+V TPGR+ D + N+  LS +   +KM VLDEAD +L  GF+  + +
Sbjct: 150 AEVQKLQMEAPHIIVGTPGRVFDML-NRRYLSPKY--IKMFVLDEADEMLSRGFKDQIYD 206
Query: 558 IVDCLPRRRQSLLFSATMPKELV 580
           I   L    Q +L SATMP +++
Sbjct: 207 IFQKLNSNTQVVLLSATMPSDVL 229

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 70/180 (38%), Positives = 111/180 (61%), Gaps = 14/180 (7%)
Query: 398 GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAV-LKATSSSTTQLVPPI 456
           G+ + + +QE ++   L G+D + +AK GTGKS A+L+P +E + LK  +         I
Sbjct: 22  GWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDN---------I 72
Query: 457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPG 516
             +++ PTRELA Q++   I + K+  G  V+   GGT  + D  RL+ D   +++ATPG
Sbjct: 73  QAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-DTVHVVIATPG 131
Query: 517 RLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP 576
           R+LD I  K G++ ++  ++M+VLDEAD LL   F + +E+I+  LP+ RQ LL+SAT P
Sbjct: 132 RILDLI--KKGVA-KVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFP 188

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  113 bits (282), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 69/203 (33%), Positives = 114/203 (56%), Gaps = 18/203 (8%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF---LLPA 437
           FD+  +S   ++ + A G+ + + +Q+  +  C++G D + +A++GTGK+  F   +L  
Sbjct: 16  FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQ 75
Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           IE  LKAT +           L+L PTRELA QI    +A L ++ G      +GGT  +
Sbjct: 76  IELDLKATQA-----------LVLAPTRELAQQIQKVVMA-LGDYMGASCHACIGGTNVR 123
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            + ++L+ +   I+V TPGR+ D + N+  LS +   +KM VLDEAD +L  GF+  + +
Sbjct: 124 AEVQKLQMEAPHIIVGTPGRVFDML-NRRYLSPKY--IKMFVLDEADEMLSRGFKDQIYD 180
Query: 558 IVDCLPRRRQSLLFSATMPKELV 580
           I   L    Q +L SATMP +++
Sbjct: 181 IFQKLNSNTQVVLLSATMPSDVL 203

>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion) Bound To Ssrna And Amp-Pnp Length = 512

Iteration: 1
 Score =  113 bits (282), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 77/219 (35%), Positives = 118/219 (53%), Gaps = 25/219 (11%)
Query: 392 KALTAAGYIQMTRVQEATLSACL--EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSST 449
           KA+T   +  +T VQ+ T+   L  E  D + +AKTGTGK+ AFL+P  + ++     S 
Sbjct: 34  KAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ 93
Query: 450 TQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI---GVLTLVGGTRFKVDQRRLESD 506
                 +  +I+ PTR+LA QI AE   +   + G+     ++LVGGT F+    ++   
Sbjct: 94  YM----VKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKL 149
Query: 507 PCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRR 566
              I++ATPGRL+D +E  S    R +  K  VLDEAD LL++GFR D+E I   L  + 
Sbjct: 150 RPNIVIATPGRLIDVLEKYSNKFFRFVDYK--VLDEADRLLEIGFRDDLETISGILNEKN 207
Query: 567 -------QSLLFSAT-------MPKELVLKREHTYIDTV 591
                  ++LLFSAT       +   ++ K+E  ++DTV
Sbjct: 208 SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTV 246

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  112 bits (280), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 71/192 (36%), Positives = 103/192 (53%), Gaps = 16/192 (8%)
Query: 397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI 456
           AG+ + + +QE  +   + G+D + +AK GTGK+ AF++P +E V    +         I
Sbjct: 39  AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNK--------I 90
Query: 457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPG 516
             LI+ PTRELA Q  ++ +  L  H GI  +   GGT  + D  RL ++   ILV TPG
Sbjct: 91  QALIMVPTRELALQ-TSQVVRTLGKHCGISCMVTTGGTNLRDDILRL-NETVHILVGTPG 148
Query: 517 RLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP 576
           R+LD    K      L    + ++DEAD +L   F+  +E I+  LP   QSLLFSAT P
Sbjct: 149 RVLDLASRKVA---DLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFP 205
Query: 577 ---KELVLKREH 585
              KE ++K  H
Sbjct: 206 LTVKEFMVKHLH 217

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  111 bits (278), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 73/196 (37%), Positives = 112/196 (57%), Gaps = 12/196 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++AL   G    T +Q A L   LEGKD + +A+TGTGK++AF LP  E 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +  +              L+L PTRELA Q+A+E  A+  +   + V+ + GGT +   +
Sbjct: 63  LAPSQERGRKP-----RALVLTPTRELALQVASELTAVAPH---LKVVAVYGGTGYGKQK 114
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
             L       +VATPGR LD++  + G+ + L  +++ VLDEAD +L +GF ++VE ++ 
Sbjct: 115 EALLRG-ADAVVATPGRALDYL--RQGV-LDLSRVEVAVLDEADEMLSMGFEEEVEALLS 170
Query: 561 CLPRRRQSLLFSATMP 576
             P  RQ+LLFSAT+P
Sbjct: 171 ATPPSRQTLLFSATLP 186

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  110 bits (274), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 72/196 (36%), Positives = 112/196 (57%), Gaps = 12/196 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++AL   G    T ++ A L   LEGKD + +A+TGTGK++AF LP  E 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +  +              L+L PTRELA Q+A+E  A+  +   + V+ + GGT +   +
Sbjct: 63  LAPSQERGRKP-----RALVLTPTRELALQVASELTAVAPH---LKVVAVYGGTGYGKQK 114
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
             L       +VATPGR LD++  + G+ + L  +++ VLDEAD +L +GF ++VE ++ 
Sbjct: 115 EALLRG-ADAVVATPGRALDYL--RQGV-LDLSRVEVAVLDEADEMLSMGFEEEVEALLS 170
Query: 561 CLPRRRQSLLFSATMP 576
             P  RQ+LLFSAT+P
Sbjct: 171 ATPPSRQTLLFSATLP 186

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

Iteration: 1
 Score =  108 bits (271), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 72/201 (35%), Positives = 113/201 (56%), Gaps = 16/201 (7%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIE 439
           F+E  +S   + A+   G+ + T +Q   +   L  + + V +A+TG+GK+ +F +P IE
Sbjct: 8   FNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE 67
Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            V +            I  +IL PTRELA Q+A E I  LK +  + +  + GG      
Sbjct: 68  LVNENNG---------IEAIILTPTRELAIQVADE-IESLKGNKNLKIAKIYGGKAIYPQ 117
Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
            + L++    I+V TPGR+LDHI N+  L+  L  +K  +LDEAD  L+ GF KDVE I+
Sbjct: 118 IKALKN--ANIVVGTPGRILDHI-NRGTLN--LKNVKYFILDEADEXLNXGFIKDVEKIL 172
Query: 560 DCLPRRRQSLLFSATMPKELV 580
           +   + ++ LLFSAT P+E++
Sbjct: 173 NACNKDKRILLFSATXPREIL 193

>pdb|1WRB|A Chain A, Crystal Structure Of The N-Terminal Reca-Like Domain Of Djvlgb, A Pranarian Vasa-Like Rna Helicase Length = 253

Iteration: 1
 Score =  108 bits (270), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 75/207 (36%), Positives = 111/207 (53%), Gaps = 12/207 (5%)
Query: 379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAI 438
           + FDE  + P     +  A Y + T +Q+  + A LE +D +  A+TG+GK+ AFL+P I
Sbjct: 23  ENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPII 82
Query: 439 EAVL--KATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF 496
             ++         ++   P   LIL PTRELA QI +E+     N   +    + GG   
Sbjct: 83  NHLVCQDLNQQRYSKTAYP-KCLILAPTRELAIQILSESQKFSLN-TPLRSCVVYGGADT 140
Query: 497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE 556
               R ++   C +LVATPGRL+D IE      + L   K +VLDEAD +LD+GF   + 
Sbjct: 141 HSQIREVQMG-CHLLVATPGRLVDFIEKN---KISLEFCKYIVLDEADRMLDMGFEPQIR 196
Query: 557 NIVD--CLPR--RRQSLLFSATMPKEL 579
            I++   +P    RQ+L+FSAT PKE+
Sbjct: 197 KIIEESNMPSGINRQTLMFSATFPKEI 223

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 70/204 (34%), Positives = 115/204 (56%), Gaps = 12/204 (5%)
Query: 379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAI 438
           + F    +  + I  +  +GY   T +Q+ ++     G+D +  A+TG+GK+ AFLLP +
Sbjct: 56  QHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPIL 115
Query: 439 EAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL-LKNHDGIGVLTLVGGTRFK 497
             +L+       +L  P  V+I+ PTRELA QI  EA     +++  IG+  + GGT F+
Sbjct: 116 SKLLE--DPHELELGRP-QVVIVSPTRELAIQIFNEARKFAFESYLKIGI--VYGGTSFR 170
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
             Q    +  C +++ATPGRLLD ++      +     + +VLDEAD +LD+GF +D+  
Sbjct: 171 -HQNECITRGCHVVIATPGRLLDFVDRT---FITFEDTRFVVLDEADRMLDMGFSEDMRR 226
Query: 558 IVDCLPRR--RQSLLFSATMPKEL 579
           I+  +  R   Q+L+FSAT P+E+
Sbjct: 227 IMTHVTMRPEHQTLMFSATFPEEI 250

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  106 bits (265), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 68/200 (34%), Positives = 105/200 (52%), Gaps = 12/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L    A
Sbjct: 9   FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL----A 64
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
            L+     T Q    + VL++C TRELA QI+ E     K    + V    GG   K D+
Sbjct: 65  TLQQLEPVTGQ----VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 120
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIV 559
             L+ +   I+V TPGR+L    NK   S+ L  +K  +LDEAD +L+ L  R+DV+ I 
Sbjct: 121 EVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILDEADKMLEQLDMRRDVQEIF 177
Query: 560 DCLPRRRQSLLFSATMPKEL 579
              P  +Q ++FSAT+ KE+
Sbjct: 178 RMTPHEKQVMMFSATLSKEI 197

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  106 bits (264), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 68/201 (33%), Positives = 109/201 (54%), Gaps = 14/201 (6%)
Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
           +FD+  +    ++ +   G+ + + +Q+  +   +EG D + +A++GTGK+  F + A++
Sbjct: 22  KFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 81
Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            +   TS    Q       L+L PTRELA QI    +AL  + D I V   +GGT F  D
Sbjct: 82  RI--DTSVKAPQ------ALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVED 132
Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
              L     QI+V TPGR+ D+I+ +     R   +KM +LDEAD +L  GF++ +  I 
Sbjct: 133 AEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIF 187
Query: 560 DCLPRRRQSLLFSATMPKELV 580
             LP   Q +L SATMP +++
Sbjct: 188 TLLPPTTQVVLLSATMPNDVL 208

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 68/201 (33%), Positives = 109/201 (54%), Gaps = 14/201 (6%)
Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
           +FD+  +    ++ +   G+ + + +Q+  +   +EG D + +A++GTGK+  F + A++
Sbjct: 23  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 82
Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            +   TS    Q       L+L PTRELA QI    +AL  + D I V   +GGT F  D
Sbjct: 83  RI--DTSVKAPQ------ALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVED 133
Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
              L     QI+V TPGR+ D+I+ +     R   +KM +LDEAD +L  GF++ +  I 
Sbjct: 134 AEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIF 188
Query: 560 DCLPRRRQSLLFSATMPKELV 580
             LP   Q +L SATMP +++
Sbjct: 189 TLLPPTTQVVLLSATMPNDVL 209

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score =  105 bits (263), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 68/201 (33%), Positives = 109/201 (54%), Gaps = 14/201 (6%)
Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
           +FD+  +    ++ +   G+ + + +Q+  +   +EG D + +A++GTGK+  F + A++
Sbjct: 15  KFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 74
Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            +   TS    Q       L+L PTRELA QI    +AL  + D I V   +GGT F  D
Sbjct: 75  RI--DTSVKAPQ------ALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVED 125
Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
              L     QI+V TPGR+ D+I+ +     R   +KM +LDEAD +L  GF++ +  I 
Sbjct: 126 AEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIF 180
Query: 560 DCLPRRRQSLLFSATMPKELV 580
             LP   Q +L SATMP +++
Sbjct: 181 TLLPPTTQVVLLSATMPNDVL 201

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  105 bits (263), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 65/203 (32%), Positives = 111/203 (54%), Gaps = 18/203 (8%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF---LLPA 437
           FD+  +    ++ + A G+ + + +Q+  +  C++G D + +A++GTGK+  F   +L  
Sbjct: 32  FDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQ 91
Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           +E   K T +           L+L PTRELA QI  + I  L ++ G      +GGT  +
Sbjct: 92  LEIEFKETQA-----------LVLAPTRELAQQI-QKVILALGDYMGATCHACIGGTNVR 139
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            + ++L+++   I+V TPGR+ D + N+  LS +   +KM VLDEAD +L  GF+  +  
Sbjct: 140 NEMQKLQAEAPHIVVGTPGRVFDML-NRRYLSPKW--IKMFVLDEADEMLSRGFKDQIYE 196
Query: 558 IVDCLPRRRQSLLFSATMPKELV 580
           I   L    Q +L SATMP +++
Sbjct: 197 IFQKLNTSIQVVLLSATMPTDVL 219

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 67/200 (33%), Positives = 104/200 (52%), Gaps = 12/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L    A
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL----A 65
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
            L+     T Q    + VL++C TRELA QI+ E     K    + V    GG   K D+
Sbjct: 66  TLQQLEPVTGQ----VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIV 559
             L+ +   I+V TPGR+L    NK   S+ L  +K  +LDE D +L+ L  R+DV+ I 
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178
Query: 560 DCLPRRRQSLLFSATMPKEL 579
              P  +Q ++FSAT+ KE+
Sbjct: 179 RMTPHEKQVMMFSATLSKEI 198

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 67/200 (33%), Positives = 104/200 (52%), Gaps = 12/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L    A
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL----A 65
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
            L+     T Q    + VL++C TRELA QI+ E     K    + V    GG   K D+
Sbjct: 66  TLQQLEPVTGQ----VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIV 559
             L+ +   I+V TPGR+L    NK   S+ L  +K  +LDE D +L+ L  R+DV+ I 
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178
Query: 560 DCLPRRRQSLLFSATMPKEL 579
              P  +Q ++FSAT+ KE+
Sbjct: 179 RMTPHEKQVMMFSATLSKEI 198

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 110/200 (55%), Gaps = 13/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           FD  G+    ++ + A G+ + + +Q+  +   ++G+D + ++++GTGK+  F +  ++ 
Sbjct: 39  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 98
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +        TQ       LIL PTRELA QI    +AL  ++  +     +GGT    D 
Sbjct: 99  L--DIQVRETQ------ALILAPTRELAVQIQKGLLAL-GDYMNVQCHACIGGTNVGEDI 149
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
           R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD +L+ GF++ + ++  
Sbjct: 150 RKLDYGQ-HVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 205
Query: 561 CLPRRRQSLLFSATMPKELV 580
            LP   Q +L SAT+P E++
Sbjct: 206 YLPPATQVVLISATLPHEIL 225

>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 411

Iteration: 1
 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 110/200 (55%), Gaps = 13/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           FD  G+    ++ + A G+ + + +Q+  +   ++G+D + ++++GTGK+  F +  ++ 
Sbjct: 40  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 99
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +        TQ       LIL PTRELA QI    +AL  ++  +     +GGT    D 
Sbjct: 100 L--DIQVRETQ------ALILAPTRELAVQIQKGLLAL-GDYMNVQCHACIGGTNVGEDI 150
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
           R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD +L+ GF++ + ++  
Sbjct: 151 RKLDYGQ-HVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 206
Query: 561 CLPRRRQSLLFSATMPKELV 580
            LP   Q +L SAT+P E++
Sbjct: 207 YLPPATQVVLISATLPHEIL 226

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 110/200 (55%), Gaps = 13/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           FD  G+    ++ + A G+ + + +Q+  +   ++G+D + ++++GTGK+  F +  ++ 
Sbjct: 18  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 77
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +        TQ       LIL PTRELA QI    +AL  ++  +     +GGT    D 
Sbjct: 78  L--DIQVRETQ------ALILAPTRELAVQIQKGLLAL-GDYMNVQCHACIGGTNVGEDI 128
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
           R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD +L+ GF++ + ++  
Sbjct: 129 RKLDYGQ-HVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 184
Query: 561 CLPRRRQSLLFSATMPKELV 580
            LP   Q +L SAT+P E++
Sbjct: 185 YLPPATQVVLISATLPHEIL 204

>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 413

Iteration: 1
 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/200 (31%), Positives = 110/200 (55%), Gaps = 13/200 (6%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           FD  G+    ++ + A G+ + + +Q+  +   ++G+D + ++++GTGK+  F +  ++ 
Sbjct: 40  FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQC 99
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +        TQ       LIL PTRELA QI    +AL  ++  +     +GGT    D 
Sbjct: 100 L--DIQVRETQ------ALILAPTRELAVQIQKGLLAL-GDYMNVQCHACIGGTNVGEDI 150
Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
           R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD +L+ GF++ + ++  
Sbjct: 151 RKLDYGQ-HVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEADEMLNKGFKEQIYDVYR 206
Query: 561 CLPRRRQSLLFSATMPKELV 580
            LP   Q +L SAT+P E++
Sbjct: 207 YLPPATQVVLISATLPHEIL 226

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 66/195 (33%), Positives = 102/195 (52%), Gaps = 12/195 (6%)
Query: 386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKAT 445
           + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L    A L+  
Sbjct: 21  LKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVL----ATLQQL 76
Query: 446 SSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLES 505
              T Q    + VL++C TRELA QI+ E     K    + V    GG   K D+  L+ 
Sbjct: 77  EPVTGQ----VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKK 132
Query: 506 DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPR 564
           +   I+V TPGR+L    NK   S+ L  +K  +LDE D +L+ L  R+DV+ I    P 
Sbjct: 133 NCPHIVVGTPGRILALARNK---SLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 189
Query: 565 RRQSLLFSATMPKEL 579
            +Q ++FSAT+ KE+
Sbjct: 190 EKQVMMFSATLSKEI 204

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  103 bits (257), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 62/203 (30%), Positives = 112/203 (55%), Gaps = 19/203 (9%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF---LLPA 437
           FD  G+    ++ + A G+ + + +Q+  +   ++G+D + ++++GTGK+  F   +L  
Sbjct: 3   FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQC 62
Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           ++  ++ T +           LIL PTRELA Q+    +AL  ++  +     +GGT   
Sbjct: 63  LDIQVRETQA-----------LILAPTRELAVQVQKGLLAL-GDYMNVQCHACIGGTNVG 110
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            D R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD +L+ GF++ + +
Sbjct: 111 EDIRKLDYGQ-HVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEADEMLNKGFKEQIYD 166
Query: 558 IVDCLPRRRQSLLFSATMPKELV 580
           +   LP   Q +L SAT+P E++
Sbjct: 167 VYRYLPPATQVVLISATLPHEIL 189

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  102 bits (255), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 62/203 (30%), Positives = 112/203 (55%), Gaps = 19/203 (9%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF---LLPA 437
           FD  G+    ++ + A G+ + + +Q+  +   ++G+D + ++++GTGK+  F   +L  
Sbjct: 3   FDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQC 62
Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           ++  ++ T +           LIL PTRELA Q+    +AL  ++  +     +GGT   
Sbjct: 63  LDIQVRETQA-----------LILAPTRELAVQVQKGLLAL-GDYMNVQSHACIGGTNVG 110
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            D R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD +L+ GF++ + +
Sbjct: 111 EDIRKLDYGQ-HVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEADEMLNKGFKEQIYD 166
Query: 558 IVDCLPRRRQSLLFSATMPKELV 580
           +   LP   Q +L SAT+P E++
Sbjct: 167 VYRYLPPATQVVLISATLPHEVL 189

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 66/203 (32%), Positives = 106/203 (52%), Gaps = 18/203 (8%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF---LLPA 437
           FD+  +S   ++ + A G+   + +Q+  +  C+ G D + +A++GTG +  F   +L  
Sbjct: 17  FDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQ 76
Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           IE  L AT +           L+L PTRELA QI    +AL  ++ G      +GGT  +
Sbjct: 77  IELDLXATQA-----------LVLAPTRELAQQIQXVVMAL-GDYMGASCHACIGGTNVR 124
Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            + + L+ +   I+V TPGR+ D + N+  LS     + M VLDEAD +L  GF   + +
Sbjct: 125 AEVQXLQMEAPHIIVGTPGRVFDML-NRRYLSPXY--IXMFVLDEADEMLSRGFXDQIYD 181
Query: 558 IVDCLPRRRQSLLFSATMPKELV 580
           I   L    Q +L SATMP +++
Sbjct: 182 IFQXLNSNTQVVLLSATMPSDVL 204

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  101 bits (251), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 67/206 (32%), Positives = 107/206 (51%), Gaps = 15/206 (7%)
Query: 377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLP 436
           ++ +F      P  I+A+    + + T +QE  +   L G+  V +++TGTGK+ A+LLP
Sbjct: 2   AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLP 61
Query: 437 AIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK---NHDGIGVLTLVGG 493
             E +    +         +  +I  PTRELA+QI  E + + K       I    L+GG
Sbjct: 62  IXEKIKPERAE--------VQAVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGG 113
Query: 494 TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK 553
           T  +    +L   P  I++ TPGR+ D I  +   ++ +    +LV+DEAD  LD GF  
Sbjct: 114 TDKQKALEKLNVQP-HIVIGTPGRINDFIREQ---ALDVHTAHILVVDEADLXLDXGFIT 169
Query: 554 DVENIVDCLPRRRQSLLFSATMPKEL 579
           DV+ I    P+  Q L+FSAT+P++L
Sbjct: 170 DVDQIAARXPKDLQXLVFSATIPEKL 195

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 99.8 bits (247), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 63/188 (33%), Positives = 105/188 (55%), Gaps = 20/188 (10%)
Query: 392 KALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQ 451
           +A+   G+   T VQ  T+   L+GK+ VV+AKTG+GK+ A+ +P +E  +K+       
Sbjct: 7   QAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKS------- 59
Query: 452 LVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQIL 511
                  L++ PTREL  Q+A+    + +  D   V  + GG  +K    R+ +    I+
Sbjct: 60  -------LVVTPTRELTRQVASHIRDIGRYMD-TKVAEVYGGMPYKAQINRVRN--ADIV 109
Query: 512 VATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLF 571
           VATPGRLLD     S   + L   +++++DEAD + ++GF  D++ I+     R+ + LF
Sbjct: 110 VATPGRLLDLW---SKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLF 166
Query: 572 SATMPKEL 579
           SAT+P+E+
Sbjct: 167 SATIPEEI 174

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 99.4 bits (246), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 104/201 (51%), Gaps = 14/201 (6%)
Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
           +FD+  +    ++ +   G+ + + +Q+  +   +EG D + +A++GTGK+  F + A++
Sbjct: 22  KFDDXELDENLLRGVFGYGFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFSIAALQ 81
Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            +   TS    Q       L L PTRELA QI  + +  L  H  I V   +GGT F  D
Sbjct: 82  RI--DTSVKAPQ------ALXLAPTRELALQIQ-KVVXALAFHXDIKVHACIGGTSFVED 132
Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
              L     QI+V TPGR+ D+I+ +     R   +K  +LDEAD  L  GF++ +  I 
Sbjct: 133 AEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKIKXFILDEADEXLSSGFKEQIYQIF 187
Query: 560 DCLPRRRQSLLFSATMPKELV 580
             LP   Q +L SAT P +++
Sbjct: 188 TLLPPTTQVVLLSATXPNDVL 208

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/215 (34%), Positives = 107/215 (49%), Gaps = 23/215 (10%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  +  + +  +    Y + T VQ+  +    E +D +  A+TG+GK+ AFLLP +  
Sbjct: 17  FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQ 76
Query: 441 V-----------LKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLT 489
           +           +K       +   PI  L+L PTRELA QI  EA         +    
Sbjct: 77  IYSDGPGEALRAMKENGRYGRRKQYPI-SLVLAPTRELAVQIYEEARK-FSYRSRVRPCV 134
Query: 490 LVGGTRFKVDQRRLESDPCQILVATPGRLLDHIE-NKSGLSVRLMGLKMLVLDEADHLLD 548
           + GG       R LE   C +LVATPGRL+D +E  K GL       K LVLDEAD +LD
Sbjct: 135 VYGGADIGQQIRDLERG-CHLLVATPGRLVDMMERGKIGLDF----CKYLVLDEADRMLD 189
Query: 549 LGFRKDVENIV--DCLPRR--RQSLLFSATMPKEL 579
           +GF   +  IV  D +P +  R +++FSAT PKE+
Sbjct: 190 MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEI 224

>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human Dead-Box Rna Helicase Ddx5 (P68) Length = 253

Iteration: 1
 Score = 91.7 bits (226), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/206 (33%), Positives = 101/206 (49%), Gaps = 11/206 (5%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF 433
           P+L+   F E       +  +    + + T +Q       L G D V  A+TG+GK++++
Sbjct: 41  PVLN---FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSY 97
Query: 434 LLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGG 493
           LLPAI  +             PI  L+L PTRELA Q+   A    +    +    + GG
Sbjct: 98  LLPAIVHINHQPFLERGD--GPI-CLVLAPTRELAQQVQQVAAEYCRACR-LKSTCIYGG 153
Query: 494 TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK 553
                  R LE    +I +ATPGRL+D +E        L     LVLDEAD +LD+GF  
Sbjct: 154 APKGPQIRDLERG-VEICIATPGRLIDFLECGK---TNLRRTTYLVLDEADRMLDMGFEP 209
Query: 554 DVENIVDCLPRRRQSLLFSATMPKEL 579
            +  IVD +   RQ+L++SAT PKE+
Sbjct: 210 QIRKIVDQIRPDRQTLMWSATWPKEV 235

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/206 (33%), Positives = 101/206 (49%), Gaps = 11/206 (5%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF 433
           P+L+   F E       +  +    + + T +Q       L G D V  A+TG+GK++++
Sbjct: 27  PVLN---FYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSY 83
Query: 434 LLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGG 493
           LLPAI  +             PI  L+L PTRELA Q+   A    +    +    + GG
Sbjct: 84  LLPAIVHINHQPFLERGD--GPI-CLVLAPTRELAQQVQQVAAEYCRACR-LKSTCIYGG 139
Query: 494 TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK 553
                  R LE    +I +ATPGRL+D +E        L     LVLDEAD +LD+GF  
Sbjct: 140 APKGPQIRDLERG-VEICIATPGRLIDFLECGK---TNLRRTTYLVLDEADRMLDMGFEP 195
Query: 554 DVENIVDCLPRRRQSLLFSATMPKEL 579
            +  IVD +   RQ+L++SAT PKE+
Sbjct: 196 QIRKIVDQIRPDRQTLMWSATWPKEV 221

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/205 (32%), Positives = 107/205 (52%), Gaps = 24/205 (11%)
Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F+   +S   ++ L AAG+ + + VQ   +     G D +V+AK+GTGK+  F   A+++
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           ++    S+         +LIL PTRE+A QI +   A+    +G+     +GGT    D+
Sbjct: 86  LVLENLSTQ--------ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDK 137
Query: 501 RRLESDPCQILVATPGRL-----LDHIENKSGLSVRLMGLKMLVLDEADHLLDLG-FRKD 554
            RL+   C I V +PGR+     LD++   S        +++ +LDEAD LL+ G F++ 
Sbjct: 138 TRLKK--CHIAVGSPGRIKQLIELDYLNPGS--------IRLFILDEADKLLEEGSFQEQ 187
Query: 555 VENIVDCLPRRRQSLLFSATMPKEL 579
           +  I   LP  +Q L  SAT P+ L
Sbjct: 188 INWIYSSLPASKQMLAVSATYPEFL 212

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 86.7 bits (213), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/189 (34%), Positives = 101/189 (53%), Gaps = 8/189 (4%)
Query: 388 PLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSS 447
           P  +K++   G ++ T +Q       L+G D +V A+TGTGK++++L+P     L +   
Sbjct: 29  PDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGF-IHLDSQPI 87
Query: 448 STTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDP 507
           S  Q   P  +L+L PTRELA  + AE      ++ G+  + + GG R +  Q    S  
Sbjct: 88  SREQRNGP-GMLVLTPTRELALHVEAECSKY--SYKGLKSICIYGG-RNRNGQIEDISKG 143
Query: 508 CQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQ 567
             I++ATPGRL D   N    SV L  +  LV+DEAD +LD+ F   +  I+  +   RQ
Sbjct: 144 VDIIIATPGRLNDLQMNN---SVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQ 200
Query: 568 SLLFSATMP 576
           +++ SAT P
Sbjct: 201 TVMTSATWP 209

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 75.5 bits (184), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 101/204 (49%), Gaps = 20/204 (9%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSI 431
           P+ S K FDE G++P  +K + A  + + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 17  PLYSAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTA 76
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF L  +  V    +S           + L P+RELA Q   E +  +     I    +V
Sbjct: 77  AFSLTMLTRVNPEDASPQA--------ICLAPSRELARQ-TLEVVQEMGKFTKITSQLIV 127
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LG 550
             +  K  Q        Q++V TPG +LD +  K    ++L  +K+ VLDEAD++LD  G
Sbjct: 128 PDSFEKNKQIN-----AQVIVGTPGTVLDLMRRK---LMQLQKIKIFVLDEADNMLDQQG 179
Query: 551 FRKDVENIVDCLPRRRQSLLFSAT 574
                  +   LP+  Q +LFSAT
Sbjct: 180 LGDQCIRVKRFLPKDTQLVLFSAT 203

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 108/235 (45%), Gaps = 31/235 (13%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSI 431
           P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 20  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 79
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF+L  +  V  A              L L PT ELA Q       + K +  + +   V
Sbjct: 80  AFVLAMLSQVEPANKYPQC--------LCLSPTYELALQTGKVIEQMGKFYPELKLAYAV 131
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G 550
            G + +  Q+  E    QI++ TPG +LD       +  +   +K+ VLDEAD ++   G
Sbjct: 132 RGNKLERGQKISE----QIVIGTPGTVLDWCSKLKFIDPK--KIKVFVLDEADVMIATQG 185
Query: 551 FRKDVENIVDCLPRRRQSLLFSATM--------------PKELVLKREHTYIDTV 591
            +     I   LPR  Q LLFSAT               P  + LKRE   +DT+
Sbjct: 186 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTI 240

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 108/235 (45%), Gaps = 31/235 (13%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSI 431
           P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 57  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 116
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF+L  +  V  A              L L PT ELA Q       + K +  + +   V
Sbjct: 117 AFVLAMLSQVEPANKYPQC--------LCLSPTYELALQTGKVIEQMGKFYPELKLAYAV 168
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G 550
            G + +  Q+  E    QI++ TPG +LD       +  +   +K+ VLDEAD ++   G
Sbjct: 169 RGNKLERGQKISE----QIVIGTPGTVLDWCSKLKFIDPK--KIKVFVLDEADVMIATQG 222
Query: 551 FRKDVENIVDCLPRRRQSLLFSATM--------------PKELVLKREHTYIDTV 591
            +     I   LPR  Q LLFSAT               P  + LKRE   +DT+
Sbjct: 223 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTI 277

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 108/235 (45%), Gaps = 31/235 (13%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSI 431
           P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 36  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 95
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF+L  +  V  A              L L PT ELA Q       + K +  + +   V
Sbjct: 96  AFVLAMLSQVEPANKYPQC--------LCLSPTYELALQTGKVIEQMGKFYPELKLAYAV 147
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G 550
            G + +  Q+  E    QI++ TPG +LD       +  +   +K+ VLDEAD ++   G
Sbjct: 148 RGNKLERGQKISE----QIVIGTPGTVLDWCSKLKFIDPK--KIKVFVLDEADVMIATQG 201
Query: 551 FRKDVENIVDCLPRRRQSLLFSATM--------------PKELVLKREHTYIDTV 591
            +     I   LPR  Q LLFSAT               P  + LKRE   +DT+
Sbjct: 202 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTI 256

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 108/235 (45%), Gaps = 31/235 (13%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSI 431
           P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 87  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 146
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF+L  +  V  A              L L PT ELA Q       + K +  + +   V
Sbjct: 147 AFVLAMLSQVEPANKYPQ--------CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV 198
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G 550
            G + +  Q+  E    QI++ TPG +LD       +  +   +K+ VLDEAD ++   G
Sbjct: 199 RGNKLERGQKISE----QIVIGTPGTVLDWCSKLKFIDPK--KIKVFVLDEADVMIATQG 252
Query: 551 FRKDVENIVDCLPRRRQSLLFSATM--------------PKELVLKREHTYIDTV 591
            +     I   LPR  Q LLFSAT               P  + LKRE   +DT+
Sbjct: 253 HQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTI 307

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 71.6 bits (174), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 98/205 (47%), Gaps = 17/205 (8%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE--GKDAVVKAKTGTGKSI 431
           P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 20  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 79
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF+L  +  V  A              L L PT ELA Q       + K +  + +   V
Sbjct: 80  AFVLAMLSQVEPANKYPQC--------LCLSPTYELALQTGKVIEQMGKFYPELKLAYAV 131
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G 550
            G + +  Q+  E    QI++ TPG +LD       +  +   +K+ VLDEAD ++   G
Sbjct: 132 RGNKLERGQKISE----QIVIGTPGTVLDWCSKLKFIDPK--KIKVFVLDEADVMIATQG 185
Query: 551 FRKDVENIVDCLPRRRQSLLFSATM 575
            +     I   LPR  Q LLFSAT 
Sbjct: 186 HQDQSIRIQRMLPRNCQMLLFSATF 210

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 71.2 bits (173), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 98/199 (49%), Gaps = 20/199 (10%)
Query: 379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLP 436
           K FDE G++P  +K + A  + + +++QE  L   L    ++ + ++++GTGK+ AF L 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 437 AIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF 496
            +  V    +S           + L P+RELA Q   E +  +     I    +V  +  
Sbjct: 65  MLTRVNPEDASPQA--------ICLAPSRELARQ-TLEVVQEMGKFTKITSQLIVPDSFE 115
Query: 497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDV 555
           K  Q        Q++V TPG +LD +  K    ++L  +K+ VLDEAD++LD  G     
Sbjct: 116 KNKQIN-----AQVIVGTPGTVLDLMRRK---LMQLQKIKIFVLDEADNMLDQQGLGDQC 167
Query: 556 ENIVDCLPRRRQSLLFSAT 574
             +   LP+  Q +LFSAT
Sbjct: 168 IRVKRFLPKDTQLVLFSAT 186

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/199 (30%), Positives = 98/199 (49%), Gaps = 20/199 (10%)
Query: 379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLP 436
           K FDE G++P  +K + A  + + +++QE  L   L    ++ + ++++GTGK+ AF L 
Sbjct: 5   KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 64
Query: 437 AIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRF 496
            +  V    +S           + L P+RELA Q   E +  +     I    +V  +  
Sbjct: 65  MLTRVNPEDASPQA--------ICLAPSRELARQ-TLEVVQEMGKFTKITSQLIVPDSFE 115
Query: 497 KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDV 555
           K  Q        Q++V TPG +LD +  K    ++L  +K+ VLDEAD++LD  G     
Sbjct: 116 KNKQIN-----AQVIVGTPGTVLDLMRRK---LMQLQKIKIFVLDEADNMLDQQGLGDQC 167
Query: 556 ENIVDCLPRRRQSLLFSAT 574
             +   LP+  Q +LFSAT
Sbjct: 168 IRVKRFLPKDTQLVLFSAT 186

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 70.9 bits (172), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/204 (29%), Positives = 98/204 (48%), Gaps = 17/204 (8%)
Query: 374 PILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE--GKDAVVKAKTGTGKSI 431
           P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + ++++GTGK+ 
Sbjct: 87  PLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTA 146
Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           AF+L  +  V  A              L L PT ELA Q       + K +  + +   V
Sbjct: 147 AFVLAMLSQVEPANKYPQ--------CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV 198
Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDL-G 550
            G + +  Q+  E    QI++ TPG +LD       +  +   +K+ VLDEAD ++   G
Sbjct: 199 RGNKLERGQKISE----QIVIGTPGTVLDWCSKLKFIDPK--KIKVFVLDEADVMIATQG 252
Query: 551 FRKDVENIVDCLPRRRQSLLFSAT 574
            +     I   LPR  Q LLFSAT
Sbjct: 253 HQDQSIRIQRMLPRNCQMLLFSAT 276

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/213 (28%), Positives = 102/213 (47%), Gaps = 26/213 (12%)
Query: 374 PILSQKRFD-ECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA 432
           PI + ++ D E  I+   ++ +  AG+   T +Q   +   L G++ +  A TG+GK++A
Sbjct: 23  PIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLA 82
Query: 433 FLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVL---- 488
           F +P +  + +  +            LI+ PTRELASQI  E   L+K  +G G      
Sbjct: 83  FSIPILMQLKQPANKG-------FRALIISPTRELASQIHRE---LIKISEGTGFRIHMI 132
Query: 489 --TLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL 546
               V   +F        S    ILV TP RL+ ++  +    + L  ++ LV+DE+D L
Sbjct: 133 HKAAVAAKKFGPK----SSKKFDILVTTPNRLI-YLLKQDPPGIDLASVEWLVVDESDKL 187
Query: 547 LD---LGFRKDVENI-VDCLPRRRQSLLFSATM 575
            +    GFR  + +I + C   + +  +FSAT 
Sbjct: 188 FEDGKTGFRDQLASIFLACTSHKVRRAMFSATF 220

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	633
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	4e-80
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	2e-76
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-72
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	5e-69
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	8e-69
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	3e-66
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	3e-65
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	3e-65
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-64
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-64
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	7e-63
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	5e-62
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	5e-62
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	7e-62
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	7e-62
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-61
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	5e-61
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	6e-60
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	9e-58
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-56
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	2e-55
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	5e-55
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-54
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	2e-54
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-52
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	2e-52
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	5e-52
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-49
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-48
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	3e-47
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-45
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-12
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	1e-10
3b6e_A	216	Interferon-induced helicase C domain-containing P;	3e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-04
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	1e-08
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	6e-08
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	4e-07
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	8e-06
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	2e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	5e-05
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	7e-05
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	9e-05
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	1e-04
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	2e-04
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-04
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	3e-04
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	9e-04

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* Length = 563

 Score =  263 bits (673), Expect = 4e-80
 Identities = 84/331 (25%), Positives = 144/331 (43%), Gaps = 38/331 (11%)

Query: 300 SEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNK 359
             D +     +   ++  +S            R   +  +DE  F++             
Sbjct: 4   YNDGNRDQRNFGRNQRNNNSNRYRNSRFNSRPRTRSREDDDEVHFDKT-----------T 52

Query: 360 LNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL--EGK 417
            +      ++   + +      +E  +     KA+T   +  +T VQ+ T+   L  E  
Sbjct: 53  FSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDH 112

Query: 418 DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA 477
           D + +AKTGTGK+ AFL+P  + ++     S       +  +I+ PTR+LA QI AE   
Sbjct: 113 DVIARAKTGTGKTFAFLIPIFQHLINTKFDSQ----YMVKAVIVAPTRDLALQIEAEVKK 168

Query: 478 LLKNHDG---IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG 534
           +   + G      ++LVGGT F+    ++      I++ATPGRL+D +E  S    R   
Sbjct: 169 IHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFR--F 226

Query: 535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRR-------QSLLFSATMPKE------LVL 581
           +   VLDEAD LL++GFR D+E I   L  +        ++LLFSAT+  +       ++
Sbjct: 227 VDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIM 286

Query: 582 K-REHTYIDTVGLGSVETPVKVSKYNIYVFV 611
             +E  ++DTV     E   ++ +    V  
Sbjct: 287 NKKECLFLDTVDKNEPEAHERIDQS--VVIS 315

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C} Length = 579

 Score =  253 bits (648), Expect = 2e-76
 Identities = 79/266 (29%), Positives = 129/266 (48%), Gaps = 27/266 (10%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL--EGKDAVVK 422
              ++   + +      +E  +     KA+T   +  +T VQ+ T+   L  E  D + +
Sbjct: 7   HVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIAR 66

Query: 423 AKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH 482
           AKTGTGK+ AFL+P  + ++     S       +  +I+ PTR+LA QI AE   +   +
Sbjct: 67  AKTGTGKTFAFLIPIFQHLINTKFDSQ----YMVKAVIVAPTRDLALQIEAEVKKIHDMN 122

Query: 483 DG---IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV 539
            G      ++LVGGT F+    ++      I++ATPGRL+D +E  S    R   +   V
Sbjct: 123 YGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFR--FVDYKV 180

Query: 540 LDEADHLLDLGFRKDVENIVDCLPRRR-------QSLLFSATMPKE-------LVLKREH 585
           LDEAD LL++GFR D+E I   L  +        ++LLFSAT+  +       ++ K+E 
Sbjct: 181 LDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKEC 240

Query: 586 TYIDTVGLGSVETPVKVSKYNIYVFV 611
            ++DTV     E   ++ +    V  
Sbjct: 241 LFLDTVDKNEPEAHERIDQS--VVIS 264

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens} Length = 236

 Score =  231 bits (591), Expect = 3e-72
 Identities = 82/215 (38%), Positives = 123/215 (57%), Gaps = 9/215 (4%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAK 424
              +  E+  +    RF +  +S  T+K L  A Y  +T +Q+ T+   L+GKD +  AK
Sbjct: 11  RLMQNYEKINVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAK 70

Query: 425 TGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDG 484
           TG+GK++AFL+P +EA+ +   +ST      + VLI+ PTRELA Q       + KNHD 
Sbjct: 71  TGSGKTLAFLVPVLEALYRLQWTST----DGLGVLIISPTRELAYQTFEVLRKVGKNHD- 125

Query: 485 IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD 544
                ++GG   K +  R+ +    ILV TPGRLL H++           L+MLVLDEAD
Sbjct: 126 FSAGLIIGGKDLKHEAERINN--INILVCTPGRLLQHMDETVSFHAT--DLQMLVLDEAD 181

Query: 545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL 579
            +LD+GF   +  +++ LP++RQ+LLFSAT  K +
Sbjct: 182 RILDMGFADTMNAVIENLPKKRQTLLFSATQTKSV 216

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens} Length = 262

 Score =  224 bits (573), Expect = 5e-69
 Identities = 81/253 (32%), Positives = 131/253 (51%), Gaps = 20/253 (7%)

Query: 338 LEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEP----------ILSQKRFDECG-- 385
           +   H     V+L  + +    +N   +     +E                  F      
Sbjct: 1   MHHHHHHSSGVDLGTENLYFQSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNL 60

Query: 386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKAT 445
           ++  T+KA+   G+  MT +Q  ++   LEG+D +  AKTG+GK++AFL+PA+E ++K  
Sbjct: 61  VNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLR 120

Query: 446 SSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLES 505
                       VLIL PTRELA Q       L+ +H       ++GG+    + ++L +
Sbjct: 121 FMP----RNGTGVLILSPTRELAMQTFGVLKELMTHHV-HTYGLIMGGSNRSAEAQKLGN 175

Query: 506 DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRR 565
               I+VATPGRLLDH++N  G   +   L+ LV+DEAD +LD+GF ++++ I+  LP R
Sbjct: 176 GI-NIIVATPGRLLDHMQNTPGFMYK--NLQCLVIDEADRILDVGFEEELKQIIKLLPTR 232

Query: 566 RQSLLFSATMPKE 578
           RQ++LFSAT  ++
Sbjct: 233 RQTMLFSATQTRK 245

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  222 bits (567), Expect = 8e-69
 Identities = 68/206 (33%), Positives = 111/206 (53%), Gaps = 15/206 (7%)

Query: 377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLP 436
           ++ +F      P  I+A+    + + T +QE  +   L G+  V +++TGTGK+ A+LLP
Sbjct: 2   AETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLP 61

Query: 437 AIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK---NHDGIGVLTLVGG 493
            +E +      +  Q       +I  PTRELA+QI  E + + K       I    L+GG
Sbjct: 62  IMEKI--KPERAEVQ------AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGG 113

Query: 494 TRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK 553
           T  +    +L   P  I++ TPGR+ D I  ++   + +    +LV+DEAD +LD+GF  
Sbjct: 114 TDKQKALEKLNVQP-HIVIGTPGRINDFIREQA---LDVHTAHILVVDEADLMLDMGFIT 169

Query: 554 DVENIVDCLPRRRQSLLFSATMPKEL 579
           DV+ I   +P+  Q L+FSAT+P++L
Sbjct: 170 DVDQIAARMPKDLQMLVFSATIPEKL 195

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19 Length = 206

 Score =  215 bits (549), Expect = 3e-66
 Identities = 67/198 (33%), Positives = 111/198 (56%), Gaps = 12/198 (6%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F++  +    +  +   G+ + + +QE ++   L G+D + +AK GTGKS A+L+P +E 
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +         Q       +++ PTRELA Q++   I + K+  G  V+   GGT  + D 
Sbjct: 65  L--DLKKDNIQ------AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI 116

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
            RL+ D   +++ATPGR+LD I+       ++  ++M+VLDEAD LL   F + +E+I+ 
Sbjct: 117 MRLD-DTVHVVIATPGRILDLIKKGV---AKVDHVQMIVLDEADKLLSQDFVQIMEDIIL 172

Query: 561 CLPRRRQSLLFSATMPKE 578
            LP+ RQ LL+SAT P  
Sbjct: 173 TLPKNRQILLYSATFPLS 190

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens} Length = 249

 Score =  213 bits (545), Expect = 3e-65
 Identities = 78/265 (29%), Positives = 131/265 (49%), Gaps = 21/265 (7%)

Query: 339 EDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAG 398
              H              ++    +   +  +        K F + G++ +  +A    G
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQLG 62

Query: 399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV 458
           + + T++Q   +   L+G+D +  A+TG+GK+ AF LP + A+L+            ++ 
Sbjct: 63  WTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQ--------RLFA 114

Query: 459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL 518
           L+L PTRELA QI+ E    L +  G+    +VGG         L   P  I++ATPGRL
Sbjct: 115 LVLTPTRELAFQIS-EQFEALGSSIGVQSAVIVGGIDSMSQSLALAKKP-HIIIATPGRL 172

Query: 519 LDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           +DH+EN  G +  L  LK LV+DEAD +L++ F  +V+ I+  +PR R++ LFSATM K+
Sbjct: 173 IDHLENTKGFN--LRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKK 230

Query: 579 LVLKREHTYIDTVGLGSVETPVKVS 603
                    +  +   +++ PVK +
Sbjct: 231 ---------VQKLQRAALKNPVKCA 246

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A* Length = 230

 Score =  212 bits (543), Expect = 3e-65
 Identities = 65/215 (30%), Positives = 109/215 (50%), Gaps = 14/215 (6%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAK 424
             + +  +  +     F+   +S   ++ L AAG+ + + VQ   +     G D +V+AK
Sbjct: 10  SPRTRTGDVLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAK 69

Query: 425 TGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDG 484
           +GTGK+  F   A++++     + +TQ      +LIL PTRE+A QI +   A+    +G
Sbjct: 70  SGTGKTCVFSTIALDSL--VLENLSTQ------ILILAPTREIAVQIHSVITAIGIKMEG 121

Query: 485 IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD 544
           +     +GGT    D+ RL+   C I V +PGR+   IE      +    +++ +LDEAD
Sbjct: 122 LECHVFIGGTPLSQDKTRLKK--CHIAVGSPGRIKQLIELD---YLNPGSIRLFILDEAD 176

Query: 545 HLLDLG-FRKDVENIVDCLPRRRQSLLFSATMPKE 578
            LL+ G F++ +  I   LP  +Q L  SAT P+ 
Sbjct: 177 KLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEF 211

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19 Length = 220

 Score =  210 bits (537), Expect = 2e-64
 Identities = 63/200 (31%), Positives = 101/200 (50%), Gaps = 12/200 (6%)

Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
            F +  + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L  ++
Sbjct: 15  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74

Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            +     +          VL++C TRELA QI+ E     K    + V    GG   K D
Sbjct: 75  QL--EPVTGQVS------VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKD 126

Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENI 558
           +  L+ +   I+V TPGR+L    NK   S+ L  +K  +LDE D +L+ L  R+DV+ I
Sbjct: 127 EEVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILDECDKMLEQLDMRRDVQEI 183

Query: 559 VDCLPRRRQSLLFSATMPKE 578
               P  +Q ++FSAT+ KE
Sbjct: 184 FRMTPHEKQVMMFSATLSKE 203

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A* Length = 237

 Score =  211 bits (539), Expect = 2e-64
 Identities = 64/222 (28%), Positives = 112/222 (50%), Gaps = 15/222 (6%)

Query: 357 KNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG 416
           +  L   G   E    E + +   FD+  +    ++ + A G+ + + +Q+  +  C++G
Sbjct: 11  RENLYFQGGVIESNWNEIVDN---FDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKG 67

Query: 417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI 476
            D + +A++GTGK+  F +  ++ +        TQ       L+L PTRELA QI  + I
Sbjct: 68  YDVIAQAQSGTGKTATFAISILQQL--EIEFKETQ------ALVLAPTRELAQQIQ-KVI 118

Query: 477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK 536
             L ++ G      +GGT  + + ++L+++   I+V TPGR+ D +  +    +    +K
Sbjct: 119 LALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRY---LSPKWIK 175

Query: 537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           M VLDEAD +L  GF+  +  I   L    Q +L SATMP +
Sbjct: 176 MFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTD 217

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens} Length = 414

 Score =  212 bits (543), Expect = 7e-63
 Identities = 63/223 (28%), Positives = 112/223 (50%), Gaps = 12/223 (5%)

Query: 356 SKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE 415
           S++      E +   E         FD+  +S   ++ + A G+ + + +Q+  +  C++
Sbjct: 17  SRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIK 76

Query: 416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA 475
           G D + +A++GTGK+  F +  ++ +        TQ       L+L PTRELA QI  + 
Sbjct: 77  GYDVIAQAQSGTGKTATFAISILQQI--ELDLKATQ------ALVLAPTRELAQQIQ-KV 127

Query: 476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL 535
           +  L ++ G      +GGT  + + ++L+ +   I+V TPGR+ D +  +    +    +
Sbjct: 128 VMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRY---LSPKYI 184

Query: 536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           KM VLDEAD +L  GF+  + +I   L    Q +L SATMP +
Sbjct: 185 KMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSD 227

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A Length = 410

 Score =  210 bits (537), Expect = 5e-62
 Identities = 65/214 (30%), Positives = 112/214 (52%), Gaps = 13/214 (6%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAK 424
            K E    E +     FD  G+    ++ + A G+ + + +Q+  +   ++G+D + +++
Sbjct: 23  TKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQ 82

Query: 425 TGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDG 484
           +GTGK+  F +  ++ +        TQ       LIL PTRELA QI  + +  L ++  
Sbjct: 83  SGTGKTATFSISVLQCL--DIQVRETQ------ALILAPTRELAVQIQ-KGLLALGDYMN 133

Query: 485 IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD 544
           +     +GGT    D R+L+     ++  TPGR+ D I  +S   +R   +KMLVLDEAD
Sbjct: 134 VQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFDMIRRRS---LRTRAIKMLVLDEAD 189

Query: 545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
            +L+ GF++ + ++   LP   Q +L SAT+P E
Sbjct: 190 EMLNKGFKEQIYDVYRYLPPATQVVLISATLPHE 223

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A Length = 391

 Score =  209 bits (535), Expect = 5e-62
 Identities = 63/199 (31%), Positives = 101/199 (50%), Gaps = 12/199 (6%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L  ++ 
Sbjct: 10  FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQ 69

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +     +          VL++C TRELA QI+ E     K    + V    GG   K D+
Sbjct: 70  L--EPVTGQVS------VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 121

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIV 559
             L+ +   I+V TPGR+L    NK   S+ L  +K  +LDE D +L+ L  R+DV+ I 
Sbjct: 122 EVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 178

Query: 560 DCLPRRRQSLLFSATMPKE 578
              P  +Q ++FSAT+ KE
Sbjct: 179 RMTPHEKQVMMFSATLSKE 197

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A* Length = 394

 Score =  209 bits (535), Expect = 7e-62
 Identities = 69/223 (30%), Positives = 113/223 (50%), Gaps = 17/223 (7%)

Query: 356 SKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE 415
           S+   +    + +   ++ +     FD+  +    ++ +   G+ + + +Q+  +   +E
Sbjct: 1   SEGITDIEESQIQTNYDKVVYK---FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIE 57

Query: 416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA 475
           G D + +A++GTGK+  F + A++ +   TS    Q       L+L PTRELA QI    
Sbjct: 58  GHDVLAQAQSGTGKTGTFSIAALQRI--DTSVKAPQ------ALMLAPTRELALQIQKVV 109

Query: 476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL 535
           +AL   H  I V   +GGT F  D   L     QI+V TPGR+ D+I+ +     R   +
Sbjct: 110 MALAF-HMDIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKI 163

Query: 536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           KM +LDEAD +L  GF++ +  I   LP   Q +L SATMP +
Sbjct: 164 KMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPND 206

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score =  203 bits (520), Expect = 7e-62
 Identities = 67/211 (31%), Positives = 109/211 (51%), Gaps = 17/211 (8%)

Query: 368 EKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGT 427
           +   ++ +     FD+  +    ++ +   G+ + + +Q+  +   +EG D + +A++GT
Sbjct: 6   QTNYDKVVYK---FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGT 62

Query: 428 GKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGV 487
           GK+  F + A++ +   TS    Q       L+L PTRELA QI  + +  L  H  I V
Sbjct: 63  GKTGTFSIAALQRI--DTSVKAPQ------ALMLAPTRELALQIQ-KVVMALAFHMDIKV 113

Query: 488 LTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL 547
              +GGT F  D   L     QI+V TPGR+ D+I+ +     R   +KM +LDEAD +L
Sbjct: 114 HACIGGTSFVEDAEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKIKMFILDEADEML 168

Query: 548 DLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
             GF++ +  I   LP   Q +L SATMP +
Sbjct: 169 SSGFKEQIYQIFTLLPPTTQVVLLSATMPND 199

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A Length = 207

 Score =  202 bits (516), Expect = 1e-61
 Identities = 71/199 (35%), Positives = 107/199 (53%), Gaps = 12/199 (6%)

Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
            F +  + P  ++AL   G    T +Q A L   LEGKD + +A+TGTGK++AF LP  E
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
            +  +              L+L PTRELA Q+A   +  +  H  + V+ + GGT +   
Sbjct: 62  RLAPSQERGR-----KPRALVLTPTRELALQVA-SELTAVAPH--LKVVAVYGGTGYGKQ 113

Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
           +  L       +VATPGR LD++       + L  +++ VLDEAD +L +GF ++VE ++
Sbjct: 114 KEALLRGA-DAVVATPGRALDYLRQGV---LDLSRVEVAVLDEADEMLSMGFEEEVEALL 169

Query: 560 DCLPRRRQSLLFSATMPKE 578
              P  RQ+LLFSAT+P  
Sbjct: 170 SATPPSRQTLLFSATLPSW 188

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A Length = 400

 Score =  207 bits (529), Expect = 5e-61
 Identities = 69/198 (34%), Positives = 100/198 (50%), Gaps = 13/198 (6%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F++  +    +  +  AG+ + + +QE  +   + G+D + +AK GTGK+ AF++P +E 
Sbjct: 23  FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 82

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           V      +  Q       LI+ PTRELA Q +     L K H GI  +   GGT  + D 
Sbjct: 83  V--KPKLNKIQ------ALIMVPTRELALQTSQVVRTLGK-HCGISCMVTTGGTNLRDDI 133

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
            RL      ILV TPGR+LD    K      L    + ++DEAD +L   F+  +E I+ 
Sbjct: 134 LRLNE-TVHILVGTPGRVLDLASRKV---ADLSDCSLFIMDEADKMLSRDFKTIIEQILS 189

Query: 561 CLPRRRQSLLFSATMPKE 578
            LP   QSLLFSAT P  
Sbjct: 190 FLPPTHQSLLFSATFPLT 207

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19 Length = 367

 Score =  203 bits (520), Expect = 6e-60
 Identities = 68/203 (33%), Positives = 112/203 (55%), Gaps = 16/203 (7%)

Query: 377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLL 435
               F+E  +S   + A+   G+ + T +Q   +   L  + + V +A+TG+GK+ +F +
Sbjct: 4   EYMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAI 63

Query: 436 PAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTR 495
           P IE       ++  +       +IL PTRELA Q+A + I  LK +  + +  + GG  
Sbjct: 64  PLIE---LVNENNGIE------AIILTPTRELAIQVA-DEIESLKGNKNLKIAKIYGGKA 113

Query: 496 FKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV 555
                + L++    I+V TPGR+LDHI   +   + L  +K  +LDEAD +L++GF KDV
Sbjct: 114 IYPQIKALKN--ANIVVGTPGRILDHINRGT---LNLKNVKYFILDEADEMLNMGFIKDV 168

Query: 556 ENIVDCLPRRRQSLLFSATMPKE 578
           E I++   + ++ LLFSATMP+E
Sbjct: 169 EKILNACNKDKRILLFSATMPRE 191

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii} Length = 337

 Score =  196 bits (502), Expect = 9e-58
 Identities = 62/193 (32%), Positives = 104/193 (53%), Gaps = 20/193 (10%)

Query: 386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKAT 445
           ++    +A+   G+   T VQ  T+   L+GK+ VV+AKTG+GK+ A+ +P +E  +K+ 
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKS- 59

Query: 446 SSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLES 505
                        L++ PTREL  Q+A   I  +  +    V  + GG  +K    R+ +
Sbjct: 60  -------------LVVTPTRELTRQVA-SHIRDIGRYMDTKVAEVYGGMPYKAQINRVRN 105

Query: 506 DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRR 565
               I+VATPGRLLD         + L   +++++DEAD + ++GF  D++ I+     R
Sbjct: 106 --ADIVVATPGRLLDLWSKGV---IDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNR 160

Query: 566 RQSLLFSATMPKE 578
           + + LFSAT+P+E
Sbjct: 161 KITGLFSATIPEE 173

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens} Length = 300

 Score =  193 bits (491), Expect = 1e-56
 Identities = 69/248 (27%), Positives = 117/248 (47%), Gaps = 19/248 (7%)

Query: 336 KSLEDEHDFEEQVELIRKEISKNKLNGNG--EKKEKREEEPILSQKRFDECGISPLTIKA 393
           K+ E+E +      L+ K I  N ++     E  ++    P+ S K F+E  + P  ++ 
Sbjct: 47  KTDEEEKEDRAAQSLLNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQG 106

Query: 394 LTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQ 451
           + A G+ + +++QE  L   L    ++ + ++++GTGK+ AF+L  +  V    ++   Q
Sbjct: 107 VYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV--EPANKYPQ 164

Query: 452 LVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQIL 511
                  L L PT ELA Q       + K +  + +   V G + +  Q+  E    QI+
Sbjct: 165 ------CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE----QIV 214

Query: 512 VATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLL 570
           + TPG +LD   +K    +    +K+ VLDEAD ++   G +     I   LPR  Q LL
Sbjct: 215 IGTPGTVLDWC-SKLK-FIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLL 272

Query: 571 FSATMPKE 578
           FSAT    
Sbjct: 273 FSATFEDS 280

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B Length = 412

 Score =  193 bits (492), Expect = 2e-55
 Identities = 62/217 (28%), Positives = 104/217 (47%), Gaps = 17/217 (7%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVK 422
           E  ++    P+ S K F+E  + P  ++ + A G+ + +++QE  L   L    ++ + +
Sbjct: 11  EVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQ 70

Query: 423 AKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNH 482
           +++GTGK+ AF+L  +  V    ++   Q       L L PT ELA Q       + K +
Sbjct: 71  SQSGTGKTAAFVLAMLSQV--EPANKYPQ------CLCLSPTYELALQTGKVIEQMGKFY 122

Query: 483 DGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDE 542
             + +   V G + +  Q+  E    QI++ TPG +LD   +K    +    +K+ VLDE
Sbjct: 123 PELKLAYAVRGNKLERGQKISE----QIVIGTPGTVLDWC-SKLK-FIDPKKIKVFVLDE 176

Query: 543 ADHLLDL-GFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           AD ++   G +     I   LPR  Q LLFSAT    
Sbjct: 177 ADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDS 213

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens} Length = 479

 Score =  193 bits (493), Expect = 5e-55
 Identities = 70/295 (23%), Positives = 124/295 (42%), Gaps = 19/295 (6%)

Query: 287 NESSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLEDEHDFEE 346
              S +    + ++          ++ K    +           ++   +  ED      
Sbjct: 2   ATDSWALAVDEQEAAAESLSNLHLKEEKIKPDTNGAVVKTNANAEKTDEEEKEDRAAQSL 61

Query: 347 QVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQ 406
             +LIR  +  N      E  ++    P+ S K F+E  + P  ++ + A G+ + +++Q
Sbjct: 62  LNKLIRSNLVDNTNQV--EVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQ 119

Query: 407 EATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT 464
           E  L   L    ++ + ++++GTGK+ AF+L  +  V    ++   Q       L L PT
Sbjct: 120 ENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV--EPANKYPQ------CLCLSPT 171

Query: 465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIEN 524
            ELA Q       + K +  + +   V G + +  Q+  E    QI++ TPG +LD   +
Sbjct: 172 YELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKISE----QIVIGTPGTVLDWC-S 226

Query: 525 KSGLSVRLMGLKMLVLDEADHLLDL-GFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           K    +    +K+ VLDEAD ++   G +     I   LPR  Q LLFSAT    
Sbjct: 227 KLK-FIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDS 280

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19 Length = 253

 Score =  185 bits (471), Expect = 2e-54
 Identities = 76/212 (35%), Positives = 108/212 (50%), Gaps = 15/212 (7%)

Query: 373 EPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA 432
             I +   FDE  + P     +  A Y + T +Q+  + A LE +D +  A+TG+GK+ A
Sbjct: 20  NVIEN---FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAA 76

Query: 433 FLLPAIEAVLK--ATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTL 490
           FL+P I  ++         ++   P   LIL PTRELA QI +E+     N   +    +
Sbjct: 77  FLIPIINHLVCQDLNQQRYSKTAYPK-CLILAPTRELAIQILSESQKFSLNT-PLRSCVV 134

Query: 491 VGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG 550
            GG      Q R     C +LVATPGRL+D IE      + L   K +VLDEAD +LD+G
Sbjct: 135 YGGAD-THSQIREVQMGCHLLVATPGRLVDFIEKN---KISLEFCKYIVLDEADRMLDMG 190

Query: 551 FRKDVENIVDCL----PRRRQSLLFSATMPKE 578
           F   +  I++         RQ+L+FSAT PKE
Sbjct: 191 FEPQIRKIIEESNMPSGINRQTLMFSATFPKE 222

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens} Length = 245

 Score =  184 bits (470), Expect = 2e-54
 Identities = 56/214 (26%), Positives = 97/214 (45%), Gaps = 20/214 (9%)

Query: 373 EPILSQKRFDEC----GISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTG 428
           +PI +   F +      I+   ++ +  AG+   T +Q   +   L G++ +  A TG+G
Sbjct: 22  DPIAT---FQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSG 78

Query: 429 KSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVL 488
           K++AF +P +  + +  +            LI+ PTRELASQI  E I + +   G  + 
Sbjct: 79  KTLAFSIPILMQLKQPANK------GFR-ALIISPTRELASQIHRELIKISE-GTGFRIH 130

Query: 489 TLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD 548
            +              S    ILV TP RL+  ++      + L  ++ LV+DE+D L +
Sbjct: 131 MIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP-GIDLASVEWLVVDESDKLFE 189

Query: 549 ---LGFRKDVENIVD-CLPRRRQSLLFSATMPKE 578
               GFR  + +I   C   + +  +FSAT   +
Sbjct: 190 DGKTGFRDQLASIFLACTSHKVRRAMFSATFAYD 223

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  180 bits (458), Expect = 1e-52
 Identities = 75/240 (31%), Positives = 111/240 (46%), Gaps = 30/240 (12%)

Query: 345 EEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTR 404
            ++VE  R+     ++   G    K    P+L+   F E       +  +    + + T 
Sbjct: 5   AQEVETYRRS---KEITVRGHNCPK----PVLN---FYEANFPANVMDVIARQNFTEPTA 54

Query: 405 VQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI------YV 458
           +Q       L G D V  A+TG+GK++++LLPAI  +         Q  P +        
Sbjct: 55  IQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINH-------Q--PFLERGDGPIC 105

Query: 459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL 518
           L+L PTRELA Q+   A    +    +    + GG   K  Q R      +I +ATPGRL
Sbjct: 106 LVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAP-KGPQIRDLERGVEICIATPGRL 163

Query: 519 LDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           +D +E        L     LVLDEAD +LD+GF   +  IVD +   RQ+L++SAT PKE
Sbjct: 164 IDFLECGK---TNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKE 220

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens} Length = 228

 Score =  178 bits (454), Expect = 2e-52
 Identities = 66/207 (31%), Positives = 102/207 (49%), Gaps = 12/207 (5%)

Query: 373 EPILSQKRFDEC-GISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSI 431
           +P      F +     P  +K++   G ++ T +Q       L+G D +V A+TGTGK++
Sbjct: 16  KPTCR---FKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTL 72

Query: 432 AFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
           ++L+P     L +   S  Q   P  +L+L PTRELA  + AE         G+  + + 
Sbjct: 73  SYLMPGFIH-LDSQPISREQRNGPG-MLVLTPTRELALHVEAECSKYSYK--GLKSICIY 128

Query: 492 GGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF 551
           GG   +  Q    S    I++ATPGRL D   N S   V L  +  LV+DEAD +LD+ F
Sbjct: 129 GGRN-RNGQIEDISKGVDIIIATPGRLNDLQMNNS---VNLRSITYLVIDEADKMLDMEF 184

Query: 552 RKDVENIVDCLPRRRQSLLFSATMPKE 578
              +  I+  +   RQ+++ SAT P  
Sbjct: 185 EPQIRKILLDVRPDRQTVMTSATWPDT 211

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A* Length = 395

 Score =  183 bits (466), Expect = 5e-52
 Identities = 60/205 (29%), Positives = 97/205 (47%), Gaps = 20/205 (9%)

Query: 377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFL 434
             K FDE G++P  +K + A  + + +++QE  L   L    ++ + ++++GTGK+ AF 
Sbjct: 3   MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS 62

Query: 435 LPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT 494
           L  +  V      ++ Q       + L P+RELA Q       + K       L  V  +
Sbjct: 63  LTMLTRV--NPEDASPQ------AICLAPSRELARQTLEVVQEMGKFTKITSQLI-VPDS 113

Query: 495 RFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRK 553
             K  Q        Q++V TPG +LD +  K    ++L  +K+ VLDEAD++LD  G   
Sbjct: 114 FEKNKQIN-----AQVIVGTPGTVLDLMRRKL---MQLQKIKIFVLDEADNMLDQQGLGD 165

Query: 554 DVENIVDCLPRRRQSLLFSATMPKE 578
               +   LP+  Q +LFSAT    
Sbjct: 166 QCIRVKRFLPKDTQLVLFSATFADA 190

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster} Length = 434

 Score =  174 bits (443), Expect = 2e-48
 Identities = 68/208 (32%), Positives = 108/208 (51%), Gaps = 13/208 (6%)

Query: 373 EPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA 432
           +PI     F    +  + I  +  +GY   T +Q+ ++     G+D +  A+TG+GK+ A
Sbjct: 53  QPIQH---FTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAA 109

Query: 433 FLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG 492
           FLLP +  +L+           P  V+I+ PTRELA QI  EA         + +  + G
Sbjct: 110 FLLPILSKLLEDPHELELGR--PQ-VVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYG 165

Query: 493 GTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFR 552
           GT     Q    +  C +++ATPGRLLD ++      +     + +VLDEAD +LD+GF 
Sbjct: 166 GTS-FRHQNECITRGCHVVIATPGRLLDFVDRT---FITFEDTRFVVLDEADRMLDMGFS 221

Query: 553 KDVENIVDCLPRR--RQSLLFSATMPKE 578
           +D+  I+  +  R   Q+L+FSAT P+E
Sbjct: 222 EDMRRIMTHVTMRPEHQTLMFSATFPEE 249

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  170 bits (433), Expect = 3e-47
 Identities = 69/220 (31%), Positives = 100/220 (45%), Gaps = 22/220 (10%)

Query: 373 EPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA 432
             I S   F +  +  + +  +    Y + T VQ+  +    E +D +  A+TG+GK+ A
Sbjct: 12  PHIES---FSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAA 68

Query: 433 FLLPAIEAVLKATSSSTTQLVPPI----------YVLILCPTRELASQIAAEAIALLKNH 482
           FLLP +  +         + +               L+L PTRELA QI  EA       
Sbjct: 69  FLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS 128

Query: 483 DGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDE 542
             +    + GG      Q R     C +LVATPGRL+D +E      + L   K LVLDE
Sbjct: 129 -RVRPCVVYGGAD-IGQQIRDLERGCHLLVATPGRLVDMMERG---KIGLDFCKYLVLDE 183

Query: 543 ADHLLDLGFRKDVENIVDCLPRR----RQSLLFSATMPKE 578
           AD +LD+GF   +  IV+         R +++FSAT PKE
Sbjct: 184 ADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKE 223

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  166 bits (421), Expect = 2e-45
 Identities = 29/192 (15%), Positives = 58/192 (30%), Gaps = 21/192 (10%)

Query: 391 IKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTT 450
                      +T  Q       ++GK   + A TG GK+   ++ A+    K       
Sbjct: 11  RSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG------ 64

Query: 451 QLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV---DQRRLESDP 507
                    ++ PT  L  Q       L      + +       + +     ++  E D 
Sbjct: 65  -----KKSALVFPTVTLVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEKSFEEDD 117

Query: 508 CQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQ 567
             ILV +   +  + E      +       + +D+ D +L      D   ++  +P    
Sbjct: 118 YHILVFSTQFVSKNREK-----LSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEII 172

Query: 568 SLLFSATMPKEL 579
              FS     ++
Sbjct: 173 RKAFSTIKQGKI 184

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19 Length = 494

 Score = 68.7 bits (167), Expect = 2e-12
 Identities = 35/224 (15%), Positives = 74/224 (33%), Gaps = 25/224 (11%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           QE   + C    + ++   TG GK++  ++ A   + K              VL+L PT+
Sbjct: 14  QEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTK----------YGGKVLMLAPTK 62

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVGGT-RFKVDQRRLESDPCQILVATPGRLLDHIEN 524
            L  Q A       +    +    +V  T     ++R       +++VATP  + + +  
Sbjct: 63  PLVLQHAES----FRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLA 118

Query: 525 KSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK------E 578
                + L  + ++V DEA   +       +        +    +  +A+         E
Sbjct: 119 GR---ISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIME 175

Query: 579 LVLKREHTYIDTVGLGSVETPVKVSKYNIYVFVLVLSIKIQAFY 622
           ++      +I+     S +    V         + L    +   
Sbjct: 176 VINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVR 219

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 63.9 bits (155), Expect = 1e-10
 Identities = 33/216 (15%), Positives = 61/216 (28%), Gaps = 46/216 (21%)

Query: 391 IKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTT 450
           ++++       +     +  +     + A + A TG+GK                   +T
Sbjct: 207 VESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGK-------------------ST 247

Query: 451 QLVPPIY------VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLE 504
           + VP  Y      VL+L P+        A           I                R  
Sbjct: 248 K-VPAAYAAQGYKVLVLNPSVAATLGFGAYMSKAHGIDPNIRT------------GVRTI 294

Query: 505 SDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPR 564
           +    +  +T G+ L                 +++ DE  H  D      +  ++D    
Sbjct: 295 TTGAPVTYSTYGKFLAD------GGCSGGAYDIIICDEC-HSTDSTTILGIGTVLDQAET 347

Query: 565 RRQSLLFSATMPKELVLKREHTYIDTVGLGSVETPV 600
               L+  AT      +   H  I+ V L S    +
Sbjct: 348 AGARLVVLATATPPGSVTVPHPNIEEVAL-SNTGEI 382

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 56.4 bits (136), Expect = 3e-09
 Identities = 31/144 (21%), Positives = 53/144 (36%), Gaps = 12/144 (8%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKS-IAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT 464
           Q       LEGK+ ++   TG+GK+ +A        + K       +   P  V++L   
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVY------IAKDHLDKKKKASEPGKVIVLVNK 91

Query: 465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIEN 524
             L  Q                V+ L G T+ K          C I+++T   L + + N
Sbjct: 92  VLLVEQ-LFRKEFQPFLKKWYRVIGLSGDTQLK-ISFPEVVKSCDIIISTAQILENSLLN 149

Query: 525 KSGLS---VRLMGLKMLVLDEADH 545
                   V+L    ++++DE  H
Sbjct: 150 LENGEDAGVQLSDFSLIIIDECHH 173

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 57.9 bits (139), Expect = 8e-09
 Identities = 61/412 (14%), Positives = 124/412 (30%), Gaps = 118/412 (28%)

Query: 298 IDSEDVDEKVEGWRDVKKMGSSASLGKYDMK----ITKRVPLKSLEDEH-----DFEEQV 348
           +D E   E    ++D+  +   A +  +D K    + K + L   E +H     D     
Sbjct: 7   MDFE-TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSI-LSKEEIDHIIMSKDAVSGT 64

Query: 349 ELI-------RKEISK----NKLNGN----GEKKEKREEEPILSQKRFDEC-----GISP 388
             +       ++E+ +      L  N        +  + +P +  + + E        + 
Sbjct: 65  LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ 124

Query: 389 LTIKALTAAGYIQMTRVQE-ATLSACLE----GKDAVVKAKTGTGKSIAFLLPAIEAVLK 443
           +  K         ++R+Q    L   L      K+ ++    G+GK+    + A++    
Sbjct: 125 VFAK-------YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW---V-ALDVC-- 171

Query: 444 ATSSSTTQLVPP--IY----------VLILCPTRELASQIAAEAIALLKNHDGIGVLTLV 491
              S   Q      I+            +L   ++L  QI     +   +   I +    
Sbjct: 172 --LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229

Query: 492 GGTRFK--VDQRRLE---------SDP---------CQILVATPGR---LLDHIENKSGL 528
                +  +  +  E          +          C+IL+ T  R   + D +   +  
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT--RFKQVTDFLSAATTT 287

Query: 529 SVRLMGL-KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLK----- 582
            + L      L  DE   L      K ++     LPR   +     T P    L      
Sbjct: 288 HISLDHHSMTLTPDEVKSL----LLKYLDCRPQDLPREVLT-----TNP--RRLSIIAES 336

Query: 583 -REHT----YIDTVGLGSVETPVKVSKYNIYVFVLVLS-IKIQAFYIICFVY 628
            R+          V    + T ++ S       + VL   + +  +    V+
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESS-------LNVLEPAEYRKMFDRLSVF 381

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.8 bits (105), Expect = 9e-05
 Identities = 105/641 (16%), Positives = 182/641 (28%), Gaps = 192/641 (29%)

Query: 49  KKAKEKEKRLLEQE--KQLYQARVRSQIRTKLFDKADPDSETNQHKPMSPDEHVKALADR 106
           K  ++  K +L +E    +  ++       +LF        + Q          + +  +
Sbjct: 36  KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL----LSKQ----------EEMVQK 81

Query: 107 FMKEGAED----LWNEDDGPVKSEQRPRSGAEAN---QRPRLAGAP-------------- 145
           F++E        L +    P+K+EQR  S        QR RL                  
Sbjct: 82  FVEEVLRINYKFLMS----PIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPY 137

Query: 146 IDLR-GLISDKRNS-VNNSGNLNSGSNVKT-------RNYSVLSESKFSDRSKSASLIFM 196
           + LR  L+  +    V   G L SG   KT        +Y V  + K   +      IF 
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGSG---KTWVALDVCLSYKV--QCKMDFK------IFW 186

Query: 197 PNL-ECNDGETVIPSRNVMDFVRRAYFSGTDKRNFCRNDGSSTRDKAGFDTGNKAKPFAR 255
            NL  CN  ETV+    +   + +         N+      S+  K      +  +   R
Sbjct: 187 LNLKNCNSPETVL--EMLQKLLYQI------DPNWTSRSDHSSNIKLRI---HSIQAELR 235

Query: 256 NLGNNRENGDS---------KNMSEFMKKKC--FVGKRRFKRNESSSSDDDSDIDSEDVD 304
            L  ++   +                    C   +  R                D     
Sbjct: 236 RLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR-----------FKQVTDFLSAA 284

Query: 305 EKVEGWRDVKKMGSSASLGKYDMKITKRVPLKSLE-DEHDFEEQV------------ELI 351
                   +     S +L   +    K + LK L+    D   +V            E I
Sbjct: 285 TTTH----ISLDHHSMTLTPDE---VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI 337

Query: 352 RKEIS--KNKLNGNGEKKEK------REEEPILSQKRFDECGISPLTIKALTAAGYIQMT 403
           R  ++   N  + N +K            EP   +K FD   + P +             
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH----------- 386

Query: 404 RVQEATLSAC-LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILC 462
            +    LS    +   + V         +   L     V K    ST  + P IY+ +  
Sbjct: 387 -IPTILLSLIWFDVIKSDV-------MVVVNKLHKYSLVEKQPKESTISI-PSIYLELKV 437

Query: 463 PTRELAS--QIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ-------RRL-ESDPCQILV 512
                 +  +   +   + K  D   ++         +DQ         L   +  + + 
Sbjct: 438 KLENEYALHRSIVDHYNIPKTFDSDDLIPP------YLDQYFYSHIGHHLKNIEHPERMT 491

Query: 513 ATPGRLLDH--IENKSGLSVRLMGLKM-LVLDEADHLLDLGFRKD------------VEN 557
                 LD   +E K    +R             + L  L F K             V  
Sbjct: 492 LFRMVFLDFRFLEQK----IRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547

Query: 558 IVDCLPRRRQSLLFS--------ATMPKELVLKREHTYIDT 590
           I+D LP+  ++L+ S        A M ++     E  + + 
Sbjct: 548 ILDFLPKIEENLICSKYTDLLRIALMAED-----EAIFEEA 583

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.4 bits (96), Expect = 9e-04
 Identities = 61/448 (13%), Positives = 115/448 (25%), Gaps = 172/448 (38%)

Query: 7   LQRSKPLTNILWFNRVFARPMGG-G--------------PRTFPGGLNKWQWKRMHEKKA 51
           L   +P  N+L    +    + G G                     +    W  +   K 
Sbjct: 144 LLELRPAKNVL----IDG--VLGSGKTWVALDVCLSYKVQCKMDFKI---FWLNL---KN 191

Query: 52  KEKEKRLLEQEKQLYQARVRSQIRTKLFDKADPDSETNQHKPMSPDEHVKALADRFMKEG 111
               + +LE  ++L       QI        DP+  +      +    + ++        
Sbjct: 192 CNSPETVLEMLQKLL-----YQI--------DPNWTSRSDHSSNIKLRIHSIQAEL---- 234

Query: 112 AEDLWNEDDGPVKSEQRPRSGAEANQRPRLAGAPIDLRGLISDKRNSVNNSGNLNSGSNV 171
              L        KS+              L         L+     +V N+   N+    
Sbjct: 235 -RRLL-------KSKPYENC---------L---------LVLL---NVQNAKAWNA---- 261

Query: 172 KTRNYSVLSESKFSDRSKSASLIFMPNLECNDGETVIPSRN--VMDFVRRAYFSGTDKRN 229
                       F             NL C   + ++ +R   V DF+     S     +
Sbjct: 262 ------------F-------------NLSC---KILLTTRFKQVTDFL-----SAATTTH 288

Query: 230 FCRNDGSSTRDKAGFDTGNKAKPFARNLGNN-----RE--NGDSKNMS---EFMKKKCFV 279
              +  S                  + L        RE    + + +S   E ++     
Sbjct: 289 ISLDHHSM-----TLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD---- 339

Query: 280 GKRRFKRNESSSSDD-----DSDIDSEDVDEKVEGWRDVKKMGSSASLGKYDMKITKRVP 334
           G   +   +  + D      +S ++  +  E        +KM    S+      I   + 
Sbjct: 340 GLATWDNWKHVNCDKLTTIIESSLNVLEPAE-------YRKMFDRLSVFPPSAHIPTIL- 391

Query: 335 LKSLEDEHDFEEQVELIRKEISKNKL-NGNG------------EKKEKREEEP-----IL 376
           L  +  +    + V ++  ++ K  L                 E K K E E      I+
Sbjct: 392 LSLIWFDVIKSD-VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIV 450

Query: 377 SQ----KRFDECGISPLTIKALTAAGYI 400
                 K FD   + P  +       Y 
Sbjct: 451 DHYNIPKTFDSDDLIPPYLD-----QYF 473

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A Length = 702

 Score = 57.1 bits (138), Expect = 1e-08
 Identities = 43/196 (21%), Positives = 73/196 (37%), Gaps = 25/196 (12%)

Query: 385 GISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKA 444
            IS   +  L   G  ++   Q   +     GK+ ++   T  GK++   +  +   +K 
Sbjct: 9   SISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG 68

Query: 445 TSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLE 504
             S        +YV+   P R LA +         +   G+ +    G    +     L 
Sbjct: 69  GKS--------LYVV---PLRALAGEKYES-FKKWEKI-GLRIGISTGDY--ESRDEHLG 113

Query: 505 SDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV-ENIVDCLP 563
              C I+V T  +  D +       ++ +    LV+DE  HLLD   R    E +V  + 
Sbjct: 114 D--CDIIVTTSEK-ADSLIRNRASWIKAVSC--LVVDEI-HLLDSEKRGATLEILVTKMR 167

Query: 564 RRRQSLLF---SATMP 576
           R  ++L     SAT P
Sbjct: 168 RMNKALRVIGLSATAP 183

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 54.7 bits (132), Expect = 6e-08
 Identities = 43/199 (21%), Positives = 75/199 (37%), Gaps = 27/199 (13%)

Query: 382 DECGISPLTIKALTAAGYIQMTRVQEATLSACL-EGKDAVVKAKTGTGKSIAFLLPAIEA 440
           ++  +    I+ +   G  ++   Q   +   L EG   ++ + TG+GK++   +  I +
Sbjct: 11  EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEM-GIIS 69

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKN--HDGIGVLTLVGGTRFKV 498
            L             IYV    P R L ++         K+    G  V    G      
Sbjct: 70  FLLKNGGKA------IYVT---PLRALTNEKYLT----FKDWELIGFKVAMTSGDY--DT 114

Query: 499 DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV-EN 557
           D   L++    I++ T  + LD +       +  +     VLDE  H L+   R  V E+
Sbjct: 115 DDAWLKN--YDIIITTYEK-LDSLWRHRPEWLNEVNY--FVLDEL-HYLNDPERGPVVES 168

Query: 558 IVDCLPRRRQSLLFSATMP 576
           +     +RR  L  SAT+ 
Sbjct: 169 VT-IRAKRRNLLALSATIS 186

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A* Length = 472

 Score = 51.8 bits (124), Expect = 4e-07
 Identities = 34/184 (18%), Positives = 61/184 (33%), Gaps = 45/184 (24%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           QE  L   L  K   +   TG+GK+      A+ A+ + ++            LI+ PT 
Sbjct: 98  QEKALERWLVDKRGCIVLPTGSGKTHV----AMAAINELSTP----------TLIVVPTL 143

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENK 525
            LA Q         + +  +G  +  G  +          +   + V+T      + E  
Sbjct: 144 ALAEQWKERLGIFGEEY--VGEFS--GRIK----------ELKPLTVSTYDSAYVNAEKL 189

Query: 526 SGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLKREH 585
                      +L+ DE  HL    + +  +  +      R  L  +AT       +RE 
Sbjct: 190 GN------RFMLLIFDEVHHLPAESYVQIAQMSI---APFR--LGLTAT------FERED 232

Query: 586 TYID 589
              +
Sbjct: 233 GRHE 236

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos} Length = 797

 Score = 48.1 bits (113), Expect = 8e-06
 Identities = 37/212 (17%), Positives = 74/212 (34%), Gaps = 17/212 (8%)

Query: 336 KSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALT 395
           +  +   D  + V+    + S++ L  +    E+ E +  LS+   +    +    K   
Sbjct: 186 ELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSE---NLGSAAEGIGKPPP 242

Query: 396 AAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPP 455
                +    Q       + GK+A++ A TG+GK+   +L          +    +    
Sbjct: 243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAK---- 298

Query: 456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG--GTRFKVDQRRLESDPCQILVA 513
             V+ L     +  Q         K+H      ++ G  G  F         +   I+V 
Sbjct: 299 --VVFLATKVPVYEQQKNV----FKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVV 352

Query: 514 TPGRLLDHIENKSGLSVRLMGLKMLVLDEADH 545
           TP  L++  E+  G    L    +++ DE  +
Sbjct: 353 TPQILVNSFED--GTLTSLSIFTLMIFDECHN 382

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A Length = 451

 Score = 46.8 bits (111), Expect = 2e-05
 Identities = 25/171 (14%), Positives = 53/171 (30%), Gaps = 45/171 (26%)

Query: 415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE 474
           + +  ++    G GK+   L   +   L                LIL PTR +A+++   
Sbjct: 18  KKRLTIMDLHPGAGKTKRILPSIVREALLRRLR----------TLILAPTRVVAAEMEEA 67

Query: 475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQ---ILVATPGRLLDHIENKSGLSVR 531
                           + G   +     ++SD      + +         + + + +   
Sbjct: 68  ----------------LRGLPIRYQTPAVKSDHTGREIVDLMCHATFTTRLLSSTRVP-- 109

Query: 532 LMGLKMLVLDEADHLLD------LGFRKDVENIVDCLPRRRQSLLFSATMP 576
                ++V+DEA H  D       G+      + +        +  +AT P
Sbjct: 110 --NYNLIVMDEA-HFTDPCSVAARGYISTRVEMGEAAA-----IFMTATPP 152

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A* Length = 440

 Score = 45.2 bits (107), Expect = 5e-05
 Identities = 27/167 (16%), Positives = 51/167 (30%), Gaps = 37/167 (22%)

Query: 415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE 474
           +G   V+    G GK+  FL   +    +               L+L PTR + S++   
Sbjct: 7   KGMTTVLDFHPGAGKTRRFLPQILAECARRRLR----------TLVLAPTRVVLSEMKEA 56

Query: 475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG 534
                    G+ V             R +      I       L   +   + +      
Sbjct: 57  F-------HGLDVKFHTQAFSAHGSGREV------IDAMCHATLTYRMLEPTRVV----N 99

Query: 535 LKMLVLDEADHL-----LDLGFRKDVENIVDCLPRRRQSLLFSATMP 576
            +++++DEA  L        G+        +       ++L +AT P
Sbjct: 100 WEVIIMDEAHFLDPASIAARGWAAHRARANES-----ATILMTATPP 141

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 44.9 bits (105), Expect = 7e-05
 Identities = 26/141 (18%), Positives = 53/141 (37%), Gaps = 12/141 (8%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKS-IAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT 464
           Q        +GK+ ++ A TG GK+ ++ L+   E  LK         V     +     
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLI--CEHHLKKFPCGQKGKV-----VFFANQ 61

Query: 465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIEN 524
             +  Q  A   +      G  + ++ G T       +   +   I++ TP  L++++  
Sbjct: 62  IPVYEQ-QATVFSRYFERLGYNIASISGATS-DSVSVQHIIEDNDIIILTPQILVNNL-- 117

Query: 525 KSGLSVRLMGLKMLVLDEADH 545
            +G    L    +++ DE  +
Sbjct: 118 NNGAIPSLSVFTLMIFDECHN 138

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae} Length = 1108

 Score = 44.8 bits (105), Expect = 9e-05
 Identities = 62/352 (17%), Positives = 114/352 (32%), Gaps = 58/352 (16%)

Query: 262 ENGDSKNMSEFMKKKCFVGKRRFKRNESSSSDDDSDIDSEDVDEKVEGWRDVKKMGSSAS 321
              D K+  E  K++        K+ +S+ S  +       V    + +         AS
Sbjct: 72  HTQDKKHGLEEEKEEHEENNSENKKIKSNKSKTEDKNKKVVVPVLADSFEQEASREVDAS 131

Query: 322 LGKYDMKITKRVPLKSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRF 381
            G  + +  +      +   H    QV L                    +  PI   KR 
Sbjct: 132 KGLTNSETLQVEQDGKVRLSHQVRHQVAL----------------PPNYDYTPIAEHKRV 175

Query: 382 DECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAV 441
           +E    P T           +   Q+  +S    G+  +V A T  GK+    + A  A+
Sbjct: 176 NEARTYPFT-----------LDPFQDTAISCIDRGESVLVSAHTSAGKT----VVAEYAI 220

Query: 442 LKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQR 501
            ++  +          V+   P + L++Q   E   LL     +G++T  G      D  
Sbjct: 221 AQSLKNKQ-------RVIYTSPIKALSNQKYRE---LLAEFGDVGLMT--GDITINPD-- 266

Query: 502 RLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDC 561
                    LV T   L   +   S +   +  +  ++ DE  ++ D       E  +  
Sbjct: 267 ------AGCLVMTTEILRSMLYRGSEV---MREVAWVIFDEVHYMRDKERGVVWEETIIL 317

Query: 562 LPRRRQSLLFSATMPKELVLKR--EHTYIDTVGLGSVETPVKVSKYNIYVFV 611
           LP + + +  SAT+P  +         +     +  V T  + +    Y+F 
Sbjct: 318 LPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHI--VYTNFRPTPLQHYLFP 367

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 44.1 bits (104), Expect = 1e-04
 Identities = 28/177 (15%), Positives = 51/177 (28%), Gaps = 59/177 (33%)

Query: 416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY----------VLILCPTR 465
            +  V+    G GK                   T + V P             +IL PTR
Sbjct: 2   RELTVLDLHPGAGK-------------------TRR-VLPQLVREAVKKRLRTVILAPTR 41

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENK 525
            +AS++       L+      +             +   +    +           +   
Sbjct: 42  VVASEMYEA----LRGEPIRYM-----TPAV----QSERTGNEIVDFMCHSTFTMKLLQ- 87

Query: 526 SGLSVRLMGLKMLVLDEADHLLD------LGFRKDVENIVDCLPRRRQSLLFSATMP 576
               VR+    + ++DEA H LD       G+ +   ++ D        +  +AT P
Sbjct: 88  ---GVRVPNYNLYIMDEA-HFLDPASVAARGYIETRVSMGDAGA-----IFMTATPP 135

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 43.4 bits (101), Expect = 2e-04
 Identities = 26/140 (18%), Positives = 52/140 (37%), Gaps = 10/140 (7%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           Q       ++GK+ ++ A TG GK+   LL     + K       +      V+      
Sbjct: 18  QLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGK------VVFFANQI 71

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENK 525
            +  Q      +      G  V  + G T   V   ++  +   I++ TP  L+++++  
Sbjct: 72  PVYEQN-KSVFSKYFERHGYRVTGISGATAENVPVEQIVEN-NDIIILTPQILVNNLKK- 128

Query: 526 SGLSVRLMGLKMLVLDEADH 545
            G    L    +++ DE  +
Sbjct: 129 -GTIPSLSIFTLMIFDECHN 147

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A* Length = 556

 Score = 43.0 bits (100), Expect = 3e-04
 Identities = 35/188 (18%), Positives = 69/188 (36%), Gaps = 19/188 (10%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           Q       + GK+A++ A TG+GK+   +L          +    +      V+ L    
Sbjct: 12  QIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAK------VVFLATKV 65

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVG--GTRFKVDQRRLESDPCQILVATPGRLLDHIE 523
            +  Q         K+H      ++ G  G  F         +   I+V TP  L++  E
Sbjct: 66  PVYEQQKNV----FKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFE 121

Query: 524 NKSGLSVRLMGLKMLVLDEA-----DHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE 578
           + +  S+ +  L  ++ DE      +H  ++   + +E   +   +  Q L  +A++   
Sbjct: 122 DGTLTSLSIFTL--MIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVG 179

Query: 579 LVLKREHT 586
                E T
Sbjct: 180 NAKNIEET 187

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 42.9 bits (100), Expect = 3e-04
 Identities = 35/172 (20%), Positives = 67/172 (38%), Gaps = 27/172 (15%)

Query: 406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR 465
           Q+  +S    G+  +V A T  GK+    + A  A+ ++  +          V+   P +
Sbjct: 91  QDTAISCIDRGESVLVSAHTSAGKT----VVAEYAIAQSLKNKQ-------RVIYTSPIK 139

Query: 466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENK 525
            L++Q   E   LL     +G++T   G          ++     LV T   L   +   
Sbjct: 140 ALSNQKYRE---LLAEFGDVGLMT---GD----ITINPDAG---CLVMTTEILRSMLYRG 186

Query: 526 SGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK 577
           S +   +  +  ++ DE  ++ D       E  +  LP + + +  SAT+P 
Sbjct: 187 SEV---MREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPN 235

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos} Length = 936

 Score = 41.5 bits (96), Expect = 9e-04
 Identities = 37/212 (17%), Positives = 76/212 (35%), Gaps = 17/212 (8%)

Query: 336 KSLEDEHDFEEQVELIRKEISKNKLNGNGEKKEKREEEPILSQKRFDECGISPLTIKALT 395
           +  +   D  + V+    + S++ L  +    E+ E +  LS+   +    +    K   
Sbjct: 186 ELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSE---NLGSAAEGIGKPPP 242

Query: 396 AAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPP 455
                +    Q       + GK+A++ A TG+GK+   +L          +    +    
Sbjct: 243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAGRKAK---- 298

Query: 456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG--GTRFKVDQRRLESDPCQILVA 513
             V+ L     +  Q         K+H      ++ G  G  F         +   I+V 
Sbjct: 299 --VVFLATKVPVYEQQKNV----FKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVV 352

Query: 514 TPGRLLDHIENKSGLSVRLMGLKMLVLDEADH 545
           TP  L++  E+ +  S+ +  L  ++ DE  +
Sbjct: 353 TPQILVNSFEDGTLTSLSIFTL--MIFDECHN 382

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	633
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.98
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.98
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.98
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.98
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.97
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.97
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.97
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.97
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.97
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.97
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.97
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.97
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.97
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.96
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.95
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.94
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.94
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.94
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.94
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.94
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.93
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.91
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.91
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.9
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.9
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.9
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.89
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.89
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.88
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.88
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.87
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.86
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.85
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.84
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.84
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.84
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.84
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.83
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.83
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.82
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.82
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.82
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.8
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.8
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.79
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.78
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.77
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.75
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.75
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.74
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.71
3h1t_A	590	Type I site-specific restriction-modification syst	99.62
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.59
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.59
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.52
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.42
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.39
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.3
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.18
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.17
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.14
3jux_A	822	Protein translocase subunit SECA; protein transloc	98.88
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.74
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	97.83
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.81
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.8
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.67
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	97.67
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	97.63
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	96.99
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.85
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	96.64
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.49
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	96.35
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.0
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	95.43
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	95.26
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	95.21
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	95.03
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	95.01
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.88
3bos_A	242	Putative DNA replication factor; P-loop containing	94.74
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	94.67
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	94.44
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	94.38
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	94.34
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	94.31
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	94.17
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.02
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	93.91
2chg_A	226	Replication factor C small subunit; DNA-binding pr	93.8
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	93.49
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	93.41
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	93.21
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.21
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	93.19
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	93.12
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	93.04
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	92.94
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	92.9
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	92.85
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	92.85
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	92.67
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	92.48
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	92.34
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	92.29
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	92.16
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	91.98
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	91.9
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	91.84
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	91.78
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	91.63
2qgz_A	308	Helicase loader, putative primosome component; str	91.57
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	91.55
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	91.24
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	91.22
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	91.18
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	91.01
2r6a_A	454	DNAB helicase, replicative helicase; replication,	90.94
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	90.93
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	90.87
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	90.46
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	90.29
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	90.16
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	90.11
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	90.07
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	89.93
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	89.87
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	89.48
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	89.46
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	89.38
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	89.16
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	89.08
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	88.91
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	88.82
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	88.78
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	88.28
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	87.88
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	87.87
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	87.72
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	87.65
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	87.6
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	87.47
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	87.46
3pvs_A	447	Replication-associated recombination protein A; ma	87.33
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	87.05
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	87.03
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	86.97
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	86.83
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	86.65
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	86.28
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	85.72
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	85.56
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	85.49
2cvh_A	220	DNA repair and recombination protein RADB; filamen	85.18
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	84.49
2fna_A	357	Conserved hypothetical protein; structural genomic	84.4
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	84.37
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	84.32
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	84.29
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	83.88
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	83.77
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	83.31
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	83.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	82.8
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	82.62
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	82.08
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	81.93
1yks_A	440	Genome polyprotein [contains: flavivirin protease	81.84
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	81.84
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	81.51
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	81.28
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	81.12
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	80.71
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	80.4

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=3e-35  Score=321.41  Aligned_cols=245  Identities=30%  Similarity=0.456  Sum_probs=198.1

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +..+|++++|++.++++|.++||..||++|.++||.+++|+|++++|+||||||++|++|+++++......   ....++
T Consensus        54 ~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~---~~~~~~  130 (434)
T 2db3_A           54 PIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE---LELGRP  130 (434)
T ss_dssp             CCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC---CCTTCC
T ss_pred             CcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc---cccCCc
Confidence            35679999999999999999999999999999999999999999999999999999999999998875431   122356


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+|||+||.|+++.+.+++... ++++.+++||.....+...+.. +++|+|+||++|++++.+.   ...+.+++
T Consensus       131 ~~lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~-~~~Ivv~Tp~~l~~~l~~~---~~~l~~~~  205 (434)
T 2db3_A          131 QVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITR-GCHVVIATPGRLLDFVDRT---FITFEDTR  205 (434)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHHTT-CCSEEEECHHHHHHHHHTT---SCCCTTCC
T ss_pred             cEEEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHhhc-CCCEEEEChHHHHHHHHhC---CcccccCC
Confidence            79999999999999999999997654 6888999999987766665554 5899999999999999866   35689999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHC--CCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeeh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCL--PRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYV  609 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~l--pk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v  609 (633)
                      +|||||||+|++++|...+..|+..+  ++.+|+++||||+++.+.     +..++.++.....  .....++.|.++.+
T Consensus       206 ~lVlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~--~~~~~~i~~~~~~~  283 (434)
T 2db3_A          206 FVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIV--GGACSDVKQTIYEV  283 (434)
T ss_dssp             EEEEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESST--TCCCTTEEEEEEEC
T ss_pred             eEEEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccc--cccccccceEEEEe
Confidence            99999999999999999999999875  578999999999998853     2233444332221  23455778877765


Q ss_pred             h------hHHHHhhcCCceEEEEEcccc
Q 006737          610 F------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       610 ~------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      .      .+..........+||||+|+.
T Consensus       284 ~~~~k~~~l~~~l~~~~~~~lVF~~t~~  311 (434)
T 2db3_A          284 NKYAKRSKLIEILSEQADGTIVFVETKR  311 (434)
T ss_dssp             CGGGHHHHHHHHHHHCCTTEEEECSSHH
T ss_pred             CcHHHHHHHHHHHHhCCCCEEEEEeCcH
Confidence            3      222222333445999999974

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=100.00  E-value=7.5e-36  Score=311.75  Aligned_cols=198  Identities=30%  Similarity=0.419  Sum_probs=173.8

Q ss_pred             cCCCCCcccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcC
Q 006737          369 KREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATS  446 (633)
Q Consensus       369 ~~~~~p~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~  446 (633)
                      ...+.|..+..+|++++|++.++++|..+||..||++|.++||.++.|  +|++++||||||||++|++|+++++.... 
T Consensus        82 ~~~~~p~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~~-  160 (300)
T 3fmo_B           82 RDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN-  160 (300)
T ss_dssp             SSTTCCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTTS-
T ss_pred             CCCCCCcCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhccC-
Confidence            345566677889999999999999999999999999999999999998  99999999999999999999998874332 


Q ss_pred             CCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhccc
Q 006737          447 SSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKS  526 (633)
Q Consensus       447 ~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~  526 (633)
                             .++++|||+|||+||.|+++.+..+.....++.+.+++|+.......    ...++||||||++|++++.+..
T Consensus       161 -------~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~TP~~l~~~l~~~~  229 (300)
T 3fmo_B          161 -------KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLK  229 (300)
T ss_dssp             -------CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC----CCCCSEEEECHHHHHHHHTTTC
T ss_pred             -------CCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh----cCCCCEEEECHHHHHHHHHhcC
Confidence                   24579999999999999999999998877788999999987754322    3457999999999999996532


Q ss_pred             CcccccCCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          527 GLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       527 ~~~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                        .+.+.++++|||||||+|++ .+|...+..|+..+++.+|+|+||||+++.+.
T Consensus       230 --~~~l~~l~~lVlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~  282 (300)
T 3fmo_B          230 --FIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVW  282 (300)
T ss_dssp             --CCCGGGCSEEEETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHH
T ss_pred             --CCChhhceEEEEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHH
Confidence              35688999999999999997 78999999999999999999999999999863

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=100.00  E-value=3.7e-34  Score=288.15  Aligned_cols=195  Identities=34%  Similarity=0.496  Sum_probs=173.5

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      +..+|.++++++.++++|.++||..|+++|.++|+.++.|+|+++++|||||||++|++|++..+......   ....++
T Consensus        27 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~~---~~~~~~  103 (242)
T 3fe2_A           27 PVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFL---ERGDGP  103 (242)
T ss_dssp             CCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCCC---CTTCCC
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhcccc---ccCCCC
Confidence            34679999999999999999999999999999999999999999999999999999999999988754321   112356


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||++|+.|+++.+..++... ++.+.+++|+.....+...+..+ ++|+|+||++|.+++...   ...+.+++
T Consensus       104 ~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~I~v~Tp~~l~~~l~~~---~~~~~~~~  178 (242)
T 3fe2_A          104 ICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERG-VEICIATPGRLIDFLECG---KTNLRRTT  178 (242)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEECHHHHHHHHHHT---SCCCTTCC
T ss_pred             EEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHhcCC-CCEEEECHHHHHHHHHcC---CCCccccc
Confidence            79999999999999999999998766 78999999998877766666554 799999999999999765   35688999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +|||||||++++++|...+..|+..+++++|+++||||+|+.+
T Consensus       179 ~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~  221 (242)
T 3fe2_A          179 YLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEV  221 (242)
T ss_dssp             EEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHH
T ss_pred             EEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHH
Confidence            9999999999999999999999999999999999999999985

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=4.1e-33  Score=271.95  Aligned_cols=190  Identities=35%  Similarity=0.590  Sum_probs=168.9

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+|+++++++.++++|.++||..|+++|.++++.+++++|+++++|||+|||++|++|+++.+....        .++++
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~--------~~~~~   74 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK--------DNIQA   74 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS--------CSCCE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhcccC--------CCeeE
Confidence            4699999999999999999999999999999999999999999999999999999999998764321        23579


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      |||+||++|+.|+++.+..+....+++.+..++|+.....+...+. ..++|+|+||++|..++...   ...+.++++|
T Consensus        75 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~~---~~~~~~~~~l  150 (206)
T 1vec_A           75 MVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLD-DTVHVVIATPGRILDLIKKG---VAKVDHVQMI  150 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTT-SCCSEEEECHHHHHHHHHTT---CSCCTTCCEE
T ss_pred             EEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcC-CCCCEEEeCHHHHHHHHHcC---CcCcccCCEE
Confidence            9999999999999999999987766788999999988766555554 45799999999999998765   3568899999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      ||||||++++.+|...+..++..+++.+|+++||||+++.+.
T Consensus       151 ViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~  192 (206)
T 1vec_A          151 VLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQ  192 (206)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHH
T ss_pred             EEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHH
Confidence            999999999999999999999999999999999999998853

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=100.00  E-value=3.2e-33  Score=277.99  Aligned_cols=196  Identities=31%  Similarity=0.460  Sum_probs=163.0

Q ss_pred             cccCccc-cCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCC
Q 006737          377 SQKRFDE-CGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPP  455 (633)
Q Consensus       377 ~~~~F~e-l~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~  455 (633)
                      +..+|.+ +++++.++++|.++||..|+++|.++++.+++|+|+++++|||||||++|++|++..+.......  ....+
T Consensus        17 p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~--~~~~~   94 (228)
T 3iuy_A           17 PTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISR--EQRNG   94 (228)
T ss_dssp             CCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-----------CC
T ss_pred             ChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchh--hccCC
Confidence            3456888 79999999999999999999999999999999999999999999999999999998875432111  11234


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      +++|||+||++||.|+++.+..+.  ..++.+.+++|+.....+...+.. +++|+|+||++|.+++...   ...+.++
T Consensus        95 ~~~lil~Pt~~L~~q~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~~~iiv~Tp~~l~~~~~~~---~~~~~~~  168 (228)
T 3iuy_A           95 PGMLVLTPTRELALHVEAECSKYS--YKGLKSICIYGGRNRNGQIEDISK-GVDIIIATPGRLNDLQMNN---SVNLRSI  168 (228)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHC--CTTCCEEEECC------CHHHHHS-CCSEEEECHHHHHHHHHTT---CCCCTTC
T ss_pred             CcEEEEeCCHHHHHHHHHHHHHhc--ccCceEEEEECCCChHHHHHHhcC-CCCEEEECHHHHHHHHHcC---CcCcccc
Confidence            679999999999999999999985  237889999999887766665554 4799999999999988765   3568899


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      ++|||||||++++++|...+..++..+++++|+++||||+++.+.
T Consensus       169 ~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~  213 (228)
T 3iuy_A          169 TYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVR  213 (228)
T ss_dssp             CEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHH
T ss_pred             eEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHH
Confidence            999999999999999999999999999999999999999999853

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=100.00  E-value=1.9e-32  Score=293.74  Aligned_cols=247  Identities=31%  Similarity=0.458  Sum_probs=192.2

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCC----------
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSS----------  447 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~----------  447 (633)
                      ..+|+++++++.++++|..+||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+......          
T Consensus        14 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~~   93 (417)
T 2i4i_A           14 IESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENG   93 (417)
T ss_dssp             CSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHCB
T ss_pred             cCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhcccccc
Confidence            4569999999999999999999999999999999999999999999999999999999999988765321          


Q ss_pred             CCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC
Q 006737          448 STTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG  527 (633)
Q Consensus       448 ~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~  527 (633)
                      .......++++|||+||++||.|+++.+..++... ++.+..++|+.....+...+.. +++|+|+||++|..++...  
T Consensus        94 ~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~I~v~Tp~~l~~~l~~~--  169 (417)
T 2i4i_A           94 RYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPCVVYGGADIGQQIRDLER-GCHLLVATPGRLVDMMERG--  169 (417)
T ss_dssp             TTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCHHHHHHHHTT-CCSEEEECHHHHHHHHHTT--
T ss_pred             ccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC-CceEEEEECCCCHHHHHHHhhC-CCCEEEEChHHHHHHHHcC--
Confidence            00011123579999999999999999999987654 7889999999887766666654 4799999999999999765  


Q ss_pred             cccccCCeeEEEEecccccCCcChHHHHHHHHHH--CCC--CCcEEEEeccCChhhh-----ccccceEeeecccccccc
Q 006737          528 LSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDC--LPR--RRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVET  598 (633)
Q Consensus       528 ~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~--lpk--~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~  598 (633)
                       ...+..+++|||||||++++++|...+..++..  ++.  .+|+++||||+++.+.     +...+..+....  ....
T Consensus       170 -~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~  246 (417)
T 2i4i_A          170 -KIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGR--VGST  246 (417)
T ss_dssp             -SBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC------C
T ss_pred             -CcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCC--CCCC
Confidence             356889999999999999999999999999884  333  6899999999998742     122233332211  1234


Q ss_pred             CccceEEEeehh-------hHHHHhhc-CCceEEEEEcccc
Q 006737          599 PVKVSKYNIYVF-------VLVLSIKI-QAFYIICFVYTIS  631 (633)
Q Consensus       599 ~~~V~q~~i~v~-------~l~~~~k~-~~~~~LVFcnT~s  631 (633)
                      ..++.+.++.+.       +....... ...++||||+|+.
T Consensus       247 ~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~  287 (417)
T 2i4i_A          247 SENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKK  287 (417)
T ss_dssp             CSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHH
T ss_pred             ccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHH
Confidence            556777777653       12222222 4568999999975

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=100.00  E-value=7e-33  Score=276.73  Aligned_cols=189  Identities=34%  Similarity=0.523  Sum_probs=167.7

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.++++|.++||..|+++|.++++.++.|+|+++++|||+|||++|++|++..+....        .+.+
T Consensus        23 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~--------~~~~   94 (230)
T 2oxc_A           23 PADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLEN--------LSTQ   94 (230)
T ss_dssp             -CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTS--------CSCC
T ss_pred             CCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC--------CCce
Confidence            45699999999999999999999999999999999999999999999999999999999998764332        2357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..+.....++.+.+++|+.....+...+.  .++|+|+||++|.+++...   ...+.++++
T Consensus        95 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~--~~~Iiv~Tp~~l~~~~~~~---~~~~~~~~~  169 (230)
T 2oxc_A           95 ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KCHIAVGSPGRIKQLIELD---YLNPGSIRL  169 (230)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHTT--SCSEEEECHHHHHHHHHTT---SSCGGGCCE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhcc--CCCEEEECHHHHHHHHhcC---CcccccCCE
Confidence            99999999999999999999987666889999999988765555443  4799999999999998765   356789999


Q ss_pred             EEEecccccCCcC-hHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          538 LVLDEADHLLDLG-FRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       538 LVIDEAD~Lld~g-f~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      |||||||++++++ |...+..|+..++..+|+++||||+++++
T Consensus       170 lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~  212 (230)
T 2oxc_A          170 FILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFL  212 (230)
T ss_dssp             EEESSHHHHHSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHH
T ss_pred             EEeCCchHhhcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHH
Confidence            9999999999997 99999999999999999999999999885

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=100.00  E-value=3.8e-33  Score=307.13  Aligned_cols=246  Identities=27%  Similarity=0.349  Sum_probs=172.7

Q ss_pred             CCCCCcccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCC
Q 006737          370 REEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSS  447 (633)
Q Consensus       370 ~~~~p~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~  447 (633)
                      ..+.|..+..+|.+++|++.++++|.++||..|+++|.++|+.++.+  +|+|++||||||||++|++|+++.+....  
T Consensus        83 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~~--  160 (479)
T 3fmp_B           83 DPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--  160 (479)
T ss_dssp             STTSCCCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTTS--
T ss_pred             CCCCCccCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhcC--
Confidence            44556667788999999999999999999999999999999999997  89999999999999999999987764322  


Q ss_pred             CCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC
Q 006737          448 STTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG  527 (633)
Q Consensus       448 ~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~  527 (633)
                            .++++|||+||++||.|+++.+..+.....++.+.++.++.......    ...++|+|+||++|++++.+.. 
T Consensus       161 ------~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~-  229 (479)
T 3fmp_B          161 ------KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLK-  229 (479)
T ss_dssp             ------CSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC----CCCCSEEEECHHHHHHHHTTSC-
T ss_pred             ------CCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc----cCCCCEEEECchHHHHHHHhcC-
Confidence                  23579999999999999999999998877788888888887654321    2346999999999999996542 


Q ss_pred             cccccCCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCcc
Q 006737          528 LSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVK  601 (633)
Q Consensus       528 ~~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~  601 (633)
                       ...+.++.+|||||||++++ .+|...+..++..++..+|+|+||||+++.+.     ....+..+....  .......
T Consensus       230 -~~~~~~~~~iViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~--~~~~~~~  306 (479)
T 3fmp_B          230 -FIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR--EEETLDT  306 (479)
T ss_dssp             -CCCGGGCCEEEECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC----------
T ss_pred             -CcCcccCCEEEEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccc--cccCcCC
Confidence             35578999999999999987 68999999999999999999999999999852     222333333221  1234456


Q ss_pred             ceEEEeehh--------hHHHHhhcCCceEEEEEcccc
Q 006737          602 VSKYNIYVF--------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       602 V~q~~i~v~--------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      +.|.++.+.        +..........++||||+|+.
T Consensus       307 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~  344 (479)
T 3fmp_B          307 IKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRK  344 (479)
T ss_dssp             --------------------------------------
T ss_pred             ceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHH
Confidence            666666553        111122334468999999975

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=100.00  E-value=9.5e-33  Score=282.24  Aligned_cols=196  Identities=38%  Similarity=0.616  Sum_probs=168.0

Q ss_pred             cccCccccC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCC
Q 006737          377 SQKRFDECG--ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVP  454 (633)
Q Consensus       377 ~~~~F~el~--L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~  454 (633)
                      ...+|++++  +++.++++|.++||..|+++|.++++.++.|+|++++||||||||++|++|+++.+......    ...
T Consensus        50 ~~~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~----~~~  125 (262)
T 3ly5_A           50 EDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM----PRN  125 (262)
T ss_dssp             GGGCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCC----GGG
T ss_pred             ccCChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhcccc----ccC
Confidence            345678887  99999999999999999999999999999999999999999999999999999998764321    112


Q ss_pred             CeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          455 PIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       455 ~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      +.++|||+||++||.|+++.+..++... ++.+.+++|+.....+...+..+ ++|+|+||++|.+++....  ...+.+
T Consensus       126 ~~~~lil~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~-~~Iiv~Tp~~l~~~~~~~~--~~~~~~  201 (262)
T 3ly5_A          126 GTGVLILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNG-INIIVATPGRLLDHMQNTP--GFMYKN  201 (262)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHHHC-CSEEEECHHHHHHHHHHCT--TCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhcCC-CCEEEEcHHHHHHHHHccC--Cccccc
Confidence            4579999999999999999999998755 78889999998877666666554 7999999999999887653  245789


Q ss_pred             eeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      +++|||||||++++++|...+..|+..+++.+|+|+||||+++.+.
T Consensus       202 l~~lViDEah~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~  247 (262)
T 3ly5_A          202 LQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE  247 (262)
T ss_dssp             CCEEEECSHHHHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHH
T ss_pred             CCEEEEcChHHHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHH
Confidence            9999999999999999999999999999999999999999999863

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=100.00  E-value=5.9e-33  Score=280.62  Aligned_cols=198  Identities=37%  Similarity=0.580  Sum_probs=169.0

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCC-CCCCCCC
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSS-TTQLVPP  455 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~-~~~~~~~  455 (633)
                      +..+|+++++++.++++|..+||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+....... ......+
T Consensus        21 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~~  100 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY  100 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccCC
Confidence            456799999999999999999999999999999999999999999999999999999999999887543210 0011234


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      +++|||+||++|+.|+++.+..+.... ++.+..++|+.....+...+.. +++|+|+||++|.+++...   ...+.++
T Consensus       101 ~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~Ivv~Tp~~l~~~l~~~---~~~~~~~  175 (253)
T 1wrb_A          101 PKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQM-GCHLLVATPGRLVDFIEKN---KISLEFC  175 (253)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSS-CCSEEEECHHHHHHHHHTT---SBCCTTC
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhCC-CCCEEEECHHHHHHHHHcC---CCChhhC
Confidence            679999999999999999999987654 6888999999887766665544 5799999999999999765   3568899


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHH--CCC--CCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDC--LPR--RRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~--lpk--~~Q~IlfSATl~~el  579 (633)
                      ++|||||||++++++|...+..|+..  ++.  .+|+++||||+++++
T Consensus       176 ~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~  223 (253)
T 1wrb_A          176 KYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEI  223 (253)
T ss_dssp             CEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHH
T ss_pred             CEEEEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHH
Confidence            99999999999999999999999995  444  689999999999985

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=2.1e-32  Score=273.47  Aligned_cols=194  Identities=41%  Similarity=0.644  Sum_probs=168.2

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ...+|+++++++.++++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+......    ...++
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~~----~~~~~   98 (236)
T 2pl3_A           23 EITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWT----STDGL   98 (236)
T ss_dssp             GCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTCC----GGGCC
T ss_pred             ccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhccc----ccCCc
Confidence            34679999999999999999999999999999999999999999999999999999999999988764221    12245


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||++|+.|+++.+..++... ++.+.+++|+.....+...+.  +++|+|+||++|.+++....  ...+.+++
T Consensus        99 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~--~~~iiv~Tp~~l~~~l~~~~--~~~~~~~~  173 (236)
T 2pl3_A           99 GVLIISPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERIN--NINILVCTPGRLLQHMDETV--SFHATDLQ  173 (236)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHHT--TCSEEEECHHHHHHHHHHCS--SCCCTTCC
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhCC--CCCEEEECHHHHHHHHHhcC--Cccccccc
Confidence            79999999999999999999987654 688999999988776555553  47999999999999887542  24578999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +|||||||++++++|...+..++..+++.+|+++||||+++.+
T Consensus       174 ~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~  216 (236)
T 2pl3_A          174 MLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSV  216 (236)
T ss_dssp             EEEETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHH
T ss_pred             EEEEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHH
Confidence            9999999999999999999999999999999999999999985

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=4e-33  Score=275.87  Aligned_cols=191  Identities=35%  Similarity=0.563  Sum_probs=166.3

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      .++|+++++++.++++|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....        .+++
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~~--------~~~~   74 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPER--------AEVQ   74 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTS--------CSCC
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhCc--------CCce
Confidence            35699999999999999999999999999999999999999999999999999999999998764321        2357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCC---CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHD---GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~---~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      +|||+||++|+.|+++.+..+.....   ++.+.+++|+.........+. .+++|+|+||++|.+++...   ...+..
T Consensus        75 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~l~~~---~~~~~~  150 (219)
T 1q0u_A           75 AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN-VQPHIVIGTPGRINDFIREQ---ALDVHT  150 (219)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCS-SCCSEEEECHHHHHHHHHTT---CCCGGG
T ss_pred             EEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcC-CCCCEEEeCHHHHHHHHHcC---CCCcCc
Confidence            99999999999999999999986543   578888899877654443333 35799999999999998765   356789


Q ss_pred             eeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      +++|||||||++++++|...+..++..+++.+|+++||||+++++.
T Consensus       151 ~~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~  196 (219)
T 1q0u_A          151 AHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLK  196 (219)
T ss_dssp             CCEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGH
T ss_pred             ceEEEEcCchHHhhhChHHHHHHHHHhCCcccEEEEEecCCCHHHH
Confidence            9999999999999999999999999999999999999999999853

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=100.00  E-value=5.7e-33  Score=278.91  Aligned_cols=190  Identities=31%  Similarity=0.538  Sum_probs=159.9

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.++++|.++||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+....        .+.+
T Consensus        29 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~~--------~~~~  100 (237)
T 3bor_A           29 VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEF--------KETQ  100 (237)
T ss_dssp             CCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTTS--------CSCC
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhcC--------CCce
Confidence            46799999999999999999999999999999999999999999999999999999999998764321        2357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..++... ++.+..++|+.....+...+..+.++|+|+||++|.+++...   ...+..+++
T Consensus       101 ~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~---~~~~~~~~~  176 (237)
T 3bor_A          101 ALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRR---YLSPKWIKM  176 (237)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEEEECHHHHHHHHHTT---SSCSTTCCE
T ss_pred             EEEEECcHHHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhC---CcCcccCcE
Confidence            9999999999999999999987654 678888899887776666666666899999999999998765   356788999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      |||||||++++++|...+..++..++..+|+|+||||+++.+
T Consensus       177 lViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~  218 (237)
T 3bor_A          177 FVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDV  218 (237)
T ss_dssp             EEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHH
T ss_pred             EEECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHH
Confidence            999999999999999999999999999999999999999885

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=2.6e-32  Score=292.79  Aligned_cols=240  Identities=28%  Similarity=0.440  Sum_probs=193.2

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ...+|+++++++.++++|.++||..|+++|.++++.++.|+|+++++|||+|||++|++|+++.+...        ..+.
T Consensus        35 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~--------~~~~  106 (410)
T 2j0s_A           35 VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ--------VRET  106 (410)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT--------SCSC
T ss_pred             CCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc--------cCCc
Confidence            34579999999999999999999999999999999999999999999999999999999999775322        1234


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||++|+.|+++.+..+.... ++.+..++|+.....+...+.. +++|+|+||++|.+++...   ...+..++
T Consensus       107 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~ivv~Tp~~l~~~l~~~---~~~~~~~~  181 (410)
T 2j0s_A          107 QALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGRVFDMIRRR---SLRTRAIK  181 (410)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHH-CCSEEEECHHHHHHHHHTT---SSCCTTCC
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhhc-CCCEEEcCHHHHHHHHHhC---CccHhhee
Confidence            79999999999999999999987654 7889999999887766666554 4799999999999999765   35678899


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhcc-----ccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVLK-----REHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l~-----~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +|||||||++++++|...+..++..+++..|+++||||+++.+...     ..+..+..  .........+.+.++.+. 
T Consensus       182 ~vViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  259 (410)
T 2j0s_A          182 MLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILV--KRDELTLEGIKQFFVAVER  259 (410)
T ss_dssp             EEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECC--CGGGCSCTTEEEEEEEESS
T ss_pred             EEEEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEe--cCccccCCCceEEEEEeCc
Confidence            9999999999999999999999999999999999999999875321     22222211  111234456777776543 


Q ss_pred             -------hHHHHhhcCCceEEEEEcccc
Q 006737          611 -------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 -------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                             +..........++||||+|+.
T Consensus       260 ~~~k~~~l~~~~~~~~~~~~lVf~~~~~  287 (410)
T 2j0s_A          260 EEWKFDTLCDLYDTLTITQAVIFCNTKR  287 (410)
T ss_dssp             TTHHHHHHHHHHHHHTSSEEEEECSSHH
T ss_pred             HHhHHHHHHHHHHhcCCCcEEEEEcCHH
Confidence                   222233445569999999975

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=100.00  E-value=1.5e-32  Score=278.79  Aligned_cols=191  Identities=38%  Similarity=0.638  Sum_probs=169.8

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ...+|+++++++.++++|.++||..|+++|.++++.+++|+|+++++|||||||++|++|+++.+.....        ++
T Consensus        41 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~~--------~~  112 (249)
T 3ber_A           41 ETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQ--------RL  112 (249)
T ss_dssp             HHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSCC--------SS
T ss_pred             ccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCCC--------Cc
Confidence            3467999999999999999999999999999999999999999999999999999999999998876532        34


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||++|+.|+++.+..++... ++.+.+++|+.....+...+.. +++|+|+||++|.+++....  ...+..++
T Consensus       113 ~~lil~Ptr~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~I~v~Tp~~l~~~l~~~~--~~~l~~~~  188 (249)
T 3ber_A          113 FALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAK-KPHIIIATPGRLIDHLENTK--GFNLRALK  188 (249)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHHHT-CCSEEEECHHHHHHHHHHST--TCCCTTCC
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHhcC-CCCEEEECHHHHHHHHHcCC--CcCccccC
Confidence            69999999999999999999987755 7889999999876655555543 57999999999999987642  24578999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +|||||||++++++|...+..++..+++.+|+++||||+++.+
T Consensus       189 ~lViDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v  231 (249)
T 3ber_A          189 YLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKV  231 (249)
T ss_dssp             EEEECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHH
T ss_pred             EEEEcChhhhhccChHHHHHHHHHhCCCCCeEEEEeccCCHHH
Confidence            9999999999999999999999999999999999999999985

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=100.00  E-value=2.3e-32  Score=270.05  Aligned_cols=191  Identities=33%  Similarity=0.560  Sum_probs=169.6

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.++++|.++||..|+++|.++++.+++++|+++++|||+|||++|++|++..+...        ..+++
T Consensus        13 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~--------~~~~~   84 (220)
T 1t6n_A           13 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--------TGQVS   84 (220)
T ss_dssp             -CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--------TTCCC
T ss_pred             CCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc--------CCCEE
Confidence            3569999999999999999999999999999999999999999999999999999999999775321        12357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..+....+++.+.+++|+.....+...+....++|+|+||++|..++...   ...+.++++
T Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~---~~~~~~~~~  161 (220)
T 1t6n_A           85 VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKH  161 (220)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTT---SSCCTTCCE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhC---CCCcccCCE
Confidence            99999999999999999999987766889999999988777777776666899999999999998765   356889999


Q ss_pred             EEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          538 LVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       538 LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      |||||||++++ .+|...+..++..+++.+|+++||||+++.+
T Consensus       162 lViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~  204 (220)
T 1t6n_A          162 FILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI  204 (220)
T ss_dssp             EEEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTT
T ss_pred             EEEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHH
Confidence            99999999987 5789999999999999999999999999885

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.98  E-value=4.3e-32  Score=268.44  Aligned_cols=188  Identities=34%  Similarity=0.569  Sum_probs=160.3

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.+++.|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+....        .+++
T Consensus        13 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~~--------~~~~   84 (224)
T 1qde_A           13 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------KAPQ   84 (224)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------CSCC
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhccC--------CCce
Confidence            45799999999999999999999999999999999999999999999999999999999998764322        2357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..++... ++.+..++|+.....+...+..  ++|+|+||++|.+++...   ...+.++++
T Consensus        85 ~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~--~~iiv~Tp~~l~~~~~~~---~~~~~~~~~  158 (224)
T 1qde_A           85 ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGRVFDNIQRR---RFRTDKIKM  158 (224)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTT--CSEEEECHHHHHHHHHTT---SSCCTTCCE
T ss_pred             EEEEECCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcCCC--CCEEEECHHHHHHHHHhC---CcchhhCcE
Confidence            9999999999999999999987654 7888999998876655544433  799999999999998765   356789999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      |||||||++++++|...+..++..+++.+|+++||||+++.+
T Consensus       159 iViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~  200 (224)
T 1qde_A          159 FILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV  200 (224)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHH
T ss_pred             EEEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHH
Confidence            999999999999999999999999999999999999999985

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.98  E-value=6.2e-32  Score=263.46  Aligned_cols=188  Identities=38%  Similarity=0.581  Sum_probs=165.4

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      +|+++++++.+++.|.++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....     ...++++|
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~-----~~~~~~~l   76 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQE-----RGRKPRAL   76 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCC-----TTCCCSEE
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccc-----cCCCCcEE
Confidence            5999999999999999999999999999999999999999999999999999999999988753211     12346799


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      |++||++|+.|+++.+..++.   .+.+..++|+.........+.. +++|+|+||++|..++...   ...+.++++||
T Consensus        77 il~P~~~L~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~---~~~~~~~~~iV  149 (207)
T 2gxq_A           77 VLTPTRELALQVASELTAVAP---HLKVVAVYGGTGYGKQKEALLR-GADAVVATPGRALDYLRQG---VLDLSRVEVAV  149 (207)
T ss_dssp             EECSSHHHHHHHHHHHHHHCT---TSCEEEECSSSCSHHHHHHHHH-CCSEEEECHHHHHHHHHHT---SSCCTTCSEEE
T ss_pred             EEECCHHHHHHHHHHHHHHhh---cceEEEEECCCChHHHHHHhhC-CCCEEEECHHHHHHHHHcC---CcchhhceEEE
Confidence            999999999999999998865   4778889999887665555544 4799999999999998765   35688999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      |||||++++++|...+..++..+++.+|+++||||+++.+
T Consensus       150 iDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~  189 (207)
T 2gxq_A          150 LDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWA  189 (207)
T ss_dssp             EESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSSCCHHH
T ss_pred             EEChhHhhccchHHHHHHHHHhCCccCeEEEEEEecCHHH
Confidence            9999999999999999999999999999999999999875

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.98  E-value=2.2e-31  Score=284.27  Aligned_cols=246  Identities=27%  Similarity=0.349  Sum_probs=195.2

Q ss_pred             CCCCCcccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCC
Q 006737          370 REEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSS  447 (633)
Q Consensus       370 ~~~~p~~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~  447 (633)
                      ....|+....+|+++++++.++++|.++||..|+++|.++++.++.+  +++++++|||+|||++|++|+++.+....  
T Consensus        16 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~~--   93 (412)
T 3fht_A           16 DPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPAN--   93 (412)
T ss_dssp             CTTSTTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTS--
T ss_pred             cCCCCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhcC--
Confidence            34556667788999999999999999999999999999999999997  89999999999999999999998764332  


Q ss_pred             CCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC
Q 006737          448 STTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG  527 (633)
Q Consensus       448 ~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~  527 (633)
                            .++++|||+||++|+.|+++.+..+....+++.+....++.......    ...++|+|+||++|.+++.... 
T Consensus        94 ------~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ivv~T~~~l~~~~~~~~-  162 (412)
T 3fht_A           94 ------KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLK-  162 (412)
T ss_dssp             ------CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC----CCCCSEEEECHHHHHHHHTTSC-
T ss_pred             ------CCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh----cCCCCEEEECchHHHHHHHhcC-
Confidence                  23479999999999999999999998877788898888887654321    3357999999999999986532 


Q ss_pred             cccccCCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCcc
Q 006737          528 LSVRLMGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVK  601 (633)
Q Consensus       528 ~~~~Ls~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~  601 (633)
                       ...+.++++|||||||++++ .++...+..++..++..+|+++||||+++.+.     ....+..+....  .......
T Consensus       163 -~~~~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~  239 (412)
T 3fht_A          163 -FIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR--EEETLDT  239 (412)
T ss_dssp             -SSCGGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCG--GGSSCTT
T ss_pred             -CcChhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeecc--ccccccC
Confidence             34578999999999999987 67999999999999999999999999999752     122223332211  2334556


Q ss_pred             ceEEEeehh--------hHHHHhhcCCceEEEEEcccc
Q 006737          602 VSKYNIYVF--------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       602 V~q~~i~v~--------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      +.+.++.+.        +..........++||||+|+.
T Consensus       240 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~  277 (412)
T 3fht_A          240 IKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRK  277 (412)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHH
T ss_pred             ceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHH
Confidence            777776653        222333445679999999974

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.98  E-value=1.6e-31  Score=283.72  Aligned_cols=242  Identities=29%  Similarity=0.441  Sum_probs=193.5

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ...|+++++++.++++|.++||..|+++|.++++.++.++|+++++|||+|||++|++|++..+....        .+.+
T Consensus         7 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~~--------~~~~   78 (391)
T 1xti_A            7 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVT--------GQVS   78 (391)
T ss_dssp             --CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCCT--------TCCC
T ss_pred             CCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhcccC--------CCee
Confidence            35699999999999999999999999999999999999999999999999999999999987753221        2346


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..+....+++.+..++|+.........+..+.++|+|+||++|..++...   ...+.++++
T Consensus        79 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~---~~~~~~~~~  155 (391)
T 1xti_A           79 VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKH  155 (391)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTT---SSCCTTCSE
T ss_pred             EEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcC---CccccccCE
Confidence            99999999999999999999987777899999999988777777777666899999999999988765   356889999


Q ss_pred             EEEecccccCCc-ChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh-
Q 006737          538 LVLDEADHLLDL-GFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       538 LVIDEAD~Lld~-gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      |||||||+++++ ++...+..++..+++..|+++||||+++.+..     ...+..+... .........+.+.++.+. 
T Consensus       156 vViDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~  234 (391)
T 1xti_A          156 FILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVD-DETKLTLHGLQQYYVKLKD  234 (391)
T ss_dssp             EEECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECC-CCCCCCCTTCEEEEEECCG
T ss_pred             EEEeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEec-CccccCcccceEEEEEcCc
Confidence            999999999984 78899999999999999999999999987421     1222222111 111223445667666543 


Q ss_pred             ------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                            +..........++||||+|+.
T Consensus       235 ~~~~~~l~~~l~~~~~~~~lvf~~~~~  261 (391)
T 1xti_A          235 NEKNRKLFDLLDVLEFNQVVIFVKSVQ  261 (391)
T ss_dssp             GGHHHHHHHHHHHSCCSEEEEECSCHH
T ss_pred             hhHHHHHHHHHHhcCCCcEEEEeCcHH
Confidence                  222333445679999999975

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.97  E-value=2.9e-31  Score=283.85  Aligned_cols=240  Identities=28%  Similarity=0.450  Sum_probs=195.4

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.+++.|.++||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+....        .+.+
T Consensus        39 ~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~--------~~~~  110 (414)
T 3eiq_A           39 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL--------KATQ  110 (414)
T ss_dssp             CCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTTS--------CSCC
T ss_pred             hcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhcC--------Ccee
Confidence            35799999999999999999999999999999999999999999999999999999999998764321        2346


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..++... ++.+..++|+.........+....++|+|+||++|.+++...   ...+..+++
T Consensus       111 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~---~~~~~~~~~  186 (414)
T 3eiq_A          111 ALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRR---YLSPKYIKM  186 (414)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHT---SSCSTTCCE
T ss_pred             EEEEeChHHHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcC---CcccccCcE
Confidence            9999999999999999999987655 788888999988877777777677899999999999999775   356788999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh--
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      |||||||++++++|...+..++..+++.+|+|+||||+++.+..     ...+..+...  ........+.+.++.+.  
T Consensus       187 vViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~  264 (414)
T 3eiq_A          187 FVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK--KEELTLEGIRQFYINVERE  264 (414)
T ss_dssp             EEECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCC--CCCCCTTSCCEEEEECSSS
T ss_pred             EEEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEec--CCccCCCCceEEEEEeChH
Confidence            99999999999999999999999999999999999999987431     1222222211  12234456777776543  


Q ss_pred             ------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                            +..........++||||+|+.
T Consensus       265 ~~~~~~l~~~~~~~~~~~~lvf~~~~~  291 (414)
T 3eiq_A          265 EWKLDTLCDLYETLTITQAVIFINTRR  291 (414)
T ss_dssp             TTHHHHHHHHHHSSCCSSCEEECSCHH
T ss_pred             HhHHHHHHHHHHhCCCCcEEEEeCCHH
Confidence                  222333445569999999974

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.97  E-value=2.4e-31  Score=300.43  Aligned_cols=240  Identities=31%  Similarity=0.450  Sum_probs=186.0

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHh--CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACL--EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il--~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      |++.++++|..+||..|+|+|.++|+.++  .++|+|++||||+|||+||++|+++.+......    ...++++|||+|
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~----~~~~~~~lvl~P  103 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD----SQYMVKAVIVAP  103 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS----STTSCCEEEECS
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcccc----ccCCCeEEEEcc
Confidence            99999999999999999999999999999  788999999999999999999999998876432    122467999999


Q ss_pred             cHHHHHHHHHHHHHHHhc---CCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEE
Q 006737          464 TRELASQIAAEAIALLKN---HDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVL  540 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~---~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVI  540 (633)
                      |++||.|+++.+..++..   ...+.+..++|+.....+...+....++|||+||++|.+++....  ...+..+++|||
T Consensus       104 tr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~--~~~~~~~~~lVi  181 (579)
T 3sqw_A          104 TRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYS--NKFFRFVDYKVL  181 (579)
T ss_dssp             SHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHH--HHHCTTCCEEEE
T ss_pred             hHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhcc--ccccccCCEEEE
Confidence            999999999999998743   235678889999888877777766668999999999999987542  245788999999


Q ss_pred             ecccccCCcChHHHHHHHHHHCCC-------CCcEEEEeccCChhhhc-----ccc--ceEeeeccccccccCccceEEE
Q 006737          541 DEADHLLDLGFRKDVENIVDCLPR-------RRQSLLFSATMPKELVL-----KRE--HTYIDTVGLGSVETPVKVSKYN  606 (633)
Q Consensus       541 DEAD~Lld~gf~~~l~~Il~~lpk-------~~Q~IlfSATl~~el~l-----~~~--~~~i~~~~~~~~~~~~~V~q~~  606 (633)
                      ||||+|++++|...+..|+..++.       .+|+++||||+++.+..     ...  ...+.............+.+.+
T Consensus       182 DEah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~  261 (579)
T 3sqw_A          182 DEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSV  261 (579)
T ss_dssp             ETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEE
T ss_pred             EChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEE
Confidence            999999999999999999876642       67999999999987421     111  1222222222233444566666


Q ss_pred             eehh-----------hHH-HHh-hcCCceEEEEEcccc
Q 006737          607 IYVF-----------VLV-LSI-KIQAFYIICFVYTIS  631 (633)
Q Consensus       607 i~v~-----------~l~-~~~-k~~~~~~LVFcnT~s  631 (633)
                      +.+.           .+. ... .....++||||+|+.
T Consensus       262 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~  299 (579)
T 3sqw_A          262 VISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVK  299 (579)
T ss_dssp             EEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHH
T ss_pred             EEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHH
Confidence            5442           111 111 144579999999974

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.97  E-value=2.7e-31  Score=297.82  Aligned_cols=240  Identities=32%  Similarity=0.460  Sum_probs=184.9

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHh--CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcc
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACL--EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCP  463 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il--~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvP  463 (633)
                      |++.++++|.++||..|+|+|.++|+.++  .++|+|++||||||||++|++|+++.+.......    ..++++|||+|
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~----~~~~~~lil~P  154 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDS----QYMVKAVIVAP  154 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSS----TTSCCEEEECS
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccccc----cCCeeEEEEcC
Confidence            99999999999999999999999999999  6789999999999999999999999998764321    22457999999


Q ss_pred             cHHHHHHHHHHHHHHHhcC---CCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEE
Q 006737          464 TRELASQIAAEAIALLKNH---DGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVL  540 (633)
Q Consensus       464 TReLa~Qi~~~l~~l~~~~---~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVI  540 (633)
                      |++||.|+++.+..++...   ..+.+..++|+.....+...+...+++|||+||++|.+++.+..  ...+..+++|||
T Consensus       155 tr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~--~~~~~~~~~lVi  232 (563)
T 3i5x_A          155 TRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYS--NKFFRFVDYKVL  232 (563)
T ss_dssp             SHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHH--HHHCTTCCEEEE
T ss_pred             cHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhcc--ccccccceEEEE
Confidence            9999999999999986532   35678889999887777777766668999999999999987542  235788999999


Q ss_pred             ecccccCCcChHHHHHHHHHHCC-------CCCcEEEEeccCChhhhc-----ccc--ceEeeeccccccccCccceEEE
Q 006737          541 DEADHLLDLGFRKDVENIVDCLP-------RRRQSLLFSATMPKELVL-----KRE--HTYIDTVGLGSVETPVKVSKYN  606 (633)
Q Consensus       541 DEAD~Lld~gf~~~l~~Il~~lp-------k~~Q~IlfSATl~~el~l-----~~~--~~~i~~~~~~~~~~~~~V~q~~  606 (633)
                      ||||+|++++|...+..|+..++       ..+|+|+||||+++.+..     ...  ..++.............+.+.+
T Consensus       233 DEah~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  312 (563)
T 3i5x_A          233 DEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSV  312 (563)
T ss_dssp             ETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEE
T ss_pred             eCHHHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEE
Confidence            99999999999999999887653       368999999999987421     111  1222222222233444566666


Q ss_pred             eehh--------hH---H-HH-hhcCCceEEEEEcccc
Q 006737          607 IYVF--------VL---V-LS-IKIQAFYIICFVYTIS  631 (633)
Q Consensus       607 i~v~--------~l---~-~~-~k~~~~~~LVFcnT~s  631 (633)
                      +.+.        .+   . .. ......++||||+|+.
T Consensus       313 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~  350 (563)
T 3i5x_A          313 VISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVK  350 (563)
T ss_dssp             EEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHH
T ss_pred             EECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHH
Confidence            5442        11   1 11 1145679999999974

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.97  E-value=8.3e-32  Score=270.62  Aligned_cols=194  Identities=27%  Similarity=0.433  Sum_probs=161.1

Q ss_pred             ccCcccc----CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCC
Q 006737          378 QKRFDEC----GISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLV  453 (633)
Q Consensus       378 ~~~F~el----~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~  453 (633)
                      ..+|+++    ++++.++++|.++||..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+....       .
T Consensus        24 ~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~~-------~   96 (245)
T 3dkp_A           24 IATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA-------N   96 (245)
T ss_dssp             CSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSCC-------S
T ss_pred             ccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhcc-------c
Confidence            3457766    8999999999999999999999999999999999999999999999999999998874321       1


Q ss_pred             CCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          454 PPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       454 ~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      .++++|||+||++|+.|+++.+..++... ++.+.+++|+.............+++|+|+||++|..++..... ...+.
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~-~~~~~  174 (245)
T 3dkp_A           97 KGFRALIISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPP-GIDLA  174 (245)
T ss_dssp             SSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSC-SCCCT
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCC-Ccccc
Confidence            24579999999999999999999997654 67777777765443333333445689999999999999976532 25688


Q ss_pred             CeeEEEEecccccCC---cChHHHHHHHHHHCC-CCCcEEEEeccCChhhh
Q 006737          534 GLKMLVLDEADHLLD---LGFRKDVENIVDCLP-RRRQSLLFSATMPKELV  580 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld---~gf~~~l~~Il~~lp-k~~Q~IlfSATl~~el~  580 (633)
                      ++++|||||||++++   .+|...+..++..+. ...|+++||||+++++.
T Consensus       175 ~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~  225 (245)
T 3dkp_A          175 SVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVE  225 (245)
T ss_dssp             TCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHH
T ss_pred             cCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHH
Confidence            999999999999998   468999999987764 57899999999999863

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.97  E-value=7.5e-31  Score=280.13  Aligned_cols=238  Identities=32%  Similarity=0.485  Sum_probs=188.8

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|++++|++.++++|.++||..|+++|.++++.++.++++++++|||+|||++|++|++..+....        .+.+
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~~--------~~~~   91 (400)
T 1s2m_A           20 GNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL--------NKIQ   91 (400)
T ss_dssp             -CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS--------CSCC
T ss_pred             cCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhcc--------CCcc
Confidence            45799999999999999999999999999999999999999999999999999999999998764321        2346


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..++... ++.+..++|+.....+...+. ..++|+|+||++|..++...   ...+.++++
T Consensus        92 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~Ivv~T~~~l~~~~~~~---~~~~~~~~~  166 (400)
T 1s2m_A           92 ALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLN-ETVHILVGTPGRVLDLASRK---VADLSDCSL  166 (400)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTT-SCCSEEEECHHHHHHHHHTT---CSCCTTCCE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHhc-CCCCEEEEchHHHHHHHHhC---CcccccCCE
Confidence            9999999999999999999987654 788889999887665544443 45799999999999988765   355789999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh--
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      |||||||++++.+|...+..++..+++..|+++||||++..+..     ...+..+...   .......+.+++..+.  
T Consensus       167 vIiDEaH~~~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~  243 (400)
T 1s2m_A          167 FIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM---EELTLKGITQYYAFVEER  243 (400)
T ss_dssp             EEEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC---SSCBCTTEEEEEEECCGG
T ss_pred             EEEeCchHhhhhchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEec---cccccCCceeEEEEechh
Confidence            99999999999889999999999999999999999999987421     1112222111   1223456677766543  


Q ss_pred             -----hHHHHhhcCCceEEEEEcccc
Q 006737          611 -----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 -----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                           +..........++||||+|+.
T Consensus       244 ~k~~~l~~~~~~~~~~~~lVf~~~~~  269 (400)
T 1s2m_A          244 QKLHCLNTLFSKLQINQAIIFCNSTN  269 (400)
T ss_dssp             GHHHHHHHHHHHSCCSEEEEECSSHH
T ss_pred             hHHHHHHHHHhhcCCCcEEEEEecHH
Confidence                 222233345579999999974

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.97  E-value=7.1e-31  Score=278.62  Aligned_cols=239  Identities=30%  Similarity=0.455  Sum_probs=168.9

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|+++++++.++++|..+||..|+++|.++++.++.++|+++++|||+|||++|++|+++.+....        .+++
T Consensus        20 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~~--------~~~~   91 (394)
T 1fuu_A           20 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------KAPQ   91 (394)
T ss_dssp             CCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTTC--------CSCC
T ss_pred             cCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhccC--------CCCC
Confidence            35699999999999999999999999999999999999999999999999999999999998764321        2357


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +|||+||++|+.|+++.+..++... ++.+..++|+.........+.  .++|+|+||++|...+...   ...+.++++
T Consensus        92 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~--~~~i~v~T~~~l~~~~~~~---~~~~~~~~~  165 (394)
T 1fuu_A           92 ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRR---RFRTDKIKM  165 (394)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHH--HCSEEEECHHHHHHHHHTT---SSCCTTCCE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcC--CCCEEEECHHHHHHHHHhC---CcchhhCcE
Confidence            9999999999999999999987654 788999999988766555554  3699999999999998765   355788999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh-----ccccceEeeeccccccccCccceEEEeehh--
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV-----LKREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~-----l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      |||||||++++++|...+..++..+++..|+++||||+++.+.     ....+..+....  .......+.+.++.+.  
T Consensus       166 vIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~  243 (394)
T 1fuu_A          166 FILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK--DELTLEGIKQFYVNVEEE  243 (394)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC--------------------
T ss_pred             EEEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecC--ccccCCCceEEEEEcCch
Confidence            9999999999999999999999999999999999999998742     112222221111  1122334444444322  


Q ss_pred             ------hHHHHhhcCCceEEEEEccccC
Q 006737          611 ------VLVLSIKIQAFYIICFVYTISM  632 (633)
Q Consensus       611 ------~l~~~~k~~~~~~LVFcnT~s~  632 (633)
                            +..........++||||+|+.+
T Consensus       244 ~~~~~~l~~~~~~~~~~~~lVf~~~~~~  271 (394)
T 1fuu_A          244 EYKYECLTDLYDSISVTQAVIFCNTRRK  271 (394)
T ss_dssp             ----------------------------
T ss_pred             hhHHHHHHHHHhcCCCCcEEEEECCHHH
Confidence                  1111222345689999999753

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.97  E-value=2.2e-30  Score=271.35  Aligned_cols=233  Identities=33%  Similarity=0.538  Sum_probs=188.4

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ..+|+++++++.++++|.++||..|+++|.++++.++++ +++++++|||+|||++|++|++..+...         .+.
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~---------~~~   75 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN---------NGI   75 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS---------SSC
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc---------CCC
Confidence            356999999999999999999999999999999999988 6999999999999999999998765321         234


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++|||+||++|+.|+++.+..++... ++.+..++|+.....+...+.  .++|+|+||++|..++...   ...+.+++
T Consensus        76 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~--~~~iiv~T~~~l~~~~~~~---~~~~~~~~  149 (367)
T 1hv8_A           76 EAIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK--NANIVVGTPGRILDHINRG---TLNLKNVK  149 (367)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH--TCSEEEECHHHHHHHHHTT---CSCTTSCC
T ss_pred             cEEEEcCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcC--CCCEEEecHHHHHHHHHcC---CcccccCC
Confidence            69999999999999999999997654 688889999988766655554  3699999999999998765   35578999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh-
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF-  610 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-  610 (633)
                      +|||||||++.+++|...+..++..+++..|+++||||++..+..     .....++.      ......+.+.++.+. 
T Consensus       150 ~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~  223 (367)
T 1hv8_A          150 YFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIK------AKINANIEQSYVEVNE  223 (367)
T ss_dssp             EEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEE------CCSSSSSEEEEEECCG
T ss_pred             EEEEeCchHhhhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEE------ecCCCCceEEEEEeCh
Confidence            999999999999999999999999999999999999999987421     12222221      122335666666543 


Q ss_pred             -----hHHHHhhcCCceEEEEEcccc
Q 006737          611 -----VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 -----~l~~~~k~~~~~~LVFcnT~s  631 (633)
                           .+.........++||||+|+.
T Consensus       224 ~~~~~~l~~~l~~~~~~~lvf~~~~~  249 (367)
T 1hv8_A          224 NERFEALCRLLKNKEFYGLVFCKTKR  249 (367)
T ss_dssp             GGHHHHHHHHHCSTTCCEEEECSSHH
T ss_pred             HHHHHHHHHHHhcCCCcEEEEECCHH
Confidence                 233334456679999999974

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.97  E-value=4.2e-30  Score=271.93  Aligned_cols=235  Identities=27%  Similarity=0.348  Sum_probs=183.7

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCC
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPP  455 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~  455 (633)
                      ..+|++++|++.++++|.++||..|+++|.++++.++.+  +++++++|||+|||++|++|++..+....        .+
T Consensus         4 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~~--------~~   75 (395)
T 3pey_A            4 AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPED--------AS   75 (395)
T ss_dssp             CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTTC--------CS
T ss_pred             ccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccCC--------CC
Confidence            367999999999999999999999999999999999998  89999999999999999999998764322        23


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      .++|||+||++|+.|+++.+..++... ++.+..++++.....     ....++|+|+||++|..++...   ...+.++
T Consensus        76 ~~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~-----~~~~~~iiv~T~~~l~~~~~~~---~~~~~~~  146 (395)
T 3pey_A           76 PQAICLAPSRELARQTLEVVQEMGKFT-KITSQLIVPDSFEKN-----KQINAQVIVGTPGTVLDLMRRK---LMQLQKI  146 (395)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSCTT-----SCBCCSEEEECHHHHHHHHHTT---CBCCTTC
T ss_pred             ccEEEECCCHHHHHHHHHHHHHHhccc-CeeEEEEecCchhhh-----ccCCCCEEEEcHHHHHHHHHcC---CcccccC
Confidence            469999999999999999999987644 677777777654332     1235799999999999998765   3568899


Q ss_pred             eEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeeh
Q 006737          536 KMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYV  609 (633)
Q Consensus       536 ~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v  609 (633)
                      ++|||||||++.+ .++...+..+...+++..|+++||||+++.+..     ......+....  .......+.+.+..+
T Consensus       147 ~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~  224 (395)
T 3pey_A          147 KIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQT--NEVNVDAIKQLYMDC  224 (395)
T ss_dssp             CEEEEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCG--GGCSCTTEEEEEEEC
T ss_pred             CEEEEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccc--cccccccccEEEEEc
Confidence            9999999999987 789999999999999999999999999987421     12222222111  123344566666654


Q ss_pred             h--------hHHHHhhcCCceEEEEEcccc
Q 006737          610 F--------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       610 ~--------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      .        +..........++||||+|+.
T Consensus       225 ~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~  254 (395)
T 3pey_A          225 KNEADKFDVLTELYGLMTIGSSIIFVATKK  254 (395)
T ss_dssp             SSHHHHHHHHHHHHTTTTSSEEEEECSCHH
T ss_pred             CchHHHHHHHHHHHHhccCCCEEEEeCCHH
Confidence            2        222233345579999999974

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.97  E-value=9.8e-30  Score=263.79  Aligned_cols=221  Identities=30%  Similarity=0.458  Sum_probs=178.2

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      |++.+.++|.++||..|+++|.++++.+++++++++++|||+|||++|++|+++.              +.++|||+||+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~--------------~~~~liv~P~~   66 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL--------------GMKSLVVTPTR   66 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH--------------TCCEEEECSSH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh--------------cCCEEEEeCCH
Confidence            5789999999999999999999999999999999999999999999999998763              13599999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc
Q 006737          466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH  545 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~  545 (633)
                      +|+.|+++.+..++... ++.+..++|+.........+..  ++|+|+||++|..++...   ...+.++++|||||||+
T Consensus        67 ~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~--~~i~v~T~~~l~~~~~~~---~~~~~~~~~iViDEah~  140 (337)
T 2z0m_A           67 ELTRQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVRN--ADIVVATPGRLLDLWSKG---VIDLSSFEIVIIDEADL  140 (337)
T ss_dssp             HHHHHHHHHHHHHTTTS-CCCEEEECTTSCHHHHHHHHTT--CSEEEECHHHHHHHHHTT---SCCGGGCSEEEEESHHH
T ss_pred             HHHHHHHHHHHHHhhhc-CCcEEEEECCcchHHHHhhcCC--CCEEEECHHHHHHHHHcC---CcchhhCcEEEEEChHH
Confidence            99999999999987654 6788999998877665555543  799999999999988765   35578899999999999


Q ss_pred             cCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhhc-----cccceEeeeccccccccCccceEEEeehh-----hHHHH
Q 006737          546 LLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELVL-----KREHTYIDTVGLGSVETPVKVSKYNIYVF-----VLVLS  615 (633)
Q Consensus       546 Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~l-----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~-----~l~~~  615 (633)
                      +.++++...+..++..++...|+++||||+++.+..     ...+..+.     ......++.+.++.+.     .+...
T Consensus       141 ~~~~~~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~  215 (337)
T 2z0m_A          141 MFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIE-----ACIGLANVEHKFVHVKDDWRSKVQAL  215 (337)
T ss_dssp             HHHTTCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEE-----CSGGGGGEEEEEEECSSSSHHHHHHH
T ss_pred             hhccccHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeee-----cccccCCceEEEEEeChHHHHHHHHH
Confidence            999999999999999999999999999999988421     11222221     1123345566555443     33334


Q ss_pred             hhcCCceEEEEEcccc
Q 006737          616 IKIQAFYIICFVYTIS  631 (633)
Q Consensus       616 ~k~~~~~~LVFcnT~s  631 (633)
                      ......++||||+|+.
T Consensus       216 ~~~~~~~~lvf~~~~~  231 (337)
T 2z0m_A          216 RENKDKGVIVFVRTRN  231 (337)
T ss_dssp             HTCCCSSEEEECSCHH
T ss_pred             HhCCCCcEEEEEcCHH
Confidence            4556679999999974

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.96  E-value=4.3e-29  Score=269.24  Aligned_cols=222  Identities=18%  Similarity=0.186  Sum_probs=166.4

Q ss_pred             HHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHH
Q 006737          389 LTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTREL  467 (633)
Q Consensus       389 ~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReL  467 (633)
                      .+.+.+.+ .|| .|+++|.++++.++.|+|+++++|||||||++|++|++..+.           .++++|||+||++|
T Consensus         9 ~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~-----------~~~~~lil~Pt~~L   76 (414)
T 3oiy_A            9 DFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-----------KGKKSALVFPTVTL   76 (414)
T ss_dssp             HHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT-----------TTCCEEEEESSHHH
T ss_pred             HHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc-----------CCCEEEEEECCHHH
Confidence            44555555 356 899999999999999999999999999999999999887651           12469999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEEEECCccc---hHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          468 ASQIAAEAIALLKNHDGIGVLTLVGGTRF---KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       468 a~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~---~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      |.|+++.+..++.  .++++..++|+...   ..+...+..+.++|+|+||++|.+++..     ..+.++++|||||||
T Consensus        77 ~~q~~~~~~~~~~--~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~-----~~~~~~~~iViDEaH  149 (414)
T 3oiy_A           77 VKQTLERLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-----LSQKRFDFVFVDDVD  149 (414)
T ss_dssp             HHHHHHHHHHHCC--SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH-----HTTCCCSEEEESCHH
T ss_pred             HHHHHHHHHHHcc--CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH-----hccccccEEEEeChH
Confidence            9999999999866  48899999999887   4455666666689999999999888763     456789999999998


Q ss_pred             ccCC-----------cChHHH-HHHHHHHCC-----------CCCcEEEEecc-CChhhh--ccccceEeeecccccccc
Q 006737          545 HLLD-----------LGFRKD-VENIVDCLP-----------RRRQSLLFSAT-MPKELV--LKREHTYIDTVGLGSVET  598 (633)
Q Consensus       545 ~Lld-----------~gf~~~-l~~Il~~lp-----------k~~Q~IlfSAT-l~~el~--l~~~~~~i~~~~~~~~~~  598 (633)
                      ++++           ++|... +..++..++           ..+|+++|||| .|..+.  +......+..  ......
T Consensus       150 ~~~~~~~~~d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~--~~~~~~  227 (414)
T 3oiy_A          150 AVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTV--GRLVSV  227 (414)
T ss_dssp             HHHHCHHHHHHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHSCCS--SCCCCC
T ss_pred             hhhhccchhhhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhccCc--Cccccc
Confidence            7654           677777 788888876           78999999999 554432  1111111111  112334


Q ss_pred             CccceEEEeehh---hHHHHhhcCCceEEEEEcccc
Q 006737          599 PVKVSKYNIYVF---VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       599 ~~~V~q~~i~v~---~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      ..++.+.++.+.   .+.........++||||||+.
T Consensus       228 ~~~i~~~~~~~~~~~~l~~~l~~~~~~~lVF~~~~~  263 (414)
T 3oiy_A          228 ARNITHVRISSRSKEKLVELLEIFRDGILIFAQTEE  263 (414)
T ss_dssp             CCSEEEEEESSCCHHHHHHHHHHHCSSEEEEESSHH
T ss_pred             cccchheeeccCHHHHHHHHHHHcCCCEEEEECCHH
Confidence            557788777654   222222224579999999974

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.95  E-value=2e-28  Score=295.11  Aligned_cols=172  Identities=19%  Similarity=0.211  Sum_probs=151.8

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      .|..+++++.+...+...++..|+++|.++|+.++.|+|+|++||||||||++|++|++..+...           .++|
T Consensus       163 ~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~g-----------~rvl  231 (1108)
T 3l9o_A          163 NYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNK-----------QRVI  231 (1108)
T ss_dssp             CCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHTT-----------CEEE
T ss_pred             CcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhcC-----------CeEE
Confidence            46777888877777777778889999999999999999999999999999999999999887432           4799


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||+||++|+.|+++.+..++.     .+++++|+....        ..++|+|+||++|.+++...   ...+.++.+||
T Consensus       232 vl~PtraLa~Q~~~~l~~~~~-----~VglltGd~~~~--------~~~~IlV~Tpe~L~~~L~~~---~~~l~~l~lVV  295 (1108)
T 3l9o_A          232 YTSPIKALSNQKYRELLAEFG-----DVGLMTGDITIN--------PDAGCLVMTTEILRSMLYRG---SEVMREVAWVI  295 (1108)
T ss_dssp             EEESSHHHHHHHHHHHHHHTS-----SEEEECSSCBCC--------CSCSEEEEEHHHHHHHHHHC---SSHHHHEEEEE
T ss_pred             EEcCcHHHHHHHHHHHHHHhC-----CccEEeCccccC--------CCCCEEEeChHHHHHHHHcC---ccccccCCEEE
Confidence            999999999999999999864     577888887643        34799999999999999776   24578999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      |||||++++++|...+..++..+++.+|+|+||||+++.
T Consensus       296 IDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~  334 (1108)
T 3l9o_A          296 FDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNA  334 (1108)
T ss_dssp             EETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSC
T ss_pred             EhhhhhccccchHHHHHHHHHhcCCCceEEEEcCCCCCH
Confidence            999999999999999999999999999999999999886

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.94  E-value=1.4e-26  Score=262.98  Aligned_cols=177  Identities=19%  Similarity=0.284  Sum_probs=145.4

Q ss_pred             CccccCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          380 RFDECGISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      .+.++++++.+.+.|.+ +||..|+|+|.++|+.++.|+|+++++|||+|||+||++|++..              ..++
T Consensus        22 ~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~--------------~g~~   87 (591)
T 2v1x_A           22 NKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS--------------DGFT   87 (591)
T ss_dssp             CCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS--------------SSEE
T ss_pred             ccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc--------------CCcE
Confidence            34568999999999999 69999999999999999999999999999999999999999742              1369


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHH---H--hcCCCcEEEECchhhH------HHHhcccC
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRR---L--ESDPCQILVATPGRLL------DHIENKSG  527 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~---l--~~~~~dILIaTPgrLl------~lL~~~~~  527 (633)
                      |||+|+++|+.|+++.+..+     ++.+..++|+.........   +  ....++|||+||++|.      +.+..   
T Consensus        88 lVisP~~~L~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~---  159 (591)
T 2v1x_A           88 LVICPLISLMEDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK---  159 (591)
T ss_dssp             EEECSCHHHHHHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH---
T ss_pred             EEEeCHHHHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh---
Confidence            99999999999999999887     6788888888775543322   2  3456899999999874      23332   


Q ss_pred             cccccCCeeEEEEecccccCCcC--hHHHHHH--HHHHCCCCCcEEEEeccCChhh
Q 006737          528 LSVRLMGLKMLVLDEADHLLDLG--FRKDVEN--IVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       528 ~~~~Ls~l~~LVIDEAD~Lld~g--f~~~l~~--Il~~lpk~~Q~IlfSATl~~el  579 (633)
                       ...+..+.+|||||||++++||  |...+..  ++....+..|+|+||||+++.+
T Consensus       160 -~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v  214 (591)
T 2v1x_A          160 -AYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHV  214 (591)
T ss_dssp             -HHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHH
T ss_pred             -hhhccCCcEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHH
Confidence             2457799999999999999998  7777665  3444445799999999999874

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=99.94  E-value=1.7e-26  Score=267.45  Aligned_cols=180  Identities=23%  Similarity=0.261  Sum_probs=156.5

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      +|++++|++.+.+.+.+.||..|+++|.++++. ++.++++++++|||||||++|.+|+++.+....          .++
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~~----------~~~   71 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQG----------GKA   71 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHHC----------SEE
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhCC----------CEE
Confidence            589999999999999999999999999999998 889999999999999999999999998887432          369


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      ||++|+++||.|+++.+..+.. . ++.+..++|+.......  +  ..++|+|+||++|..++...   ...+.++++|
T Consensus        72 l~i~P~raLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~~--~--~~~~Iiv~Tpe~l~~~~~~~---~~~l~~~~~v  142 (720)
T 2zj8_A           72 VYIVPLKALAEEKFQEFQDWEK-I-GLRVAMATGDYDSKDEW--L--GKYDIIIATAEKFDSLLRHG---SSWIKDVKIL  142 (720)
T ss_dssp             EEECSSGGGHHHHHHHTGGGGG-G-TCCEEEECSCSSCCCGG--G--GGCSEEEECHHHHHHHHHHT---CTTGGGEEEE
T ss_pred             EEEcCcHHHHHHHHHHHHHHHh-c-CCEEEEecCCCCccccc--c--CCCCEEEECHHHHHHHHHcC---hhhhhcCCEE
Confidence            9999999999999999965443 2 78899999986654321  2  24799999999999988765   2347899999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ||||||++.++++...+..++..++...|+|+||||+++.
T Consensus       143 IiDE~H~l~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n~  182 (720)
T 2zj8_A          143 VADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNP  182 (720)
T ss_dssp             EEETGGGGGCTTTHHHHHHHHHHHBTTBEEEEEECCCSCH
T ss_pred             EEECCcccCCCcccHHHHHHHHHhhcCCeEEEEcCCcCCH
Confidence            9999999999889999999999887789999999999864

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.94  E-value=1e-26  Score=280.20  Aligned_cols=214  Identities=19%  Similarity=0.209  Sum_probs=165.3

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      +|| +|+++|.++|+.++.|+|++++||||||||++|+++++..+.           .++++|||+||++||.|+++.+.
T Consensus        75 ~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~-----------~~~~~Lil~PtreLa~Q~~~~l~  142 (1104)
T 4ddu_A           75 FGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR-----------KGKKSALVFPTVTLVKQTLERLQ  142 (1104)
T ss_dssp             SSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT-----------TTCCEEEEESSHHHHHHHHHHHH
T ss_pred             cCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh-----------cCCeEEEEechHHHHHHHHHHHH
Confidence            678 699999999999999999999999999999998888877651           13469999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccc---hHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC-----
Q 006737          477 ALLKNHDGIGVLTLVGGTRF---KVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-----  548 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~---~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld-----  548 (633)
                      .++  ..++.+.+++|+...   ..+...+..+.++|||+||++|.+++..     +.+.++++|||||||+++.     
T Consensus       143 ~l~--~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~-----l~~~~l~~lViDEaH~l~~~~r~~  215 (1104)
T 4ddu_A          143 KLA--DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-----LSQKRFDFVFVDDVDAVLKASRNI  215 (1104)
T ss_dssp             TTS--CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH-----HHTSCCSEEEESCHHHHTTSSHHH
T ss_pred             Hhh--CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh-----hcccCcCEEEEeCCCccccccccc
Confidence            965  448899999999987   5566677776689999999999888763     4578999999999977654     


Q ss_pred             ------cChHHH-HHHHHHHCC-----------CCCcEEEEecc-CChhhh--ccccceEeeeccccccccCccceEEEe
Q 006737          549 ------LGFRKD-VENIVDCLP-----------RRRQSLLFSAT-MPKELV--LKREHTYIDTVGLGSVETPVKVSKYNI  607 (633)
Q Consensus       549 ------~gf~~~-l~~Il~~lp-----------k~~Q~IlfSAT-l~~el~--l~~~~~~i~~~~~~~~~~~~~V~q~~i  607 (633)
                            +||... +..++..++           .++|+++|||| .|..+.  +......+...  .......++.|.++
T Consensus       216 Dr~L~~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~i~v~--~~~~~~~~i~~~~~  293 (1104)
T 4ddu_A          216 DTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVG--RLVSVARNITHVRI  293 (1104)
T ss_dssp             HHHHHTSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTCCCCC--BCCCCCCCEEEEEE
T ss_pred             hhhhHhcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhcceeEEec--cCCCCcCCceeEEE
Confidence                  788888 889998887           78999999999 455432  11111111111  12345667888887


Q ss_pred             ehh---hHHHHhhcCCceEEEEEcccc
Q 006737          608 YVF---VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       608 ~v~---~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      .+.   .+.........++||||||+.
T Consensus       294 ~~~k~~~L~~ll~~~~~~~LVF~~s~~  320 (1104)
T 4ddu_A          294 SSRSKEKLVELLEIFRDGILIFAQTEE  320 (1104)
T ss_dssp             SCCCHHHHHHHHHHHCSSEEEEESSSH
T ss_pred             ecCHHHHHHHHHHhcCCCEEEEECcHH
Confidence            664   222222224579999999974

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.94  E-value=4e-26  Score=263.83  Aligned_cols=180  Identities=21%  Similarity=0.216  Sum_probs=154.7

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      .+|++++|++.+.+.+.+.||..|+++|.++++. +..+++++++||||||||++|.+|+++.+...          +.+
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~----------~~~   77 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN----------GGK   77 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS----------CSE
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC----------CCe
Confidence            5699999999999999999999999999999999 78899999999999999999999999887643          237


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +||++|+++||.|+++.++.+.. . ++.+..++|+......  .+.  .++|+|+||++|..++...   ...+.++++
T Consensus        78 il~i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~--~~~--~~~Iiv~Tpe~l~~~~~~~---~~~l~~~~~  148 (715)
T 2va8_A           78 AIYVTPLRALTNEKYLTFKDWEL-I-GFKVAMTSGDYDTDDA--WLK--NYDIIITTYEKLDSLWRHR---PEWLNEVNY  148 (715)
T ss_dssp             EEEECSCHHHHHHHHHHHGGGGG-G-TCCEEECCSCSSSCCG--GGG--GCSEEEECHHHHHHHHHHC---CGGGGGEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhc-C-CCEEEEEeCCCCCchh--hcC--CCCEEEEcHHHHHHHHhCC---hhHhhccCE
Confidence            99999999999999999854432 3 7889999998665432  122  4799999999999988765   244789999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      |||||||++.+.++...+..++..++ +.|+|+||||+++.
T Consensus       149 vIiDE~H~l~~~~~~~~l~~i~~~~~-~~~ii~lSATl~n~  188 (715)
T 2va8_A          149 FVLDELHYLNDPERGPVVESVTIRAK-RRNLLALSATISNY  188 (715)
T ss_dssp             EEECSGGGGGCTTTHHHHHHHHHHHH-TSEEEEEESCCTTH
T ss_pred             EEEechhhcCCcccchHHHHHHHhcc-cCcEEEEcCCCCCH
Confidence            99999999998889999998888776 89999999999864

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.93  E-value=1.9e-26  Score=258.17  Aligned_cols=178  Identities=20%  Similarity=0.278  Sum_probs=144.6

Q ss_pred             cCccccCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          379 KRFDECGISPLTIKALTA-AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..|++++|++.+.+.|.+ +||..|+++|.++|+.+++|+|+++++|||+|||+||++|++..   .           ..
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~---~-----------g~   67 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL---N-----------GL   67 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS---S-----------SE
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh---C-----------CC
Confidence            358999999999999999 89999999999999999999999999999999999999999732   1           25


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      +|||+|+++|+.|+++.+..+     ++.+..++++.......   ..+..+.++|+|+||++|.......   .+...+
T Consensus        68 ~lvi~P~~aL~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~---~l~~~~  139 (523)
T 1oyw_A           68 TVVVSPLISLMKDQVDQLQAN-----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLE---HLAHWN  139 (523)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHH---HHTTSC
T ss_pred             EEEECChHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHH---HHhhCC
Confidence            899999999999999988875     67788888876654332   3444566899999999995321111   133468


Q ss_pred             eeEEEEecccccCCcC--hHHHHHH---HHHHCCCCCcEEEEeccCChhh
Q 006737          535 LKMLVLDEADHLLDLG--FRKDVEN---IVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       535 l~~LVIDEAD~Lld~g--f~~~l~~---Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +.+|||||||++++||  |...+..   ++..++ +.|+++||||+++.+
T Consensus       140 ~~~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~~~  188 (523)
T 1oyw_A          140 PVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTT  188 (523)
T ss_dssp             EEEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHH
T ss_pred             CCEEEEeCccccCcCCCccHHHHHHHHHHHHhCC-CCCEEEEeCCCCHHH
Confidence            9999999999999988  6666554   455554 689999999999874

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=99.93  E-value=1.4e-26  Score=267.44  Aligned_cols=179  Identities=20%  Similarity=0.262  Sum_probs=149.7

Q ss_pred             CccccC--CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          380 RFDECG--ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       380 ~F~el~--L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      +|++++  |++.+.+.|.+.||..|+++|.++++.++.++|+++++|||||||++|.+|+++.+...           .+
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-----------~~   70 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG-----------GK   70 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT-----------CC
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-----------Cc
Confidence            588898  99999999999999999999999999999999999999999999999999999887532           35


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +||++|+++||.|+++.++.+. .. ++++..++|+......  .  ...++|+|+||++|..++.+.   ...+.++++
T Consensus        71 ~l~i~P~r~La~q~~~~~~~~~-~~-g~~v~~~~G~~~~~~~--~--~~~~~Iiv~Tpe~l~~~l~~~---~~~l~~~~~  141 (702)
T 2p6r_A           71 SLYVVPLRALAGEKYESFKKWE-KI-GLRIGISTGDYESRDE--H--LGDCDIIVTTSEKADSLIRNR---ASWIKAVSC  141 (702)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTT-TT-TCCEEEECSSCBCCSS--C--STTCSEEEEEHHHHHHHHHTT---CSGGGGCCE
T ss_pred             EEEEeCcHHHHHHHHHHHHHHH-hc-CCEEEEEeCCCCcchh--h--ccCCCEEEECHHHHHHHHHcC---hhHHhhcCE
Confidence            9999999999999999985443 22 7889999998765432  1  125799999999999988775   234789999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHC---CCCCcEEEEeccCChh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCL---PRRRQSLLFSATMPKE  578 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~l---pk~~Q~IlfSATl~~e  578 (633)
                      |||||||++.++++...+..++..+   .++.|+|+||||+++.
T Consensus       142 vIiDE~H~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n~  185 (702)
T 2p6r_A          142 LVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNV  185 (702)
T ss_dssp             EEETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTTH
T ss_pred             EEEeeeeecCCCCcccHHHHHHHHHHhcCcCceEEEECCCcCCH
Confidence            9999999999988888888776655   5789999999999964

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.91  E-value=2.4e-24  Score=268.56  Aligned_cols=227  Identities=20%  Similarity=0.228  Sum_probs=161.3

Q ss_pred             CCCCCcHHHHHHHHHHhC-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLE-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ||+.|+++|.+++|.++. ++|+|++||||||||++|.+++++.+.+...........+.++|||+|+++||.|+++.+.
T Consensus        76 g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP~kALa~e~~~~l~  155 (1724)
T 4f92_B           76 GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFG  155 (1724)
T ss_dssp             TCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECCHHHHHHHHHHHHH
Confidence            799999999999998774 7899999999999999999999999887543332233446789999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      +.+... +++|..++|+.......  .  ..++||||||+++..++.+. .....+..|++|||||+|.+.+ ..+..++
T Consensus       156 ~~~~~~-gi~V~~~tGd~~~~~~~--~--~~~~IlVtTpEkld~llr~~-~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE  228 (1724)
T 4f92_B          156 KRLATY-GITVAELTGDHQLCKEE--I--SATQIIVCTPEKWDIITRKG-GERTYTQLVRLIILDEIHLLHD-DRGPVLE  228 (1724)
T ss_dssp             HHHTTT-TCCEEECCSSCSSCCTT--G--GGCSEEEECHHHHHHHTTSS-TTHHHHTTEEEEEETTGGGGGS-TTHHHHH
T ss_pred             HHHhhC-CCEEEEEECCCCCCccc--c--CCCCEEEECHHHHHHHHcCC-ccchhhcCcCEEEEecchhcCC-ccHHHHH
Confidence            988765 89999999997654321  1  24799999999986666443 2223478999999999998876 4555555


Q ss_pred             HHH-------HHCCCCCcEEEEeccCChhhhccccceE---eeeccccccccCccceEEEeehh---------------h
Q 006737          557 NIV-------DCLPRRRQSLLFSATMPKELVLKREHTY---IDTVGLGSVETPVKVSKYNIYVF---------------V  611 (633)
Q Consensus       557 ~Il-------~~lpk~~Q~IlfSATl~~el~l~~~~~~---i~~~~~~~~~~~~~V~q~~i~v~---------------~  611 (633)
                      .++       ..++...|+|+||||+|+...+...-..   ...........|..+++.++.+.               .
T Consensus       229 ~~l~rl~~~~~~~~~~~riI~LSATl~N~~dvA~wL~~~~~~~~~~~~~~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~  308 (1724)
T 4f92_B          229 ALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVY  308 (1724)
T ss_dssp             HHHHHHHHHHHHHTCCCEEEEEECSCTTHHHHHHHTTCCHHHHEEECCGGGCSSCEEEECCEECCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCcEEEEecccCCHHHHHHHhCCCCCCCeEEECCCCccCccEEEEeccCCcchhhhhHHHHHHHH
Confidence            444       3457789999999999986433211000   00001112234556666654321               1


Q ss_pred             HHHHhhcCCceEEEEEcccc
Q 006737          612 LVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       612 l~~~~k~~~~~~LVFcnT~s  631 (633)
                      ..........++||||+|+.
T Consensus       309 ~~v~~~~~~~~~LVF~~sR~  328 (1724)
T 4f92_B          309 EKIMEHAGKNQVLVFVHSRK  328 (1724)
T ss_dssp             HHHTTCCSSCCEEEECSSTT
T ss_pred             HHHHHHhcCCcEEEECCCHH
Confidence            11112234568999999975

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=99.91  E-value=1.2e-24  Score=261.55  Aligned_cols=209  Identities=19%  Similarity=0.141  Sum_probs=157.6

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          396 AAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       396 ~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .+||. | ++|.++|+.++.|+|++++||||||||+ |++|++..+...          ++++|||+||++||.|+++.+
T Consensus        53 ~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~----------~~~~lil~PtreLa~Q~~~~l  119 (1054)
T 1gku_B           53 CVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALK----------GKRCYVIFPTSLLVIQAAETI  119 (1054)
T ss_dssp             TTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTT----------SCCEEEEESCHHHHHHHHHHH
T ss_pred             hcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhc----------CCeEEEEeccHHHHHHHHHHH
Confidence            37999 9 9999999999999999999999999998 999999887642          246999999999999999999


Q ss_pred             HHHHhcCCCc----eEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC
Q 006737          476 IALLKNHDGI----GVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       476 ~~l~~~~~~i----~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      ..++... ++    .+.+++|+.....+   ...+..  ++|+|+||++|.+++.+       |.++++|||||||+|++
T Consensus       120 ~~l~~~~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~--~~IlV~TP~~L~~~l~~-------L~~l~~lViDEah~~l~  189 (1054)
T 1gku_B          120 RKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRN--FKIVITTTQFLSKHYRE-------LGHFDFIFVDDVDAILK  189 (1054)
T ss_dssp             HHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGG--CSEEEEEHHHHHHCSTT-------SCCCSEEEESCHHHHHT
T ss_pred             HHHHhhc-CCCccceEEEEeCCCChhhHHHHHhhccC--CCEEEEcHHHHHHHHHH-------hccCCEEEEeChhhhhh
Confidence            9998765 66    89999999887653   233333  79999999999987653       56899999999999998


Q ss_pred             cChHHHHHHHHHHC-----------CCCCcEEEEeccCChhhhc----cccceEeeeccccccccCccceEEEeehh---
Q 006737          549 LGFRKDVENIVDCL-----------PRRRQSLLFSATMPKELVL----KREHTYIDTVGLGSVETPVKVSKYNIYVF---  610 (633)
Q Consensus       549 ~gf~~~l~~Il~~l-----------pk~~Q~IlfSATl~~el~l----~~~~~~i~~~~~~~~~~~~~V~q~~i~v~---  610 (633)
                      +  ...+..++..+           +..+|+++||||+++...+    ......+..  ........++.+.++...   
T Consensus       190 ~--~~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~~~~~~~~~~~~~~i~v--~~~~~~~~~i~~~~~~~~k~~  265 (1054)
T 1gku_B          190 A--SKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLNFDI--GSSRITVRNVEDVAVNDESIS  265 (1054)
T ss_dssp             S--THHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTHHHHHHHHCCCC--SCCEECCCCEEEEEESCCCTT
T ss_pred             c--cccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCchhHHHHHhhcceEEEc--cCcccCcCCceEEEechhHHH
Confidence            4  67777777766           3568999999999987211    111111111  111223446777666321   


Q ss_pred             hHHHHhhcCCceEEEEEcccc
Q 006737          611 VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ~l~~~~k~~~~~~LVFcnT~s  631 (633)
                      .+.........++||||||+.
T Consensus       266 ~L~~ll~~~~~~~LVF~~t~~  286 (1054)
T 1gku_B          266 TLSSILEKLGTGGIIYARTGE  286 (1054)
T ss_dssp             TTHHHHTTSCSCEEEEESSHH
T ss_pred             HHHHHHhhcCCCEEEEEcCHH
Confidence            222333333678999999974

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.91  E-value=7.3e-24  Score=264.25  Aligned_cols=180  Identities=16%  Similarity=0.216  Sum_probs=144.5

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEccc
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLE-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT  464 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPT  464 (633)
                      |.....++|...+|..|+|+|.++++.+++ ++|++++||||||||++|.+|+++.+.....         .++|||+||
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~~~---------~kavyi~P~  981 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSE---------GRCVYITPM  981 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHCTT---------CCEEEECSC
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhCCC---------CEEEEEcCh
Confidence            556788888888999999999999999976 5689999999999999999999999876432         369999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          465 RELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       465 ReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      ++||.|+++.+.+.+....+++|..++|+.....  ..+.  .++||||||+++..++.+... ...+.+|++|||||+|
T Consensus       982 raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~--~~~~--~~~IiV~TPEkld~llr~~~~-~~~l~~v~lvViDE~H 1056 (1724)
T 4f92_B          982 EALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDL--KLLG--KGNIIISTPEKWDILSRRWKQ-RKNVQNINLFVVDEVH 1056 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHHH--HHHH--HCSEEEECHHHHHHHHTTTTT-CHHHHSCSEEEECCGG
T ss_pred             HHHHHHHHHHHHHHhchhcCCEEEEEECCCCcch--hhcC--CCCEEEECHHHHHHHHhCccc-ccccceeeEEEeechh
Confidence            9999999999988776655889999999876432  2222  269999999999777754322 2347899999999999


Q ss_pred             ccCCcChHHHHHHHH-------HHCCCCCcEEEEeccCChhhh
Q 006737          545 HLLDLGFRKDVENIV-------DCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il-------~~lpk~~Q~IlfSATl~~el~  580 (633)
                      .|.+. .+..+..++       ..+++.+|+|+||||+++...
T Consensus      1057 ~l~d~-rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N~~d 1098 (1724)
T 4f92_B         1057 LIGGE-NGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKD 1098 (1724)
T ss_dssp             GGGST-THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTTHHH
T ss_pred             hcCCC-CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCCHHH
Confidence            98874 444444443       345678999999999998743

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.91  E-value=5.6e-24  Score=254.51  Aligned_cols=155  Identities=20%  Similarity=0.249  Sum_probs=136.8

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .+|. |+++|.++++.++.|+++++++|||+|||++|+++++..+..           +.++||++||++|+.|+++.+.
T Consensus        83 ~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~-----------g~rvL~l~PtkaLa~Q~~~~l~  150 (1010)
T 2xgj_A           83 YPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN-----------KQRVIYTSPIKALSNQKYRELL  150 (1010)
T ss_dssp             CSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT-----------TCEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc-----------CCeEEEECChHHHHHHHHHHHH
Confidence            4664 999999999999999999999999999999999999877632           2479999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      .++.     .+++++|+.....        .++|+|+||++|..++.+.   ...+.++++|||||||++.++++...+.
T Consensus       151 ~~~~-----~vglltGd~~~~~--------~~~IvV~Tpe~L~~~L~~~---~~~l~~l~lVViDEaH~l~d~~rg~~~e  214 (1010)
T 2xgj_A          151 AEFG-----DVGLMTGDITINP--------DAGCLVMTTEILRSMLYRG---SEVMREVAWVIFDEVHYMRDKERGVVWE  214 (1010)
T ss_dssp             HHHS-----CEEEECSSCEECT--------TCSEEEEEHHHHHHHHHHT---CTTGGGEEEEEEETGGGGGCTTTHHHHH
T ss_pred             HHhC-----CEEEEeCCCccCC--------CCCEEEEcHHHHHHHHHcC---cchhhcCCEEEEechhhhcccchhHHHH
Confidence            9874     5788888876542        3699999999999988765   3567899999999999999999999999


Q ss_pred             HHHHHCCCCCcEEEEeccCChhh
Q 006737          557 NIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       557 ~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      .++..++...|+|+||||+++..
T Consensus       215 ~il~~l~~~~~il~LSATi~n~~  237 (1010)
T 2xgj_A          215 ETIILLPDKVRYVFLSATIPNAM  237 (1010)
T ss_dssp             HHHHHSCTTCEEEEEECCCTTHH
T ss_pred             HHHHhcCCCCeEEEEcCCCCCHH
Confidence            99999999999999999999863

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.90  E-value=6.4e-24  Score=253.83  Aligned_cols=156  Identities=17%  Similarity=0.222  Sum_probs=135.3

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ++| .|+++|.++|+.++.|+|+++++|||||||++|+++++..+..           +.++|||+||++|+.|+++.+.
T Consensus        36 ~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~-----------g~~vlvl~PtraLa~Q~~~~l~  103 (997)
T 4a4z_A           36 WPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN-----------MTKTIYTSPIKALSNQKFRDFK  103 (997)
T ss_dssp             CSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT-----------TCEEEEEESCGGGHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc-----------CCeEEEEeCCHHHHHHHHHHHH
Confidence            345 4899999999999999999999999999999999998876432           2479999999999999999988


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      +++.   ++.+..++|+....        ..++|+|+||++|..++...   ...+.++.+|||||||++.+++|...+.
T Consensus       104 ~~~~---~~~v~~l~G~~~~~--------~~~~IlV~Tpe~L~~~l~~~---~~~l~~l~lvViDEaH~l~d~~~g~~~e  169 (997)
T 4a4z_A          104 ETFD---DVNIGLITGDVQIN--------PDANCLIMTTEILRSMLYRG---ADLIRDVEFVIFDEVHYVNDQDRGVVWE  169 (997)
T ss_dssp             TTC-----CCEEEECSSCEEC--------TTSSEEEEEHHHHHHHHHHT---CSGGGGEEEEEECCTTCCCTTCTTCCHH
T ss_pred             HHcC---CCeEEEEeCCCccC--------CCCCEEEECHHHHHHHHHhC---chhhcCCCEEEEECcccccccchHHHHH
Confidence            7653   67899999987643        23799999999999988765   3457899999999999999999999999


Q ss_pred             HHHHHCCCCCcEEEEeccCChh
Q 006737          557 NIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       557 ~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .++..+++..|+|+||||+++.
T Consensus       170 ~ii~~l~~~v~iIlLSAT~~n~  191 (997)
T 4a4z_A          170 EVIIMLPQHVKFILLSATVPNT  191 (997)
T ss_dssp             HHHHHSCTTCEEEEEECCCTTH
T ss_pred             HHHHhcccCCCEEEEcCCCCCh
Confidence            9999999999999999999865

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.90  E-value=9.2e-24  Score=244.13  Aligned_cols=164  Identities=21%  Similarity=0.217  Sum_probs=136.3

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          396 AAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       396 ~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .+|| .||++|..++|.++.|+  |+.++||+|||++|+||++...+.           +..|+||+||++||.|+++.+
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~-----------g~~vlVltptreLA~qd~e~~  144 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT-----------GKGVHVVTVNEYLASRDAEQM  144 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT-----------SSCEEEEESSHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc-----------CCCEEEEeCCHHHHHHHHHHH
Confidence            4799 99999999999999999  999999999999999999854322           235999999999999999999


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC-CcC
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL-DLG  550 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll-d~g  550 (633)
                      ..++.+. ++++.+++||.+.......   .+|||+|+||++| .++|...-.   ....++.+.++||||||.|| +.+
T Consensus       145 ~~l~~~l-gl~v~~i~gg~~~~~r~~~---~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea  220 (844)
T 1tf5_A          145 GKIFEFL-GLTVGLNLNSMSKDEKREA---YAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEA  220 (844)
T ss_dssp             HHHHHHT-TCCEEECCTTSCHHHHHHH---HHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTT
T ss_pred             HHHHhhc-CCeEEEEeCCCCHHHHHHh---cCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhcc
Confidence            9998876 8999999999875533322   2489999999999 676654311   12557899999999999998 653


Q ss_pred             ---------------hHHHHHHHHHHCC---------CCCcEE-----------------EEeccCCh
Q 006737          551 ---------------FRKDVENIVDCLP---------RRRQSL-----------------LFSATMPK  577 (633)
Q Consensus       551 ---------------f~~~l~~Il~~lp---------k~~Q~I-----------------lfSATl~~  577 (633)
                                     |...+..|+..++         +.+|++                 +||||++.
T Consensus       221 ~tplIisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~  288 (844)
T 1tf5_A          221 RTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVA  288 (844)
T ss_dssp             TCEEEEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHH
T ss_pred             ccchhhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccch
Confidence                           7889999999997         478888                 99999873

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.90  E-value=3.3e-23  Score=229.83  Aligned_cols=170  Identities=17%  Similarity=0.190  Sum_probs=130.1

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ++..+|+++|.++++.++.|+|+++++|||+|||++|++|+++.+.....      ..+.++|||+||++|+.|+++.+.
T Consensus         3 ~~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~~~~~   76 (556)
T 4a2p_A            3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKVVFLATKVPVYEQQKNVFK   76 (556)
T ss_dssp             -----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS------SCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc------cCCCeEEEEeCCHHHHHHHHHHHH
Confidence            34568999999999999999999999999999999999999988865432      113469999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccc-ccCCeeEEEEecccccCCcChHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSV-RLMGLKMLVLDEADHLLDLGFRKDV  555 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~-~Ls~l~~LVIDEAD~Lld~gf~~~l  555 (633)
                      .++... ++.+..++|+.........+.. +++|+|+||++|.+++...   .. .+.++++|||||||++.+++....+
T Consensus        77 ~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~---~~~~~~~~~~vViDEah~~~~~~~~~~~  151 (556)
T 4a2p_A           77 HHFERQ-GYSVQGISGENFSNVSVEKVIE-DSDIIVVTPQILVNSFEDG---TLTSLSIFTLMIFDECHNTTGNHPYNVL  151 (556)
T ss_dssp             HHHGGG-TCCEEECCCC-----CHHHHHH-HCSEEEECHHHHHHHHHSS---SCCCSTTCSEEEEETGGGCSTTSHHHHH
T ss_pred             HHhccc-CceEEEEeCCCCcchhHHHhhC-CCCEEEECHHHHHHHHHhC---cccccccCCEEEEECCcccCCcchHHHH
Confidence            998765 7889999999866554444433 3799999999999999765   24 5889999999999999988754444


Q ss_pred             H-HHHHH-C---CCCCcEEEEeccCCh
Q 006737          556 E-NIVDC-L---PRRRQSLLFSATMPK  577 (633)
Q Consensus       556 ~-~Il~~-l---pk~~Q~IlfSATl~~  577 (633)
                      . .++.. +   ++..|+|+||||++.
T Consensus       152 ~~~~~~~~~~~~~~~~~~l~lSAT~~~  178 (556)
T 4a2p_A          152 MTRYLEQKFNSASQLPQILGLTASVGV  178 (556)
T ss_dssp             HHHHHHHHHCC---CCEEEEEESCCCC
T ss_pred             HHHHHHhhhcccCCCCeEEEEeCCccc
Confidence            2 33322 1   356899999999954

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.89  E-value=7.7e-23  Score=226.15  Aligned_cols=166  Identities=17%  Similarity=0.201  Sum_probs=134.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      +|+++|.++++.++.|+|+++++|||+|||++|++|+++.+.....      ..+.++|||+||++|+.|+++.+..++.
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~------~~~~~~lil~P~~~L~~q~~~~~~~~~~   77 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC------GQKGKVVFFANQIPVYEQQATVFSRYFE   77 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS------SCCCCEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc------CCCCEEEEEeCCHHHHHHHHHHHHHHhc
Confidence            7999999999999999999999999999999999999998876432      1134699999999999999999999987


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccc-ccCCeeEEEEecccccCCcC-hHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSV-RLMGLKMLVLDEADHLLDLG-FRKDVENI  558 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~-~Ls~l~~LVIDEAD~Lld~g-f~~~l~~I  558 (633)
                      .. ++.+..++|+.........+.. +++|+|+||++|..++....   . .+.++++|||||||++.+.+ +...+..+
T Consensus        78 ~~-~~~~~~~~g~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~---~~~~~~~~~vViDEah~~~~~~~~~~~~~~~  152 (555)
T 3tbk_A           78 RL-GYNIASISGATSDSVSVQHIIE-DNDIIILTPQILVNNLNNGA---IPSLSVFTLMIFDECHNTSKNHPYNQIMFRY  152 (555)
T ss_dssp             TT-TCCEEEECTTTGGGSCHHHHHH-HCSEEEECHHHHHHHHHTSS---SCCGGGCSEEEETTGGGCSTTCHHHHHHHHH
T ss_pred             cC-CcEEEEEcCCCcchhhHHHHhc-CCCEEEECHHHHHHHHhcCc---ccccccCCEEEEECccccCCcchHHHHHHHH
Confidence            65 7899999999876654444433 37999999999999997652   3 57889999999999999875 33333344


Q ss_pred             HHHC-----CCCCcEEEEeccCCh
Q 006737          559 VDCL-----PRRRQSLLFSATMPK  577 (633)
Q Consensus       559 l~~l-----pk~~Q~IlfSATl~~  577 (633)
                      +...     ....|+++||||++.
T Consensus       153 ~~~~~~~~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          153 LDHKLGESRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             HHHHTSSCCSCCCEEEEEESCCCC
T ss_pred             HHhhhccccCCCCeEEEEecCccc
Confidence            4332     245899999999965

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.89  E-value=9.4e-23  Score=233.92  Aligned_cols=175  Identities=17%  Similarity=0.202  Sum_probs=137.1

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHH
Q 006737          391 IKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQ  470 (633)
Q Consensus       391 l~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Q  470 (633)
                      ..+|..+||..|+++|.++++.++.|+|+|+++|||+|||++|++|+++.+......      .+.++|||+||++|+.|
T Consensus         3 ~~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~~------~~~~~lvl~Pt~~L~~Q   76 (696)
T 2ykg_A            3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQG------QKGKVVFFANQIPVYEQ   76 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCTT------CCCCEEEECSSHHHHHH
T ss_pred             CCcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCccC------CCCeEEEEECCHHHHHH
Confidence            356677899999999999999999999999999999999999999999988764321      12469999999999999


Q ss_pred             HHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccc-ccCCeeEEEEecccccCCc
Q 006737          471 IAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSV-RLMGLKMLVLDEADHLLDL  549 (633)
Q Consensus       471 i~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~-~Ls~l~~LVIDEAD~Lld~  549 (633)
                      +++.+.+++... ++.+..++|+.....+...+.. .++|+|+||++|.+++....   . .+.++++|||||||++.+.
T Consensus        77 ~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~~~~-~~~Iiv~Tp~~L~~~l~~~~---~~~l~~~~~vViDEaH~~~~~  151 (696)
T 2ykg_A           77 NKSVFSKYFERH-GYRVTGISGATAENVPVEQIVE-NNDIIILTPQILVNNLKKGT---IPSLSIFTLMIFDECHNTSKQ  151 (696)
T ss_dssp             HHHHHHHHTTTT-TCCEEEECSSSCSSSCHHHHHH-TCSEEEECHHHHHHHHHTTS---SCCGGGCSEEEEETGGGCSTT
T ss_pred             HHHHHHHHhccC-CceEEEEeCCccccccHHHhcc-CCCEEEECHHHHHHHHhcCc---ccccccccEEEEeCCCcccCc
Confidence            999999998643 7899999999866554444443 37999999999999997652   3 5788999999999999866


Q ss_pred             C-hHHHHHHHHHH-----CCCCCcEEEEeccCC
Q 006737          550 G-FRKDVENIVDC-----LPRRRQSLLFSATMP  576 (633)
Q Consensus       550 g-f~~~l~~Il~~-----lpk~~Q~IlfSATl~  576 (633)
                      . +...+..++..     .++..|+|+||||+.
T Consensus       152 ~~~~~i~~~~l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          152 HPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             CHHHHHHHHHHHHHHTTCCSCCCEEEEEESCCC
T ss_pred             ccHHHHHHHHHHHhhcccCCCCCeEEEEeCccc
Confidence            5 33333333332     245789999999997

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=99.88  E-value=4.3e-23  Score=201.21  Aligned_cols=170  Identities=23%  Similarity=0.288  Sum_probs=120.3

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHH-HHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQ-IAAEA  475 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Q-i~~~l  475 (633)
                      .....|+++|.++++.++.++++++++|||+|||++|+++++..+.......     .+.++|||+|+++|+.| +.+.+
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~~~-----~~~~~lil~p~~~L~~q~~~~~~  103 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKAS-----EPGKVIVLVNKVLLVEQLFRKEF  103 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHHTT-----CCCCEEEEESSHHHHHHHHHHTH
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccccc-----CCCcEEEEECHHHHHHHHHHHHH
Confidence            3456899999999999999999999999999999999999998776543111     13469999999999999 67778


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC---cccccCCeeEEEEecccccCCcChH
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG---LSVRLMGLKMLVLDEADHLLDLGFR  552 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~---~~~~Ls~l~~LVIDEAD~Lld~gf~  552 (633)
                      ..+...  ++.+..++|+.........+.. .++|+|+||+.|..++.....   ....+.++.+|||||||+++..++.
T Consensus       104 ~~~~~~--~~~v~~~~g~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~  180 (216)
T 3b6e_A          104 QPFLKK--WYRVIGLSGDTQLKISFPEVVK-SCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVY  180 (216)
T ss_dssp             HHHHTT--TSCEEECCC---CCCCHHHHHH-HCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CH
T ss_pred             HHHhcc--CceEEEEeCCcccchhHHhhcc-CCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcH
Confidence            777653  6788888888765543333333 369999999999998876421   0144678999999999999877665


Q ss_pred             HHHH-HHHHHC-------------CCCCcEEEEecc
Q 006737          553 KDVE-NIVDCL-------------PRRRQSLLFSAT  574 (633)
Q Consensus       553 ~~l~-~Il~~l-------------pk~~Q~IlfSAT  574 (633)
                      ..+. .++...             .+..++|+||||
T Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          181 NNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            5553 332221             157899999998

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=99.88  E-value=2.8e-22  Score=201.06  Aligned_cols=173  Identities=17%  Similarity=0.224  Sum_probs=130.0

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHH
Q 006737          388 PLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTREL  467 (633)
Q Consensus       388 ~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReL  467 (633)
                      +.+.+.+.......++++|.++++.+..|++++++|+||||||+++.++++..+.....      ...+++|+++|+++|
T Consensus        48 ~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~------~~~~~~l~~~p~~~l  121 (235)
T 3llm_A           48 HDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR------AAECNIVVTQPRRIS  121 (235)
T ss_dssp             HHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC------GGGCEEEEEESSHHH
T ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC------CCceEEEEeccchHH
Confidence            34444444444456899999999999999999999999999999999999887765432      123579999999999


Q ss_pred             HHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccccc-
Q 006737          468 ASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL-  546 (633)
Q Consensus       468 a~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~L-  546 (633)
                      +.|+.+.+........+..++.......      ......++|+||||++|++++..      .+.++++|||||||.+ 
T Consensus       122 a~q~~~~~~~~~~~~~~~~~g~~~~~~~------~~~~~~~~Ivv~Tpg~l~~~l~~------~l~~~~~lVlDEah~~~  189 (235)
T 3llm_A          122 AVSVAERVAFERGEEPGKSCGYSVRFES------ILPRPHASIMFCTVGVLLRKLEA------GIRGISHVIVDEIHERD  189 (235)
T ss_dssp             HHHHHHHHHHTTTCCTTSSEEEEETTEE------ECCCSSSEEEEEEHHHHHHHHHH------CCTTCCEEEECCTTSCC
T ss_pred             HHHHHHHHHHHhccccCceEEEeechhh------ccCCCCCeEEEECHHHHHHHHHh------hhcCCcEEEEECCccCC
Confidence            9999888876654333344433221111      11123479999999999999865      3789999999999996 


Q ss_pred             CCcChH-HHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          547 LDLGFR-KDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       547 ld~gf~-~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      ++.+|. ..+..++... +++|+|+||||++.+.
T Consensus       190 ~~~~~~~~~l~~i~~~~-~~~~~il~SAT~~~~~  222 (235)
T 3llm_A          190 INTDFLLVVLRDVVQAY-PEVRIVLMSATIDTSM  222 (235)
T ss_dssp             HHHHHHHHHHHHHHHHC-TTSEEEEEECSSCCHH
T ss_pred             cchHHHHHHHHHHHhhC-CCCeEEEEecCCCHHH
Confidence            677777 4666666665 4799999999999885

>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.40A {Anas platyrhynchos}

Probab=99.87  E-value=6.2e-22  Score=231.82  Aligned_cols=169  Identities=17%  Similarity=0.187  Sum_probs=131.4

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      +|+..|+++|.++|+.++.|+|+|+++|||+|||++|++|++..+.....      ..+.++|||+||++|+.|+++.+.
T Consensus       244 ~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~------~~~~~~Lvl~Pt~~L~~Q~~~~~~  317 (797)
T 4a2q_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKVVFLATKVPVYEQQKNVFK  317 (797)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS------SCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc------cCCCeEEEEeCCHHHHHHHHHHHH
Confidence            57889999999999999999999999999999999999999998876431      113469999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCccc-ccCCeeEEEEecccccCCcChHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSV-RLMGLKMLVLDEADHLLDLGFRKDV  555 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~-~Ls~l~~LVIDEAD~Lld~gf~~~l  555 (633)
                      .++... ++.+..++|+.........+.. +++|+|+||++|.+++...   .. .+.++++|||||||++...+....+
T Consensus       318 ~~~~~~-~~~v~~~~g~~~~~~~~~~~~~-~~~Ivv~Tp~~l~~~l~~~---~~~~~~~~~~iViDEaH~~~~~~~~~~i  392 (797)
T 4a2q_A          318 HHFERQ-GYSVQGISGENFSNVSVEKVIE-DSDIIVVTPQILVNSFEDG---TLTSLSIFTLMIFDECHNTTGNHPYNVL  392 (797)
T ss_dssp             HHHGGG-TCCEEEECCC-----CHHHHHH-TCSEEEECHHHHHHHHHSS---SCCCGGGCSEEEETTGGGCSTTSHHHHH
T ss_pred             HhcccC-CceEEEEeCCcchhhhHHHhhC-CCCEEEEchHHHHHHHHhc---cccccccCCEEEEECccccCCCccHHHH
Confidence            998765 7899999999876655444443 4799999999999999765   23 5788999999999999976543333


Q ss_pred             -HHHHHHC----CCCCcEEEEeccCC
Q 006737          556 -ENIVDCL----PRRRQSLLFSATMP  576 (633)
Q Consensus       556 -~~Il~~l----pk~~Q~IlfSATl~  576 (633)
                       ..++...    .+..|+|+||||++
T Consensus       393 ~~~~~~~~~~~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          393 MTRYLEQKFNSASQLPQILGLTASVG  418 (797)
T ss_dssp             HHHHHHHHHTTCCCCCEEEEEESCCC
T ss_pred             HHHHHHHhhccCCCCCeEEEEcCCcc
Confidence             3333321    45689999999995

>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A {Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19 c.37.1.19

Probab=99.86  E-value=2e-21  Score=226.50  Aligned_cols=165  Identities=16%  Similarity=0.237  Sum_probs=130.0

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEE
Q 006737          388 PLTIKALTAAGYIQMTRVQEATLSACLEG------KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLIL  461 (633)
Q Consensus       388 ~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g------rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLIL  461 (633)
                      +.+.+.+..++| .||++|.++|+.++.+      .|++++++||||||++|++|++..+...           .++||+
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~g-----------~qvlvl  423 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAG-----------FQTAFM  423 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHT-----------SCEEEE
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHcC-----------CeEEEE
Confidence            445555677899 9999999999999876      5999999999999999999999887543           359999


Q ss_pred             cccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          462 CPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       462 vPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      +||++||.|+++.+.+++... ++++.+++|+......   ...+..+.++|+|+||+.|.+        ...+.++.+|
T Consensus       424 aPtr~La~Q~~~~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~--------~~~~~~l~lV  494 (780)
T 1gm5_A          424 VPTSILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE--------DVHFKNLGLV  494 (780)
T ss_dssp             CSCHHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH--------CCCCSCCCEE
T ss_pred             eCcHHHHHHHHHHHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh--------hhhccCCceE
Confidence            999999999999999998655 7899999999876543   344556678999999987743        2457899999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ||||+|++....     ...+.......|+++||||..+.
T Consensus       495 VIDEaHr~g~~q-----r~~l~~~~~~~~vL~mSATp~p~  529 (780)
T 1gm5_A          495 IIDEQHRFGVKQ-----REALMNKGKMVDTLVMSATPIPR  529 (780)
T ss_dssp             EEESCCCC----------CCCCSSSSCCCEEEEESSCCCH
T ss_pred             EecccchhhHHH-----HHHHHHhCCCCCEEEEeCCCCHH
Confidence            999999974221     11122223468999999997665

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=99.85  E-value=1.7e-21  Score=214.13  Aligned_cols=153  Identities=17%  Similarity=0.183  Sum_probs=115.0

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcE-EEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLEGKDA-VVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~grDv-Lv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      |+.+++|+|+ +||.++.++++ ++++|||||||++|++|++.++....          .++|||+|||+||.|+++.+.
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~----------~~~lvl~Ptr~La~Q~~~~l~   69 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRR----------LRTLILAPTRVVAAEMEEALR   69 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHTT----------CCEEEEESSHHHHHHHHHHTT
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhcC----------CcEEEECCCHHHHHHHHHHhc
Confidence            7889999986 79999999887 99999999999999999998876532          469999999999999998774


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                             ++.+.........      .......|.|+|++.|.+.+...    ..+.++++|||||||++ +..+...+.
T Consensus        70 -------g~~v~~~~~~~~~------~~~~~~~i~~~t~~~l~~~l~~~----~~l~~~~~iViDEah~~-~~~~~~~~~  131 (451)
T 2jlq_A           70 -------GLPIRYQTPAVKS------DHTGREIVDLMCHATFTTRLLSS----TRVPNYNLIVMDEAHFT-DPCSVAARG  131 (451)
T ss_dssp             -------TSCEEECCTTCSC------CCCSSCCEEEEEHHHHHHHHHHC----SCCCCCSEEEEETTTCC-SHHHHHHHH
T ss_pred             -------Cceeeeeeccccc------cCCCCceEEEEChHHHHHHhhCc----ccccCCCEEEEeCCccC-CcchHHHHH
Confidence                   3333222111110      11223579999999998888654    45789999999999987 444444444


Q ss_pred             HHHH-HCCCCCcEEEEeccCChhh
Q 006737          557 NIVD-CLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       557 ~Il~-~lpk~~Q~IlfSATl~~el  579 (633)
                      .+.. ..++++|+|+||||++..+
T Consensus       132 ~~~~~~~~~~~~~i~~SAT~~~~~  155 (451)
T 2jlq_A          132 YISTRVEMGEAAAIFMTATPPGST  155 (451)
T ss_dssp             HHHHHHHTTSCEEEEECSSCTTCC
T ss_pred             HHHHhhcCCCceEEEEccCCCccc
Confidence            3433 3456799999999999874

>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.70A {Anas platyrhynchos}

Probab=99.84  E-value=5.4e-21  Score=227.67  Aligned_cols=170  Identities=17%  Similarity=0.171  Sum_probs=129.3

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|+..|+++|.++|+.++.|+|+++++|||+|||++|++|+++.+.....      ..+.++|||+||++|+.|++..+.
T Consensus       244 ~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~~------~~~~~vLvl~Pt~~L~~Q~~~~~~  317 (936)
T 4a2w_A          244 YETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA------GRKAKVVFLATKVPVYEQQKNVFK  317 (936)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCCS------SCCCCEEEECSSHHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhccc------cCCCeEEEEeCCHHHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999877654321      113469999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChH-HHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFR-KDV  555 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~-~~l  555 (633)
                      .++... ++.+..++|+.....+...+.. .++|+|+||++|.+++....  ...+.++++|||||||++...+.. ..+
T Consensus       318 ~~~~~~-~~~v~~~~G~~~~~~~~~~~~~-~~~IvI~Tp~~L~~~l~~~~--~~~l~~~~liViDEaH~~~~~~~~~~i~  393 (936)
T 4a2w_A          318 HHFERQ-GYSVQGISGENFSNVSVEKVIE-DSDIIVVTPQILVNSFEDGT--LTSLSIFTLMIFDECHNTTGNHPYNVLM  393 (936)
T ss_dssp             HHHHTT-TCCEEEECCC-----CCHHHHH-HCSEEEECHHHHHHHHHSSS--CCCGGGCSEEEEETGGGCSTTCHHHHHH
T ss_pred             HHhccc-CceEEEEECCcchhhHHHHhcc-CCCEEEecHHHHHHHHHcCc--cccccCCCEEEEECccccCCCccHHHHH
Confidence            998755 7899999999865544444433 36999999999999997652  125788999999999999977533 333


Q ss_pred             HHHHHHC----CCCCcEEEEeccCC
Q 006737          556 ENIVDCL----PRRRQSLLFSATMP  576 (633)
Q Consensus       556 ~~Il~~l----pk~~Q~IlfSATl~  576 (633)
                      ..++...    .+..|+++||||..
T Consensus       394 ~~~~~~~~~~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          394 TRYLEQKFNSASQLPQILGLTASVG  418 (936)
T ss_dssp             HHHHHHHHTTCSCCCEEEEEESCCC
T ss_pred             HHHHHHhhccCCCcCeEEEecCCcc
Confidence            3333321    45689999999995

>2fsf_A Preprotein translocase SECA subunit; ATPase, DNA-RNA helicase, protein translocation, protein transport; 2.00A {Escherichia coli} PDB: 2fsg_A* 2fsh_A* 2fsi_A* 2vda_A 3bxz_A*

Probab=99.84  E-value=3.5e-21  Score=222.32  Aligned_cols=150  Identities=23%  Similarity=0.208  Sum_probs=111.8

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|. .|+++|..++|.++.|+  |+.++||+|||++|+||++...+.           +.+|+||+||++||.|+++.+.
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~-----------g~~vlVltPTreLA~Q~~e~~~  136 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT-----------GKGVHVVTVNDYLAQRDAENNR  136 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT-----------SSCCEEEESSHHHHHHHHHHHH
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHHHH
Confidence            464 89999999999999998  999999999999999999865432           2359999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC-Cc--
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL-DL--  549 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll-d~--  549 (633)
                      .++.+. ++++.+++||.+....  .+.. +++|+||||++| .++|...-.   ....++.+.++||||||.|| +.  
T Consensus       137 ~l~~~l-gl~v~~i~GG~~~~~r--~~~~-~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~  212 (853)
T 2fsf_A          137 PLFEFL-GLTVGINLPGMPAPAK--REAY-AADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEAR  212 (853)
T ss_dssp             HHHHHT-TCCEEECCTTCCHHHH--HHHH-HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTT
T ss_pred             HHHHhc-CCeEEEEeCCCCHHHH--HHhc-CCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCc
Confidence            999877 8999999999875432  2222 489999999999 788865421   12457899999999999998 54  


Q ss_pred             -------------ChHHHHHHHHHHCCC
Q 006737          550 -------------GFRKDVENIVDCLPR  564 (633)
Q Consensus       550 -------------gf~~~l~~Il~~lpk  564 (633)
                                   +|...+..|+..+++
T Consensus       213 tpLIiSg~~~~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          213 TPLIISGPAEDSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             CEEEEEEC--------------------
T ss_pred             ccccccCCCccchhHHHHHHHHHHhchh
Confidence                         367888889888874

>1nkt_A Preprotein translocase SECA 1 subunit; preprotein translocation, ATPase, transmembrane transport, helicase-like motor domain; HET: ADP; 2.60A {Mycobacterium tuberculosis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1nl3_A

Probab=99.84  E-value=7.5e-21  Score=219.94  Aligned_cols=163  Identities=20%  Similarity=0.215  Sum_probs=136.8

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|+ +|+++|..++|.++.|+  |+.++||+|||++|+||++...+..           ..|+||+||++||.|+++.+.
T Consensus       108 lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~g-----------~~v~VvTpTreLA~Qdae~m~  173 (922)
T 1nkt_A          108 LDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALAG-----------NGVHIVTVNDYLAKRDSEWMG  173 (922)
T ss_dssp             HSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTTT-----------SCEEEEESSHHHHHHHHHHHH
T ss_pred             cCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHhC-----------CCeEEEeCCHHHHHHHHHHHH
Confidence            688 99999999999999998  9999999999999999997544322           249999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC-C---
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL-D---  548 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll-d---  548 (633)
                      .++.+. ++++++++||.+........   .|||+|+||++| .++|...-.   ....++.+.++||||||.|| +   
T Consensus       174 ~l~~~l-GLsv~~i~gg~~~~~r~~~y---~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDear  249 (922)
T 1nkt_A          174 RVHRFL-GLQVGVILATMTPDERRVAY---NADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEAR  249 (922)
T ss_dssp             HHHHHT-TCCEEECCTTCCHHHHHHHH---HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGG
T ss_pred             HHHhhc-CCeEEEEeCCCCHHHHHHhc---CCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCc
Confidence            999876 89999999998754332222   379999999999 788765411   13557899999999999998 4   


Q ss_pred             ------------cChHHHHHHHHHHCC---------CCCcEE-----------------EEeccCCh
Q 006737          549 ------------LGFRKDVENIVDCLP---------RRRQSL-----------------LFSATMPK  577 (633)
Q Consensus       549 ------------~gf~~~l~~Il~~lp---------k~~Q~I-----------------lfSATl~~  577 (633)
                                  .+|...+..|+..++         +.+|++                 +||||++.
T Consensus       250 tPLiiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~  316 (922)
T 1nkt_A          250 TPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSP  316 (922)
T ss_dssp             SCEEEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCC
T ss_pred             cceeecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchh
Confidence                        358899999999998         789998                 99999875

>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase, ATP-binding, reticulum, nucleotidyltransferase, multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4} PDB: 2vbc_A 2wzq_A

Probab=99.84  E-value=1.2e-21  Score=223.45  Aligned_cols=171  Identities=17%  Similarity=0.157  Sum_probs=124.6

Q ss_pred             ccc-cCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          381 FDE-CGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       381 F~e-l~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      |.. +++++.++++|... ...++|+|+.+++.++.|+|++++||||||||++|++|+++.+...          ++++|
T Consensus       151 ~~~~l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~----------~~~vL  219 (618)
T 2whx_A          151 GNGVVTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR----------RLRTL  219 (618)
T ss_dssp             CC---------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT----------TCCEE
T ss_pred             ccccccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC----------CCeEE
Confidence            344 56677766666543 5789999988999999999999999999999999999999988753          24699


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      ||+|||+||.|+++.+.       +..+. +.+.. .    ......+..|.++|.+.|...+...    ..+.++++||
T Consensus       220 vl~PtreLa~Qi~~~l~-------~~~v~-~~~~~-l----~~~~tp~~~i~~~t~~~l~~~l~~~----~~l~~~~~iV  282 (618)
T 2whx_A          220 ILAPTRVVAAEMEEALR-------GLPIR-YQTPA-V----KSDHTGREIVDLMCHATFTTRLLSS----TRVPNYNLIV  282 (618)
T ss_dssp             EEESSHHHHHHHHHHTT-------TSCEE-ECCTT-S----SCCCCSSSCEEEEEHHHHHHHHHHC----SSCCCCSEEE
T ss_pred             EEcChHHHHHHHHHHhc-------CCcee-Eeccc-c----eeccCCCceEEEEChHHHHHHHhcc----ccccCCeEEE
Confidence            99999999999997765       22333 11111 0    0011223356677888777666543    4578999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCC-CCCcEEEEeccCChhhh
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLP-RRRQSLLFSATMPKELV  580 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSATl~~el~  580 (633)
                      |||||++ +.+|...+..|+..++ +++|+|+||||++..+.
T Consensus       283 iDEah~~-~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~  323 (618)
T 2whx_A          283 MDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTD  323 (618)
T ss_dssp             EESTTCC-SHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCC
T ss_pred             EECCCCC-CccHHHHHHHHHHHhcccCccEEEEECCCchhhh
Confidence            9999998 6778888888888775 68999999999998853

>4gl2_A Interferon-induced helicase C domain-containing P; MDA5, dsRNA, anti-viral signaling, RIG-I, MAVS, oligomerizat helicase, ATPase; HET: ANP; 3.56A {Homo sapiens}

Probab=99.83  E-value=5.1e-21  Score=219.60  Aligned_cols=169  Identities=22%  Similarity=0.262  Sum_probs=125.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH-HHHHHHHH
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI-AAEAIALL  479 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi-~~~l~~l~  479 (633)
                      .|+++|.++++.++.|+|+|+++|||+|||++|++|+++.+......     ..+.++|||+||++|+.|+ ++.+..++
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~~-----~~~~~vlvl~P~~~L~~Q~~~~~l~~~~   81 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKA-----SEPGKVIVLVNKVLLVEQLFRKEFQPFL   81 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHHH-----TCCCCBCCEESCSHHHHHHHHHTHHHHH
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccc-----CCCCeEEEEECCHHHHHHHHHHHHHHHc
Confidence            79999999999999999999999999999999999999888765320     0113589999999999999 99999998


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhccc---CcccccCCeeEEEEecccccCCcChH-HHH
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKS---GLSVRLMGLKMLVLDEADHLLDLGFR-KDV  555 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~---~~~~~Ls~l~~LVIDEAD~Lld~gf~-~~l  555 (633)
                      ..  .+.+..++|+.........+.. .++|||+||++|..++....   .....+..+++|||||||++...++. ..+
T Consensus        82 ~~--~~~v~~~~g~~~~~~~~~~~~~-~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~  158 (699)
T 4gl2_A           82 KK--WYRVIGLSGDTQLKISFPEVVK-SCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIM  158 (699)
T ss_dssp             TT--TSCEEEEC----CCCCHHHHHH-SCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHH
T ss_pred             Cc--CceEEEEeCCcchhhHHHhhhc-CCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHH
Confidence            64  4889999999776554444433 47999999999998884321   11346788999999999998754422 222


Q ss_pred             HHHHHH----C---------CCCCcEEEEeccCCh
Q 006737          556 ENIVDC----L---------PRRRQSLLFSATMPK  577 (633)
Q Consensus       556 ~~Il~~----l---------pk~~Q~IlfSATl~~  577 (633)
                      ..++..    .         .+..|+|+||||.+.
T Consensus       159 ~~~l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          159 RHYLMQKLKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHHHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             HHHHHhhhcccccccccccCCCCCEEEEecccccc
Confidence            222221    1         156799999999997

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=99.83  E-value=1.7e-20  Score=192.73  Aligned_cols=153  Identities=16%  Similarity=0.158  Sum_probs=122.4

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.++++.++.+++.+++++||+|||+++++++...+....          .++|||+||++|+.|+++++.++..
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~----------~~~lil~Pt~~L~~q~~~~l~~~~~  182 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE----------GKILIIVPTTALTTQMADDFVDYRL  182 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHCS----------SEEEEECSSHHHHHHHHHHHHHHTS
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcCC----------CeEEEEECCHHHHHHHHHHHHHhcc
Confidence            799999999999999889999999999999999888777654321          2699999999999999999998854


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                      . ....+..++++.....    .....++|+|+||+.|....      ...+.++++|||||||++..    ..+..++.
T Consensus       183 ~-~~~~~~~~~~~~~~~~----~~~~~~~I~v~T~~~l~~~~------~~~~~~~~~vIiDEaH~~~~----~~~~~il~  247 (282)
T 1rif_A          183 F-SHAMIKKIGGGASKDD----KYKNDAPVVVGTWQTVVKQP------KEWFSQFGMMMNDECHLATG----KSISSIIS  247 (282)
T ss_dssp             C-CGGGEEECSTTCSSTT----CCCTTCSEEEECHHHHTTSC------GGGGGGEEEEEEETGGGCCH----HHHHHHTT
T ss_pred             c-ccceEEEEeCCCcchh----hhccCCcEEEEchHHHHhhH------HHHHhhCCEEEEECCccCCc----ccHHHHHH
Confidence            3 2567777777765432    11234799999998875432      13467899999999999974    47778888


Q ss_pred             HCCCCCcEEEEeccCChh
Q 006737          561 CLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl~~e  578 (633)
                      .+.+..++++||||+++.
T Consensus       248 ~~~~~~~~l~lSATp~~~  265 (282)
T 1rif_A          248 GLNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             TCTTCCEEEEECSSCCTT
T ss_pred             HhhcCCeEEEEeCCCCCc
Confidence            887789999999999876

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.82  E-value=1e-19  Score=195.54  Aligned_cols=160  Identities=20%  Similarity=0.213  Sum_probs=131.5

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|+++|.++++.++.+ ++++++|||+|||++++++++..+...          +.++|||+|+++|+.|+++++.+++.
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~~----------~~~~liv~P~~~L~~q~~~~~~~~~~   77 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTKY----------GGKVLMLAPTKPLVLQHAESFRRLFN   77 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHHS----------CSCEEEECSSHHHHHHHHHHHHHHBC
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhcC----------CCeEEEEECCHHHHHHHHHHHHHHhC
Confidence            6899999999999999 999999999999999999998876521          23599999999999999999998863


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                       .+...+..++|+...........  .++|+|+||+.|...+...   ...+.++++|||||||++.+......+...+.
T Consensus        78 -~~~~~v~~~~g~~~~~~~~~~~~--~~~ivv~T~~~l~~~~~~~---~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~  151 (494)
T 1wp9_A           78 -LPPEKIVALTGEKSPEERSKAWA--RAKVIVATPQTIENDLLAG---RISLEDVSLIVFDEAHRAVGNYAYVFIAREYK  151 (494)
T ss_dssp             -SCGGGEEEECSCSCHHHHHHHHH--HCSEEEECHHHHHHHHHTT---SCCTTSCSEEEEETGGGCSTTCHHHHHHHHHH
T ss_pred             -cchhheEEeeCCcchhhhhhhcc--CCCEEEecHHHHHHHHhcC---CcchhhceEEEEECCcccCCCCcHHHHHHHHH
Confidence             23458888999877654333332  3699999999999988765   35678899999999999987666666666666


Q ss_pred             HCCCCCcEEEEeccCCh
Q 006737          561 CLPRRRQSLLFSATMPK  577 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl~~  577 (633)
                      ...+..++++||||..+
T Consensus       152 ~~~~~~~~l~lTaTp~~  168 (494)
T 1wp9_A          152 RQAKNPLVIGLTASPGS  168 (494)
T ss_dssp             HHCSSCCEEEEESCSCS
T ss_pred             hcCCCCeEEEEecCCCC
Confidence            66778999999999974

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=99.82  E-value=1.7e-19  Score=218.65  Aligned_cols=169  Identities=20%  Similarity=0.155  Sum_probs=131.9

Q ss_pred             cCCCHHHHHHHHH-cCCCCCcHHHHHHHHHHhC----CC--cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          384 CGISPLTIKALTA-AGYIQMTRVQEATLSACLE----GK--DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       384 l~L~~~Ll~~L~~-~g~~~pt~iQ~~aIp~il~----gr--DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ++++....+.+.. ++|. +|++|.++|+.++.    ++  |+|++++||+|||++|+++++..+..           +.
T Consensus       586 ~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~-----------g~  653 (1151)
T 2eyq_A          586 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN-----------HK  653 (1151)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT-----------TC
T ss_pred             CCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh-----------CC
Confidence            4566677777654 5775 79999999999987    66  99999999999999999998876432           24


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++|||+||++||.|+++.+.+.+... ++.+..+++.......   ...+..+.++|+|+||+.|.    .    ...+.
T Consensus       654 ~vlvlvPt~~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~----~----~~~~~  724 (1151)
T 2eyq_A          654 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ----S----DVKFK  724 (1151)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH----S----CCCCS
T ss_pred             eEEEEechHHHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh----C----Ccccc
Confidence            79999999999999999999887654 6788888876554432   34455667899999997553    2    25678


Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ++.+|||||||++.     .....++..++..+++++||||..+.
T Consensus       725 ~l~lvIiDEaH~~g-----~~~~~~l~~l~~~~~vl~lSATp~p~  764 (1151)
T 2eyq_A          725 DLGLLIVDEEHRFG-----VRHKERIKAMRANVDILTLTATPIPR  764 (1151)
T ss_dssp             SEEEEEEESGGGSC-----HHHHHHHHHHHTTSEEEEEESSCCCH
T ss_pred             ccceEEEechHhcC-----hHHHHHHHHhcCCCCEEEEcCCCChh
Confidence            99999999999953     23455566666789999999998665

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.82  E-value=8.5e-21  Score=216.77  Aligned_cols=147  Identities=18%  Similarity=0.134  Sum_probs=117.0

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .+...|..+++.+..++|++++||||||||++|.+|+++.              +.++||++|||+||.|+++.+.+.+ 
T Consensus       217 P~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~--------------g~~vLVl~PTReLA~Qia~~l~~~~-  281 (666)
T 3o8b_A          217 PVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ--------------GYKVLVLNPSVAATLGFGAYMSKAH-  281 (666)
T ss_dssp             CSCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT--------------TCCEEEEESCHHHHHHHHHHHHHHH-
T ss_pred             CcHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC--------------CCeEEEEcchHHHHHHHHHHHHHHh-
Confidence            4455666666777788999999999999999999988752              2369999999999999998877665 


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                         +..+...+|+..        ....++|+|+||++|+   ...   .+.++++++|||||||+ ++.+|...+..|+.
T Consensus       282 ---g~~vg~~vG~~~--------~~~~~~IlV~TPGrLl---~~~---~l~l~~l~~lVlDEAH~-l~~~~~~~l~~Il~  343 (666)
T 3o8b_A          282 ---GIDPNIRTGVRT--------ITTGAPVTYSTYGKFL---ADG---GCSGGAYDIIICDECHS-TDSTTILGIGTVLD  343 (666)
T ss_dssp             ---SCCCEEECSSCE--------ECCCCSEEEEEHHHHH---HTT---SCCTTSCSEEEETTTTC-CSHHHHHHHHHHHH
T ss_pred             ---CCCeeEEECcEe--------ccCCCCEEEECcHHHH---hCC---CcccCcccEEEEccchh-cCccHHHHHHHHHH
Confidence               445666777654        2345799999999983   332   35678899999999965 56779999999999


Q ss_pred             HCCCCCc--EEEEeccCChhhh
Q 006737          561 CLPRRRQ--SLLFSATMPKELV  580 (633)
Q Consensus       561 ~lpk~~Q--~IlfSATl~~el~  580 (633)
                      .++..+|  +++||||++..+.
T Consensus       344 ~l~~~~~~llil~SAT~~~~i~  365 (666)
T 3o8b_A          344 QAETAGARLVVLATATPPGSVT  365 (666)
T ss_dssp             HTTTTTCSEEEEEESSCTTCCC
T ss_pred             hhhhcCCceEEEECCCCCcccc
Confidence            9988777  7778999998654

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=99.80  E-value=4.9e-19  Score=206.70  Aligned_cols=228  Identities=18%  Similarity=0.145  Sum_probs=150.0

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLE-GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~-grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      ..+|.++++++.+.+.|...+ ..|+++|+.+|+.++. +++++++||||||||+  ++|++........      ..+.
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~~------~~g~  141 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMPH------LENT  141 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCGG------GGTC
T ss_pred             CCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhcccc------CCCc
Confidence            356999999999999999988 7899999999988775 5689999999999999  6777722211111      0135


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      +++|++|+|+||.|+++.+........+..++.......       .....++|+|+|||+|.+.+...    ..+.+++
T Consensus       142 ~ilvl~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~-------~~~~~~~I~v~T~G~l~r~l~~~----~~l~~~~  210 (773)
T 2xau_A          142 QVACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN-------KTSNKTILKYMTDGMLLREAMED----HDLSRYS  210 (773)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE-------ECCTTCSEEEEEHHHHHHHHHHS----TTCTTEE
T ss_pred             eEEecCchHHHHHHHHHHHHHHhCCchhheecceecccc-------ccCCCCCEEEECHHHHHHHHhhC----ccccCCC
Confidence            799999999999999987766543221222221111111       11234799999999999887654    4588999


Q ss_pred             EEEEecccc-cCCcCh-HHHHHHHHHHCCCCCcEEEEeccCChhhh--ccccceEeeeccccccccCccceEEEeehh--
Q 006737          537 MLVLDEADH-LLDLGF-RKDVENIVDCLPRRRQSLLFSATMPKELV--LKREHTYIDTVGLGSVETPVKVSKYNIYVF--  610 (633)
Q Consensus       537 ~LVIDEAD~-Lld~gf-~~~l~~Il~~lpk~~Q~IlfSATl~~el~--l~~~~~~i~~~~~~~~~~~~~V~q~~i~v~--  610 (633)
                      +|||||||. .++..+ ...+..++... ++.|+|+||||++.+..  +.....++...     .....++++|+.+.  
T Consensus       211 ~lIlDEah~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~~~l~~~~~~~~vi~v~-----gr~~pv~~~~~~~~~~  284 (773)
T 2xau_A          211 CIILDEAHERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDAEKFQRYFNDAPLLAVP-----GRTYPVELYYTPEFQR  284 (773)
T ss_dssp             EEEECSGGGCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCCHHHHHHTTSCCEEECC-----CCCCCEEEECCSSCCS
T ss_pred             EEEecCccccccchHHHHHHHHHHHHhC-CCceEEEEeccccHHHHHHHhcCCCccccc-----CcccceEEEEecCCch
Confidence            999999996 565432 33444454444 57999999999976521  11112222211     11224555554321  


Q ss_pred             ---------hHHHHhhcCCceEEEEEcccc
Q 006737          611 ---------VLVLSIKIQAFYIICFVYTIS  631 (633)
Q Consensus       611 ---------~l~~~~k~~~~~~LVFcnT~s  631 (633)
                               ++..........+|||||++.
T Consensus       285 ~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~  314 (773)
T 2xau_A          285 DYLDSAIRTVLQIHATEEAGDILLFLTGED  314 (773)
T ss_dssp             CHHHHHHHHHHHHHHHSCSCEEEEECSCHH
T ss_pred             hHHHHHHHHHHHHHHhcCCCCEEEECCCHH
Confidence                     112222335679999999864

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.80  E-value=9.9e-20  Score=201.51  Aligned_cols=155  Identities=17%  Similarity=0.177  Sum_probs=126.4

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ...|+++|.++++.++.+++++++++||+|||++|+++++..+....          .++|||+||++|+.|+++.+..+
T Consensus       111 ~~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~~----------~~vlvl~P~~~L~~Q~~~~~~~~  180 (510)
T 2oca_A          111 RIEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYE----------GKILIIVPTTALTTQMADDFVDY  180 (510)
T ss_dssp             EECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHCS----------SEEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCCC----------CeEEEEECcHHHHHHHHHHHHHh
Confidence            34899999999999999999999999999999999999887765321          26999999999999999999877


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                      .. .+++.+..++|+.....+    ....++|+|+||+.|...   .   ...+.++.+|||||||++..    ..+..+
T Consensus       181 ~~-~~~~~v~~~~~~~~~~~~----~~~~~~I~i~T~~~l~~~---~---~~~~~~~~liIiDE~H~~~~----~~~~~i  245 (510)
T 2oca_A          181 RL-FSHAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVKQ---P---KEWFSQFGMMMNDECHLATG----KSISSI  245 (510)
T ss_dssp             TS-SCGGGEEECGGGCCTTGG----GCTTCSEEEEEHHHHTTS---C---GGGGGGEEEEEEETGGGCCH----HHHHHH
T ss_pred             hc-CCccceEEEecCCccccc----cccCCcEEEEeHHHHhhc---h---hhhhhcCCEEEEECCcCCCc----ccHHHH
Confidence            43 335788888888765433    234579999999976432   1   24567899999999999875    467778


Q ss_pred             HHHCCCCCcEEEEeccCChh
Q 006737          559 VDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~~e  578 (633)
                      +..+++..++++||||.++.
T Consensus       246 l~~~~~~~~~l~lSATp~~~  265 (510)
T 2oca_A          246 ISGLNNCMFKFGLSGSLRDG  265 (510)
T ss_dssp             GGGCTTCCEEEEEESCGGGC
T ss_pred             HHhcccCcEEEEEEeCCCCC
Confidence            88888889999999999766

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.79  E-value=8.7e-21  Score=218.18  Aligned_cols=154  Identities=18%  Similarity=0.260  Sum_probs=105.8

Q ss_pred             HHHcCCC-----CCcHHHH-----HHHHHHh------CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          394 LTAAGYI-----QMTRVQE-----ATLSACL------EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       394 L~~~g~~-----~pt~iQ~-----~aIp~il------~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      |..+||.     .||++|+     .+||.++      .++|+|++||||||||++|++|+++.+...          +++
T Consensus       203 l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~----------~~~  272 (673)
T 2wv9_A          203 LYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK----------RLR  272 (673)
T ss_dssp             EEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT----------TCC
T ss_pred             eeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC----------CCc
Confidence            3445666     8999999     9999988      899999999999999999999999887653          246


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-----ccccc
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-----LSVRL  532 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-----~~~~L  532 (633)
                      +|||+||++||.|+++.+..+     ++.  ...+.         +.      .++||+++++++.....     ....+
T Consensus       273 ~lilaPTr~La~Q~~~~l~~~-----~i~--~~~~~---------l~------~v~tp~~ll~~l~~~~l~~~l~~~~~l  330 (673)
T 2wv9_A          273 TAVLAPTRVVAAEMAEALRGL-----PVR--YLTPA---------VQ------REHSGNEIVDVMCHATLTHRLMSPLRV  330 (673)
T ss_dssp             EEEEESSHHHHHHHHHHTTTS-----CCE--ECCC------------------CCCCSCCCEEEEEHHHHHHHHHSSSCC
T ss_pred             EEEEccHHHHHHHHHHHHhcC-----Cee--eeccc---------cc------ccCCHHHHHHHHHhhhhHHHHhccccc
Confidence            999999999999999877643     221  11100         00      14555555433221100     01357


Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCC-CCCcEEEEeccCChhhh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLP-RRRQSLLFSATMPKELV  580 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k~~Q~IlfSATl~~el~  580 (633)
                      .++++|||||||++ +..+...+..+...++ ..+|+|+||||+++.+.
T Consensus       331 ~~l~lvViDEaH~~-~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~  378 (673)
T 2wv9_A          331 PNYNLFVMDEAHFT-DPASIAARGYIATRVEAGEAAAIFMTATPPGTSD  378 (673)
T ss_dssp             CCCSEEEEESTTCC-CHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCC
T ss_pred             ccceEEEEeCCccc-CccHHHHHHHHHHhccccCCcEEEEcCCCChhhh
Confidence            89999999999998 3333344444444443 67999999999998853

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.78  E-value=1e-19  Score=199.39  Aligned_cols=134  Identities=19%  Similarity=0.256  Sum_probs=96.7

Q ss_pred             HHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEE
Q 006737          412 ACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLV  491 (633)
Q Consensus       412 ~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~  491 (633)
                      .+++|+|+++++|||||||++|++|+++.+...          ++++||++||++||.|+++.+..+       .+....
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~----------~~~~lil~Ptr~La~Q~~~~l~~~-------~v~~~~   66 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR----------RLRTLVLAPTRVVLSEMKEAFHGL-------DVKFHT   66 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHTTTS-------CEEEES
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc----------CCeEEEEcchHHHHHHHHHHHhcC-------CeEEec
Confidence            467899999999999999999999999987654          246999999999999999877632       222111


Q ss_pred             CCccchHHHHHHhcCCCcE-EEECchhhHHHHhccc-----CcccccCCeeEEEEecccccCCcChHHHHHHHHHHC-CC
Q 006737          492 GGTRFKVDQRRLESDPCQI-LVATPGRLLDHIENKS-----GLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCL-PR  564 (633)
Q Consensus       492 Gg~~~~~~~~~l~~~~~dI-LIaTPgrLl~lL~~~~-----~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~l-pk  564 (633)
                      +                .+ +|+||+++++++....     .....+.++++|||||||++ +.++...+..+...+ +.
T Consensus        67 ~----------------~~~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~  129 (440)
T 1yks_A           67 Q----------------AFSAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARAN  129 (440)
T ss_dssp             S----------------CCCCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTT
T ss_pred             c----------------cceeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhccC
Confidence            1                11 3788887765443221     00123789999999999998 444544444444433 36


Q ss_pred             CCcEEEEeccCChhh
Q 006737          565 RRQSLLFSATMPKEL  579 (633)
Q Consensus       565 ~~Q~IlfSATl~~el  579 (633)
                      ++|+++||||+++.+
T Consensus       130 ~~~~l~~SAT~~~~~  144 (440)
T 1yks_A          130 ESATILMTATPPGTS  144 (440)
T ss_dssp             SCEEEEECSSCTTCC
T ss_pred             CceEEEEeCCCCchh
Confidence            799999999998875

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A

Probab=99.77  E-value=4.1e-19  Score=195.61  Aligned_cols=139  Identities=18%  Similarity=0.214  Sum_probs=97.5

Q ss_pred             HHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEE
Q 006737          410 LSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLT  489 (633)
Q Consensus       410 Ip~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~  489 (633)
                      ...+..++++|+++|||||||++|++|+++.+...          ++++|||+|||+||.|+++.+.       ++.+..
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~----------~~~~lvl~Ptr~La~Q~~~~l~-------g~~v~~   77 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ----------RLRTAVLAPTRVVAAEMAEALR-------GLPVRY   77 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT----------TCCEEEEECSHHHHHHHHHHTT-------TSCEEE
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC----------CCcEEEECchHHHHHHHHHHhc-------CceEeE
Confidence            44567789999999999999999999999988653          2469999999999999998875       233322


Q ss_pred             EECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccccc-----CCcChHHHHHHHHHHCCC
Q 006737          490 LVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL-----LDLGFRKDVENIVDCLPR  564 (633)
Q Consensus       490 l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~L-----ld~gf~~~l~~Il~~lpk  564 (633)
                      ..+....      ....+..|.++|.+.+...+...    ..+.++++|||||||++     +..+|...+.     .++
T Consensus        78 ~~~~~~~------~~t~~~~i~~~~~~~l~~~l~~~----~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~-----~~~  142 (459)
T 2z83_A           78 QTSAVQR------EHQGNEIVDVMCHATLTHRLMSP----NRVPNYNLFVMDEAHFTDPASIAARGYIATKV-----ELG  142 (459)
T ss_dssp             CC--------------CCCSEEEEEHHHHHHHHHSC----C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH-----HTT
T ss_pred             Eeccccc------CCCCCcEEEEEchHHHHHHhhcc----ccccCCcEEEEECCccCCchhhHHHHHHHHHh-----ccC
Confidence            2211110      01223357788888887766544    45789999999999984     3333322221     236


Q ss_pred             CCcEEEEeccCChhhh
Q 006737          565 RRQSLLFSATMPKELV  580 (633)
Q Consensus       565 ~~Q~IlfSATl~~el~  580 (633)
                      ++|+|+||||++..+.
T Consensus       143 ~~~~il~SAT~~~~~~  158 (459)
T 2z83_A          143 EAAAIFMTATPPGTTD  158 (459)
T ss_dssp             SCEEEEECSSCTTCCC
T ss_pred             CccEEEEEcCCCcchh
Confidence            8999999999998753

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.75  E-value=4.7e-18  Score=185.70  Aligned_cols=138  Identities=18%  Similarity=0.202  Sum_probs=98.8

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      .|+|+++++|||||||++|++|+++.+....          .++|||+||++||.|+++.+.       ++.+..+.|+.
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~g----------~~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~   63 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKKR----------LRTVILAPTRVVASEMYEALR-------GEPIRYMTPAV   63 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHTT----------CCEEEEESSHHHHHHHHHHTT-------TSCEEEC----
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhCC----------CCEEEECcHHHHHHHHHHHhC-------CCeEEEEecCc
Confidence            3789999999999999999999997776532          369999999999999887664       44555554432


Q ss_pred             cchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHC-CCCCcEEEEec
Q 006737          495 RFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCL-PRRRQSLLFSA  573 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~l-pk~~Q~IlfSA  573 (633)
                      ..      ......-+.++|.+.+...+...    ..+.++.+|||||||++ +.++...+..+.... +..+|+|+|||
T Consensus        64 ~~------~~~~~~~~~~~~~~~l~~~l~~~----~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SA  132 (431)
T 2v6i_A           64 QS------ERTGNEIVDFMCHSTFTMKLLQG----VRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTA  132 (431)
T ss_dssp             -----------CCCSEEEEEHHHHHHHHHHT----CCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEES
T ss_pred             cc------cCCCCceEEEEchHHHHHHHhcC----ccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeC
Confidence            21      11222457778888887666543    45789999999999997 444555555555443 56899999999


Q ss_pred             cCChhhh
Q 006737          574 TMPKELV  580 (633)
Q Consensus       574 Tl~~el~  580 (633)
                      |+++.+.
T Consensus       133 T~~~~~~  139 (431)
T 2v6i_A          133 TPPGTTE  139 (431)
T ss_dssp             SCTTCCC
T ss_pred             CCCcchh
Confidence            9998753

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=99.75  E-value=7.8e-18  Score=184.51  Aligned_cols=137  Identities=24%  Similarity=0.216  Sum_probs=113.2

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..|+++|.++++.++.+++++++++||+|||++|++++...              +.++|||+||++|+.|+++.+..+ 
T Consensus        92 ~~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~--------------~~~~Lvl~P~~~L~~Q~~~~~~~~-  156 (472)
T 2fwr_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL--------------STPTLIVVPTLALAEQWKERLGIF-  156 (472)
T ss_dssp             CCBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH--------------CSCEEEEESSHHHHHHHHHHGGGG-
T ss_pred             CCcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc--------------CCCEEEEECCHHHHHHHHHHHHhC-
Confidence            37999999999999999999999999999999999987653              125999999999999999998883 


Q ss_pred             hcCCCce-EEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          480 KNHDGIG-VLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       480 ~~~~~i~-v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                          ++. +.+++|+...          .++|+|+||+.|...+...      ..++.+|||||||++.+.+|..    +
T Consensus       157 ----~~~~v~~~~g~~~~----------~~~Ivv~T~~~l~~~~~~~------~~~~~liIvDEaH~~~~~~~~~----~  212 (472)
T 2fwr_A          157 ----GEEYVGEFSGRIKE----------LKPLTVSTYDSAYVNAEKL------GNRFMLLIFDEVHHLPAESYVQ----I  212 (472)
T ss_dssp             ----CGGGEEEBSSSCBC----------CCSEEEEEHHHHHHTHHHH------TTTCSEEEEETGGGTTSTTTHH----H
T ss_pred             ----CCcceEEECCCcCC----------cCCEEEEEcHHHHHHHHHh------cCCCCEEEEECCcCCCChHHHH----H
Confidence                677 8888887653          3689999999988766421      2468999999999999887654    4


Q ss_pred             HHHCCCCCcEEEEeccCC
Q 006737          559 VDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~  576 (633)
                      +..++ ..++++||||..
T Consensus       213 ~~~~~-~~~~l~lSATp~  229 (472)
T 2fwr_A          213 AQMSI-APFRLGLTATFE  229 (472)
T ss_dssp             HHTCC-CSEEEEEESCCC
T ss_pred             HHhcC-CCeEEEEecCcc
Confidence            55553 678999999997

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=99.74  E-value=1.6e-17  Score=167.45  Aligned_cols=139  Identities=24%  Similarity=0.226  Sum_probs=110.2

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..|+++|.+++..++.++++++++|||+|||++++.++...              +.++||++|+++|+.|+++.+..+ 
T Consensus        92 ~~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~--------------~~~~liv~P~~~L~~q~~~~~~~~-  156 (237)
T 2fz4_A           92 ISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL--------------STPTLIVVPTLALAEQWKERLGIF-  156 (237)
T ss_dssp             CCCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS--------------CSCEEEEESSHHHHHHHHHHHGGG-
T ss_pred             CCcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc--------------CCCEEEEeCCHHHHHHHHHHHHhC-
Confidence            47999999999999999999999999999999988776532              124999999999999999888773 


Q ss_pred             hcCCCce-EEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          480 KNHDGIG-VLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       480 ~~~~~i~-v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                          ++. +..+.|+...          ..+|+|+|++.+...+...      ...+++|||||||++.+..+.    .+
T Consensus       157 ----~~~~v~~~~g~~~~----------~~~i~v~T~~~l~~~~~~~------~~~~~llIiDEaH~l~~~~~~----~i  212 (237)
T 2fz4_A          157 ----GEEYVGEFSGRIKE----------LKPLTVSTYDSAYVNAEKL------GNRFMLLIFDEVHHLPAESYV----QI  212 (237)
T ss_dssp             ----CGGGEEEESSSCBC----------CCSEEEEEHHHHHHTHHHH------TTTCSEEEEECSSCCCTTTHH----HH
T ss_pred             ----CCCeEEEEeCCCCC----------cCCEEEEeHHHHHhhHHHh------cccCCEEEEECCccCCChHHH----HH
Confidence                566 7777776542          3589999999987665421      246899999999999876544    45


Q ss_pred             HHHCCCCCcEEEEeccCChh
Q 006737          559 VDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~~e  578 (633)
                      +..++ ..++++||||....
T Consensus       213 ~~~~~-~~~~l~LSATp~r~  231 (237)
T 2fz4_A          213 AQMSI-APFRLGLTATFERE  231 (237)
T ss_dssp             HHTCC-CSEEEEEEESCC--
T ss_pred             HHhcc-CCEEEEEecCCCCC
Confidence            55554 67899999998754

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.71  E-value=1.3e-17  Score=192.75  Aligned_cols=133  Identities=21%  Similarity=0.217  Sum_probs=110.8

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      +|+ .|+++|..++|.++.|+  |++++||+|||++|+||++...+..           .+|+||+||++||.|+++.+.
T Consensus        76 lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~G-----------~qv~VvTPTreLA~Qdae~m~  141 (997)
T 2ipc_A           76 LGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALTG-----------KGVHVVTVNDYLARRDAEWMG  141 (997)
T ss_dssp             TCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTTC-----------SCCEEEESSHHHHHHHHHHHH
T ss_pred             hCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHhC-----------CCEEEEeCCHHHHHHHHHHHH
Confidence            689 99999999999999998  9999999999999999996544321           249999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccC---cccccC---CeeEEEEecccccC
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSG---LSVRLM---GLKMLVLDEADHLL  547 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~---~~~~Ls---~l~~LVIDEAD~Ll  547 (633)
                      .++.++ ++++++++||.+.......  . .+||+|+||++| .++|...-.   ....++   .+.++||||||.||
T Consensus       142 ~l~~~l-GLsv~~i~Gg~~~~~r~~a--y-~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          142 PVYRGL-GLSVGVIQHASTPAERRKA--Y-LADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             HHHHTT-TCCEEECCTTCCHHHHHHH--H-TSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             HHHHhc-CCeEEEEeCCCCHHHHHHH--c-CCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            999876 8999999999874432222  2 489999999999 888876521   124577   89999999999987

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.62  E-value=5.2e-16  Score=175.27  Aligned_cols=160  Identities=14%  Similarity=0.134  Sum_probs=91.4

Q ss_pred             CCCcHHHHHHHHHHhC----C-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH-H
Q 006737          400 IQMTRVQEATLSACLE----G-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA-A  473 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~----g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~-~  473 (633)
                      ..|+++|.++++.++.    + ++++++++||+|||++++ +++..+....... .......++|||+||++|+.|++ +
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~-~~~~~l~~~~~~~-~~~~~~~~vlil~P~~~L~~Q~~~~  254 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAF-QISWKLWSARWNR-TGDYRKPRILFLADRNVLVDDPKDK  254 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHH-HHHHHHHHTTCCS-SCSSSCCCEEEEEC-----------
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHH-HHHHHHHhccccc-ccccCCCeEEEEeCCHHHHHHHHHH
Confidence            3799999999999876    4 679999999999999954 4555555442100 01112357999999999999998 6


Q ss_pred             HHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC-cccccCCeeEEEEecccccCCcChH
Q 006737          474 EAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG-LSVRLMGLKMLVLDEADHLLDLGFR  552 (633)
Q Consensus       474 ~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~-~~~~Ls~l~~LVIDEAD~Lld~gf~  552 (633)
                      .+..+     +..+..+.++.         .....+|+|+||++|...+..... ..+....+++|||||||++...+ .
T Consensus       255 ~~~~~-----~~~~~~~~~~~---------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~  319 (590)
T 3h1t_A          255 TFTPF-----GDARHKIEGGK---------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-N  319 (590)
T ss_dssp             CCTTT-----CSSEEECCC-----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC--------
T ss_pred             HHHhc-----chhhhhhhccC---------CCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-h
Confidence            66544     22333333321         123469999999999887642211 12345678999999999997642 3


Q ss_pred             HHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          553 KDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       553 ~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ..+..++..++ ..++|+||||...
T Consensus       320 ~~~~~il~~~~-~~~~l~lTATP~~  343 (590)
T 3h1t_A          320 SNWREILEYFE-PAFQIGMTATPLR  343 (590)
T ss_dssp             --CHHHHHHST-TSEEEEEESSCSC
T ss_pred             HHHHHHHHhCC-cceEEEecccccc
Confidence            56677777776 4789999999764

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.59  E-value=6.6e-16  Score=177.61  Aligned_cols=138  Identities=17%  Similarity=0.075  Sum_probs=104.0

Q ss_pred             HHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCc
Q 006737          406 QEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI  485 (633)
Q Consensus       406 Q~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i  485 (633)
                      |.......+.+++++++||||||||+    ++++.+....           .+||++|||+||.|+++.+..+     ++
T Consensus       145 ~~~p~ar~l~rk~vlv~apTGSGKT~----~al~~l~~~~-----------~gl~l~PtR~LA~Qi~~~l~~~-----g~  204 (677)
T 3rc3_A          145 NWYPDARAMQRKIIFHSGPTNSGKTY----HAIQKYFSAK-----------SGVYCGPLKLLAHEIFEKSNAA-----GV  204 (677)
T ss_dssp             GGCHHHHTSCCEEEEEECCTTSSHHH----HHHHHHHHSS-----------SEEEEESSHHHHHHHHHHHHHT-----TC
T ss_pred             hhCHHHHhcCCCEEEEEcCCCCCHHH----HHHHHHHhcC-----------CeEEEeCHHHHHHHHHHHHHhc-----CC
Confidence            33344456789999999999999998    4555555442           2689999999999999998775     67


Q ss_pred             eEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC-C
Q 006737          486 GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP-R  564 (633)
Q Consensus       486 ~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp-k  564 (633)
                      .+.+++|+.....   .......+++++|++.+           ..+..+++|||||||++++.+|...+..++..++ .
T Consensus       205 ~v~lltG~~~~iv---~TpGr~~~il~~T~e~~-----------~l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~  270 (677)
T 3rc3_A          205 PCDLVTGEERVTV---QPNGKQASHVSCTVEMC-----------SVTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAE  270 (677)
T ss_dssp             CEEEECSSCEECC---STTCCCCSEEEEEGGGC-----------CSSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEE
T ss_pred             cEEEEECCeeEEe---cCCCcccceeEecHhHh-----------hhcccCCEEEEecceecCCccchHHHHHHHHccCcc
Confidence            8888888765411   00001245666666443           1246789999999999999999999999999888 6


Q ss_pred             CCcEEEEeccCCh
Q 006737          565 RRQSLLFSATMPK  577 (633)
Q Consensus       565 ~~Q~IlfSATl~~  577 (633)
                      ..|++++|||.+.
T Consensus       271 ~i~il~~SAT~~~  283 (677)
T 3rc3_A          271 EVHLCGEPAAIDL  283 (677)
T ss_dssp             EEEEEECGGGHHH
T ss_pred             ceEEEeccchHHH
Confidence            8899999999643

>2w00_A HSDR, R.ECOR124I; ATP-binding, DNA-binding, restriction system, helicase, HYDR R.ECOR124I, nucleotide-binding; HET: ATP; 2.6A {Escherichia coli} PDB: 2y3t_A* 2w74_B*

Probab=99.59  E-value=2.6e-15  Score=179.63  Aligned_cols=156  Identities=19%  Similarity=0.155  Sum_probs=115.6

Q ss_pred             CCcHHHHHHHHHHhC--------------CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHH
Q 006737          401 QMTRVQEATLSACLE--------------GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRE  466 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~--------------grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTRe  466 (633)
                      .|+++|..|++.++.              +++++++++||||||+++ ++++..+ ....       ...++|||+|+++
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll-~~~~-------~~~rvLvlvpr~e  341 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLA-TELD-------FIDKVFFVVDRKD  341 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHH-TTCT-------TCCEEEEEECGGG
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHH-HhcC-------CCceEEEEeCcHH
Confidence            599999999999875              368999999999999997 6666443 2211       1247999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccccc
Q 006737          467 LASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHL  546 (633)
Q Consensus       467 La~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~L  546 (633)
                      |+.|+.+.+..+...       .+.++.+.......+....++|+|+||++|..++...... ..+....+|||||||++
T Consensus       342 L~~Q~~~~f~~f~~~-------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~-~~~~~~~lvIiDEAHrs  413 (1038)
T 2w00_A          342 LDYQTMKEYQRFSPD-------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDL-PVYNQQVVFIFDECHRS  413 (1038)
T ss_dssp             CCHHHHHHHHTTSTT-------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCC-GGGGSCEEEEEESCCTT
T ss_pred             HHHHHHHHHHHhccc-------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccch-hccccccEEEEEccchh
Confidence            999999988876532       1234444444445555556799999999999987653211 23557889999999997


Q ss_pred             CCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          547 LDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       547 ld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ..   ...+..|+..++ +.++++||||...
T Consensus       414 ~~---~~~~~~I~~~~p-~a~~lgfTATP~~  440 (1038)
T 2w00_A          414 QF---GEAQKNLKKKFK-RYYQFGFTGTPIF  440 (1038)
T ss_dssp             HH---HHHHHHHHHHCS-SEEEEEEESSCCC
T ss_pred             cc---hHHHHHHHHhCC-cccEEEEeCCccc
Confidence            63   344566777776 4799999999864

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.52  E-value=9.2e-15  Score=164.43  Aligned_cols=131  Identities=19%  Similarity=0.121  Sum_probs=98.1

Q ss_pred             CCcHHHHHHHHH----HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSA----CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~aIp~----il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .++|.|.+++..    +..|+++++.||||+|||++|++|++..              +.++||++||++|+.|+.+++.
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~--------------~~~v~i~~pt~~l~~q~~~~~~   68 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV--------------KPKVLFVVRTHNEFYPIYRDLT   68 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH--------------CSEEEEEESSGGGHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC--------------CCeEEEEcCCHHHHHHHHHHHH
Confidence            689999987764    5679999999999999999999999861              2479999999999999998888


Q ss_pred             HHHhcCCCceEEEEECCccc---------------------------------hHHHH-----------------HHhcC
Q 006737          477 ALLKNHDGIGVLTLVGGTRF---------------------------------KVDQR-----------------RLESD  506 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~---------------------------------~~~~~-----------------~l~~~  506 (633)
                      .+.... ++++.++.|...+                                 .....                 .....
T Consensus        69 ~l~~~~-~~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~  147 (551)
T 3crv_A           69 KIREKR-NITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLY  147 (551)
T ss_dssp             TCCCSS-CCCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGG
T ss_pred             HHhhhc-CccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhh
Confidence            776544 6778777774321                                 00010                 11112


Q ss_pred             CCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC
Q 006737          507 PCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       507 ~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      .++|||+|+..|++.+.... .. ......+|||||||.|.+
T Consensus       148 ~adIVV~~~~~l~~~~~~~~-~~-~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          148 KADVIALTYPYFFIDRYREF-ID-IDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             GCSEEEEETHHHHCHHHHTT-SC-CCSTTEEEEETTGGGGGG
T ss_pred             cCCEEEeCchHhcCHHHHHh-cC-CCcCCeEEEEecccchHH
Confidence            47999999999998764432 11 124677999999999987

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.42  E-value=1.5e-13  Score=154.40  Aligned_cols=132  Identities=23%  Similarity=0.237  Sum_probs=86.3

Q ss_pred             cCCCCCcHHHHHHHH----HHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLS----ACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp----~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      .|| .|+++|.+++.    .+..|+++++.||||+|||++|++|++..              ..++||++||++|+.|++
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~--------------~~~~~~~~~t~~l~~q~~   68 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL--------------KKKVLIFTRTHSQLDSIY   68 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH--------------TCEEEEEESCHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC--------------CCcEEEEcCCHHHHHHHH
Confidence            466 89999999865    45689999999999999999999998753              136999999999999999


Q ss_pred             HHHHHHHhcCCCceEEEEECCccc--------hH------------------------HHHH--------------HhcC
Q 006737          473 AEAIALLKNHDGIGVLTLVGGTRF--------KV------------------------DQRR--------------LESD  506 (633)
Q Consensus       473 ~~l~~l~~~~~~i~v~~l~Gg~~~--------~~------------------------~~~~--------------l~~~  506 (633)
                      +.+..+     ++++..+.|....        ..                        ....              ....
T Consensus        69 ~~~~~l-----~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~  143 (540)
T 2vl7_A           69 KNAKLL-----GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLK  143 (540)
T ss_dssp             HHHGGG-----TCCEEEC---------------------------------------------------------CTTGG
T ss_pred             HHHHhc-----CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhh
Confidence            887764     3444444432210        00                        0000              0012


Q ss_pred             CCcEEEECchhhHHHHhcccCc----ccccCCeeEEEEecccccCC
Q 006737          507 PCQILVATPGRLLDHIENKSGL----SVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       507 ~~dILIaTPgrLl~lL~~~~~~----~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      .++|||+|+..|++.+......    ...+....+|||||||.|.+
T Consensus       144 ~adiVV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~~  189 (540)
T 2vl7_A          144 DKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLE  189 (540)
T ss_dssp             GCSEEEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGGG
T ss_pred             cCCEEEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHHH
Confidence            4699999999998755432100    00245678999999999953

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.39  E-value=6.4e-13  Score=146.46  Aligned_cols=150  Identities=15%  Similarity=0.200  Sum_probs=106.9

Q ss_pred             CCCcHHHHHHHHHH----hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSAC----LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       400 ~~pt~iQ~~aIp~i----l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      ..|+|+|.+++..+    ..++++|++.+||+|||++++. ++..+.....        ..++|||||+ .|+.|..+++
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~-~i~~~~~~~~--------~~~~LIv~P~-~l~~qw~~e~  105 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKENE--------LTPSLVICPL-SVLKNWEEEL  105 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTTC--------CSSEEEEECS-TTHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHH-HHHHHHhcCC--------CCCEEEEccH-HHHHHHHHHH
Confidence            36999999999876    3578999999999999998654 4444443321        1249999994 6899999999


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHH
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDV  555 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l  555 (633)
                      .+++.   .+.+.+++|+...      ......+|+|+|++.|.....      +....+++|||||||++.+..  ...
T Consensus       106 ~~~~~---~~~v~~~~g~~~~------~~~~~~~ivi~t~~~l~~~~~------l~~~~~~~vIvDEaH~~kn~~--~~~  168 (500)
T 1z63_A          106 SKFAP---HLRFAVFHEDRSK------IKLEDYDIILTTYAVLLRDTR------LKEVEWKYIVIDEAQNIKNPQ--TKI  168 (500)
T ss_dssp             HHHCT---TSCEEECSSSTTS------CCGGGSSEEEEEHHHHTTCHH------HHTCCEEEEEEETGGGGSCTT--SHH
T ss_pred             HHHCC---CceEEEEecCchh------ccccCCcEEEeeHHHHhccch------hcCCCcCEEEEeCccccCCHh--HHH
Confidence            88753   5677777766532      111236999999999865432      223468899999999997653  234


Q ss_pred             HHHHHHCCCCCcEEEEeccCCh
Q 006737          556 ENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       556 ~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ...+..++ ..+.+++|||...
T Consensus       169 ~~~l~~l~-~~~~l~LTaTP~~  189 (500)
T 1z63_A          169 FKAVKELK-SKYRIALTGTPIE  189 (500)
T ss_dssp             HHHHHTSC-EEEEEEECSSCST
T ss_pred             HHHHHhhc-cCcEEEEecCCCC
Confidence            44555554 4578999999743

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}

Probab=99.30  E-value=2.7e-12  Score=153.37  Aligned_cols=161  Identities=17%  Similarity=0.129  Sum_probs=106.4

Q ss_pred             CCCcHHHHHHHHHHhCC--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEG--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ..|+|+|..++..++..  ..+|++.+||+|||++++..+...+.....         -++|||||+ .|+.|...++.+
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g~~---------~rvLIVvP~-sLl~Qw~~E~~~  221 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSGAA---------ERVLIIVPE-TLQHQWLVEMLR  221 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTSSC---------CCEEEECCT-TTHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhCCC---------CeEEEEeCH-HHHHHHHHHHHH
Confidence            47999999999988764  489999999999999987766555433221         249999999 999999999877


Q ss_pred             HHhcCCCceEEEEECCccchHHHHH-HhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChH--HH
Q 006737          478 LLKNHDGIGVLTLVGGTRFKVDQRR-LESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFR--KD  554 (633)
Q Consensus       478 l~~~~~~i~v~~l~Gg~~~~~~~~~-l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~--~~  554 (633)
                      .+    ++.+.++.|+......... ......+|+|+|++.|.......  ..+....+.+|||||||++...+..  ..
T Consensus       222 ~f----~l~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~--~~l~~~~~dlVIvDEAH~~kn~~~~~s~~  295 (968)
T 3dmq_A          222 RF----NLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRL--EHLCEAEWDLLVVDEAHHLVWSEDAPSRE  295 (968)
T ss_dssp             HS----CCCCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTT--HHHHTSCCCEEEECCSSCCCCBTTBCCHH
T ss_pred             Hh----CCCEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHH--HHhhhcCCCEEEehhhHhhcCCCCcchHH
Confidence            65    4556555544322111110 11124689999998875421110  0133457899999999999764421  11


Q ss_pred             HHHHHHHCCCCCcEEEEeccCC
Q 006737          555 VENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       555 l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      +..+.....+..+++++|||.-
T Consensus       296 ~~~l~~L~~~~~~~L~LTATPi  317 (968)
T 3dmq_A          296 YQAIEQLAEHVPGVLLLTATPE  317 (968)
T ss_dssp             HHHHHHHHTTCSSEEESCSSCS
T ss_pred             HHHHHHHhhcCCcEEEEEcCCc
Confidence            2222223334567999999974

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.18  E-value=5.6e-11  Score=139.34  Aligned_cols=156  Identities=12%  Similarity=0.166  Sum_probs=109.2

Q ss_pred             CCCcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      ..++++|.+++..++    .++++|++.+||.|||+..+..+...+......        ..+||||| ..|+.|..+++
T Consensus       235 ~~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~~~--------~~~LIV~P-~sll~qW~~E~  305 (800)
T 3mwy_W          235 GELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQN--------GPHIIVVP-LSTMPAWLDTF  305 (800)
T ss_dssp             SCCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHSCC--------SCEEEECC-TTTHHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcCCC--------CCEEEEEC-chHHHHHHHHH
Confidence            379999999998665    788999999999999998665444333332211        13899999 77888998888


Q ss_pred             HHHHhcCCCceEEEEECCccchHHHHHH-----------hcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          476 IALLKNHDGIGVLTLVGGTRFKVDQRRL-----------ESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       476 ~~l~~~~~~i~v~~l~Gg~~~~~~~~~l-----------~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      .+++   +++.+.+++|+..........           ....++|+|+|++.+......     +......+|||||||
T Consensus       306 ~~~~---p~~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~-----l~~~~w~~vIvDEaH  377 (800)
T 3mwy_W          306 EKWA---PDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE-----LGSIKWQFMAVDEAH  377 (800)
T ss_dssp             HHHS---TTCCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH-----HHTSEEEEEEETTGG
T ss_pred             HHHC---CCceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH-----HhcCCcceeehhhhh
Confidence            8775   477888888876544333221           223578999999999765432     222367899999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      ++-+..  ..+...+..++ ....+++|||.
T Consensus       378 ~lkn~~--s~~~~~l~~l~-~~~rl~LTgTP  405 (800)
T 3mwy_W          378 RLKNAE--SSLYESLNSFK-VANRMLITGTP  405 (800)
T ss_dssp             GGCCSS--SHHHHHHTTSE-EEEEEEECSCC
T ss_pred             hhcCch--hHHHHHHHHhh-hccEEEeeCCc
Confidence            996432  23444444443 34568899997

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.17  E-value=2.5e-11  Score=138.55  Aligned_cols=83  Identities=20%  Similarity=0.259  Sum_probs=67.8

Q ss_pred             CCcHHHHHHHH----HHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLS----ACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~aIp----~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      +|++.|.+.+.    .+.+|+++++.||||+|||++|++|++..+....          .++||++||++|+.|+.+.+.
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~~----------~kvli~t~T~~l~~Qi~~el~   72 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERK----------LKVLYLVRTNSQEEQVIKELR   72 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHHT----------CEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhcC----------CeEEEECCCHHHHHHHHHHHH
Confidence            57899988875    5668999999999999999999999999876532          479999999999999999999


Q ss_pred             HHHhcCCCceEEEEECCc
Q 006737          477 ALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~  494 (633)
                      .+.... .+++..+.|+.
T Consensus        73 ~l~~~~-~~~~~~l~gr~   89 (620)
T 4a15_A           73 SLSSTM-KIRAIPMQGRV   89 (620)
T ss_dssp             HHHHHS-CCCEEECCCHH
T ss_pred             HHhhcc-CeEEEEEECCC
Confidence            887654 67776666643

>1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination-DNA binding COM; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19

Probab=99.14  E-value=5.5e-10  Score=127.91  Aligned_cols=161  Identities=16%  Similarity=0.197  Sum_probs=107.2

Q ss_pred             CCcHHHHHHHHHHh---------CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          401 QMTRVQEATLSACL---------EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       401 ~pt~iQ~~aIp~il---------~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      .+.|+|.+++..+.         .+..+|+..+||+|||+..+..+... .......   .....++|||+|+ .|+.|.
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l-~~~~~~~---~p~~~~~LiV~P~-sll~qW  129 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTL-LKQSPDC---KPEIDKVIVVSPS-SLVRNW  129 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHH-HHCCTTS---SCSCSCEEEEECH-HHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHH-HHhCccc---cCCCCcEEEEecH-HHHHHH
Confidence            68999999998874         45689999999999999876655443 3322110   0011248999997 899999


Q ss_pred             HHHHHHHHhcCCCceEEEEECCccchHH--HHHHhc-----CCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          472 AAEAIALLKNHDGIGVLTLVGGTRFKVD--QRRLES-----DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       472 ~~~l~~l~~~~~~i~v~~l~Gg~~~~~~--~~~l~~-----~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      .+++.+++..  .+.+..++++......  ......     ...+|+|+|++.+......     +....+.+|||||||
T Consensus       130 ~~E~~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~~-----l~~~~~~~vI~DEaH  202 (644)
T 1z3i_X          130 YNEVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV-----LHKGKVGLVICDEGH  202 (644)
T ss_dssp             HHHHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT-----TTTSCCCEEEETTGG
T ss_pred             HHHHHHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHHH-----hhcCCccEEEEECce
Confidence            9999998753  3566667776543221  111111     1368999999998765421     223467899999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      ++-+..  ......+..++ ....+++|||.-
T Consensus       203 ~ikn~~--~~~~~al~~l~-~~~rl~LTgTPi  231 (644)
T 1z3i_X          203 RLKNSD--NQTYLALNSMN-AQRRVLISGTPI  231 (644)
T ss_dssp             GCCTTC--HHHHHHHHHHC-CSEEEEECSSCS
T ss_pred             ecCChh--hHHHHHHHhcc-cCcEEEEecCcc
Confidence            997543  22333333443 456899999963

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=98.88  E-value=1e-08  Score=117.25  Aligned_cols=133  Identities=23%  Similarity=0.180  Sum_probs=99.3

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          397 AGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       397 ~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .|. .|+++|.-..-.+..|+  |+.+.||+|||+++.+|++-..+..           ..|.||+||+.||.|-++.+.
T Consensus        72 lg~-r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~G-----------~~vhVvT~ndyLA~rdae~m~  137 (822)
T 3jux_A           72 LGM-RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALIG-----------KGVHLVTVNDYLARRDALWMG  137 (822)
T ss_dssp             TSC-CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTTS-----------SCEEEEESSHHHHHHHHHHHH
T ss_pred             hCC-CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhcC-----------CceEEEeccHHHHHhHHHHHH
Confidence            344 68999999998898887  9999999999999999997444332           248999999999999999999


Q ss_pred             HHHhcCCCceEEEEECC--------------------------------------------------ccchHHHHHHhcC
Q 006737          477 ALLKNHDGIGVLTLVGG--------------------------------------------------TRFKVDQRRLESD  506 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg--------------------------------------------------~~~~~~~~~l~~~  506 (633)
                      .+..++ |+.|++++..                                                  ..... .+...  
T Consensus       138 ~l~~~L-glsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~e-rr~aY--  213 (822)
T 3jux_A          138 PVYLFL-GLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEIT-RKEAY--  213 (822)
T ss_dssp             HHHHHT-TCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCC-HHHHH--
T ss_pred             HHHHHh-CCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHH-HHHHh--
Confidence            998877 8999998872                                                  11111 11111  


Q ss_pred             CCcEEEECchhh-HHHHhcccC---cccccCCeeEEEEecccccC
Q 006737          507 PCQILVATPGRL-LDHIENKSG---LSVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       507 ~~dILIaTPgrL-l~lL~~~~~---~~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .|||.++|..-| .++|...-.   .......+.+.||||+|.+|
T Consensus       214 ~~DItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          214 LCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HSSEEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             cCCCEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            379999999877 455543210   11224678899999999775

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=98.74  E-value=1.9e-08  Score=114.46  Aligned_cols=145  Identities=21%  Similarity=0.306  Sum_probs=89.8

Q ss_pred             cHHHHHHHHHHhCCCcEEEEccCCCCch--hhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          403 TRVQEATLSACLEGKDAVVKAKTGTGKS--IAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       403 t~iQ~~aIp~il~grDvLv~ApTGSGKT--laylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      ++.|+.+++.++.+++++++|++|||||  ++++++++..+...         .+.++++++||..+|.++.+.+.....
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~~---------~~~~vll~APTg~AA~~L~e~~~~~~~  221 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMADG---------ERCRIRLAAPTGKAAARLTESLGKALR  221 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCSS---------CCCCEEEEBSSHHHHHHHHHHHTHHHH
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhhc---------CCCeEEEEeCChhHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999  66777776543111         134699999999999999888776654


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                      .. ++..... .+...  ....+    -.++-.+|+.. . +....   .....+++||||||+. ++   ...+..|+.
T Consensus       222 ~l-~l~~~~~-~~~~~--~~~Ti----h~ll~~~~~~~-~-~~~~~---~~~l~~d~lIIDEAsm-l~---~~~~~~Ll~  284 (608)
T 1w36_D          222 QL-PLTDEQK-KRIPE--DASTL----HRLLGAQPGSQ-R-LRHHA---GNPLHLDVLVVDEASM-ID---LPMMSRLID  284 (608)
T ss_dssp             HS-SCCSCCC-CSCSC--CCBTT----TSCC-------------CT---TSCCSCSEEEECSGGG-CB---HHHHHHHHH
T ss_pred             cC-CCCHHHH-hccch--hhhhh----HhhhccCCCch-H-HHhcc---CCCCCCCEEEEechhh-CC---HHHHHHHHH
Confidence            33 2110000 00000  00000    01222223221 1 11110   1123788999999994 44   457788899


Q ss_pred             HCCCCCcEEEEec
Q 006737          561 CLPRRRQSLLFSA  573 (633)
Q Consensus       561 ~lpk~~Q~IlfSA  573 (633)
                      .++...|+|++.=
T Consensus       285 ~l~~~~~liLvGD  297 (608)
T 1w36_D          285 ALPDHARVIFLGD  297 (608)
T ss_dssp             TCCTTCEEEEEEC
T ss_pred             hCCCCCEEEEEcc
Confidence            9999999999853

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=97.83  E-value=0.00012  Score=83.33  Aligned_cols=70  Identities=14%  Similarity=0.199  Sum_probs=54.3

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      +..+++.|..|+..++...-++|+||+|||||.+. ..++..+....         +.++|+++||...+.++.+.+...
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~-~~~i~~l~~~~---------~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQG---------NGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHH-HHHHHHHHTSS---------SCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHH-HHHHHHHHHcC---------CCeEEEEeCcHHHHHHHHHHHHhc
Confidence            45789999999999998888899999999999863 33444444321         135999999999999988777543

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.81  E-value=8.2e-05  Score=84.07  Aligned_cols=125  Identities=19%  Similarity=0.243  Sum_probs=78.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .+++.|..++..++.++.+++.|+.|||||... ..++..+...          +.++++++||...+..+.+.+     
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~~----------g~~Vl~~ApT~~Aa~~L~e~~-----  252 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAESL----------GLEVGLCAPTGKAARRLGEVT-----  252 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHHT----------TCCEEEEESSHHHHHHHHHHH-----
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHhc----------CCeEEEecCcHHHHHHhHhhh-----
Confidence            689999999999999999999999999999752 2233333322          135899999999998765432     


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                         +.....          ...+..    +   .|..+    ...   .......++||||||+.+..    ..+..++.
T Consensus       253 ---~~~a~T----------ih~ll~----~---~~~~~----~~~---~~~~~~~dvlIIDEasml~~----~~~~~Ll~  301 (574)
T 3e1s_A          253 ---GRTAST----------VHRLLG----Y---GPQGF----RHN---HLEPAPYDLLIVDEVSMMGD----ALMLSLLA  301 (574)
T ss_dssp             ---TSCEEE----------HHHHTT----E---ETTEE----SCS---SSSCCSCSEEEECCGGGCCH----HHHHHHHT
T ss_pred             ---cccHHH----------HHHHHc----C---Ccchh----hhh---hcccccCCEEEEcCccCCCH----HHHHHHHH
Confidence               111111          011110    0   00000    000   11233678999999998753    36677778


Q ss_pred             HCCCCCcEEEEe
Q 006737          561 CLPRRRQSLLFS  572 (633)
Q Consensus       561 ~lpk~~Q~IlfS  572 (633)
                      .++...++|++.
T Consensus       302 ~~~~~~~lilvG  313 (574)
T 3e1s_A          302 AVPPGARVLLVG  313 (574)
T ss_dssp             TSCTTCEEEEEE
T ss_pred             hCcCCCEEEEEe
Confidence            888777777764

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=97.80  E-value=5.7e-05  Score=82.73  Aligned_cols=138  Identities=14%  Similarity=0.201  Sum_probs=80.7

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCC----C-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHH
Q 006737          395 TAAGYIQMTRVQEATLSACLEG----K-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELAS  469 (633)
Q Consensus       395 ~~~g~~~pt~iQ~~aIp~il~g----r-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~  469 (633)
                      .-+.|..+++-|++++..++..    . .+++.|+.|||||.+ +..++..+.....         ..+++++||...|.
T Consensus        19 ~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~l-l~~~~~~l~~~~~---------~~il~~a~T~~Aa~   88 (459)
T 3upu_A           19 SHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTL-TKFIIEALISTGE---------TGIILAAPTHAAKK   88 (459)
T ss_dssp             --CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHH-HHHHHHHHHHTTC---------CCEEEEESSHHHHH
T ss_pred             CCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHH-HHHHHHHHHhcCC---------ceEEEecCcHHHHH
Confidence            4467889999999999977543    3 899999999999964 3344555544322         13889999999887


Q ss_pred             HHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhc-CCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCC
Q 006737          470 QIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLES-DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD  548 (633)
Q Consensus       470 Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~-~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld  548 (633)
                      .+.+.+        ++.+..++.-...     .... .....+..          ..   ...+...++|||||++.+. 
T Consensus        89 ~l~~~~--------~~~~~T~h~~~~~-----~~~~~~~~~~~~~----------~~---~~~~~~~~~iiiDE~~~~~-  141 (459)
T 3upu_A           89 ILSKLS--------GKEASTIHSILKI-----NPVTYEENVLFEQ----------KE---VPDLAKCRVLICDEVSMYD-  141 (459)
T ss_dssp             HHHHHH--------SSCEEEHHHHHTE-----EEEECSSCEEEEE----------CS---CCCCSSCSEEEESCGGGCC-
T ss_pred             HHHhhh--------ccchhhHHHHhcc-----Ccccccccchhcc----------cc---cccccCCCEEEEECchhCC-
Confidence            765443        1112111100000     0000 00000000          00   1335678999999999764 


Q ss_pred             cChHHHHHHHHHHCCCCCcEEEEe
Q 006737          549 LGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       549 ~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                         ...+..++..++...+++++.
T Consensus       142 ---~~~~~~l~~~~~~~~~~~~vG  162 (459)
T 3upu_A          142 ---RKLFKILLSTIPPWCTIIGIG  162 (459)
T ss_dssp             ---HHHHHHHHHHSCTTCEEEEEE
T ss_pred             ---HHHHHHHHHhccCCCEEEEEC
Confidence               335666677777666666654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.67  E-value=9.6e-05  Score=84.42  Aligned_cols=67  Identities=19%  Similarity=0.286  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHHHHhCCCc-EEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLEGKD-AVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grD-vLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .+++-|.+|+..++..++ .||+||.|||||.+- ..++..+....          .++|+++||...+.++.+.+...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti-~~~I~~l~~~~----------~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTV-VEIILQAVKQG----------LKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHH-HHHHHHHHHTT----------CCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHH-HHHHHHHHhCC----------CeEEEEcCchHHHHHHHHHHHhc
Confidence            578999999999988775 589999999999863 34444444432          35999999999999988877543

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=97.67  E-value=0.00027  Score=82.88  Aligned_cols=70  Identities=20%  Similarity=0.306  Sum_probs=55.0

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      +..+++.|..|+..++.+.-++|.||.|||||.+. ..++..+....         +.++|+++||...+.++.+.+...
T Consensus       358 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i-~~~i~~l~~~~---------~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          358 FAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTS-ATIVYHLSKIH---------KDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHH-HHHHHHHHHHH---------CCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHH-HHHHHHHHhCC---------CCeEEEEcCcHHHHHHHHHHHHhh
Confidence            45789999999999988777899999999999763 33444444321         125999999999999998888764

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=97.63  E-value=0.00023  Score=83.38  Aligned_cols=70  Identities=14%  Similarity=0.199  Sum_probs=54.4

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          399 YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       399 ~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ...+++.|..|+..++.+.-++|.||+|||||.+. ..++..+....         +.++|+++||...+.++.+.+...
T Consensus       354 ~~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti-~~~i~~l~~~~---------~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          354 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQG---------NGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTTC---------SSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHcC---------CCcEEEEcCcHHHHHHHHHHHHHh
Confidence            45789999999999998888899999999999863 34444444321         135999999999999988777543

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=96.99  E-value=0.0041  Score=70.25  Aligned_cols=72  Identities=17%  Similarity=0.253  Sum_probs=53.6

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+++-|.+++..  ....++|.|+.|||||.+.+ .-+.++.....      .++-++|+|++|+..+.++.+.+..+.
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~-~ri~~l~~~~~------~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLV-HRIAWLMSVEN------CSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHH-HHHHHHHHTSC------CCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHH-HHHHHHHHhCC------CChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            4789999999973  35689999999999998643 33334443321      112359999999999999999998886


Q ss_pred             h
Q 006737          480 K  480 (633)
Q Consensus       480 ~  480 (633)
                      .
T Consensus        79 ~   79 (647)
T 3lfu_A           79 G   79 (647)
T ss_dssp             C
T ss_pred             c
Confidence            4

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=96.85  E-value=0.0053  Score=57.68  Aligned_cols=18  Identities=33%  Similarity=0.481  Sum_probs=16.0

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .|+.+++.||+|+|||..
T Consensus        37 ~g~~~~l~G~~G~GKTtL   54 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHL   54 (180)
T ss_dssp             GCCEEEECCSSSSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            478899999999999974

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=96.64  E-value=0.0085  Score=64.31  Aligned_cols=74  Identities=14%  Similarity=0.064  Sum_probs=56.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .++|+|...+..+...+-+++..+-+.|||.+...-++..+...         ++..+++++||++.|..+++.+..+..
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~---------~g~~v~~vA~t~~qA~~vf~~i~~mi~  233 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN---------KDKAVGILAHKGSMSAEVLDRTKQAIE  233 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS---------SSCEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC---------CCCeEEEEeCCHHHHHHHHHHHHHHHH
Confidence            68999999998775556789999999999987665555433321         134699999999999999988888876


Q ss_pred             cCC
Q 006737          481 NHD  483 (633)
Q Consensus       481 ~~~  483 (633)
                      ..+
T Consensus       234 ~~P  236 (385)
T 2o0j_A          234 LLP  236 (385)
T ss_dssp             HSC
T ss_pred             hCh
Confidence            544

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=96.49  E-value=0.025  Score=63.88  Aligned_cols=74  Identities=14%  Similarity=0.068  Sum_probs=57.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .++++|...+..+...+-+++..+-|+|||.+...-++-.+....         +..++++.|+++.|..++..+..++.
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~~---------~~~i~~va~t~~qA~~~~~~i~~~i~  233 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFNK---------DKAVGILAHKGSMSAEVLDRTKQAIE  233 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTSS---------SCEEEEEESSHHHHHHHHHHHHHHHT
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhCC---------CCeEEEEECCHHHHHHHHHHHHHHHH
Confidence            689999999987755677999999999999876554444443221         23699999999999999998888876


Q ss_pred             cCC
Q 006737          481 NHD  483 (633)
Q Consensus       481 ~~~  483 (633)
                      ..+
T Consensus       234 ~~p  236 (592)
T 3cpe_A          234 LLP  236 (592)
T ss_dssp             TSC
T ss_pred             hCh
Confidence            554

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=96.35  E-value=0.0065  Score=69.66  Aligned_cols=68  Identities=32%  Similarity=0.421  Sum_probs=51.3

Q ss_pred             CCCCCcHHHHHHHHHHhC----CC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHH
Q 006737          398 GYIQMTRVQEATLSACLE----GK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIA  472 (633)
Q Consensus       398 g~~~pt~iQ~~aIp~il~----gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~  472 (633)
                      +| .|++.|..+|..+..    |. ..++.+.||||||+++.- ++..+   ..          .+|||+|+..+|.|++
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~---~~----------~~lvv~~~~~~A~ql~   70 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEAL---GR----------PALVLAPNKILAAQLA   70 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH---TC----------CEEEEESSHHHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHh---CC----------CEEEEecCHHHHHHHH
Confidence            56 899999888876553    32 577889999999986432 22222   11          2899999999999999


Q ss_pred             HHHHHHHh
Q 006737          473 AEAIALLK  480 (633)
Q Consensus       473 ~~l~~l~~  480 (633)
                      ..+..++.
T Consensus        71 ~el~~~~~   78 (664)
T 1c4o_A           71 AEFRELFP   78 (664)
T ss_dssp             HHHHHHCT
T ss_pred             HHHHHHCC
Confidence            99999964

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.00  E-value=0.0051  Score=56.86  Aligned_cols=44  Identities=14%  Similarity=0.188  Sum_probs=26.8

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCC-CCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk-~~Q~IlfSATl~~e  578 (633)
                      +.++|||||++.+.... ...+..+++.+.. ...++++++..++.
T Consensus        83 ~~~lLilDE~~~~~~~~-~~~l~~li~~~~~~g~~~iiits~~~p~  127 (149)
T 2kjq_A           83 EAEYLAVDQVEKLGNEE-QALLFSIFNRFRNSGKGFLLLGSEYTPQ  127 (149)
T ss_dssp             GCSEEEEESTTCCCSHH-HHHHHHHHHHHHHHTCCEEEEEESSCTT
T ss_pred             CCCEEEEeCccccChHH-HHHHHHHHHHHHHcCCcEEEEECCCCHH
Confidence            46789999999866543 5556666654432 34435556665443

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=95.43  E-value=0.012  Score=64.13  Aligned_cols=43  Identities=33%  Similarity=0.388  Sum_probs=30.3

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      +=.++.|+.|+|||....     .+....           ..+|++||++++..+.+.+
T Consensus       162 ~v~~I~G~aGsGKTt~I~-----~~~~~~-----------~~lVlTpT~~aa~~l~~kl  204 (446)
T 3vkw_A          162 KVVLVDGVPGCGKTKEIL-----SRVNFE-----------EDLILVPGRQAAEMIRRRA  204 (446)
T ss_dssp             EEEEEEECTTSCHHHHHH-----HHCCTT-----------TCEEEESCHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHH-----HHhccC-----------CeEEEeCCHHHHHHHHHHh
Confidence            346789999999998421     121110           2689999999998877655

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=95.26  E-value=0.061  Score=55.29  Aligned_cols=43  Identities=16%  Similarity=0.301  Sum_probs=24.8

Q ss_pred             eeEEEEecccccCCc-ChHHHHHHHHHHC-CCCCcEEEEeccCChh
Q 006737          535 LKMLVLDEADHLLDL-GFRKDVENIVDCL-PRRRQSLLFSATMPKE  578 (633)
Q Consensus       535 l~~LVIDEAD~Lld~-gf~~~l~~Il~~l-pk~~Q~IlfSATl~~e  578 (633)
                      ..+|+|||+|.+... .....+..+++.+ ....+ ++++++.+..
T Consensus        99 ~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~-iii~~~~~~~  143 (324)
T 1l8q_A           99 VDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQ-IILASDRHPQ  143 (324)
T ss_dssp             CSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCE-EEEEESSCGG
T ss_pred             CCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCe-EEEEecCChH
Confidence            568999999998752 2334444555433 23344 5555565443

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=95.21  E-value=0.023  Score=64.80  Aligned_cols=81  Identities=14%  Similarity=0.118  Sum_probs=56.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .+++-|.+++...  +..++|.|+.|||||.+.+--+...+.....       ++-++|+|+.|+..|.++.+.+..+..
T Consensus         2 ~L~~~Q~~av~~~--~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~-------~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEFV--TGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-------QARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHCC--SSEEEECCCTTSCHHHHHHHHHHHHHHHHCC-------CGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhCC--CCCEEEEeCCCCChHHHHHHHHHHHHHhcCC-------CHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            4789999999763  6689999999999998644333333333221       123599999999999999999988754


Q ss_pred             cC--CCceEEEE
Q 006737          481 NH--DGIGVLTL  490 (633)
Q Consensus       481 ~~--~~i~v~~l  490 (633)
                      ..  .++.|..+
T Consensus        73 ~~~~~~~~v~Tf   84 (673)
T 1uaa_A           73 RKEARGLMISTF   84 (673)
T ss_dssp             TTTTTTSEEEEH
T ss_pred             cccccCCEEEeH
Confidence            32  23555544

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=95.03  E-value=0.011  Score=58.72  Aligned_cols=113  Identities=13%  Similarity=0.139  Sum_probs=58.7

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      .|.=++++|++|+|||.+.+ -++..+....          .+++|+.|...--   .  ...+....         | .
T Consensus        11 ~G~i~litG~mGsGKTT~ll-~~~~r~~~~g----------~kVli~~~~~d~r---~--~~~i~srl---------G-~   64 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELI-RRLHRLEYAD----------VKYLVFKPKIDTR---S--IRNIQSRT---------G-T   64 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHH-HHHHHHHHTT----------CCEEEEEECCCGG---G--CSSCCCCC---------C-C
T ss_pred             CcEEEEEECCCCCcHHHHHH-HHHHHHHhcC----------CEEEEEEeccCch---H--HHHHHHhc---------C-C
Confidence            35567889999999998643 3333333322          2488887754210   0  00001100         1 0


Q ss_pred             cchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          495 RFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ..           ..+-+.+...++..+...    ..-...++||||||+.+... ....+..+..   ...++|++.
T Consensus        65 ~~-----------~~~~~~~~~~i~~~i~~~----~~~~~~dvViIDEaQ~l~~~-~ve~l~~L~~---~gi~Vil~G  123 (223)
T 2b8t_A           65 SL-----------PSVEVESAPEILNYIMSN----SFNDETKVIGIDEVQFFDDR-ICEVANILAE---NGFVVIISG  123 (223)
T ss_dssp             SS-----------CCEEESSTHHHHHHHHST----TSCTTCCEEEECSGGGSCTH-HHHHHHHHHH---TTCEEEEEC
T ss_pred             Cc-----------cccccCCHHHHHHHHHHH----hhCCCCCEEEEecCccCcHH-HHHHHHHHHh---CCCeEEEEe
Confidence            00           133456666676666543    11235789999999976432 3333433333   255555544

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=95.01  E-value=0.13  Score=53.61  Aligned_cols=26  Identities=8%  Similarity=0.038  Sum_probs=18.8

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVL  442 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~  442 (633)
                      +.++++.||+|+|||++.- .++..+.
T Consensus        45 ~~~lli~GpPGTGKT~~v~-~v~~~L~   70 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLVN-DVMDELI   70 (318)
T ss_dssp             CCEEEEECCCSHHHHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            4589999999999998643 2444443

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.88  E-value=0.083  Score=50.37  Aligned_cols=39  Identities=23%  Similarity=0.270  Sum_probs=24.9

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      |+=.+++|+.|+|||...+ -++.......          .+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll-~~~~~~~~~g----------~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELL-SFVEIYKLGK----------KKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHH-HHHHHHHHTT----------CEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHH-HHHHHHHHCC----------CeEEEEeecc
Confidence            5567899999999998643 2333332221          2588888874

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=94.74  E-value=0.033  Score=53.65  Aligned_cols=18  Identities=6%  Similarity=0.025  Sum_probs=15.8

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .++.++++||+|+|||..
T Consensus        51 ~~~~~ll~G~~G~GKT~l   68 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHL   68 (242)
T ss_dssp             SCSEEEEECSTTSSHHHH
T ss_pred             CCCeEEEECCCCCCHHHH
Confidence            467899999999999974

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=94.67  E-value=0.053  Score=62.62  Aligned_cols=82  Identities=17%  Similarity=0.284  Sum_probs=57.5

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+++-|.+++..  ....++|.|..|||||.+..- -+.+++....      ..+-++|+|+.|+..|.++.+.+..+.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~-ri~~ll~~~~------~~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTH-RIAYLMAEKH------VAPWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHH-HHHHHHHTTC------CCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHH-HHHHHHHhcC------CCHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            4789999999976  356899999999999986433 3333433211      112358999999999999999988875


Q ss_pred             hcC-CCceEEEE
Q 006737          480 KNH-DGIGVLTL  490 (633)
Q Consensus       480 ~~~-~~i~v~~l  490 (633)
                      ... .++.+..+
T Consensus        81 ~~~~~~~~v~Tf   92 (724)
T 1pjr_A           81 GGAAEDVWISTF   92 (724)
T ss_dssp             GGGGTTSEEEEH
T ss_pred             cccccCcEEeeH
Confidence            422 24555544

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=94.44  E-value=0.094  Score=50.61  Aligned_cols=39  Identities=21%  Similarity=0.186  Sum_probs=25.4

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      |+=.+++++.|+|||.+.+ -++.......          .+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~ll-~~a~r~~~~g----------~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELI-RRIRRAKIAK----------QKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHH-HHHHHHHHTT----------CCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHHH-HHHHHHHHCC----------CEEEEEEecc
Confidence            5557889999999997643 3343333222          3589998873

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=94.38  E-value=0.15  Score=51.60  Aligned_cols=18  Identities=22%  Similarity=0.274  Sum_probs=15.3

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      +.+++++||+|+|||.+.
T Consensus        67 ~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            347999999999999753

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=94.34  E-value=0.16  Score=55.17  Aligned_cols=41  Identities=15%  Similarity=0.359  Sum_probs=25.3

Q ss_pred             CeeEEEEecccccCCc-ChHHHHHHHHHHC-CCCCcEEEEeccC
Q 006737          534 GLKMLVLDEADHLLDL-GFRKDVENIVDCL-PRRRQSLLFSATM  575 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~-gf~~~l~~Il~~l-pk~~Q~IlfSATl  575 (633)
                      ...+|||||+|.+... .....+..+++.+ ....++|+ +++.
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIi-tt~~  236 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVI-CSDR  236 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEE-EESS
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEE-EECC
Confidence            4568999999999863 2444555555543 33455555 4443

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=94.31  E-value=0.13  Score=51.31  Aligned_cols=45  Identities=27%  Similarity=0.451  Sum_probs=26.5

Q ss_pred             CeeEEEEecccccCCc-----ChHHH-HHHHHHHCC----CCCcEEEEeccCChh
Q 006737          534 GLKMLVLDEADHLLDL-----GFRKD-VENIVDCLP----RRRQSLLFSATMPKE  578 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~-----gf~~~-l~~Il~~lp----k~~Q~IlfSATl~~e  578 (633)
                      ...+|||||+|.|+..     .+... +..+...+.    ...+++++.+|-.++
T Consensus       124 ~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~  178 (272)
T 1d2n_A          124 QLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKD  178 (272)
T ss_dssp             SEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHH
T ss_pred             CCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChh
Confidence            4678999999998531     12222 233333333    345677777777664

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=94.17  E-value=0.053  Score=54.38  Aligned_cols=52  Identities=13%  Similarity=0.155  Sum_probs=31.1

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHH--HhCCCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSA--CLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~--il~grDvLv~ApTGSGKTla  432 (633)
                      .+|+++.-.+..++.|...- ..+ -.....+..  +...+.++++||+|+|||..
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~-~~~-~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~l   67 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVV-ELP-LKHPELFEKVGIEPPKGILLYGPPGTGKTLL   67 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHT-HHH-HHCHHHHHHHCCCCCSEEEEESSSSSSHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHH-HHH-hhCHHHHHhcCCCCCCeEEEECCCCCcHHHH
Confidence            45888877777777776531 000 000111111  23457899999999999974

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=94.02  E-value=0.13  Score=58.75  Aligned_cols=66  Identities=26%  Similarity=0.333  Sum_probs=48.1

Q ss_pred             CCcHHHHHHHHHHh----CCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACL----EGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEA  475 (633)
Q Consensus       401 ~pt~iQ~~aIp~il----~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l  475 (633)
                      .|+..|..+|..+.    .|. ..++.+.||||||++..- ++..+   ..          .+|||+|+..+|.|++..+
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~---~~----------~~lvv~~~~~~A~~l~~el   77 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEV---NK----------PTLVIAHNKTLAGQLYSEF   77 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHH---CC----------CEEEECSSHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHh---CC----------CEEEEECCHHHHHHHHHHH
Confidence            67788887776544    343 477889999999985332 22221   11          2899999999999999999


Q ss_pred             HHHHh
Q 006737          476 IALLK  480 (633)
Q Consensus       476 ~~l~~  480 (633)
                      ..++.
T Consensus        78 ~~~~~   82 (661)
T 2d7d_A           78 KEFFP   82 (661)
T ss_dssp             HHHCT
T ss_pred             HHHcC
Confidence            99964

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=93.91  E-value=0.07  Score=65.37  Aligned_cols=73  Identities=19%  Similarity=0.226  Sum_probs=53.5

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      ..+|+-|.++|..-  +++++|.|..|||||.+.+-=++..+.....     ....-++|+|++|+..|.++.+.+...+
T Consensus         9 ~~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~-----~~~~~~il~~Tft~~aa~e~~~ri~~~l   81 (1232)
T 3u4q_A            9 STWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEEN-----PIDVDRLLVVTFTNASAAEMKHRIAEAL   81 (1232)
T ss_dssp             -CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSSS-----CCCGGGEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCCC-----CCCccceEEEeccHHHHHHHHHHHHHHH
Confidence            36899999999864  7899999999999998654444444433210     1122359999999999999998887754

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=93.80  E-value=0.72  Score=43.04  Aligned_cols=39  Identities=21%  Similarity=0.280  Sum_probs=25.8

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ..-.+|||||+|.+... ....+..++...+....+|+.|
T Consensus       101 ~~~~vliiDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~~  139 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-AQAALRRTMEMYSKSCRFILSC  139 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             cCceEEEEeChhhcCHH-HHHHHHHHHHhcCCCCeEEEEe
Confidence            34568999999998643 4556666677665555555544

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=93.49  E-value=0.28  Score=50.08  Aligned_cols=39  Identities=13%  Similarity=0.189  Sum_probs=26.1

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+|||||+|.+........+..+++..+...++|+.+
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~  143 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITA  143 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEE
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            577899999999862234555666666655566666633

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=93.41  E-value=0.63  Score=47.81  Aligned_cols=49  Identities=16%  Similarity=0.158  Sum_probs=30.7

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh-----CCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL-----EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il-----~grDvLv~ApTGSGKTla  432 (633)
                      ..+|+++.-...+++.|...=.   .+   ...|.+.     ..+.++++||+|+|||+.
T Consensus        14 ~~~~~di~G~~~~~~~l~~~i~---~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~l   67 (322)
T 3eie_A           14 NVKWEDVAGLEGAKEALKEAVI---LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYL   67 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHTH---HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHH
T ss_pred             CCCHHHhcChHHHHHHHHHHHH---HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHH
Confidence            3468888777777777765310   00   0111111     135799999999999974

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=93.21  E-value=0.094  Score=59.98  Aligned_cols=115  Identities=19%  Similarity=0.176  Sum_probs=73.5

Q ss_pred             CCcHHHHHHHHHHhC--CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACLE--GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~--grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      .+|.-|.+++..++.  ..-.++.|+-|.|||.+.-+.+ ..+ .   .         .++|.+|+.+-+..+.+.    
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~-a~~-~---~---------~~~vtAP~~~a~~~l~~~----  236 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLI-SRI-A---G---------RAIVTAPAKASTDVLAQF----  236 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHH-HHS-S---S---------CEEEECSSCCSCHHHHHH----
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHH-HHH-H---h---------CcEEECCCHHHHHHHHHH----
Confidence            678999999988876  3357899999999996543322 221 1   1         268999999877654322    


Q ss_pred             HhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHH
Q 006737          479 LKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENI  558 (633)
Q Consensus       479 ~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~I  558 (633)
                      ...                           .|-+..|..+..          .+...++||||||=.+-    .+.+..+
T Consensus       237 ~~~---------------------------~i~~~~Pd~~~~----------~~~~~dlliVDEAAaIp----~pll~~l  275 (671)
T 2zpa_A          237 AGE---------------------------KFRFIAPDALLA----------SDEQADWLVVDEAAAIP----APLLHQL  275 (671)
T ss_dssp             HGG---------------------------GCCBCCHHHHHH----------SCCCCSEEEEETGGGSC----HHHHHHH
T ss_pred             hhC---------------------------CeEEeCchhhhh----------CcccCCEEEEEchhcCC----HHHHHHH
Confidence            210                           133445654321          12357899999997765    4466666


Q ss_pred             HHHCCCCCcEEEEeccCChh
Q 006737          559 VDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       559 l~~lpk~~Q~IlfSATl~~e  578 (633)
                      +...    ..|+||.|+.--
T Consensus       276 l~~~----~~v~~~tTv~GY  291 (671)
T 2zpa_A          276 VSRF----PRTLLTTTVQGY  291 (671)
T ss_dssp             HTTS----SEEEEEEEBSST
T ss_pred             HhhC----CeEEEEecCCcC
Confidence            6533    368888887543

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=93.21  E-value=0.17  Score=49.90  Aligned_cols=40  Identities=18%  Similarity=0.160  Sum_probs=24.1

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHH
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRE  466 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTRe  466 (633)
                      |+=.+++++-|+|||.+.+- .+......          +.+++|+.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~-~a~r~~~~----------g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIR-RVRRTQFA----------KQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHH-HHHHHHHT----------TCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHH-HHHHHHHC----------CCEEEEEEeccC
Confidence            44456788889999976433 33333222          235899988764

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=93.19  E-value=0.24  Score=51.52  Aligned_cols=17  Identities=29%  Similarity=0.354  Sum_probs=14.7

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      .+.++++||+|+|||..
T Consensus        45 ~~~vll~G~~G~GKT~l   61 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFV   61 (384)
T ss_dssp             CCEEEEEECTTSSHHHH
T ss_pred             CCcEEEECCCCCCHHHH
Confidence            35799999999999975

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=93.12  E-value=0.44  Score=49.30  Aligned_cols=49  Identities=16%  Similarity=0.153  Sum_probs=30.1

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHh-----CCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACL-----EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il-----~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++++-.+.+.+.|.+.-.   .|+   ..|.++     ..+.++++||+|+|||+.
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~---~p~---~~~~~~~~~~~~~~~iLL~GppGtGKT~l   61 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVI---LPI---KFPHLFTGKRTPWRGILLFGPPGTGKSYL   61 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHH---HHH---HCGGGSCTTCCCCSEEEEESSSSSCHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH---HHH---hCHHHHhCCCCCCceEEEECCCCccHHHH
Confidence            3568888777777777654200   000   011222     236799999999999974

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=93.04  E-value=0.19  Score=48.91  Aligned_cols=38  Identities=21%  Similarity=0.215  Sum_probs=25.5

Q ss_pred             CCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEccc
Q 006737          416 GKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPT  464 (633)
Q Consensus       416 grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPT  464 (633)
                      |+=.++.++.|+|||.. +|-.+.......          .+++|+.|.
T Consensus        20 g~l~fiyG~MgsGKTt~-Ll~~i~n~~~~~----------~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTE-LMRRVRRFQIAQ----------YKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHH-HHHHHHHHHHTT----------CCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHH-HHHHHHHHHHcC----------CeEEEEccc
Confidence            56678999999999953 444444433322          358898887

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=92.94  E-value=1.6  Score=39.47  Aligned_cols=17  Identities=24%  Similarity=0.460  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      ...++++|++|+|||..
T Consensus        43 ~~~~ll~G~~G~GKT~l   59 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAI   59 (195)
T ss_dssp             SCEEEEECCTTSCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            35799999999999975

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=92.90  E-value=0.26  Score=47.68  Aligned_cols=19  Identities=32%  Similarity=0.415  Sum_probs=16.1

Q ss_pred             hCCCcEEEEccCCCCchhh
Q 006737          414 LEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTla  432 (633)
                      ..|.-+++.|++|+|||..
T Consensus        21 ~~G~~~~i~G~~GsGKTtl   39 (247)
T 2dr3_A           21 PERNVVLLSGGPGTGKTIF   39 (247)
T ss_dssp             ETTCEEEEEECTTSSHHHH
T ss_pred             CCCcEEEEECCCCCCHHHH
Confidence            3567889999999999975

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=92.85  E-value=0.29  Score=50.57  Aligned_cols=18  Identities=33%  Similarity=0.490  Sum_probs=15.5

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .+..++++||+|+|||..
T Consensus        43 ~~~~vll~G~~G~GKT~l   60 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAV   60 (387)
T ss_dssp             CCCCEEECBCTTSSHHHH
T ss_pred             CCCcEEEECCCCCCHHHH
Confidence            356899999999999975

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=92.85  E-value=0.2  Score=52.01  Aligned_cols=15  Identities=33%  Similarity=0.649  Sum_probs=13.8

Q ss_pred             cEEEEccCCCCchhh
Q 006737          418 DAVVKAKTGTGKSIA  432 (633)
Q Consensus       418 DvLv~ApTGSGKTla  432 (633)
                      .++++||+|+|||..
T Consensus        46 ~~li~G~~G~GKTtl   60 (389)
T 1fnn_A           46 RATLLGRPGTGKTVT   60 (389)
T ss_dssp             EEEEECCTTSSHHHH
T ss_pred             eEEEECCCCCCHHHH
Confidence            799999999999984

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=92.67  E-value=0.41  Score=45.17  Aligned_cols=16  Identities=25%  Similarity=0.372  Sum_probs=14.7

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      +.++++||+|+|||..
T Consensus        55 ~~~~l~G~~GtGKT~l   70 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYL   70 (202)
T ss_dssp             CEEEEECSTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            7899999999999984

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=92.48  E-value=0.33  Score=49.56  Aligned_cols=52  Identities=15%  Similarity=0.158  Sum_probs=30.5

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHH-HHHHH--HhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQE-ATLSA--CLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~-~aIp~--il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++++-...+.+.|...- .  .++.. ..+..  +..++.++++||+|+|||+.
T Consensus        11 ~~~~~di~G~~~~~~~l~~~v-~--~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~l   65 (301)
T 3cf0_A           11 QVTWEDIGGLEDVKRELQELV-Q--YPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLL   65 (301)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHH-H--HHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHH-H--HHhhCHHHHHHcCCCCCceEEEECCCCcCHHHH
Confidence            356888876676666665430 0  00000 00111  23467899999999999984

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=92.34  E-value=1.9  Score=40.45  Aligned_cols=38  Identities=18%  Similarity=0.208  Sum_probs=21.9

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      .-.+|||||+|.+.. .....+..++...+....+|+.|
T Consensus       126 ~~~vlviDe~~~l~~-~~~~~l~~~l~~~~~~~~~i~~t  163 (250)
T 1njg_A          126 RFKVYLIDEVHMLSR-HSFNALLKTLEEPPEHVKFLLAT  163 (250)
T ss_dssp             SSEEEEEETGGGSCH-HHHHHHHHHHHSCCTTEEEEEEE
T ss_pred             CceEEEEECcccccH-HHHHHHHHHHhcCCCceEEEEEe
Confidence            346899999999753 23444455555444444444433

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=92.29  E-value=0.64  Score=42.70  Aligned_cols=72  Identities=19%  Similarity=0.290  Sum_probs=53.8

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++..+..+++.+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..    .+++.
T Consensus        37 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~----Gld~~  102 (163)
T 2hjv_A           37 SCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----VAAR----GIDIE  102 (163)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GGTT----TCCCS
T ss_pred             cEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhhc----CCchh
Confidence            5999999999999998887765     67889999987655433   345567789999993     2233    36778


Q ss_pred             CeeEEEEec
Q 006737          534 GLKMLVLDE  542 (633)
Q Consensus       534 ~l~~LVIDE  542 (633)
                      .+.+||.-.
T Consensus       103 ~~~~Vi~~~  111 (163)
T 2hjv_A          103 NISLVINYD  111 (163)
T ss_dssp             CCSEEEESS
T ss_pred             cCCEEEEeC
Confidence            888888643

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=92.16  E-value=0.68  Score=47.91  Aligned_cols=31  Identities=13%  Similarity=0.213  Sum_probs=21.6

Q ss_pred             cHHHHHHHHHH----hCCC---cEEEEccCCCCchhhh
Q 006737          403 TRVQEATLSAC----LEGK---DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       403 t~iQ~~aIp~i----l~gr---DvLv~ApTGSGKTlay  433 (633)
                      .|+|..++..+    .+|+   -+++.||.|+|||.+.
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a   41 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH
T ss_pred             CCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH
Confidence            46666665443    3444   4899999999999754

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=91.98  E-value=0.58  Score=50.82  Aligned_cols=46  Identities=13%  Similarity=0.283  Sum_probs=33.9

Q ss_pred             CCeeEEEEecccccC---CcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLL---DLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Ll---d~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ...++||||.+-++.   +..+...+..++..+.+..-+++++|+...+
T Consensus       178 ~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~  226 (433)
T 3kl4_A          178 NKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQK  226 (433)
T ss_dssp             TTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGG
T ss_pred             cCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchH
Confidence            467899999998653   3446777778877777666678888887654

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=91.90  E-value=0.37  Score=49.67  Aligned_cols=41  Identities=10%  Similarity=0.239  Sum_probs=28.8

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ...++|||||+|. ++......+..+++..+....+|+.|-.
T Consensus       133 ~~~~vlilDE~~~-L~~~~~~~L~~~le~~~~~~~~Il~t~~  173 (354)
T 1sxj_E          133 HRYKCVIINEANS-LTKDAQAALRRTMEKYSKNIRLIMVCDS  173 (354)
T ss_dssp             -CCEEEEEECTTS-SCHHHHHHHHHHHHHSTTTEEEEEEESC
T ss_pred             CCCeEEEEeCccc-cCHHHHHHHHHHHHhhcCCCEEEEEeCC
Confidence            3567999999999 5555667777888877666555555443

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens}

Probab=91.84  E-value=0.5  Score=43.90  Aligned_cols=73  Identities=21%  Similarity=0.270  Sum_probs=54.1

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.++++..|..++..+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..    .+++
T Consensus        35 ~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~~~----Gid~  100 (175)
T 2rb4_A           35 GQAIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN-----VCAR----GIDV  100 (175)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC-----SCCT----TTCC
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec-----chhc----CCCc
Confidence            36999999999999988777653     67899999987755433   345567789999993     2222    3678


Q ss_pred             CCeeEEEEec
Q 006737          533 MGLKMLVLDE  542 (633)
Q Consensus       533 s~l~~LVIDE  542 (633)
                      ..+.+||.-.
T Consensus       101 ~~~~~Vi~~d  110 (175)
T 2rb4_A          101 KQVTIVVNFD  110 (175)
T ss_dssp             TTEEEEEESS
T ss_pred             ccCCEEEEeC
Confidence            8899888533

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=91.78  E-value=0.48  Score=43.23  Aligned_cols=17  Identities=18%  Similarity=0.440  Sum_probs=14.9

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      ...++++||+|+|||..
T Consensus        43 ~~~vll~G~~G~GKT~l   59 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAI   59 (187)
T ss_dssp             SCEEEEESCGGGCHHHH
T ss_pred             CCceEEECCCCCCHHHH
Confidence            45899999999999974

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=91.63  E-value=1.2  Score=42.37  Aligned_cols=71  Identities=17%  Similarity=0.240  Sum_probs=54.3

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++..+..++..+...     ++.+..++|+.......   ..+..+.++|||+|     +.+..+    +++.
T Consensus        56 ~~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT-----~~~~~G----ldi~  121 (191)
T 2p6n_A           56 PVLIFAEKKADVDAIHEYLLLK-----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT-----DVASKG----LDFP  121 (191)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC-----HHHHTT----CCCC
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc-----CchhcC----CCcc
Confidence            5999999999999998888765     67889999987755433   34455678999999     344444    6778


Q ss_pred             CeeEEEEe
Q 006737          534 GLKMLVLD  541 (633)
Q Consensus       534 ~l~~LVID  541 (633)
                      .+.+||.=
T Consensus       122 ~v~~VI~~  129 (191)
T 2p6n_A          122 AIQHVINY  129 (191)
T ss_dssp             CCSEEEES
T ss_pred             cCCEEEEe
Confidence            88888873

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=91.57  E-value=0.26  Score=50.78  Aligned_cols=18  Identities=28%  Similarity=0.338  Sum_probs=15.7

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      ++++++.||+|+|||...
T Consensus       152 ~~~lll~G~~GtGKT~La  169 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLL  169 (308)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            579999999999999743

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=91.55  E-value=0.41  Score=50.20  Aligned_cols=18  Identities=28%  Similarity=0.311  Sum_probs=15.2

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      .+.++++||+|+|||+..
T Consensus        84 ~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           84 TSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCCEEEECSTTSCHHHHH
T ss_pred             CceEEEECCCCCcHHHHH
Confidence            357999999999999843

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=91.24  E-value=2.1  Score=41.64  Aligned_cols=51  Identities=14%  Similarity=0.083  Sum_probs=27.3

Q ss_pred             cCccccCCCHHHHHHHHHcC--CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAAG--YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g--~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      .+|+++.-.+.+.+.|.+.-  +..+..+...   .+...+.++++||+|+|||..
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~---g~~~~~~vll~G~~GtGKT~l   55 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQL---GAKVPKGALLLGPPGCGKTLL   55 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHc---CCCCCceEEEECCCCCCHHHH
Confidence            35777765566666665420  1111111110   012346799999999999974

>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer, ATP-binding, helicase, hydrolase, nucleotide-binding; 2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A

Probab=91.22  E-value=0.94  Score=43.70  Aligned_cols=70  Identities=17%  Similarity=0.235  Sum_probs=53.4

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++.-+..++..+...     ++.+..++|+.......   ..+..+..+|||||.     .+..    .+++.
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~~----Gidi~   98 (212)
T 3eaq_A           33 RAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----VAAR----GLDIP   98 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----TTTC----SSSCC
T ss_pred             eEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----hhhc----CCCCc
Confidence            5999999999999998888775     67889999998765543   345567789999993     2333    36778


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      .+.+||.
T Consensus        99 ~v~~Vi~  105 (212)
T 3eaq_A           99 QVDLVVH  105 (212)
T ss_dssp             CBSEEEE
T ss_pred             cCcEEEE
Confidence            8888774

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=91.18  E-value=0.42  Score=45.58  Aligned_cols=18  Identities=33%  Similarity=0.475  Sum_probs=15.4

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .|.-+++.+++|+|||..
T Consensus        22 ~G~~~~i~G~~GsGKTtl   39 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIF   39 (235)
T ss_dssp             TTCEEEEECSTTSSHHHH
T ss_pred             CCCEEEEEcCCCCCHHHH
Confidence            467789999999999974

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=91.01  E-value=1.5  Score=45.00  Aligned_cols=17  Identities=29%  Similarity=0.438  Sum_probs=15.1

Q ss_pred             CCcEEEEccCCCCchhh
Q 006737          416 GKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv~ApTGSGKTla  432 (633)
                      +..+++.||+|+|||..
T Consensus        45 ~~~vli~G~~G~GKTtl   61 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAV   61 (386)
T ss_dssp             CCCEEEEECTTSSHHHH
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            56899999999999984

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=90.94  E-value=0.4  Score=52.03  Aligned_cols=28  Identities=21%  Similarity=0.224  Sum_probs=19.4

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVL  442 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~  442 (633)
                      ..|.-+++.|++|+|||.. ++-+...+.
T Consensus       201 ~~G~liiI~G~pG~GKTtl-~l~ia~~~~  228 (454)
T 2r6a_A          201 QRSDLIIVAARPSVGKTAF-ALNIAQNVA  228 (454)
T ss_dssp             CTTCEEEEECCTTSCHHHH-HHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH-HHHHHHHHH
Confidence            3567789999999999974 333444343

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.93  E-value=0.57  Score=50.45  Aligned_cols=52  Identities=17%  Similarity=0.203  Sum_probs=31.3

Q ss_pred             ccCccccCCCHHHHHHHHHcC---CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAG---YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g---~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++.+=-+...+.|.+.=   +..|.-++..-   +..-+-+|+.||+|+|||+.
T Consensus       144 ~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          144 DSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLL  198 (405)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHH
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHH
Confidence            456999876666666666530   11111111111   11236899999999999984

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=90.87  E-value=1  Score=41.33  Aligned_cols=72  Identities=13%  Similarity=0.254  Sum_probs=53.3

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++..+..++..+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..    .+++.
T Consensus        32 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~----G~d~~   97 (165)
T 1fuk_A           32 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLAR----GIDVQ   97 (165)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GGTT----TCCCC
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----hhhc----CCCcc
Confidence            5999999999999988877664     67888999987755433   345567789999993     2233    36777


Q ss_pred             CeeEEEEec
Q 006737          534 GLKMLVLDE  542 (633)
Q Consensus       534 ~l~~LVIDE  542 (633)
                      .+.+||.-.
T Consensus        98 ~~~~Vi~~~  106 (165)
T 1fuk_A           98 QVSLVINYD  106 (165)
T ss_dssp             SCSEEEESS
T ss_pred             cCCEEEEeC
Confidence            888887743

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=90.46  E-value=1.6  Score=43.94  Aligned_cols=38  Identities=21%  Similarity=0.329  Sum_probs=25.2

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEE
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLF  571 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~Ilf  571 (633)
                      ..-.+|||||+|.+... ....+..+++..+....+|+.
T Consensus       109 ~~~~vliiDe~~~l~~~-~~~~L~~~le~~~~~~~~i~~  146 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILS  146 (327)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEE
T ss_pred             CCCeEEEEeCCCcCCHH-HHHHHHHHHHhcCCCCeEEEE
Confidence            35678999999998643 345566666666555555554

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=90.29  E-value=0.43  Score=51.59  Aligned_cols=28  Identities=18%  Similarity=0.218  Sum_probs=19.2

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVL  442 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~  442 (633)
                      ..|.-+++.|++|+|||.. ++-+...+.
T Consensus       198 ~~G~l~ii~G~pg~GKT~l-al~ia~~~a  225 (444)
T 2q6t_A          198 GPGSLNIIAARPAMGKTAF-ALTIAQNAA  225 (444)
T ss_dssp             CTTCEEEEEECTTSCHHHH-HHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHH-HHHHHHHHH
Confidence            3456789999999999964 444444443

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=90.16  E-value=0.87  Score=48.08  Aligned_cols=44  Identities=20%  Similarity=0.304  Sum_probs=28.2

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHH---------hCCCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSAC---------LEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~i---------l~grDvLv~ApTGSGKTla  432 (633)
                      .+|+++.-...+++.|...-          .++..         ...+.+|++||+|+|||++
T Consensus       112 ~~~~~iiG~~~~~~~l~~~~----------~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~l  164 (389)
T 3vfd_A          112 VKFDDIAGQDLAKQALQEIV----------ILPSLRPELFTGLRAPARGLLLFGPPGNGKTML  164 (389)
T ss_dssp             CCGGGSCSCHHHHHHHHHHT----------HHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHH
T ss_pred             CChHHhCCHHHHHHHHHHHH----------HHhccCHHHhcccCCCCceEEEECCCCCCHHHH
Confidence            45777765666666665421          11111         1247899999999999974

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=90.11  E-value=0.68  Score=50.99  Aligned_cols=43  Identities=21%  Similarity=0.384  Sum_probs=29.7

Q ss_pred             eEEEEecccccCCc-----C-----hHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          536 KMLVLDEADHLLDL-----G-----FRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       536 ~~LVIDEAD~Lld~-----g-----f~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+|+|||+|.|...     +     ....+..+++.+.....++++.||-.+.
T Consensus       299 ~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~~~  351 (489)
T 3hu3_A          299 AIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPN  351 (489)
T ss_dssp             EEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESCGG
T ss_pred             cEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCCcc
Confidence            57999999988742     1     2344555666666667788888887664

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.07  E-value=0.72  Score=50.52  Aligned_cols=52  Identities=17%  Similarity=0.217  Sum_probs=32.1

Q ss_pred             ccCccccCCCHHHHHHHHHcC---CCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAG---YIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g---~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++.+--+.+.+.|.+.=   +..|.-++..-   +.--+-+|++||+|+|||+.
T Consensus       205 ~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlL  259 (467)
T 4b4t_H          205 DVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLC  259 (467)
T ss_dssp             SCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHH
Confidence            457999987777777776531   11111111110   12346899999999999974

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=89.93  E-value=0.65  Score=47.53  Aligned_cols=38  Identities=18%  Similarity=0.270  Sum_probs=25.5

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+|||||+|.+... ....+..+++..+....+|+.+
T Consensus       133 ~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~  170 (353)
T 1sxj_D          133 PYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLIC  170 (353)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEe
Confidence            4578999999998643 3455666677666555555543

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=89.87  E-value=0.67  Score=46.23  Aligned_cols=40  Identities=18%  Similarity=0.201  Sum_probs=25.1

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      .|+=.+++|+-|+|||.+.+- .+......          +.+++|+.|..
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~-~~~r~~~~----------g~kvli~kp~~   57 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMR-RVRRFQIA----------QYKCLVIKYAK   57 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHH-HHHHHHTT----------TCCEEEEEETT
T ss_pred             ceEEEEEECCCCCcHHHHHHH-HHHHHHHC----------CCeEEEEeecC
Confidence            356667888889999975333 33222222          23588888875

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=89.48  E-value=0.8  Score=45.96  Aligned_cols=48  Identities=13%  Similarity=0.124  Sum_probs=29.0

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHH-----hCCCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSAC-----LEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~i-----l~grDvLv~ApTGSGKTla  432 (633)
                      .+|+++.-...+.+.|...-.   .+.   ..|.+     ...+.+++.||+|+|||+.
T Consensus        18 ~~~~~i~G~~~~~~~l~~~i~---~~~---~~~~~~~~~~~~~~~vll~Gp~GtGKT~l   70 (297)
T 3b9p_A           18 VEWTDIAGQDVAKQALQEMVI---LPS---VRPELFTGLRAPAKGLLLFGPPGNGKTLL   70 (297)
T ss_dssp             CCGGGSCCCHHHHHHHHHHTH---HHH---HCGGGSCGGGCCCSEEEEESSSSSCHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHH---hhh---hCHHHHhcCCCCCCeEEEECcCCCCHHHH
Confidence            457887666777766654310   000   00111     1357899999999999974

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=89.46  E-value=2  Score=47.26  Aligned_cols=41  Identities=12%  Similarity=0.105  Sum_probs=28.0

Q ss_pred             CeeEEEEecccccCCc--ChHHHHHHHHHHCCCCCcEEEEeccCC
Q 006737          534 GLKMLVLDEADHLLDL--GFRKDVENIVDCLPRRRQSLLFSATMP  576 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~--gf~~~l~~Il~~lpk~~Q~IlfSATl~  576 (633)
                      .-.+|||||+|.|...  +....+..++...  ...+|+.+++..
T Consensus       148 ~~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~~  190 (516)
T 1sxj_A          148 KHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNERN  190 (516)
T ss_dssp             TSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCTT
T ss_pred             CCeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCCC
Confidence            4568999999999753  3445666666553  456788777654

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.38  E-value=0.29  Score=53.27  Aligned_cols=52  Identities=19%  Similarity=0.310  Sum_probs=33.1

Q ss_pred             ccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++.+--+.+.+.|.+.   -+..|.-++..-+   -.-+-+|++||+|+|||+.
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHH
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHH
Confidence            45699998878777777653   1122222222211   1246899999999999974

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=89.16  E-value=1.2  Score=41.46  Aligned_cols=72  Identities=13%  Similarity=0.128  Sum_probs=53.3

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++..+..++..+...     ++.+..++|+.......   ..+..+...|||+|.-     +..    .+++.
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~-----~~~----Gldi~   98 (172)
T 1t5i_A           33 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----FGR----GMDIE   98 (172)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-----CST----TCCGG
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc-----hhc----Ccchh
Confidence            5999999999999988887764     67888999987655433   3455677899999942     222    36677


Q ss_pred             CeeEEEEec
Q 006737          534 GLKMLVLDE  542 (633)
Q Consensus       534 ~l~~LVIDE  542 (633)
                      .+.+||.-+
T Consensus        99 ~~~~Vi~~d  107 (172)
T 1t5i_A           99 RVNIAFNYD  107 (172)
T ss_dssp             GCSEEEESS
T ss_pred             hCCEEEEEC
Confidence            888888633

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=89.08  E-value=0.7  Score=47.34  Aligned_cols=16  Identities=19%  Similarity=0.364  Sum_probs=14.5

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      ..++++||+|+|||+.
T Consensus        56 ~~vll~G~~GtGKT~l   71 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTL   71 (338)
T ss_dssp             CCEEEECSTTSSHHHH
T ss_pred             CeEEEECcCCCCHHHH
Confidence            5899999999999974

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=88.91  E-value=0.34  Score=47.86  Aligned_cols=99  Identities=16%  Similarity=0.230  Sum_probs=51.1

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      .|.=.+++++-|+|||... +-.+.......          .+++|+.|...--.-    ...+.... ++..       
T Consensus        27 ~G~I~vitG~M~sGKTT~L-lr~~~r~~~~g----------~kvli~kp~~D~R~~----~~~I~Sr~-G~~~-------   83 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEEL-IRRLRRGIYAK----------QKVVVFKPAIDDRYH----KEKVVSHN-GNAI-------   83 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHH-HHHHHHHHHTT----------CCEEEEEEC---------------CBT-TBCC-------
T ss_pred             CceEEEEECCCCCCHHHHH-HHHHHHHHHcC----------CceEEEEeccCCcch----hhhHHHhc-CCce-------
Confidence            3556788999999999753 33344333322          358999886532110    01111111 1111       


Q ss_pred             cchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHH
Q 006737          495 RFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV  559 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il  559 (633)
                                   .-+.|..+.-|..++         ...+.+|+||||+.+.+ ....++..+.
T Consensus        84 -------------~a~~v~~~~di~~~i---------~~~~dvV~IDEaQFf~~-~~v~~l~~la  125 (219)
T 3e2i_A           84 -------------EAINISKASEIMTHD---------LTNVDVIGIDEVQFFDD-EIVSIVEKLS  125 (219)
T ss_dssp             -------------EEEEESSGGGGGGSC---------CTTCSEEEECCGGGSCT-HHHHHHHHHH
T ss_pred             -------------eeEEeCCHHHHHHHH---------hcCCCEEEEechhcCCH-HHHHHHHHHH
Confidence                         124444444443222         13678999999998764 3556666665

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.82  E-value=0.63  Score=50.61  Aligned_cols=52  Identities=21%  Similarity=0.213  Sum_probs=30.2

Q ss_pred             ccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++.+--+...+.|.+.   -+..|.-++..-   +.--+-+|++||+|+|||+.
T Consensus       177 ~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g---~~~prGvLL~GPPGtGKTll  231 (437)
T 4b4t_L          177 EITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG---IKPPKGVLLYGPPGTGKTLL  231 (437)
T ss_dssp             SSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTSSHHHH
T ss_pred             CCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCeEEEECCCCCcHHHH
Confidence            45689987666666666542   011111111110   11236899999999999984

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=88.78  E-value=2.6  Score=43.24  Aligned_cols=40  Identities=18%  Similarity=0.189  Sum_probs=24.0

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEecc
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSAT  574 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSAT  574 (633)
                      ..-.+|||||+|.+... ....+..+++..+....+ +++++
T Consensus       118 ~~~~vliiDe~~~l~~~-~~~~Ll~~le~~~~~~~~-Il~~~  157 (373)
T 1jr3_A          118 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKF-LLATT  157 (373)
T ss_dssp             SSSEEEEEECGGGSCHH-HHHHHHHHHHSCCSSEEE-EEEES
T ss_pred             CCeEEEEEECcchhcHH-HHHHHHHHHhcCCCceEE-EEEeC
Confidence            45678999999998643 344555555554444433 44444

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=87.88  E-value=2.1  Score=43.95  Aligned_cols=53  Identities=11%  Similarity=0.004  Sum_probs=30.6

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIAL  478 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l  478 (633)
                      ..|.-+++.|++|+|||.. ++-+...+....          -.++|++-- +-..|+...+...
T Consensus        66 ~~G~l~li~G~pG~GKTtl-~l~ia~~~a~~g----------~~vl~~slE-~s~~~l~~R~~~~  118 (315)
T 3bh0_A           66 KRRNFVLIAARPSMGKTAF-ALKQAKNMSDND----------DVVNLHSLE-MGKKENIKRLIVT  118 (315)
T ss_dssp             CTTCEEEEECCTTSSHHHH-HHHHHHHHHTTT----------CEEEEEESS-SCHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHH-HHHHHHHHHHcC----------CeEEEEECC-CCHHHHHHHHHHH
Confidence            4567789999999999963 333333333221          247776533 4445555555443

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=87.87  E-value=2.7  Score=46.09  Aligned_cols=77  Identities=17%  Similarity=0.216  Sum_probs=58.1

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.++|+.-|..++..+...+.  .++.+..++|+.......   ..+..+..+|||||.     .+..    .+++
T Consensus       340 ~~~iVF~~s~~~~~~l~~~L~~~~~--~~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~~~----GiDi  408 (563)
T 3i5x_A          340 YKAIIFAPTVKFTSFLCSILKNEFK--KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGAR----GMDF  408 (563)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHHHT--TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGTS----SCCC
T ss_pred             CcEEEEcCcHHHHHHHHHHHHHhcc--CCceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc-----hhhc----CCCc
Confidence            3699999999999999999888754  267888999987755433   445567789999994     3333    3778


Q ss_pred             CCeeEEEEecc
Q 006737          533 MGLKMLVLDEA  543 (633)
Q Consensus       533 s~l~~LVIDEA  543 (633)
                      .++.+||.-..
T Consensus       409 p~v~~VI~~~~  419 (563)
T 3i5x_A          409 PNVHEVLQIGV  419 (563)
T ss_dssp             TTCCEEEEESC
T ss_pred             ccCCEEEEECC
Confidence            88998886554

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=87.72  E-value=1.3  Score=47.90  Aligned_cols=52  Identities=15%  Similarity=0.099  Sum_probs=29.6

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHH-HH-HHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEA-TL-SACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~-aI-p~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|+++.-...+.+.|...-.   .|++.. .+ ......+.+|++||+|+|||+.
T Consensus       130 ~~~~~di~G~~~~k~~l~~~v~---~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~l  183 (444)
T 2zan_A          130 NVKWSDVAGLEGAKEALKEAVI---LPIKFPHLFTGKRTPWRGILLFGPPGTGKSYL  183 (444)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHT---HHHHCTTTTSGGGCCCSEEEEECSTTSSHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH---HHhhCHHHhhccCCCCceEEEECCCCCCHHHH
Confidence            3568888766677666654210   000000 00 0012346899999999999974

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=87.65  E-value=0.87  Score=43.00  Aligned_cols=70  Identities=17%  Similarity=0.210  Sum_probs=45.1

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++.-+..++..+...     ++.+..++|+......   ...+..+...|||+|.     .+..+    +++.
T Consensus        48 k~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~~G----ldi~  113 (185)
T 2jgn_A           48 LTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAARG----LDIS  113 (185)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSEEEEEC---------------CCC
T ss_pred             eEEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-----hhhcC----CCcc
Confidence            5999999999999988877664     6788899998764432   3455567789999993     22222    6677


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      .+.+||.
T Consensus       114 ~~~~VI~  120 (185)
T 2jgn_A          114 NVKHVIN  120 (185)
T ss_dssp             SBSEEEE
T ss_pred             cCCEEEE
Confidence            8888876

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.60  E-value=0.96  Score=49.09  Aligned_cols=53  Identities=15%  Similarity=0.248  Sum_probs=31.5

Q ss_pred             cccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          377 SQKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      +..+|++.+=-+.+.+.|.+.   -+..|.-++..-+   ---+-+|+.||+|+|||+.
T Consensus       177 p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi---~~prGvLLyGPPGTGKTlL  232 (437)
T 4b4t_I          177 PTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI---KPPKGVILYGAPGTGKTLL  232 (437)
T ss_dssp             CCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTC---CCCSEEEEESSTTTTHHHH
T ss_pred             CCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCCCceECCCCchHHHH
Confidence            346799997556666666542   1122222222111   1236899999999999983

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=87.47  E-value=3.5  Score=41.06  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=18.6

Q ss_pred             HHhCCCcEEEEccCCCCchhhhH
Q 006737          412 ACLEGKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       412 ~il~grDvLv~ApTGSGKTlayl  434 (633)
                      -+..|.-+++.+++|+|||...+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~   48 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLAL   48 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHH
Confidence            35578889999999999997543

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=87.46  E-value=1.7  Score=45.24  Aligned_cols=17  Identities=18%  Similarity=0.364  Sum_probs=14.2

Q ss_pred             CCcEEE--EccCCCCchhh
Q 006737          416 GKDAVV--KAKTGTGKSIA  432 (633)
Q Consensus       416 grDvLv--~ApTGSGKTla  432 (633)
                      +..+++  +|++|+|||..
T Consensus        50 ~~~~li~i~G~~G~GKT~L   68 (412)
T 1w5s_A           50 DVNMIYGSIGRVGIGKTTL   68 (412)
T ss_dssp             CEEEEEECTTCCSSSHHHH
T ss_pred             CCEEEEeCcCcCCCCHHHH
Confidence            346888  99999999974

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=87.33  E-value=0.72  Score=50.17  Aligned_cols=17  Identities=24%  Similarity=0.356  Sum_probs=14.6

Q ss_pred             CcEEEEccCCCCchhhh
Q 006737          417 KDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       417 rDvLv~ApTGSGKTlay  433 (633)
                      ..++++||+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            37999999999999843

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=87.05  E-value=2.2  Score=46.47  Aligned_cols=17  Identities=18%  Similarity=0.290  Sum_probs=14.2

Q ss_pred             CcEEEEccCCCCchhhh
Q 006737          417 KDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       417 rDvLv~ApTGSGKTlay  433 (633)
                      .-+++++++|+|||...
T Consensus       101 ~vIlivG~~G~GKTTt~  117 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTV  117 (443)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEECcCCCCHHHHH
Confidence            46789999999999853

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=87.03  E-value=0.94  Score=49.10  Aligned_cols=52  Identities=13%  Similarity=0.217  Sum_probs=29.8

Q ss_pred             ccCccccCCCHHHHHHHHHc---CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAA---GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~---g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++.+=-+.+.+.|.+.   -+..|.-++..-   +.--+-+|++||+|+|||+.
T Consensus       168 ~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~l  222 (428)
T 4b4t_K          168 DVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTML  222 (428)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHH
Confidence            45689987666666666542   011111111110   11235799999999999984

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=86.97  E-value=2  Score=44.74  Aligned_cols=71  Identities=17%  Similarity=0.214  Sum_probs=54.6

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.+++++.+..+++.+...     ++.+..++|+.......   ..+..+..+|||||.     .+..+    +++
T Consensus       277 ~~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~~G----idi  342 (417)
T 2i4i_A          277 SLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAARG----LDI  342 (417)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----HHHTT----SCC
T ss_pred             CeEEEEECCHHHHHHHHHHHHHC-----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhhcC----CCc
Confidence            46999999999999988887764     67889999988755433   344556789999994     45544    778


Q ss_pred             CCeeEEEE
Q 006737          533 MGLKMLVL  540 (633)
Q Consensus       533 s~l~~LVI  540 (633)
                      ..+++||.
T Consensus       343 p~v~~Vi~  350 (417)
T 2i4i_A          343 SNVKHVIN  350 (417)
T ss_dssp             CCEEEEEE
T ss_pred             ccCCEEEE
Confidence            88998885

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=86.83  E-value=1.6  Score=41.87  Aligned_cols=20  Identities=20%  Similarity=0.114  Sum_probs=16.4

Q ss_pred             CCCcEEEEccCCCCchhhhH
Q 006737          415 EGKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlayl  434 (633)
                      .|.-+++.+|+|+|||....
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~   42 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICH   42 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHH
Confidence            46788999999999997543

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=86.65  E-value=2.3  Score=43.78  Aligned_cols=39  Identities=18%  Similarity=0.463  Sum_probs=27.2

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+++||||+|.|... ....+..+++..+....+|+.+
T Consensus       109 ~~~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~  147 (340)
T 1sxj_C          109 KGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLA  147 (340)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCceEEEEeCCCCCCHH-HHHHHHHHHhcCCCCeEEEEEe
Confidence            34688999999998643 4556777777776666655543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=86.28  E-value=0.72  Score=58.80  Aligned_cols=25  Identities=24%  Similarity=0.336  Sum_probs=19.9

Q ss_pred             HHHHhC------CCcEEEEccCCCCchhhhH
Q 006737          410 LSACLE------GKDAVVKAKTGTGKSIAFL  434 (633)
Q Consensus       410 Ip~il~------grDvLv~ApTGSGKTlayl  434 (633)
                      +..++.      ++.+++++|+|+|||...+
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ 1445 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTL 1445 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHH
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHH
Confidence            555555      6899999999999998543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=85.72  E-value=4.1  Score=45.13  Aligned_cols=78  Identities=17%  Similarity=0.204  Sum_probs=58.6

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.++|+..|..++..+...+.  .++.+..++|+......   ...+..+..+|||||.     .+..    .+++
T Consensus       289 ~~~iVF~~t~~~~~~l~~~L~~~~~--~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~~~~----GiDi  357 (579)
T 3sqw_A          289 YKAIIFAPTVKFTSFLCSILKNEFK--KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGAR----GMDF  357 (579)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHHHT--TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGTS----SCCC
T ss_pred             CcEEEECCcHHHHHHHHHHHHHhhc--CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----hhhc----CCCc
Confidence            3699999999999999999887754  26788899998775543   3445567789999994     3333    3778


Q ss_pred             CCeeEEEEeccc
Q 006737          533 MGLKMLVLDEAD  544 (633)
Q Consensus       533 s~l~~LVIDEAD  544 (633)
                      .++++||.-..-
T Consensus       358 p~v~~VI~~~~p  369 (579)
T 3sqw_A          358 PNVHEVLQIGVP  369 (579)
T ss_dssp             TTCCEEEEESCC
T ss_pred             ccCCEEEEcCCC
Confidence            889988876543

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=85.56  E-value=1.9  Score=44.27  Aligned_cols=70  Identities=17%  Similarity=0.238  Sum_probs=51.6

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++|++-+..++..+...     ++.+..++|+.....+.   ..+..+..+|||||.     .+..    .+++.
T Consensus        30 ~~LVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----va~~----Gidi~   95 (300)
T 3i32_A           30 RAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----VAAR----GLDIP   95 (300)
T ss_dssp             SEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----TTTC----STTCC
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----hhhc----Ccccc
Confidence            4999999999999888776543     78899999997765543   344556789999993     2233    36677


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      .+.+||.
T Consensus        96 ~v~~VI~  102 (300)
T 3i32_A           96 QVDLVVH  102 (300)
T ss_dssp             CCSEEEE
T ss_pred             ceeEEEE
Confidence            8887774

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=85.49  E-value=1.8  Score=43.43  Aligned_cols=37  Identities=16%  Similarity=0.248  Sum_probs=24.7

Q ss_pred             eeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       535 l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      -.+|||||+|.+... ....+..+++..+....+|+.|
T Consensus       108 ~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          108 HKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEE
T ss_pred             ceEEEEECcccCCHH-HHHHHHHHHhccCCCceEEEEe
Confidence            678999999998643 3344556666665556555544

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=85.18  E-value=1.2  Score=42.13  Aligned_cols=19  Identities=21%  Similarity=0.142  Sum_probs=15.8

Q ss_pred             CCCcEEEEccCCCCchhhh
Q 006737          415 EGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlay  433 (633)
                      .|.-+++.+++|+|||...
T Consensus        19 ~G~~~~i~G~~GsGKTtl~   37 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLA   37 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHH
Confidence            4567899999999999743

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=84.49  E-value=0.69  Score=48.56  Aligned_cols=52  Identities=19%  Similarity=0.261  Sum_probs=29.9

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIA  477 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~  477 (633)
                      ..|.=+++.|++|+|||.. ++-+...+....          ..|+|++- -.-..|+..++..
T Consensus        44 ~~G~LiiIaG~pG~GKTt~-al~ia~~~a~~g----------~~Vl~fSl-Ems~~ql~~Rlls   95 (338)
T 4a1f_A           44 NKGSLVIIGARPSMGKTSL-MMNMVLSALNDD----------RGVAVFSL-EMSAEQLALRALS   95 (338)
T ss_dssp             CTTCEEEEEECTTSCHHHH-HHHHHHHHHHTT----------CEEEEEES-SSCHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHH-HHHHHHHHHHcC----------CeEEEEeC-CCCHHHHHHHHHH
Confidence            3466788999999999964 344444443321          24667654 2334455554433

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=84.40  E-value=24  Score=35.31  Aligned_cols=37  Identities=24%  Similarity=0.366  Sum_probs=24.3

Q ss_pred             eEEEEecccccCC---cChHHHHHHHHHHCCCCCcEEEEec
Q 006737          536 KMLVLDEADHLLD---LGFRKDVENIVDCLPRRRQSLLFSA  573 (633)
Q Consensus       536 ~~LVIDEAD~Lld---~gf~~~l~~Il~~lpk~~Q~IlfSA  573 (633)
                      -+|||||+|.+..   ..+...+..+....+ ...+|+.+.
T Consensus       139 ~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~-~~~~i~~g~  178 (357)
T 2fna_A          139 VIIVLDEAQELVKLRGVNLLPALAYAYDNLK-RIKFIMSGS  178 (357)
T ss_dssp             EEEEEETGGGGGGCTTCCCHHHHHHHHHHCT-TEEEEEEES
T ss_pred             eEEEEECHHHhhccCchhHHHHHHHHHHcCC-CeEEEEEcC
Confidence            4799999999864   346677777766543 344444443

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=84.37  E-value=2  Score=44.60  Aligned_cols=71  Identities=24%  Similarity=0.284  Sum_probs=54.2

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++.-|..++..+...     ++.+..++|+.......   ..+..+..+|||||.     .+..    .+++.
T Consensus       268 ~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~----Gidip  333 (412)
T 3fht_A          268 QAMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----VCAR----GIDVE  333 (412)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GGTS----SCCCT
T ss_pred             CEEEEeCCHHHHHHHHHHHHhC-----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC-----cccc----CCCcc
Confidence            6999999999999998888765     67788899987755433   345567789999994     3333    37788


Q ss_pred             CeeEEEEe
Q 006737          534 GLKMLVLD  541 (633)
Q Consensus       534 ~l~~LVID  541 (633)
                      ++++||.-
T Consensus       334 ~~~~Vi~~  341 (412)
T 3fht_A          334 QVSVVINF  341 (412)
T ss_dssp             TEEEEEES
T ss_pred             CCCEEEEE
Confidence            99988853

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=84.32  E-value=2.9  Score=47.01  Aligned_cols=22  Identities=27%  Similarity=0.469  Sum_probs=18.6

Q ss_pred             HHHhCCCcEEEEccCCCCchhh
Q 006737          411 SACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       411 p~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+..+..+++.+|+|+|||..
T Consensus        55 ~~i~~g~~vll~Gp~GtGKTtl   76 (604)
T 3k1j_A           55 TAANQKRHVLLIGEPGTGKSML   76 (604)
T ss_dssp             HHHHTTCCEEEECCTTSSHHHH
T ss_pred             ccccCCCEEEEEeCCCCCHHHH
Confidence            3456788999999999999984

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=84.29  E-value=2.2  Score=43.33  Aligned_cols=72  Identities=18%  Similarity=0.303  Sum_probs=53.6

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.+++++-+..+++.+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..+    +++.
T Consensus       240 ~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~~G----id~~  305 (367)
T 1hv8_A          240 YGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSRG----IDVN  305 (367)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHHH----CCCS
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhhcC----CCcc
Confidence            5899999999999988888765     67888999987655433   344567789999993     33333    6677


Q ss_pred             CeeEEEEec
Q 006737          534 GLKMLVLDE  542 (633)
Q Consensus       534 ~l~~LVIDE  542 (633)
                      ++++||.-.
T Consensus       306 ~~~~Vi~~~  314 (367)
T 1hv8_A          306 DLNCVINYH  314 (367)
T ss_dssp             CCSEEEESS
T ss_pred             cCCEEEEec
Confidence            888887643

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=83.88  E-value=1.4  Score=49.13  Aligned_cols=18  Identities=22%  Similarity=0.344  Sum_probs=15.9

Q ss_pred             CCCcEEEEccCCCCchhh
Q 006737          415 EGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTla  432 (633)
                      .+..+++.+|+|+|||..
T Consensus       107 ~g~~vll~Gp~GtGKTtl  124 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSL  124 (543)
T ss_dssp             CSCEEEEESSSSSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            477899999999999984

>2d7d_A Uvrabc system protein B; helicase, protein-DNA-ADP ternary complex, hydrolase/DNA complex; HET: ADP; 2.10A {Bacillus subtilis} PDB: 2nmv_A* 2fdc_A* 1t5l_A 3uwx_B 1d9z_A* 1d9x_A 2d7d_B* 2nmv_B*

Probab=83.77  E-value=3.7  Score=46.72  Aligned_cols=77  Identities=16%  Similarity=0.189  Sum_probs=58.8

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHH---HHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQR---RLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~---~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++|+..|..+.+.+...     ++.+..++|+........   .+..+..+|+|||.     .+..    .+++.
T Consensus       447 ~vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~-----~l~~----GlDip  512 (661)
T 2d7d_A          447 RVLVTTLTKKMSEDLTDYLKEI-----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LLRE----GLDIP  512 (661)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC-----CCST----TCCCT
T ss_pred             eEEEEECCHHHHHHHHHHHHhc-----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc-----hhhC----CcccC
Confidence            6999999999999988877765     678888898876554433   34557789999994     2233    37788


Q ss_pred             CeeEEEEecccccC
Q 006737          534 GLKMLVLDEADHLL  547 (633)
Q Consensus       534 ~l~~LVIDEAD~Ll  547 (633)
                      .+++||+=++|...
T Consensus       513 ~v~lVi~~d~d~~G  526 (661)
T 2d7d_A          513 EVSLVAILDADKEG  526 (661)
T ss_dssp             TEEEEEETTTTCCT
T ss_pred             CCCEEEEeCccccc
Confidence            99999999998754

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=83.31  E-value=2.2  Score=43.68  Aligned_cols=76  Identities=14%  Similarity=0.186  Sum_probs=57.1

Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCccccc
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRL  532 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~L  532 (633)
                      .++||.++++.-|..+++.+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..    .+++
T Consensus       244 ~~~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~----Gidi  309 (395)
T 3pey_A          244 GSSIIFVATKKTANVLYGKLKSE-----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN-----VLAR----GIDI  309 (395)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG-----GGSS----SCCC
T ss_pred             CCEEEEeCCHHHHHHHHHHHHhc-----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC-----hhhc----CCCc
Confidence            36999999999999988888765     67788999987655433   345567789999994     3333    3778


Q ss_pred             CCeeEEEEecccc
Q 006737          533 MGLKMLVLDEADH  545 (633)
Q Consensus       533 s~l~~LVIDEAD~  545 (633)
                      .++++||.-....
T Consensus       310 p~~~~Vi~~~~p~  322 (395)
T 3pey_A          310 PTVSMVVNYDLPT  322 (395)
T ss_dssp             TTEEEEEESSCCB
T ss_pred             ccCCEEEEcCCCC
Confidence            8999999766554

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=83.00  E-value=1.7  Score=42.04  Aligned_cols=48  Identities=17%  Similarity=0.274  Sum_probs=32.2

Q ss_pred             CCeeEEEEecccccCCcC--hHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          533 MGLKMLVLDEADHLLDLG--FRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g--f~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      ..+++|||||+-..+..+  -.+.+..++...|...-+|+.+--.|+++.
T Consensus       119 ~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~  168 (196)
T 1g5t_A          119 PLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDIL  168 (196)
T ss_dssp             TTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHH
T ss_pred             CCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHH
Confidence            568999999997655444  356677777776666555555555555554

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=82.80  E-value=2.5  Score=43.79  Aligned_cols=70  Identities=10%  Similarity=0.237  Sum_probs=53.5

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.+++++-+..+++.+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..    .+++.
T Consensus       260 ~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~-----~~~~----Gidip  325 (400)
T 1s2m_A          260 QAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD-----LLTR----GIDIQ  325 (400)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS-----CSSS----SCCCT
T ss_pred             cEEEEEecHHHHHHHHHHHHhc-----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----cccc----CCCcc
Confidence            6999999999999999888776     67788899987755433   345567789999993     2222    37788


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      .+.+||.
T Consensus       326 ~~~~Vi~  332 (400)
T 1s2m_A          326 AVNVVIN  332 (400)
T ss_dssp             TEEEEEE
T ss_pred             CCCEEEE
Confidence            8888875

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=82.62  E-value=2.2  Score=43.91  Aligned_cols=73  Identities=12%  Similarity=0.134  Sum_probs=54.7

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.+++++.+..+++.+...     ++.+..++|+.......   ..+..+...|||||.     .+..    .+++.
T Consensus       252 ~~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~~----Gidi~  317 (391)
T 1xti_A          252 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LFGR----GMDIE  317 (391)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC-----CCSS----CBCCT
T ss_pred             cEEEEeCcHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC-----hhhc----CCCcc
Confidence            6999999999999988887764     67788999987655432   345567789999993     2222    37788


Q ss_pred             CeeEEEEecc
Q 006737          534 GLKMLVLDEA  543 (633)
Q Consensus       534 ~l~~LVIDEA  543 (633)
                      .+++||.-..
T Consensus       318 ~~~~Vi~~~~  327 (391)
T 1xti_A          318 RVNIAFNYDM  327 (391)
T ss_dssp             TEEEEEESSC
T ss_pred             cCCEEEEeCC
Confidence            8999987544

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=82.08  E-value=0.86  Score=45.95  Aligned_cols=20  Identities=30%  Similarity=0.383  Sum_probs=16.6

Q ss_pred             hCCCcEEEEccCCCCchhhh
Q 006737          414 LEGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlay  433 (633)
                      ..|.-+++.|++|+|||...
T Consensus        33 ~~G~~~~i~G~~G~GKTTl~   52 (296)
T 1cr0_A           33 RGGEVIMVTSGSGMGKSTFV   52 (296)
T ss_dssp             CTTCEEEEEESTTSSHHHHH
T ss_pred             CCCeEEEEEeCCCCCHHHHH
Confidence            45778899999999999743

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=81.93  E-value=2.3  Score=46.69  Aligned_cols=49  Identities=18%  Similarity=0.238  Sum_probs=27.5

Q ss_pred             cCccccCCCHHHHHHHHHcC--CCCCcHHHHHHHHHH--hCCCcEEEEccCCCCchhh
Q 006737          379 KRFDECGISPLTIKALTAAG--YIQMTRVQEATLSAC--LEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g--~~~pt~iQ~~aIp~i--l~grDvLv~ApTGSGKTla  432 (633)
                      .+|+++.-....++.|.+.-  +..+.     .+..+  .-.+.+++++|+|+|||+.
T Consensus        13 ~~f~di~G~~~~~~~l~e~v~~l~~~~-----~~~~~g~~~p~gvLL~GppGtGKT~L   65 (476)
T 2ce7_A           13 VTFKDVGGAEEAIEELKEVVEFLKDPS-----KFNRIGARMPKGILLVGPPGTGKTLL   65 (476)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCTH-----HHHTTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHhhChH-----HHhhcCCCCCCeEEEECCCCCCHHHH
Confidence            45777765555555554420  11111     11111  1125699999999999984

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=81.84  E-value=1.2  Score=47.97  Aligned_cols=67  Identities=18%  Similarity=0.159  Sum_probs=45.4

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++||++|+++-|..+++.+...     ++.+..++|... ......+..+..+|||||.     .+..    .+++. ++
T Consensus       179 ~~lVF~~s~~~a~~l~~~L~~~-----~~~v~~lhg~~R-~~~~~~F~~g~~~vLVaT~-----v~e~----GiDip-v~  242 (440)
T 1yks_A          179 PTAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTF-EREYPTIKQKKPDFILATD-----IAEM----GANLC-VE  242 (440)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSC-C--------CCCSEEEESS-----STTC----CTTCC-CS
T ss_pred             CEEEEeCCHHHHHHHHHHHHHc-----CCCEEEecchhH-HHHHhhhcCCCceEEEECC-----hhhe----eeccC-ce
Confidence            5999999999999998887765     678889998433 3345566677889999994     2333    36677 88


Q ss_pred             EEE
Q 006737          537 MLV  539 (633)
Q Consensus       537 ~LV  539 (633)
                      +||
T Consensus       243 ~VI  245 (440)
T 1yks_A          243 RVL  245 (440)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            776

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=81.84  E-value=1.4  Score=47.89  Aligned_cols=51  Identities=12%  Similarity=0.012  Sum_probs=29.4

Q ss_pred             hCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          414 LEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       414 l~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      ..|.-+++.|++|+|||.. ++-+..++...+          ..|+|++-- +-..|+...+.
T Consensus       195 ~~G~liiIaG~pG~GKTtl-al~ia~~~a~~g----------~~vl~fSlE-ms~~ql~~R~~  245 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAF-ALKQAKNMSDND----------DVVNLHSLE-MGKKENIKRLI  245 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHH-HHHHHHHHHHTT----------CEEEEECSS-SCTTHHHHHHH
T ss_pred             CCCcEEEEEeCCCCChHHH-HHHHHHHHHHcC----------CEEEEEECC-CCHHHHHHHHH
Confidence            3466789999999999964 444444443321          247776532 33344444443

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=81.51  E-value=2.8  Score=44.74  Aligned_cols=69  Identities=13%  Similarity=0.198  Sum_probs=53.3

Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccCC
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLMG  534 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~  534 (633)
                      +||.++++.-|..+++.+...     ++.+..++|+.......   ..++.+.++|||||.     .+..    .+++.+
T Consensus       303 ~lVF~~t~~~a~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----v~~r----GlDi~~  368 (434)
T 2db3_A          303 TIVFVETKRGADFLASFLSEK-----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS-----VASR----GLDIKN  368 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG-----GGTS----SCCCTT
T ss_pred             EEEEEeCcHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch-----hhhC----CCCccc
Confidence            899999999999988877664     67889999987755433   345567789999995     3333    377889


Q ss_pred             eeEEEE
Q 006737          535 LKMLVL  540 (633)
Q Consensus       535 l~~LVI  540 (633)
                      +++||.
T Consensus       369 v~~VI~  374 (434)
T 2db3_A          369 IKHVIN  374 (434)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            998886

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=81.28  E-value=3.6  Score=46.84  Aligned_cols=76  Identities=16%  Similarity=0.142  Sum_probs=57.7

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHH---HHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQR---RLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~---~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++|+..|..+.+.+...     ++.+..++|+........   .+..+..+|+|||.     .+..    .+++.
T Consensus       441 ~vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~-----~l~~----GlDip  506 (664)
T 1c4o_A          441 RTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LLRE----GLDIP  506 (664)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CCCT----TCCCT
T ss_pred             EEEEEECCHHHHHHHHHHHHhc-----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccC-----hhhc----CccCC
Confidence            6999999999999988877765     678888898876554333   35567789999993     2222    37788


Q ss_pred             CeeEEEEeccccc
Q 006737          534 GLKMLVLDEADHL  546 (633)
Q Consensus       534 ~l~~LVIDEAD~L  546 (633)
                      .+++||+=+++..
T Consensus       507 ~v~lVI~~d~d~~  519 (664)
T 1c4o_A          507 EVSLVAILDADKE  519 (664)
T ss_dssp             TEEEEEETTTTSC
T ss_pred             CCCEEEEeCCccc
Confidence            9999999888765

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=81.12  E-value=2.7  Score=43.77  Aligned_cols=70  Identities=13%  Similarity=0.263  Sum_probs=53.1

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++++..+..+++.+...     ++.+..++|+.......   ..+..+..+|||+|.     .+..    .+++.
T Consensus       278 ~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~~----Gidi~  343 (410)
T 2j0s_A          278 QAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VWAR----GLDVP  343 (410)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GGSS----SCCCT
T ss_pred             cEEEEEcCHHHHHHHHHHHHhC-----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC-----hhhC----cCCcc
Confidence            6999999999999988887764     67788999987755433   344556789999994     2333    37788


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      .+.+||.
T Consensus       344 ~v~~Vi~  350 (410)
T 2j0s_A          344 QVSLIIN  350 (410)
T ss_dssp             TEEEEEE
T ss_pred             cCCEEEE
Confidence            9998886

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=80.71  E-value=2.1  Score=45.17  Aligned_cols=26  Identities=23%  Similarity=0.327  Sum_probs=18.7

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAV  441 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l  441 (633)
                      .|.-+++.+|+|+|||.. ++.++..+
T Consensus        60 ~G~i~~I~GppGsGKSTL-al~la~~~   85 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTL-ALHAIAEA   85 (356)
T ss_dssp             TTEEEEEEESTTSSHHHH-HHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHH-HHHHHHHH
Confidence            466789999999999974 44444433

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=80.40  E-value=1.3  Score=46.60  Aligned_cols=19  Identities=16%  Similarity=0.270  Sum_probs=15.9

Q ss_pred             CCCcEEEEccCCCCchhhh
Q 006737          415 EGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlay  433 (633)
                      .|.-+++.+++|+|||...
T Consensus        60 ~G~iv~I~G~pGsGKTtLa   78 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVA   78 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4677999999999999743

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	633
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	2e-38
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	9e-33
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	1e-31
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	4e-31
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	9e-31
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	6e-30
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	1e-27
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	1e-27
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	3e-25
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	4e-23
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	2e-20
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-20
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	1e-16
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	4e-11

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 208

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score =  139 bits (350), Expect = 2e-38
 Identities = 70/200 (35%), Positives = 111/200 (55%), Gaps = 16/200 (8%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIE 439
           F+E  +S   + A+   G+ + T +Q   +   L  + + V +A+TG+GK+ +F +P IE
Sbjct: 6   FNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIE 65

Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
                           I  +IL PTRELA Q+A E I  LK +  + +  + GG      
Sbjct: 66  ---------LVNENNGIEAIILTPTRELAIQVADE-IESLKGNKNLKIAKIYGGKAIYPQ 115

Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
            + L++    I+V TPGR+LDHI   +   + L  +K  +LDEAD +L++GF KDVE I+
Sbjct: 116 IKALKN--ANIVVGTPGRILDHINRGT---LNLKNVKYFILDEADEMLNMGFIKDVEKIL 170

Query: 560 DCLPRRRQSLLFSATMPKEL 579
           +   + ++ LLFSATMP+E+
Sbjct: 171 NACNKDKRILLFSATMPREI 190

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  123 bits (308), Expect = 9e-33
 Identities = 63/200 (31%), Positives = 102/200 (51%), Gaps = 12/200 (6%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F +  + P  ++A+   G+   + VQ   +   + G D + +AK+G GK+  F+L  ++ 
Sbjct: 3   FRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ- 61

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
                      +   + VL++C TRELA QI+ E     K    + V    GG   K D+
Sbjct: 62  -------QLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDE 114

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-LGFRKDVENIV 559
             L+ +   I+V TPGR+L    NK   S+ L  +K  +LDE D +L+ L  R+DV+ I 
Sbjct: 115 EVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFILDECDKMLEQLDMRRDVQEIF 171

Query: 560 DCLPRRRQSLLFSATMPKEL 579
              P  +Q ++FSAT+ KE+
Sbjct: 172 RMTPHEKQVMMFSATLSKEI 191

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  120 bits (301), Expect = 1e-31
 Identities = 61/212 (28%), Positives = 106/212 (50%), Gaps = 15/212 (7%)

Query: 368 EKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGT 427
           E    E + S   FD+  +S   ++ + A G+ + + +Q+  +  C++G D + +A++GT
Sbjct: 4   ESNWNEIVDS---FDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGT 60

Query: 428 GKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGV 487
           GK+  F +  ++ +                 L+L PTRELA QI    +AL         
Sbjct: 61  GKTATFAISILQQIELDL--------KATQALVLAPTRELAQQIQKVVMALGDYMGAS-C 111

Query: 488 LTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL 547
              +GGT  + + ++L+ +   I+V TPGR+ D +  +    +    +KM VLDEAD +L
Sbjct: 112 HACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRR---YLSPKYIKMFVLDEADEML 168

Query: 548 DLGFRKDVENIVDCLPRRRQSLLFSATMPKEL 579
             GF+  + +I   L    Q +L SATMP ++
Sbjct: 169 SRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV 200

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 212

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  118 bits (296), Expect = 4e-31
 Identities = 61/212 (28%), Positives = 106/212 (50%), Gaps = 17/212 (8%)

Query: 368 EKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGT 427
           +   ++ +     FD+  +    ++ +   G+ + + +Q+  +   +EG D + +A++GT
Sbjct: 2   QTNYDKVVYK---FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGT 58

Query: 428 GKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGV 487
           GK+  F + A++ +  +        V     L+L PTRE  +    + +  L  H  I V
Sbjct: 59  GKTGTFSIAALQRIDTS--------VKAPQALMLAPTRE-LALQIQKVVMALAFHMDIKV 109

Query: 488 LTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLL 547
              +GGT F  D   L     QI+V TPGR+ D+I+ +     R   +KM +LDEAD +L
Sbjct: 110 HACIGGTSFVEDAEGLRD--AQIVVGTPGRVFDNIQRRR---FRTDKIKMFILDEADEML 164

Query: 548 DLGFRKDVENIVDCLPRRRQSLLFSATMPKEL 579
             GF++ +  I   LP   Q +L SATMP ++
Sbjct: 165 SSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV 196

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 222

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  118 bits (295), Expect = 9e-31
 Identities = 55/215 (25%), Positives = 107/215 (49%), Gaps = 13/215 (6%)

Query: 365 EKKEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAK 424
            K E    E +     FD  G+    ++ + A G+ + + +Q+  +   ++G+D + +++
Sbjct: 3   TKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQ 62

Query: 425 TGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDG 484
           +GTGK+  F +  ++ +      +   ++ P   L +   + L +         L ++  
Sbjct: 63  SGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLA---------LGDYMN 113

Query: 485 IGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD 544
           +     +GGT    D R+L+     ++  TPGR+ D I  +   S+R   +KMLVLDEAD
Sbjct: 114 VQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRRR---SLRTRAIKMLVLDEAD 169

Query: 545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL 579
            +L+ GF++ + ++   LP   Q +L SAT+P E+
Sbjct: 170 EMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEI 204

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

 Score =  116 bits (290), Expect = 6e-30
 Identities = 75/218 (34%), Positives = 108/218 (49%), Gaps = 13/218 (5%)

Query: 367 KEKREEEPILSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTG 426
            +      I +   FDE  + P     +  A Y + T +Q+  + A LE +D +  A+TG
Sbjct: 12  PDYSATNVIEN---FDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTG 68

Query: 427 TGKSIAFLLPAIEAVLK-ATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGI 485
           +GK+ AFL+P I  ++    +            LIL PTRELA QI +E+     N   +
Sbjct: 69  SGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNT-PL 127

Query: 486 GVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH 545
               +V G      Q R     C +LVATPGRL+D IE      + L   K +VLDEAD 
Sbjct: 128 RS-CVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKN---KISLEFCKYIVLDEADR 183

Query: 546 LLDLGFRKDVENIVDCL----PRRRQSLLFSATMPKEL 579
           +LD+GF   +  I++         RQ+L+FSAT PKE+
Sbjct: 184 MLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEI 221

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (270), Expect = 1e-27
 Identities = 67/199 (33%), Positives = 112/199 (56%), Gaps = 12/199 (6%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F++  +    +  +   G+ + + +QE ++   L G+D + +AK GTGKS A+L+P +E 
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           +              I  +++ PTRELA Q++   I + K+  G  V+   GGT  + D 
Sbjct: 65  LDLKK--------DNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDI 116

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
            RL+ D   +++ATPGR+LD I+       ++  ++M+VLDEAD LL   F + +E+I+ 
Sbjct: 117 MRLD-DTVHVVIATPGRILDLIKKG---VAKVDHVQMIVLDEADKLLSQDFVQIMEDIIL 172

Query: 561 CLPRRRQSLLFSATMPKEL 579
            LP+ RQ LL+SAT P  +
Sbjct: 173 TLPKNRQILLYSATFPLSV 191

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 237

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  109 bits (272), Expect = 1e-27
 Identities = 39/212 (18%), Positives = 67/212 (31%), Gaps = 37/212 (17%)

Query: 391 IKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTT 450
                     +   +Q+      L  +     A TG GK+   L  ++   LK       
Sbjct: 33  FVEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGK----- 87

Query: 451 QLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQ- 509
                    ++ PT  L  Q A       +   G+G   L+G    ++ +R  E+     
Sbjct: 88  ------RCYVIFPTSLLVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNL 140

Query: 510 ----ILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLD-----------LGFRKD 554
               I++ T   L  H          L     + +D+ D +L            LGF  D
Sbjct: 141 RNFKIVITTTQFLSKHYRE-------LGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYD 193

Query: 555 VENIVDCLPRRRQSLLFSATMPKELV--LKRE 584
           ++        R   ++ +AT  K     L R+
Sbjct: 194 LKTKSWVGEARGCLMVSTATAKKGKKAELFRQ 225

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  101 bits (252), Expect = 3e-25
 Identities = 60/199 (30%), Positives = 97/199 (48%), Gaps = 13/199 (6%)

Query: 381 FDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEA 440
           F++  +    +  +  AG+ + + +QE  +   + G+D + +AK GTGK+ AF++P +E 
Sbjct: 3   FEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEK 62

Query: 441 VLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ 500
           V    +     ++ P   L L  ++ + +            H GI  +   GGT  + D 
Sbjct: 63  VKPKLNKIQALIMVPTRELALQTSQVVRTL---------GKHCGISCMVTTGGTNLRDDI 113

Query: 501 RRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD 560
            RL  +   ILV TPGR+LD    K      L    + ++DEAD +L   F+  +E I+ 
Sbjct: 114 LRLN-ETVHILVGTPGRVLDLASRK---VADLSDCSLFIMDEADKMLSRDFKTIIEQILS 169

Query: 561 CLPRRRQSLLFSATMPKEL 579
            LP   QSLLFSAT P  +
Sbjct: 170 FLPPTHQSLLFSATFPLTV 188

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]} Length = 209

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 95.9 bits (237), Expect = 4e-23
 Identities = 52/200 (26%), Positives = 93/200 (46%), Gaps = 9/200 (4%)

Query: 380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIE 439
           +F      P  I+A+    + + T +QE  +   L G+  V +++TGTGK+ A+LLP + 
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIM- 60

Query: 440 AVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD 499
              +       ++   I         ++  +         K+   +       G   K  
Sbjct: 61  ---EKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCL--IGGTDKQK 115

Query: 500 QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV 559
                +    I++ TPGR+ D I  +   ++ +    +LV+DEAD +LD+GF  DV+ I 
Sbjct: 116 ALEKLNVQPHIVIGTPGRINDFIREQ---ALDVHTAHILVVDEADLMLDMGFITDVDQIA 172

Query: 560 DCLPRRRQSLLFSATMPKEL 579
             +P+  Q L+FSAT+P++L
Sbjct: 173 ARMPKDLQMLVFSATIPEKL 192

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]} Length = 305

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

 Score = 90.4 bits (223), Expect = 2e-20
 Identities = 21/163 (12%), Positives = 48/163 (29%), Gaps = 27/163 (16%)

Query: 415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAE 474
           + +  ++    G GK+  +L   +   +K            +  LIL PTR +A+++   
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIKR----------GLRTLILAPTRVVAAEMEEA 57

Query: 475 AIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMG 534
                        L  +         R   +    + +         + +     +R+  
Sbjct: 58  -------------LRGLPIRYQTPAIRAEHTGREIVDLMCHATFTMRLLSP----IRVPN 100

Query: 535 LKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK 577
             ++++DEA                         +  +AT P 
Sbjct: 101 YNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPG 143

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]} Length = 202

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 87.7 bits (216), Expect = 2e-20
 Identities = 37/202 (18%), Positives = 70/202 (34%), Gaps = 25/202 (12%)

Query: 380 RFDE--CGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPA 437
           + +E    IS   +  L   G  ++   Q   +     GK+ ++   T  GK++   +  
Sbjct: 2   KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAM 61

Query: 438 IEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK 497
           +            + +     L + P R LA +         K    IG+      +   
Sbjct: 62  V-----------REAIKGGKSLYVVPLRALAGEKYESFKKWEKIGLRIGI------STGD 104

Query: 498 VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVEN 557
            + R      C I+V T  +    I N+   +  +  +  LV+DE   L        +E 
Sbjct: 105 YESRDEHLGDCDIIVTTSEKADSLIRNR---ASWIKAVSCLVVDEIHLLDSEKRGATLEI 161

Query: 558 IVDCL---PRRRQSLLFSATMP 576
           +V  +    +  + +  SAT P
Sbjct: 162 LVTKMRRMNKALRVIGLSATAP 183

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]} Length = 206

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

 Score = 77.0 bits (188), Expect = 1e-16
 Identities = 34/204 (16%), Positives = 65/204 (31%), Gaps = 24/204 (11%)

Query: 380 RFDECGISPLTIKALTAA-GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAI 438
           + +   +     + L    GY Q    QE  +   L G+D +V   TG GKS+ + +PA+
Sbjct: 3   QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL 62

Query: 439 EAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKV 498
                               +++ P      +   + +            T     + +V
Sbjct: 63  LLNGLT--------------VVVSPLIS-LMKDQVDQLQANGVAAACLNSTQTREQQLEV 107

Query: 499 DQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLG--FRKDVE 556
                     ++L   P RL+     +    +      +L +DEA  +   G  FR +  
Sbjct: 108 MTGCRTGQ-IRLLYIAPERLMLDNFLE---HLAHWNPVLLAVDEAHCISQWGHDFRPEYA 163

Query: 557 NIVDCLPR--RRQSLLFSATMPKE 578
            +     R      +  +AT    
Sbjct: 164 ALGQLRQRFPTLPFMALTATADDT 187

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 60.6 bits (145), Expect = 4e-11
 Identities = 33/179 (18%), Positives = 62/179 (34%), Gaps = 17/179 (9%)

Query: 398 GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY 457
             IQ    QE   + C E  + ++   TG GK++  ++ A   + K              
Sbjct: 6   DLIQPRIYQEVIYAKCKE-TNCLIVLPTGLGKTLIAMMIAEYRLTK----------YGGK 54

Query: 458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGR 517
           VL+L PT+ L  Q A     L        V      +     +R       +++VATP  
Sbjct: 55  VLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPE---ERSKAWARAKVIVATPQT 111

Query: 518 LLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMP 576
           + + +       + L  + ++V DEA   +       +        +    +  +A+  
Sbjct: 112 IENDLLAGR---ISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPG 167

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	633
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.92
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.92
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.91
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.87
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.8
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.66
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.63
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.6
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.6
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.6
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.52
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.76
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	98.49
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.37
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.31
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.82
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.05
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	96.35
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	95.85
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	95.55
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	95.45
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	94.85
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	94.72
d1ls1a2	207	GTPase domain of the signal sequence recognition p	94.53
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	94.36
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	94.08
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	94.05
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	93.94
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	93.63
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	93.15
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	92.98
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	92.88
d1okkd2	207	GTPase domain of the signal recognition particle r	92.8
d2qy9a2	211	GTPase domain of the signal recognition particle r	92.42
d1vmaa2	213	GTPase domain of the signal recognition particle r	92.39
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	92.34
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	92.32
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	91.82
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	91.76
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	91.74
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	91.5
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	90.65
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	90.28
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	90.16
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	90.03
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	89.96
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	89.47
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	89.18
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	89.0
d1j8yf2	211	GTPase domain of the signal sequence recognition p	88.47
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	86.84
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	84.63
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	83.22
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	82.78
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	82.61
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	82.41
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	81.19
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	81.1
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	80.95

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=4e-40  Score=328.32  Aligned_cols=192  Identities=32%  Similarity=0.552  Sum_probs=174.4

Q ss_pred             ccccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCC
Q 006737          376 LSQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPP  455 (633)
Q Consensus       376 ~~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~  455 (633)
                      ....+|++|+|++.++++|.++||.+||++|..+||.+++|+|++++|+||||||+||++|+++++....        ..
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~~--------~~   85 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQV--------RE   85 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTTS--------CS
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhcccccccccccc--------cC
Confidence            3445799999999999999999999999999999999999999999999999999999999998875432        24


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      +++||++||||||.|+++.+..+.... ++++.+++|+.....+...+..+ ++|||+|||+|.+++...   ...++++
T Consensus        86 ~~~lil~PtreLa~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l~~~-~~Ilv~TPgrl~~~~~~~---~~~~~~l  160 (222)
T d2j0sa1          86 TQALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYG-QHVVAGTPGRVFDMIRRR---SLRTRAI  160 (222)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHC-CSEEEECHHHHHHHHHTT---SSCCTTC
T ss_pred             ceeEEecchHHHHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHhccC-CeEEeCCCCcHHhccccc---ccccccc
Confidence            679999999999999999999998754 79999999999888777777654 799999999999998776   4678999


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      ++|||||||+|++.+|...+..|+..+++++|+++||||+++++.
T Consensus       161 ~~lVlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~  205 (222)
T d2j0sa1         161 KMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEIL  205 (222)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHH
T ss_pred             eeeeecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHH
Confidence            999999999999999999999999999999999999999999863

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-39  Score=319.77  Aligned_cols=190  Identities=35%  Similarity=0.582  Sum_probs=172.1

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ++|++|+|++.++++|.++||+.||++|+++||.+++|+|++++||||||||+||++|+++++....        .++++
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~~--------~~~~~   74 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKK--------DNIQA   74 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTTS--------CSCCE
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhcccccc--------cCcce
Confidence            5799999999999999999999999999999999999999999999999999999999998864332        34679


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      ||++||++||.|+++.+..+.....++.+....|+.....+...+.. +++|||+||++|.+++...   ...++++++|
T Consensus        75 lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~-~~~ivv~TPgrl~~~~~~~---~~~~~~l~~l  150 (206)
T d1veca_          75 MVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD-TVHVVIATPGRILDLIKKG---VAKVDHVQMI  150 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTS-CCSEEEECHHHHHHHHHTT---CSCCTTCCEE
T ss_pred             EEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHh-ccCeEEeCCccccccccch---hccccccceE
Confidence            99999999999999999999887777888888888887766555544 5899999999999999876   4678999999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      ||||||.|++.+|..++..|+..+++++|+++||||+++++.
T Consensus       151 VlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~  192 (206)
T d1veca_         151 VLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQ  192 (206)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHH
T ss_pred             EEeccccccccchHHHHHHHHHhCCCCCEEEEEEecCCHHHH
Confidence            999999999999999999999999999999999999999863

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=5e-39  Score=316.59  Aligned_cols=190  Identities=33%  Similarity=0.559  Sum_probs=173.7

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      .|++|+|++.++++|.++||++|||+|+++||.+++|+|++++||||||||+||++|+++.+...        ..++++|
T Consensus         2 ~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~--------~~~~~~l   73 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV--------TGQVSVL   73 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC--------TTCCCEE
T ss_pred             CccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc--------CCCceEE
Confidence            59999999999999999999999999999999999999999999999999999999999875332        2346799


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      |++|||+||.|+++.+..+......+.+.+++|+.....+...+....++|||+||++|.+++.+.   ...++++++||
T Consensus        74 il~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~---~~~l~~l~~lV  150 (207)
T d1t6na_          74 VMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNK---SLNLKHIKHFI  150 (207)
T ss_dssp             EECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTT---SSCCTTCCEEE
T ss_pred             EEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCC---ceeccccceee
Confidence            999999999999999999998877788899999998888888887777999999999999999876   46799999999


Q ss_pred             EecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          540 LDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       540 IDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      |||||.|++ .+|...+..|+..+++++|+++||||+++.+.
T Consensus       151 lDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~  192 (207)
T d1t6na_         151 LDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIR  192 (207)
T ss_dssp             EESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTH
T ss_pred             hhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHH
Confidence            999999997 48999999999999999999999999998853

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.4e-38  Score=314.41  Aligned_cols=191  Identities=31%  Similarity=0.556  Sum_probs=170.4

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|++++|++.++++|.++||.+||++|+++||.++.|+|++++|+||||||+||++|+++++....        .+++
T Consensus        11 i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~~--------~~~~   82 (218)
T d2g9na1          11 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDL--------KATQ   82 (218)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------CSCC
T ss_pred             cCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecccc--------cCcc
Confidence            46799999999999999999999999999999999999999999999999999999999999874332        3468


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +||++||++||.|+++.+..+.... ++.+.++.++.....+........++|||+||++|.+++.+.   ...++++++
T Consensus        83 alil~Pt~eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~---~~~~~~l~~  158 (218)
T d2g9na1          83 ALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRR---YLSPKYIKM  158 (218)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTT---SSCSTTCCE
T ss_pred             EEEEcccchhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcC---CcccccceE
Confidence            9999999999999999999998766 677777777776666555565667899999999999999876   467899999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      |||||||.|++.+|...+..|++.+++++|+++||||+++++.
T Consensus       159 lVlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~  201 (218)
T d2g9na1         159 FVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVL  201 (218)
T ss_dssp             EEEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHH
T ss_pred             EEeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHH
Confidence            9999999999999999999999999999999999999999863

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.8e-37  Score=304.41  Aligned_cols=188  Identities=34%  Similarity=0.567  Sum_probs=162.3

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeE
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIY  457 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~  457 (633)
                      ..+|++|+|++.++++|.++||++||++|..+||+++.|+|++++||||||||+||++|+++++....        .+++
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~~--------~~~~   80 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTSV--------KAPQ   80 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTTC--------CSCC
T ss_pred             ccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhccC--------CCcc
Confidence            56799999999999999999999999999999999999999999999999999999999999874332        3578


Q ss_pred             EEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeE
Q 006737          458 VLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKM  537 (633)
Q Consensus       458 vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~  537 (633)
                      +||++||++|+.|++..+..+.... .+.+..+.++.....+...++  +++|+|+||++|..++...   ...++++++
T Consensus        81 ~lil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~--~~~IvI~TP~~l~~~~~~~---~~~l~~l~~  154 (212)
T d1qdea_          81 ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQRR---RFRTDKIKM  154 (212)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CT--TCSEEEECHHHHHHHHHTT---SSCCTTCCE
T ss_pred             eEEEcccHHHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHhc--CCcEEEECCCccccccccC---ceecCcceE
Confidence            9999999999999999998887654 678888888777665555443  4799999999999999776   467999999


Q ss_pred             EEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          538 LVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       538 LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +||||||.|++.+|...+..|++.+++.+|+++||||+++.+
T Consensus       155 lVlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v  196 (212)
T d1qdea_         155 FILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV  196 (212)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHH
T ss_pred             EeehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHH
Confidence            999999999999999999999999999999999999999985

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=100.00  E-value=5.9e-37  Score=308.16  Aligned_cols=198  Identities=37%  Similarity=0.552  Sum_probs=172.8

Q ss_pred             cccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCC-CCCCCCC
Q 006737          377 SQKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSS-TTQLVPP  455 (633)
Q Consensus       377 ~~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~-~~~~~~~  455 (633)
                      ...+|++|+|++.++++|.++||..||++|..+||.+++|+|++++||||||||+||++|+++++....... ......+
T Consensus        19 ~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~~   98 (238)
T d1wrba1          19 VIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAY   98 (238)
T ss_dssp             CCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCBC
T ss_pred             ccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCCC
Confidence            457899999999999999999999999999999999999999999999999999999999999987653211 1223456


Q ss_pred             eEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          456 IYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       456 ~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      +++|||+||++||.|+++.+..+.... ++++..++|+.....+..... .++||||+||++|.+++...   ...+.++
T Consensus        99 ~~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~ivV~TP~~l~~~~~~~---~~~l~~v  173 (238)
T d1wrba1          99 PKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQ-MGCHLLVATPGRLVDFIEKN---KISLEFC  173 (238)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHS-SCCSEEEECHHHHHHHHHTT---SBCCTTC
T ss_pred             ceEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhcc-cCCceeecCHHHHHhHHccC---ceecccc
Confidence            789999999999999999999988765 789999999988776655554 46899999999999999876   4678999


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCC----CCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPR----RRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk----~~Q~IlfSATl~~el  579 (633)
                      +++||||||.|++.+|..++..|++.+..    ++|+++||||+++++
T Consensus       174 ~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v  221 (238)
T d1wrba1         174 KYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEI  221 (238)
T ss_dssp             CEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHH
T ss_pred             ceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHH
Confidence            99999999999999999999999987642    689999999999985

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=100.00  E-value=3.1e-36  Score=296.45  Aligned_cols=187  Identities=37%  Similarity=0.613  Sum_probs=168.5

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCe
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPI  456 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~  456 (633)
                      .++|++|+|++.++++|.++||..|||+|.++||.+++|+ |++++||||+|||++|++|++++...         ..++
T Consensus         3 ~msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~---------~~~~   73 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE---------NNGI   73 (208)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS---------SSSC
T ss_pred             ccCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc---------ccCc
Confidence            4689999999999999999999999999999999999985 99999999999999999999876432         2356


Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCee
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLK  536 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~  536 (633)
                      ++||++||++||.|+++.+..+.... +.++.+++|+.....+...+.  +++|||+||++|.+++.+.   ...+++++
T Consensus        74 ~~lil~pt~~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~--~~~IlV~TP~~l~~~l~~~---~~~~~~l~  147 (208)
T d1hv8a1          74 EAIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK--NANIVVGTPGRILDHINRG---TLNLKNVK  147 (208)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH--TCSEEEECHHHHHHHHHTT---CSCTTSCC
T ss_pred             ceEEEeeccccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhcC--CCCEEEEChHHHHHHHHcC---CCCcccCc
Confidence            89999999999999999999998755 788999999988777666654  4799999999999999776   46789999


Q ss_pred             EEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          537 MLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       537 ~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +|||||||+|++.++..++..|+..+++++|+++||||+|+++
T Consensus       148 ~lViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v  190 (208)
T d1hv8a1         148 YFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREI  190 (208)
T ss_dssp             EEEEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHH
T ss_pred             EEEEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEccCCHHH
Confidence            9999999999999999999999999999999999999999875

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=7.6e-36  Score=292.91  Aligned_cols=188  Identities=36%  Similarity=0.579  Sum_probs=169.7

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      +|++|+|++.++++|.++||.+|||+|+++||+++.|+|++++||||||||+||++|+++++....        ..++++
T Consensus         2 sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~~--------~~~~~~   73 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKL--------NKIQAL   73 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTTS--------CSCCEE
T ss_pred             ChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhcccccccccccc--------ccccce
Confidence            699999999999999999999999999999999999999999999999999999999998865432        235699


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEE
Q 006737          460 ILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLV  539 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LV  539 (633)
                      +++|+++++.|....+..+... .++++.+++|+.........+. .+++|||+||++|.+++...   ...+.++++||
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~g~~~~~~~~~~l~-~~~~Ili~TP~~l~~~l~~~---~~~l~~l~~lV  148 (206)
T d1s2ma1          74 IMVPTRELALQTSQVVRTLGKH-CGISCMVTTGGTNLRDDILRLN-ETVHILVGTPGRVLDLASRK---VADLSDCSLFI  148 (206)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTT-TTCCEEEECSSSCHHHHHHHTT-SCCSEEEECHHHHHHHHHTT---CSCCTTCCEEE
T ss_pred             eeccchhhhhhhhhhhhhcccc-cCeeEEeecCccchhhHHHHhc-ccceEEEECCcccccccccc---eeecccceEEE
Confidence            9999999999999888887654 4899999999998776666554 45899999999999999876   46799999999


Q ss_pred             EecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhhh
Q 006737          540 LDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKELV  580 (633)
Q Consensus       540 IDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el~  580 (633)
                      |||||.|++.+|...+..|+..+++.+|+++||||+|+++.
T Consensus       149 ~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~  189 (206)
T d1s2ma1         149 MDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVK  189 (206)
T ss_dssp             EESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHH
T ss_pred             eechhhhhhhhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHH
Confidence            99999999999999999999999999999999999998853

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=1.4e-34  Score=283.11  Aligned_cols=189  Identities=35%  Similarity=0.571  Sum_probs=163.4

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ++|++|+|++.++++|.+.||.+||++|++|||.+++|+|++++||||||||+||++|+++.+.....        .+.+
T Consensus         1 t~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~~~--------~~~~   72 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERA--------EVQA   72 (209)
T ss_dssp             CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTTSC--------SCCE
T ss_pred             CccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccccc--------cccc
Confidence            46999999999999999999999999999999999999999999999999999999999987654322        3468


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCC---CceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          459 LILCPTRELASQIAAEAIALLKNHD---GIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~---~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      ++++|+++++.+.+..+........   ...+.++.++.....+.... ..+++|+|+||++|..++.+.   ...++++
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~TP~~l~~~~~~~---~~~~~~l  148 (209)
T d1q0ua_          73 VITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL-NVQPHIVIGTPGRINDFIREQ---ALDVHTA  148 (209)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCC-SSCCSEEEECHHHHHHHHHTT---CCCGGGC
T ss_pred             cccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHh-ccCceEEEecCchhhhhhhhh---ccccccc
Confidence            9999999999999988887765442   35566677766655443333 345899999999999998776   3568999


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      +++||||||.|++++|..++..|+..+++++|+++||||+|+++
T Consensus       149 ~~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v  192 (209)
T d1q0ua_         149 HILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKL  192 (209)
T ss_dssp             CEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGG
T ss_pred             eEEEEeecccccccccHHHHHHHHHHCCCCCEEEEEEccCCHHH
Confidence            99999999999999999999999999999999999999999885

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.92  E-value=1.2e-25  Score=218.27  Aligned_cols=173  Identities=20%  Similarity=0.245  Sum_probs=137.8

Q ss_pred             CCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccH
Q 006737          386 ISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTR  465 (633)
Q Consensus       386 L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTR  465 (633)
                      +++.++..|.+.||.+|+|+|.++++.+++|+|+++++|||+|||++++++++..+.+.           .++|||+|++
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~~-----------~~vl~l~P~~   78 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG-----------GKSLYVVPLR   78 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHTT-----------CCEEEEESSH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhcc-----------CcceeecccH
Confidence            56788999999999999999999999999999999999999999999999998877543           2599999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccc
Q 006737          466 ELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADH  545 (633)
Q Consensus       466 eLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~  545 (633)
                      +|+.|+++.++++...  ...+....|+.....    .....++|+++||..+..++.+.   ...+..+++||+||+|.
T Consensus        79 ~L~~q~~~~~~~~~~~--~~~v~~~~~~~~~~~----~~~~~~~ii~~~~~~~~~~~~~~---~~~~~~~~~ii~DE~h~  149 (202)
T d2p6ra3          79 ALAGEKYESFKKWEKI--GLRIGISTGDYESRD----EHLGDCDIIVTTSEKADSLIRNR---ASWIKAVSCLVVDEIHL  149 (202)
T ss_dssp             HHHHHHHHHHTTTTTT--TCCEEEECSSCBCCS----SCSTTCSEEEEEHHHHHHHHHTT---CSGGGGCCEEEETTGGG
T ss_pred             HHHHHHHHHHHHHhhc--cccceeeccCccccc----ccccccceeeeccHHHHHHHhcc---chhhhhhhhccccHHHH
Confidence            9999999999877653  345556666554332    12234789999999999988765   34578899999999999


Q ss_pred             cCCcChHHHHHHH---HHHCCCCCcEEEEeccCChh
Q 006737          546 LLDLGFRKDVENI---VDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       546 Lld~gf~~~l~~I---l~~lpk~~Q~IlfSATl~~e  578 (633)
                      +.+..+...+..+   +..+++++|+|+||||+++.
T Consensus       150 ~~~~~r~~~~~~~l~~i~~~~~~~~~l~lSATl~n~  185 (202)
T d2p6ra3         150 LDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNV  185 (202)
T ss_dssp             GGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTTH
T ss_pred             hcccccchHHHHHHHHHHhcCCCCcEEEEcCCCCcH
Confidence            9887765554444   44556789999999999875

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.92  E-value=5.7e-26  Score=225.89  Aligned_cols=179  Identities=17%  Similarity=0.103  Sum_probs=130.2

Q ss_pred             CccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEE
Q 006737          380 RFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVL  459 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vL  459 (633)
                      .|.+..+.+.+ ..+.+.++.+|+++|+.+++.++.|+|++++||||+|||++|+++++....+.           .++|
T Consensus        23 ~~~~~~~~~~~-~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~~-----------~rvl   90 (237)
T d1gkub1          23 LFPEDFLLKEF-VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKG-----------KRCY   90 (237)
T ss_dssp             CCTTHHHHHHH-HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTTS-----------CCEE
T ss_pred             cCccchhHHHH-HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHhc-----------CeEE
Confidence            34444334443 55667789999999999999999999999999999999999999988655322           3699


Q ss_pred             EEcccHHHHHHHHHHHHHHHhcCC---CceEEEEECCccchHHHHHHh-cCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          460 ILCPTRELASQIAAEAIALLKNHD---GIGVLTLVGGTRFKVDQRRLE-SDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       460 ILvPTReLa~Qi~~~l~~l~~~~~---~i~v~~l~Gg~~~~~~~~~l~-~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      ||+||++|+.|+++.+++++....   ...+....++.........+. ...++|||+||++|.+.+       ..+.++
T Consensus        91 iv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~-------~~~~~~  163 (237)
T d1gkub1          91 VIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHY-------RELGHF  163 (237)
T ss_dssp             EEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCS-------TTSCCC
T ss_pred             EEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhh-------hhcCCC
Confidence            999999999999999999986542   122344444444443333322 234689999999876533       346789


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHH-------------CCCCCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDC-------------LPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~-------------lpk~~Q~IlfSATl~~el  579 (633)
                      ++|||||||.|++.+..  +..++..             .+...|+|++|||+++.+
T Consensus       164 ~~vVvDE~d~~l~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~  218 (237)
T d1gkub1         164 DFIFVDDVDAILKASKN--VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGK  218 (237)
T ss_dssp             SEEEESCHHHHHTSTHH--HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCT
T ss_pred             CEEEEEChhhhhhcccc--hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCccc
Confidence            99999999999876532  2222222             234678999999998764

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=99.91  E-value=5e-25  Score=214.06  Aligned_cols=177  Identities=19%  Similarity=0.235  Sum_probs=135.3

Q ss_pred             CccccCCCHHHHHHHHHc-CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          380 RFDECGISPLTIKALTAA-GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       380 ~F~el~L~~~Ll~~L~~~-g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ..+.++|.+.+.+.|++. ||..++|+|.++|++++.|+|+++++|||||||++|.+|++..              ..++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~--------------~~~~   68 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL--------------NGLT   68 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS--------------SSEE
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc--------------cCce
Confidence            357789999999999987 9999999999999999999999999999999999999998742              1269


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccch---HHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK---VDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~---~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      +|++|+++|+.|+.+.++.+..     ............   ...........+|+++||..+.......   ......+
T Consensus        69 ~~v~P~~~L~~q~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~---~~~~~~v  140 (206)
T d1oywa2          69 VVVSPLISLMKDQVDQLQANGV-----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLE---HLAHWNP  140 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHTTC-----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHH---HHTTSCE
T ss_pred             EEeccchhhhhhHHHHHHhhcc-----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcc---cchhhee
Confidence            9999999999999998887742     233333322211   2223334456799999999886543332   2456789


Q ss_pred             eEEEEecccccCCcCh--HH---HHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLGF--RK---DVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf--~~---~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      .+||+||||++.++++  ..   .+..++..++ ++|+++||||+++.+
T Consensus       141 ~~lviDEaH~~~~~~~~~~~~~~~~~~l~~~~~-~~~ii~lSATl~~~v  188 (206)
T d1oywa2         141 VLLAVDEAHCISQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTT  188 (206)
T ss_dssp             EEEEESSGGGGCTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHH
T ss_pred             eeeeeeeeeeeeccccchHHHHHHHHHHHHhCC-CCceEEEEeCCCHHH
Confidence            9999999999998763  22   3334455554 699999999999975

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.87  E-value=1.5e-21  Score=187.61  Aligned_cols=162  Identities=20%  Similarity=0.212  Sum_probs=128.1

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHH
Q 006737          400 IQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALL  479 (633)
Q Consensus       400 ~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~  479 (633)
                      -+|+++|.+++..+. ++|+|+++|||+|||+++++++...+.+..          -++|||+|+++|+.|.++.+.+++
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~~----------~~il~i~P~~~L~~q~~~~~~~~~   76 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYG----------GKVLMLAPTKPLVLQHAESFRRLF   76 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHSC----------SCEEEECSSHHHHHHHHHHHHHHB
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhcC----------CcEEEEcCchHHHHHHHHHHHHhh
Confidence            379999999999876 568999999999999999988877665432          148999999999999999999987


Q ss_pred             hcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHH
Q 006737          480 KNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIV  559 (633)
Q Consensus       480 ~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il  559 (633)
                      ... +..+..+.++.........+..  ++|+|+||+.+...+...   ...+.++++||+||||++........+...+
T Consensus        77 ~~~-~~~v~~~~~~~~~~~~~~~~~~--~~i~i~t~~~~~~~~~~~---~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~  150 (200)
T d1wp9a1          77 NLP-PEKIVALTGEKSPEERSKAWAR--AKVIVATPQTIENDLLAG---RISLEDVSLIVFDEAHRAVGNYAYVFIAREY  150 (200)
T ss_dssp             CSC-GGGEEEECSCSCHHHHHHHHHH--CSEEEECHHHHHHHHHTT---SCCTTSCSEEEEETGGGCSTTCHHHHHHHHH
T ss_pred             ccc-ccceeeeecccchhHHHHhhhc--ccccccccchhHHHHhhh---hhhccccceEEEEehhhhhcchhHHHHHHHH
Confidence            543 6778777777665544444333  589999999999888765   3567899999999999998765555555555


Q ss_pred             HHCCCCCcEEEEeccCChh
Q 006737          560 DCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       560 ~~lpk~~Q~IlfSATl~~e  578 (633)
                      .......++++||||.+..
T Consensus       151 ~~~~~~~~~l~~SATp~~~  169 (200)
T d1wp9a1         151 KRQAKNPLVIGLTASPGST  169 (200)
T ss_dssp             HHHCSSCCEEEEESCSCSS
T ss_pred             HhcCCCCcEEEEEecCCCc
Confidence            5555678999999998654

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=99.80  E-value=2e-20  Score=189.95  Aligned_cols=138  Identities=17%  Similarity=0.232  Sum_probs=98.3

Q ss_pred             HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEEC
Q 006737          413 CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG  492 (633)
Q Consensus       413 il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~G  492 (633)
                      +..++++|+.||||||||++|+++++.......          .++|||+||++||.|+++.+..+.....     ... 
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~~----------~~~lvi~Ptr~La~q~~~~l~~~~~~~~-----~~~-   69 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRG----------LRTLILAPTRVVAAEMEEALRGLPIRYQ-----TPA-   69 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHHT----------CCEEEEESSHHHHHHHHHHTTTSCCBCC-----C---
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhcC----------CEEEEEccHHHHHHHHHHHHhcCCccee-----eeE-
Confidence            457899999999999999999989887766542          3699999999999999888765532211     110 


Q ss_pred             CccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcCh--HHHHHHHHHHCCCCCcEEE
Q 006737          493 GTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGF--RKDVENIVDCLPRRRQSLL  570 (633)
Q Consensus       493 g~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf--~~~l~~Il~~lpk~~Q~Il  570 (633)
                             ..........|+++||+.|..++...    ..+.++++|||||||++..+++  ...+..+.  .....|+++
T Consensus        70 -------~~~~~~~~~~i~~~t~~~l~~~~~~~----~~~~~~~~vViDE~H~~~~~~~~~~~~l~~~~--~~~~~~~v~  136 (305)
T d2bmfa2          70 -------IRAEHTGREIVDLMCHATFTMRLLSP----IRVPNYNLIIMDEAHFTDPASIAARGYISTRV--EMGEAAGIF  136 (305)
T ss_dssp             -------------CCCSEEEEEHHHHHHHHTSS----SCCCCCSEEEEESTTCCSHHHHHHHHHHHHHH--HHTSCEEEE
T ss_pred             -------EeecccCccccccCCcHHHHHHHhcC----ccccceeEEEeeeeeecchhhHHHHHHHHHhh--ccccceEEE
Confidence                   01112234589999999988877544    4578899999999999987653  22222221  235789999


Q ss_pred             EeccCChhh
Q 006737          571 FSATMPKEL  579 (633)
Q Consensus       571 fSATl~~el  579 (633)
                      +|||.+...
T Consensus       137 ~SAT~~~~~  145 (305)
T d2bmfa2         137 MTATPPGSR  145 (305)
T ss_dssp             ECSSCTTCC
T ss_pred             eecCCCcce
Confidence            999998764

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

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=99.66  E-value=4.9e-17  Score=145.00  Aligned_cols=136  Identities=19%  Similarity=0.242  Sum_probs=90.6

Q ss_pred             HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEEC
Q 006737          413 CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVG  492 (633)
Q Consensus       413 il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~G  492 (633)
                      +..|+++++++|||+|||++++..++.......          .++||++|+++|+.|.++.+...     ...+  ...
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~~----------~~vli~~p~~~l~~q~~~~~~~~-----~~~~--~~~   66 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECARRR----------LRTLVLAPTRVVLSEMKEAFHGL-----DVKF--HTQ   66 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHHTT----------CCEEEEESSHHHHHHHHHHTTTS-----CEEE--ESS
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhhcC----------ceeeeeecchhHHHHHHHHhhhh-----hhhh--ccc
Confidence            346889999999999999988766666654432          35999999999999987665322     2222  211


Q ss_pred             CccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHH-HHHHHHHHCCCCCcEEEE
Q 006737          493 GTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRK-DVENIVDCLPRRRQSLLF  571 (633)
Q Consensus       493 g~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~-~l~~Il~~lpk~~Q~Ilf  571 (633)
                      .....      ......+.++|...+.......    ..+.++++|||||||.+...++.. .+...+.. .++.++|+|
T Consensus        67 ~~~~~------~~~~~~~~~~~~~~l~~~~~~~----~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~l  135 (140)
T d1yksa1          67 AFSAH------GSGREVIDAMCHATLTYRMLEP----TRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILM  135 (140)
T ss_dssp             CCCCC------CCSSCCEEEEEHHHHHHHHTSS----SCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEE
T ss_pred             ccccc------cccccchhhhhHHHHHHHHhcc----ccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEE
Confidence            11111      1122467888888776655443    567899999999999886443221 12222223 357999999


Q ss_pred             eccCC
Q 006737          572 SATMP  576 (633)
Q Consensus       572 SATl~  576 (633)
                      |||.|
T Consensus       136 TATPp  140 (140)
T d1yksa1         136 TATPP  140 (140)
T ss_dssp             CSSCT
T ss_pred             EcCCC
Confidence            99987

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=99.63  E-value=3.2e-15  Score=148.21  Aligned_cols=170  Identities=21%  Similarity=0.168  Sum_probs=130.0

Q ss_pred             CCCHHHHHHHHHcCCCCCcHHHHHHHHHHhC----C--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEE
Q 006737          385 GISPLTIKALTAAGYIQMTRVQEATLSACLE----G--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYV  458 (633)
Q Consensus       385 ~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~----g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~v  458 (633)
                      ..+....+.+.+.-...+|+-|..++..|.+    +  .+.+++|.||||||.+|+..++..+...           -+|
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g-----------~qv  107 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNH-----------KQV  107 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTTT-----------CEE
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHcC-----------Cce
Confidence            3456777777766556899999999988754    3  3789999999999999999887766332           369


Q ss_pred             EEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCe
Q 006737          459 LILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGL  535 (633)
Q Consensus       459 LILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l  535 (633)
                      ++++||..|+.|.++.+++++... ++.+.++++.......   ...+..+.++|||+|--.|.    .    .+.+.++
T Consensus       108 ~~l~Pt~~La~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~----~----~~~f~~L  178 (233)
T d2eyqa3         108 AVLVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ----S----DVKFKDL  178 (233)
T ss_dssp             EEECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH----S----CCCCSSE
T ss_pred             EEEccHHHhHHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc----c----CCccccc
Confidence            999999999999999999998766 7889999998775543   34667788999999954443    2    2567899


Q ss_pred             eEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChhh
Q 006737          536 KMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKEL  579 (633)
Q Consensus       536 ~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~el  579 (633)
                      .+|||||-|+..-   . +-..+ .....+..++++|||-.+..
T Consensus       179 gLiIiDEeH~fg~---k-Q~~~l-~~~~~~~~~l~~SATPiprt  217 (233)
T d2eyqa3         179 GLLIVDEEHRFGV---R-HKERI-KAMRANVDILTLTATPIPRT  217 (233)
T ss_dssp             EEEEEESGGGSCH---H-HHHHH-HHHHTTSEEEEEESSCCCHH
T ss_pred             cceeeechhhhhh---H-HHHHH-HhhCCCCCEEEEecchhHHH
Confidence            9999999998542   2 22223 22334688999999987773

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=99.60  E-value=8.2e-16  Score=156.77  Aligned_cols=153  Identities=16%  Similarity=0.179  Sum_probs=109.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .|++.|.+++..++.++..++.+|||+|||++..+ ++..+.....         .++|||||+++|+.|.++.+.+++.
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~~~---------~k~Liivp~~~Lv~Q~~~~f~~~~~  182 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQAL-LARYYLENYE---------GKILIIVPTTALTTQMADDFVDYRL  182 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHH-HHHHHHHHCS---------SEEEEECSSHHHHHHHHHHHHHHTS
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHH-HHHHhhhccc---------ceEEEEEcCchhHHHHHHHHHHhhc
Confidence            69999999999999999999999999999987544 3333333221         2699999999999999999998864


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                      .. ...+..+.+|......    .....+|+|+|+..+..+..      ..+.++++||+||||++-    ...+..|+.
T Consensus       183 ~~-~~~~~~~~~g~~~~~~----~~~~~~i~i~t~qs~~~~~~------~~~~~f~~VIvDEaH~~~----a~~~~~il~  247 (282)
T d1rifa_         183 FS-HAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVKQPK------EWFSQFGMMMNDECHLAT----GKSISSIIS  247 (282)
T ss_dssp             CC-GGGEEECSTTCSSTTC----CCTTCSEEEECHHHHTTSCG------GGGGGEEEEEEETGGGCC----HHHHHHHTT
T ss_pred             cc-cccceeecceeccccc----ccccceEEEEeeehhhhhcc------cccCCCCEEEEECCCCCC----chhHHHHHH
Confidence            32 3345555555432211    12236899999877654322      236789999999999975    346677777


Q ss_pred             HCCCCCcEEEEeccCChh
Q 006737          561 CLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl~~e  578 (633)
                      .+.+....++||||++..
T Consensus       248 ~~~~~~~rlGlTaT~~~~  265 (282)
T d1rifa_         248 GLNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             TCTTCCEEEEECSSCCTT
T ss_pred             hccCCCeEEEEEeecCCC
Confidence            665444468999998654

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.60  E-value=4.4e-15  Score=149.78  Aligned_cols=164  Identities=16%  Similarity=0.213  Sum_probs=122.3

Q ss_pred             HHHHHHH-HcCCCCCcHHHHHHHHHHhC----C--CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEE
Q 006737          389 LTIKALT-AAGYIQMTRVQEATLSACLE----G--KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLIL  461 (633)
Q Consensus       389 ~Ll~~L~-~~g~~~pt~iQ~~aIp~il~----g--rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLIL  461 (633)
                      .+.+.+. +..| .+|.-|..|+..|..    +  .+.+++|-||||||.+|+..++..+....           +|+++
T Consensus        71 ~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~-----------q~~~m  138 (264)
T d1gm5a3          71 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGF-----------QTAFM  138 (264)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHHTS-----------CEEEE
T ss_pred             HHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhccc-----------ceeEE
Confidence            4444444 4455 799999999998864    2  37899999999999999998887776543           49999


Q ss_pred             cccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEE
Q 006737          462 CPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKML  538 (633)
Q Consensus       462 vPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~L  538 (633)
                      +||..||.|.++.+.+++... ++.+.+++|+......   ...+.++.++|||||-.-|.+    .    +.+.++.+|
T Consensus       139 ~Pt~~La~Qh~~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~----~----~~f~~Lglv  209 (264)
T d1gm5a3         139 VPTSILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE----D----VHFKNLGLV  209 (264)
T ss_dssp             CSCHHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH----C----CCCSCCCEE
T ss_pred             eehHhhhHHHHHHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC----C----CCcccccee
Confidence            999999999999999999766 7889999998875542   455667889999999654432    2    557799999


Q ss_pred             EEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          539 VLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       539 VIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ||||-|+..-...     ..+..-..++.++++|||--+.
T Consensus       210 iiDEqH~fgv~Qr-----~~l~~~~~~~~~l~~SATPipr  244 (264)
T d1gm5a3         210 IIDEQHRFGVKQR-----EALMNKGKMVDTLVMSATPIPR  244 (264)
T ss_dssp             EEESCCCC----------CCCCSSSSCCCEEEEESSCCCH
T ss_pred             eeccccccchhhH-----HHHHHhCcCCCEEEEECCCCHH
Confidence            9999999763221     1111122358899999996555

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=99.60  E-value=1.6e-15  Score=147.23  Aligned_cols=136  Identities=23%  Similarity=0.199  Sum_probs=99.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      +|+++|.+++..+++++..++++|||+|||++++.. +..+   .          .++|||||+++|+.|..+.+..+..
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~-~~~~---~----------~~~Liv~p~~~L~~q~~~~~~~~~~  135 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAA-INEL---S----------TPTLIVVPTLALAEQWKERLGIFGE  135 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHH-HHHS---C----------SCEEEEESSHHHHHHHHHHHGGGCG
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhH-HHHh---c----------CceeEEEcccchHHHHHHHHHhhcc
Confidence            689999999999999999999999999999875432 2221   1          2489999999999999988876532


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVD  560 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~  560 (633)
                          ..+....|+..          ...+|+|+|...+.......      ...+++||+||||++...    .+..++.
T Consensus       136 ----~~~~~~~~~~~----------~~~~i~i~t~~~~~~~~~~~------~~~~~lvIiDEaH~~~a~----~~~~i~~  191 (206)
T d2fz4a1         136 ----EYVGEFSGRIK----------ELKPLTVSTYDSAYVNAEKL------GNRFMLLIFDEVHHLPAE----SYVQIAQ  191 (206)
T ss_dssp             ----GGEEEESSSCB----------CCCSEEEEEHHHHHHTHHHH------TTTCSEEEEECSSCCCTT----THHHHHH
T ss_pred             ----cchhhcccccc----------cccccccceehhhhhhhHhh------CCcCCEEEEECCeeCCcH----HHHHHHh
Confidence                23444444432          12479999998877654432      357889999999998643    3455565


Q ss_pred             HCCCCCcEEEEeccC
Q 006737          561 CLPRRRQSLLFSATM  575 (633)
Q Consensus       561 ~lpk~~Q~IlfSATl  575 (633)
                      .++ ....++||||+
T Consensus       192 ~~~-~~~~lgLTATl  205 (206)
T d2fz4a1         192 MSI-APFRLGLTATF  205 (206)
T ss_dssp             TCC-CSEEEEEEESC
T ss_pred             ccC-CCcEEEEecCC
Confidence            554 34578899997

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=99.52  E-value=1.9e-14  Score=129.64  Aligned_cols=127  Identities=20%  Similarity=0.135  Sum_probs=86.4

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCc
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGT  494 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~  494 (633)
                      ..+..++.+|||||||+.+  +.+  +...          +.++||++|+++|+.|+.+.+.+.+...    .....++.
T Consensus         7 ~~~~~ll~apTGsGKT~~~--~~~--~~~~----------~~~vli~~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~   68 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKV--PAA--YAAQ----------GYKVLVLNPSVAATLGFGAYMSKAHGVD----PNIRTGVR   68 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHH--HHH--HHTT----------TCCEEEEESCHHHHHHHHHHHHHHHSCC----CEEECSSC
T ss_pred             CCCEEEEEeCCCCCHHHHH--HHH--HHHc----------CCcEEEEcChHHHHHHHHHHHHHHhhcc----cccccccc
Confidence            3567899999999999743  222  2221          1359999999999999999998876432    23333333


Q ss_pred             cchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHHHHHHHCC--CCCcEEEEe
Q 006737          495 RFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVENIVDCLP--RRRQSLLFS  572 (633)
Q Consensus       495 ~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lp--k~~Q~IlfS  572 (633)
                      ...        ....++++|.+.+.....      ..+.++++|||||+|++... ....+..++..+.  .+.++|++|
T Consensus        69 ~~~--------~~~~~~~~~~~~~~~~~~------~~~~~~~~vIiDE~H~~~~~-~~~~~~~~l~~~~~~~~~~~l~~T  133 (136)
T d1a1va1          69 TIT--------TGSPITYSTYGKFLADGG------CSGGAYDIIICDECHSTDAT-SILGIGTVLDQAETAGARLVVLAT  133 (136)
T ss_dssp             EEC--------CCCSEEEEEHHHHHHTTG------GGGCCCSEEEEETTTCCSHH-HHHHHHHHHHHTTTTTCSEEEEEE
T ss_pred             ccc--------cccceEEEeeeeeccccc------hhhhcCCEEEEecccccCHH-HHHHHHHHHHHHHHCCCCcEEEEe
Confidence            221        124789999887654432      34788999999999987432 3334556666654  356789999


Q ss_pred             cc
Q 006737          573 AT  574 (633)
Q Consensus       573 AT  574 (633)
                      ||
T Consensus       134 AT  135 (136)
T d1a1va1         134 AT  135 (136)
T ss_dssp             SS
T ss_pred             CC
Confidence            98

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=98.76  E-value=9.8e-08  Score=96.25  Aligned_cols=163  Identities=16%  Similarity=0.232  Sum_probs=101.6

Q ss_pred             CCcHHHHHHHHHHh---------CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHH
Q 006737          401 QMTRVQEATLSACL---------EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQI  471 (633)
Q Consensus       401 ~pt~iQ~~aIp~il---------~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi  471 (633)
                      .+.|+|.+++.-+.         .+..+|++-..|.|||+..+ .++..+........   .....+|||+|.. |+.|.
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qai-a~l~~l~~~~~~~~---~~~~~~LIV~P~s-l~~qW  129 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCI-TLIWTLLKQSPDCK---PEIDKVIVVSPSS-LVRNW  129 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHH-HHHHHHHHCCTTSS---CSCSCEEEEECHH-HHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHH-HHHHHHHHhccccc---CCCCcEEEEccch-hhHHH
Confidence            67899999997552         34568888899999998533 34444444322110   1112489999975 88899


Q ss_pred             HHHHHHHHhcCCCceEEEEECCccchHHHHH---Hhc----CCCcEEEECchhhHHHHhcccCcccccCCeeEEEEeccc
Q 006737          472 AAEAIALLKNHDGIGVLTLVGGTRFKVDQRR---LES----DPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEAD  544 (633)
Q Consensus       472 ~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~---l~~----~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD  544 (633)
                      .+++.+++..  ...+..++++.........   ...    ...+|+|+|...+......     ..-....+||+||||
T Consensus       130 ~~Ei~k~~~~--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~-----l~~~~~~~vI~DEaH  202 (298)
T d1z3ix2         130 YNEVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV-----LHKGKVGLVICDEGH  202 (298)
T ss_dssp             HHHHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT-----TTTSCCCEEEETTGG
T ss_pred             HHHHHhhcCC--ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchhc-----ccccceeeeeccccc
Confidence            9999988753  3455566666543322211   111    2357999998877654432     222356789999999


Q ss_pred             ccCCcChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          545 HLLDLGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       545 ~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+-+..  ......+..+. ....+++|||.-..
T Consensus       203 ~ikn~~--s~~~~a~~~l~-~~~rllLTGTPi~N  233 (298)
T d1z3ix2         203 RLKNSD--NQTYLALNSMN-AQRRVLISGTPIQN  233 (298)
T ss_dssp             GCCTTC--HHHHHHHHHHC-CSEEEEECSSCSGG
T ss_pred             cccccc--chhhhhhhccc-cceeeeecchHHhh
Confidence            997653  22222333333 45578999998544

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=98.49  E-value=2e-07  Score=90.21  Aligned_cols=150  Identities=15%  Similarity=0.189  Sum_probs=93.6

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHH
Q 006737          401 QMTRVQEATLSACL----EGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAI  476 (633)
Q Consensus       401 ~pt~iQ~~aIp~il----~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~  476 (633)
                      .+.|+|.+++..+.    .+..+|+.-.+|.|||+..+ .++..+......        .++|||+| ..++.|..+++.
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i-~~~~~~~~~~~~--------~~~LIv~p-~~l~~~W~~e~~   81 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKENEL--------TPSLVICP-LSVLKNWEEELS   81 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHTTCC--------SSEEEEEC-STTHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHH-Hhhhhhhhcccc--------cccceecc-hhhhhHHHHHHH
Confidence            57899999987543    35578999999999999754 344444443221        14899999 566778888888


Q ss_pred             HHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccCcccccCCeeEEEEecccccCCcChHHHHH
Q 006737          477 ALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSGLSVRLMGLKMLVLDEADHLLDLGFRKDVE  556 (633)
Q Consensus       477 ~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~  556 (633)
                      .+..   ...+..........      .....+|+|+|...+...-.      +.--...+||+||||.+-...-  ...
T Consensus        82 ~~~~---~~~~~~~~~~~~~~------~~~~~~vvi~~~~~~~~~~~------l~~~~~~~vI~DEah~~k~~~s--~~~  144 (230)
T d1z63a1          82 KFAP---HLRFAVFHEDRSKI------KLEDYDIILTTYAVLLRDTR------LKEVEWKYIVIDEAQNIKNPQT--KIF  144 (230)
T ss_dssp             HHCT---TSCEEECSSSTTSC------CGGGSSEEEEEHHHHTTCHH------HHTCCEEEEEEETGGGGSCTTS--HHH
T ss_pred             hhcc---cccceeeccccchh------hccCcCEEEeeHHHHHhHHH------HhcccceEEEEEhhhcccccch--hhh
Confidence            7754   33343332222111      11235899999877643221      1122567899999999976532  222


Q ss_pred             HHHHHCCCCCcEEEEeccCChh
Q 006737          557 NIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       557 ~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      ..+..+. ....+++|||.-..
T Consensus       145 ~~~~~l~-a~~r~~LTgTPi~n  165 (230)
T d1z63a1         145 KAVKELK-SKYRIALTGTPIEN  165 (230)
T ss_dssp             HHHHTSC-EEEEEEECSSCSTT
T ss_pred             hhhhhhc-cceEEEEecchHHh
Confidence            3334443 33468899997544

>d1tf5a3 c.37.1.19 (A:1-226,A:349-395) Translocation ATPase SecA, nucleotide-binding domains {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Translocation ATPase SecA, nucleotide-binding domains
species: Bacillus subtilis [TaxId: 1423]

Probab=98.37  E-value=1.2e-06  Score=86.78  Aligned_cols=130  Identities=23%  Similarity=0.239  Sum_probs=98.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      +++++|.-.--.+..|+  |+...||-|||++..+|+.-..+..+           .|-||+..--||..=.+.+..+..
T Consensus        80 RhyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~g~-----------~vhvvTvNdyLA~RDae~m~~iy~  146 (273)
T d1tf5a3          80 FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALTGK-----------GVHVVTVNEYLASRDAEQMGKIFE  146 (273)
T ss_dssp             CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTTSS-----------CEEEEESSHHHHHHHHHHHHHHHH
T ss_pred             EEehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhcCC-----------CceEEecCccccchhhhHHhHHHH
Confidence            78899988888888886  89999999999999998875544432           277888889999887777888877


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhh-HHHHhcccCc---ccccCCeeEEEEecccccC
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRL-LDHIENKSGL---SVRLMGLKMLVLDEADHLL  547 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrL-l~lL~~~~~~---~~~Ls~l~~LVIDEAD~Ll  547 (633)
                      .+ |+.|.++..+..........   .|||+++|..-| .++|...-..   ......+.+.||||+|.++
T Consensus       147 ~l-Glsvg~~~~~~~~~~r~~~Y---~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsil  213 (273)
T d1tf5a3         147 FL-GLTVGLNLNSMSKDEKREAY---AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  213 (273)
T ss_dssp             HT-TCCEEECCTTSCHHHHHHHH---HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             Hc-CCCccccccccCHHHHHHHh---hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhh
Confidence            66 89999988776655444433   379999999887 4555433111   1235678999999999876

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.82  E-value=2.1e-05  Score=81.28  Aligned_cols=146  Identities=18%  Similarity=0.218  Sum_probs=86.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .....|..|+..++.++-++|+|+.|||||... ..++..+.....      ..+.++++++||-..|..+.+.+.....
T Consensus       148 ~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~~~------~~~~~I~l~ApTgkAA~~L~e~~~~~~~  220 (359)
T d1w36d1         148 DEINWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQMAD------GERCRIRLAAPTGKAAARLTESLGKALR  220 (359)
T ss_dssp             TSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH-HHHHHHHHHTCS------SCCCCEEEEBSSHHHHHHHHHHHTHHHH
T ss_pred             ccccHHHHHHHHHHcCCeEEEEcCCCCCceehH-HHHHHHHHHHHh------ccCCeEEEecCcHHHHHHHHHHHHHHHh
Confidence            456789999999999999999999999999863 333444443221      1234699999999999888777655443


Q ss_pred             cCCCceEEEEECCccchHHHHHHhcCCCcEEEECchhhHHHHhcccC---cccccCCeeEEEEecccccCCcChHHHHHH
Q 006737          481 NHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATPGRLLDHIENKSG---LSVRLMGLKMLVLDEADHLLDLGFRKDVEN  557 (633)
Q Consensus       481 ~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTPgrLl~lL~~~~~---~~~~Ls~l~~LVIDEAD~Lld~gf~~~l~~  557 (633)
                      .......      .. .         ....-..|..+++........   .......+++||||||-.+.    ...+..
T Consensus       221 ~~~~~~~------~~-~---------~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~  280 (359)
T d1w36d1         221 QLPLTDE------QK-K---------RIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSR  280 (359)
T ss_dssp             HSSCCSC------CC-C---------SCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHH
T ss_pred             hcCchhh------hh-h---------hhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHH
Confidence            2210000      00 0         000011222222211111000   01223467899999998764    346778


Q ss_pred             HHHHCCCCCcEEEEec
Q 006737          558 IVDCLPRRRQSLLFSA  573 (633)
Q Consensus       558 Il~~lpk~~Q~IlfSA  573 (633)
                      ++..++...++|++-=
T Consensus       281 ll~~~~~~~~lILvGD  296 (359)
T d1w36d1         281 LIDALPDHARVIFLGD  296 (359)
T ss_dssp             HHHTCCTTCEEEEEEC
T ss_pred             HHHHhcCCCEEEEECC
Confidence            8888888888888753

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.05  E-value=0.00048  Score=67.37  Aligned_cols=71  Identities=14%  Similarity=0.136  Sum_probs=51.2

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      +++|-|.+++..  ....++|.|+.|||||.+.+. .+..++.....      ++-++|||++|+.+|..+...+.++..
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~-rv~~ll~~~~~------~~~~ILvlt~tn~a~~~i~~~~~~~~~   71 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITN-KIAHLIRGCGY------QARHIAAVTFTNKAAREMKERVGQTLG   71 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHH-HHHHHHHHHCC------CGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHH-HHHHHHHhcCC------ChhHEEEEeCcHHHHHHHHHHHHHhcC
Confidence            478999999975  245699999999999986443 33333333211      122599999999999999888877653

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=96.35  E-value=0.0034  Score=61.68  Aligned_cols=72  Identities=17%  Similarity=0.274  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          401 QMTRVQEATLSACLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       401 ~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .+++-|.+++...  +..++|.|+.|||||.+.+- -+..++.....      ++-++|++++|+.++..+...+.....
T Consensus        11 ~L~~eQ~~~v~~~--~g~~lV~g~aGSGKTt~l~~-ri~~ll~~~~~------~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          11 HLNKEQQEAVRTT--EGPLLIMAGAGSGKTRVLTH-RIAYLMAEKHV------APWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             TSCHHHHHHHHCC--SSCEEEEECTTSCHHHHHHH-HHHHHHHTTCC------CGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhCC--CCCEEEEecCCccHHHHHHH-HHHHHHHcCCC------CHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            5889999999853  45699999999999986433 33333333211      112589999999999999988877654


Q ss_pred             c
Q 006737          481 N  481 (633)
Q Consensus       481 ~  481 (633)
                      .
T Consensus        82 ~   82 (318)
T d1pjra1          82 G   82 (318)
T ss_dssp             G
T ss_pred             c
Confidence            3

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.85  E-value=0.016  Score=54.43  Aligned_cols=45  Identities=18%  Similarity=0.255  Sum_probs=29.2

Q ss_pred             CCeeEEEEecccccCCc-ChHHHHHHHHHHCC-CCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLDL-GFRKDVENIVDCLP-RRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~-gf~~~l~~Il~~lp-k~~Q~IlfSATl~~e  578 (633)
                      ...++||||++|.+... .....+..+++.+. ...++|+ |++.++.
T Consensus        96 ~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iii-ts~~~p~  142 (213)
T d1l8qa2          96 KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIIL-ASDRHPQ  142 (213)
T ss_dssp             HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEE-EESSCGG
T ss_pred             hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEE-ecCCcch
Confidence            36778999999999753 24556667776554 3455555 5555444

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=95.45  E-value=0.013  Score=54.68  Aligned_cols=40  Identities=20%  Similarity=0.199  Sum_probs=27.2

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....+++||||||.|... -...+.++++.-+++..+|+.+
T Consensus       106 ~~~~kviIide~d~l~~~-a~n~Llk~lEep~~~~~fIl~t  145 (207)
T d1a5ta2         106 LGGAKVVWVTDAALLTDA-AANALLKTLEEPPAETWFFLAT  145 (207)
T ss_dssp             TSSCEEEEESCGGGBCHH-HHHHHHHHHTSCCTTEEEEEEE
T ss_pred             cCccceEEechhhhhhhh-hhHHHHHHHHhhcccceeeeee
Confidence            456789999999999743 3556666666666555555444

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=94.85  E-value=0.25  Score=46.24  Aligned_cols=49  Identities=14%  Similarity=0.109  Sum_probs=32.3

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCC---CcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEG---KDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~g---rDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      ++|+++-..+.+.+.|...               +.++   +.+|++||+|+|||.+.. .++..+..
T Consensus         9 ~~~~dlig~~~~~~~L~~~---------------i~~~~~~~~~Ll~Gp~G~GKtt~a~-~~~~~l~~   60 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANG---------------LSLGRIHHAYLFSGTRGVGKTSIAR-LLAKGLNC   60 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHH---------------HHTTCCCSEEEEECSTTSSHHHHHH-HHHHHHHC
T ss_pred             CCHHHccChHHHHHHHHHH---------------HHcCCCCeeEEEECCCCCcHHHHHH-HHHHHhcC
Confidence            4688887778777776542               2223   248999999999997643 34444443

>d2eyqa5 c.37.1.19 (A:779-989) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=94.72  E-value=0.02  Score=54.05  Aligned_cols=92  Identities=17%  Similarity=0.187  Sum_probs=72.0

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      +|.||+|..+-+..+++.+.+++   +++++.+++|..+..+.   ...+..+..+|||||.     .++.+    +++.
T Consensus        33 Qvy~V~p~I~~~e~~~~~l~~~~---p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIEvG----iDvp  100 (211)
T d2eyqa5          33 QVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIETG----IDIP  100 (211)
T ss_dssp             EEEEECCCSSCHHHHHHHHHHHC---TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTGGG----SCCT
T ss_pred             eEEEEEcCccchhhHHHHHHHhC---CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhhhc----cCCC
Confidence            79999999998888888877775   47899999998875543   3456677899999995     33443    7888


Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCC
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPR  564 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk  564 (633)
                      +..++||..||++.    ..++.++....-+
T Consensus       101 nA~~iiI~~a~rfG----LaQLhQLRGRVGR  127 (211)
T d2eyqa5         101 TANTIIIERADHFG----LAQLHQLRGRVGR  127 (211)
T ss_dssp             TEEEEEETTTTSSC----HHHHHHHHTTCCB
T ss_pred             CCcEEEEecchhcc----ccccccccceeee
Confidence            99999999999965    4577777766654

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=94.53  E-value=0.049  Score=51.07  Aligned_cols=46  Identities=15%  Similarity=0.195  Sum_probs=26.5

Q ss_pred             CCeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEEeccCChh
Q 006737          533 MGLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLFSATMPKE  578 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~IlfSATl~~e  578 (633)
                      .+.++|+||=|=+... ......+..+....++..-+++++||...+
T Consensus        91 ~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~  137 (207)
T d1ls1a2          91 EARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQE  137 (207)
T ss_dssp             HTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHH
T ss_pred             ccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchh
Confidence            3455666666655432 224455556666666555566777777665

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.36  E-value=0.066  Score=49.55  Aligned_cols=43  Identities=9%  Similarity=0.132  Sum_probs=31.4

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      ....+++||||||.|... -...+.++++.-|++..+|++|...
T Consensus        77 ~~~~KviIId~ad~l~~~-aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          77 LYTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             SSSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             cCCCEEEEEeCccccchh-hhhHHHHHHhCCCCCceeeeccCCh
Confidence            345679999999999643 5667777888777777777765543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.08  E-value=0.025  Score=53.15  Aligned_cols=39  Identities=10%  Similarity=0.217  Sum_probs=27.0

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ....++||||+|.|... ....+..+++..+..+.+|+.+
T Consensus       130 ~~~~iiiide~d~l~~~-~~~~l~~~~e~~~~~~~~Il~t  168 (252)
T d1sxje2         130 HRYKCVIINEANSLTKD-AQAALRRTMEKYSKNIRLIMVC  168 (252)
T ss_dssp             -CCEEEEEECTTSSCHH-HHHHHHHHHHHSTTTEEEEEEE
T ss_pred             CCceEEEeccccccccc-cchhhhcccccccccccceeee
Confidence            35678999999998543 5556777888777666555543

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.05  E-value=0.068  Score=49.46  Aligned_cols=39  Identities=18%  Similarity=0.436  Sum_probs=25.6

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEE
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLF  571 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~Ilf  571 (633)
                      .....+|||||+|.+... ....+..++...++...+++.
T Consensus        97 ~~~~kiiiiDe~d~~~~~-~~~~Ll~~le~~~~~~~~~~~  135 (227)
T d1sxjc2          97 SKGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVL  135 (227)
T ss_dssp             SCSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEE
T ss_pred             CCCeEEEEEeccccchhh-HHHHHHHHhhhcccceeeccc
Confidence            345568999999998754 455566667766655444433

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.94  E-value=0.13  Score=47.50  Aligned_cols=44  Identities=16%  Similarity=0.179  Sum_probs=29.7

Q ss_pred             CCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccCCh
Q 006737          533 MGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATMPK  577 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl~~  577 (633)
                      ..-.+||+||+|.+... ....+...+...+..+.+++.+....+
T Consensus       100 ~~~kviiiDe~d~~~~~-~~~~ll~~~e~~~~~~~~i~~~~~~~~  143 (224)
T d1sxjb2         100 GKHKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFACNQSNK  143 (224)
T ss_dssp             TCCEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEESCGGG
T ss_pred             cceEEEEEecccccchh-HHHHHhhhccccccceeeeeccCchhh
Confidence            34568999999998854 344555666666666767666655443

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=93.63  E-value=0.11  Score=47.24  Aligned_cols=77  Identities=17%  Similarity=0.144  Sum_probs=61.6

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|+|+.-|..+...+...     ++.+..++|+.+.....   ..+..+..+|||+|.     ++..    .+++.
T Consensus        33 r~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~-----v~~~----GiDip   98 (174)
T d1c4oa2          33 RTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LLRE----GLDIP   98 (174)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CCCT----TCCCT
T ss_pred             cEEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee-----eeee----eccCC
Confidence            6999999999999988887765     89999999998866543   466678899999994     3333    37889


Q ss_pred             CeeEEEEecccccC
Q 006737          534 GLKMLVLDEADHLL  547 (633)
Q Consensus       534 ~l~~LVIDEAD~Ll  547 (633)
                      ++.+||+=.++...
T Consensus        99 ~V~~Vi~~~~~~~~  112 (174)
T d1c4oa2          99 EVSLVAILDADKEG  112 (174)
T ss_dssp             TEEEEEETTTTSCS
T ss_pred             CCcEEEEecccccc
Confidence            99999997777643

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=93.15  E-value=0.13  Score=49.05  Aligned_cols=52  Identities=12%  Similarity=0.132  Sum_probs=30.2

Q ss_pred             ccCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHH--hCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAAGYIQMTRVQEATLSAC--LEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~i--l~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++++-.+.+.+.|.+. + .+ -.+.+.+..+  ..-+.+|+.||+|+|||+.
T Consensus         5 ~~~~~di~G~~~~k~~l~~~-i-~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~l   58 (247)
T d1ixza_           5 KVTFKDVAGAEEAKEELKEI-V-EF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHL   58 (247)
T ss_dssp             SCCGGGCCSCHHHHHHHHHH-H-HH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHH
T ss_pred             CCcHHHHccHHHHHHHHHHH-H-HH-HHCHHHHHHcCCCCCceEEEecCCCCChhHH
Confidence            35799997777766666542 0 00 0011122221  1124699999999999984

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=92.98  E-value=0.053  Score=56.13  Aligned_cols=54  Identities=22%  Similarity=0.388  Sum_probs=39.8

Q ss_pred             HhCC-CcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          413 CLEG-KDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       413 il~g-rDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      +..| ++.++.|-||||||++.  ..+   ......         .+|||+|+..+|.|+++.+..++.
T Consensus        27 l~~g~~~q~l~GltGS~ka~~i--A~l---~~~~~r---------p~LVVt~n~~~A~qL~~dL~~~l~   81 (413)
T d1t5la1          27 LRRGVKHQTLLGATGTGKTFTI--SNV---IAQVNK---------PTLVIAHNKTLAGQLYSELKEFFP   81 (413)
T ss_dssp             HHHTCSEEEEEECTTSCHHHHH--HHH---HHHHTC---------CEEEECSSHHHHHHHHHHHHHHCT
T ss_pred             HhcCCCcEEEeCCCCcHHHHHH--HHH---HHHhCC---------CEEEEeCCHHHHHHHHHHHHHHcC
Confidence            3344 57899999999999743  222   222111         289999999999999999999874

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=92.88  E-value=0.071  Score=48.78  Aligned_cols=101  Identities=15%  Similarity=0.144  Sum_probs=70.1

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.+++++-+..+...+...     ++.+..++|+.+.....   ..++.+..+|||||.     ++..    .+++.
T Consensus        33 ~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v~~r----GiDip   98 (181)
T d1t5la2          33 RTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LLRE----GLDIP   98 (181)
T ss_dssp             EEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----CCSS----SCCCT
T ss_pred             eEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----HHHc----cCCCC
Confidence            6999999999999887777654     88999999998866543   456668899999993     2333    37889


Q ss_pred             CeeEEEEecccccCC-cChHHHHHHHHHHCCCCCcEEEE
Q 006737          534 GLKMLVLDEADHLLD-LGFRKDVENIVDCLPRRRQSLLF  571 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld-~gf~~~l~~Il~~lpk~~Q~Ilf  571 (633)
                      ++.+||.-++..... ..+...+.++-..-......+++
T Consensus        99 ~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~g~~~~~~  137 (181)
T d1t5la2          99 EVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM  137 (181)
T ss_dssp             TEEEEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEE
T ss_pred             CCCEEEEecCCcccccccHHHHHHHHHhhccccCceeEe
Confidence            999999988886432 22344444444433333333333

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=92.80  E-value=0.11  Score=48.48  Aligned_cols=18  Identities=28%  Similarity=0.523  Sum_probs=14.6

Q ss_pred             CCcEEEEccCCCCchhhh
Q 006737          416 GKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       416 grDvLv~ApTGSGKTlay  433 (633)
                      ++-+++++|||+|||.+.
T Consensus         6 ~~vi~lvGptGvGKTTTi   23 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTI   23 (207)
T ss_dssp             SSEEEEECSTTSSHHHHH
T ss_pred             CEEEEEECCCCCCHHHHH
Confidence            345788999999999863

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=92.42  E-value=0.21  Score=46.73  Aligned_cols=15  Identities=20%  Similarity=0.426  Sum_probs=12.7

Q ss_pred             EEEEccCCCCchhhh
Q 006737          419 AVVKAKTGTGKSIAF  433 (633)
Q Consensus       419 vLv~ApTGSGKTlay  433 (633)
                      +++++|||+|||.+.
T Consensus        12 i~lvGptGvGKTTTi   26 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTI   26 (211)
T ss_dssp             EEEECCTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567999999999863

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=92.39  E-value=0.23  Score=46.49  Aligned_cols=16  Identities=31%  Similarity=0.397  Sum_probs=13.3

Q ss_pred             cEEEEccCCCCchhhh
Q 006737          418 DAVVKAKTGTGKSIAF  433 (633)
Q Consensus       418 DvLv~ApTGSGKTlay  433 (633)
                      -+++++|||+|||.+.
T Consensus        13 vi~lvGptGvGKTTTi   28 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSC   28 (213)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3678999999999863

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.34  E-value=0.22  Score=44.25  Aligned_cols=73  Identities=12%  Similarity=0.245  Sum_probs=55.3

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|.++.-+.++++.+...     ++.+..++|+.......   ..++.+...|||||.     .+.+    .+++.
T Consensus        29 k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v~~r----GiDi~   94 (162)
T d1fuka_          29 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLAR----GIDVQ   94 (162)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GGTT----TCCCC
T ss_pred             cEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----cccc----cccCC
Confidence            5999999999999998777654     77889999988766543   445567789999995     2333    37788


Q ss_pred             CeeEEEEecc
Q 006737          534 GLKMLVLDEA  543 (633)
Q Consensus       534 ~l~~LVIDEA  543 (633)
                      ++.+||.=+.
T Consensus        95 ~v~~VI~~d~  104 (162)
T d1fuka_          95 QVSLVINYDL  104 (162)
T ss_dssp             SCSEEEESSC
T ss_pred             CceEEEEecc
Confidence            8988887443

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.32  E-value=0.49  Score=43.45  Aligned_cols=42  Identities=21%  Similarity=0.203  Sum_probs=28.6

Q ss_pred             cCccccCCCHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhhh
Q 006737          379 KRFDECGISPLTIKALTAAGYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIAF  433 (633)
Q Consensus       379 ~~F~el~L~~~Ll~~L~~~g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTlay  433 (633)
                      ++|+++-..+.+.+.|...       ++.      -.-.++|++||+|+|||.+.
T Consensus        21 ~~~~diig~~~~~~~l~~~-------i~~------~~~~~lll~Gp~G~GKTtla   62 (231)
T d1iqpa2          21 QRLDDIVGQEHIVKRLKHY-------VKT------GSMPHLLFAGPPGVGKTTAA   62 (231)
T ss_dssp             CSTTTCCSCHHHHHHHHHH-------HHH------TCCCEEEEESCTTSSHHHHH
T ss_pred             CCHHHccCcHHHHHHHHHH-------HHc------CCCCeEEEECCCCCcHHHHH
Confidence            4578887777777776553       110      01247999999999999753

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.82  E-value=0.081  Score=48.92  Aligned_cols=38  Identities=18%  Similarity=0.270  Sum_probs=23.4

Q ss_pred             CeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEe
Q 006737          534 GLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFS  572 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfS  572 (633)
                      ...+|||||+|.+... ....+..++...+....+++.+
T Consensus       108 ~~~viiiDe~d~l~~~-~~~~l~~~~~~~~~~~~~i~~~  145 (237)
T d1sxjd2         108 PYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLIC  145 (237)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEecccccCHH-HHHHHhhccccccccccccccc
Confidence            4568999999998754 3344555555555444444433

>d1s2ma2 c.37.1.19 (A:252-422) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.76  E-value=0.34  Score=43.17  Aligned_cols=73  Identities=10%  Similarity=0.198  Sum_probs=56.0

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|.++.-|..++..+...     ++.+..++|+.......   ..++.+..+|||||.-     +..    .+++.
T Consensus        34 k~iVF~~~~~~~~~l~~~L~~~-----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~-----~~~----Gid~~   99 (171)
T d1s2ma2          34 QAIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL-----LTR----GIDIQ   99 (171)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC-----SSS----SCCCT
T ss_pred             ceEEEEeeeehhhHhHHhhhcc-----cccccccccccchhhhhhhhhhcccCccccccchhH-----hhh----ccccc
Confidence            7999999999999988888776     78888999988765433   4555678899999963     222    37788


Q ss_pred             CeeEEEEecc
Q 006737          534 GLKMLVLDEA  543 (633)
Q Consensus       534 ~l~~LVIDEA  543 (633)
                      .+.+||.=++
T Consensus       100 ~v~~VI~~d~  109 (171)
T d1s2ma2         100 AVNVVINFDF  109 (171)
T ss_dssp             TEEEEEESSC
T ss_pred             eeEEEEecCC
Confidence            9998885444

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=91.74  E-value=0.13  Score=49.41  Aligned_cols=52  Identities=15%  Similarity=0.155  Sum_probs=29.8

Q ss_pred             ccCccccCCCHHHHHHHHHc--CCCCCcHHHHHHHHHHhCCCcEEEEccCCCCchhh
Q 006737          378 QKRFDECGISPLTIKALTAA--GYIQMTRVQEATLSACLEGKDAVVKAKTGTGKSIA  432 (633)
Q Consensus       378 ~~~F~el~L~~~Ll~~L~~~--g~~~pt~iQ~~aIp~il~grDvLv~ApTGSGKTla  432 (633)
                      ..+|++.+-.+.+.+.|.+.  -+..+..+|..-   +-..+.+|+.||+|+|||+.
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHH
Confidence            35689988777777666542  011111111110   11235799999999999984

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=91.50  E-value=0.38  Score=41.99  Aligned_cols=70  Identities=19%  Similarity=0.323  Sum_probs=52.9

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|++++-|.+++..+...     ++.+..++|+.......   ..+..+...|+|||.     .+..+    +++.
T Consensus        30 k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-----~~~~G----id~~   95 (155)
T d1hv8a2          30 YGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSRG----IDVN   95 (155)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHHH----CCCS
T ss_pred             CEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehh-----HHhhh----hhhc
Confidence            5999999999999988877764     77888999987655433   455567789999994     23333    6778


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      .+.+||.
T Consensus        96 ~v~~Vi~  102 (155)
T d1hv8a2          96 DLNCVIN  102 (155)
T ss_dssp             CCSEEEE
T ss_pred             cCcEEEE
Confidence            8888884

>d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=90.65  E-value=0.38  Score=44.28  Aligned_cols=70  Identities=24%  Similarity=0.319  Sum_probs=53.0

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHH---HHHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVD---QRRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~---~~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.++|+..+..++..+...     ++.+..++|+......   ...+..+..+|||+|.     .+..    .+++.
T Consensus        32 ~~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~~~~----GiD~p   97 (200)
T d1oywa3          32 SGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AFGM----GINKP   97 (200)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TSCT----TTCCT
T ss_pred             CEEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----hhhh----ccCCC
Confidence            5999999999999988777654     7889999999876543   3455667889999994     2222    36778


Q ss_pred             CeeEEEE
Q 006737          534 GLKMLVL  540 (633)
Q Consensus       534 ~l~~LVI  540 (633)
                      +|++||.
T Consensus        98 ~v~~VI~  104 (200)
T d1oywa3          98 NVRFVVH  104 (200)
T ss_dssp             TCCEEEE
T ss_pred             CCCEEEE
Confidence            8888874

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=90.28  E-value=0.53  Score=44.52  Aligned_cols=16  Identities=13%  Similarity=0.275  Sum_probs=14.1

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      +.+|+.||+|+|||+.
T Consensus        41 ~~vLL~GppGtGKT~l   56 (246)
T d1d2na_          41 VSVLLEGPPHSGKTAL   56 (246)
T ss_dssp             EEEEEECSTTSSHHHH
T ss_pred             eEEEEECcCCCCHHHH
Confidence            3699999999999974

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=90.16  E-value=0.19  Score=49.93  Aligned_cols=65  Identities=15%  Similarity=0.268  Sum_probs=37.5

Q ss_pred             HHHHHHcCCCC---CcHHHHHHHHH-HhCCCcEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHH
Q 006737          391 IKALTAAGYIQ---MTRVQEATLSA-CLEGKDAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRE  466 (633)
Q Consensus       391 l~~L~~~g~~~---pt~iQ~~aIp~-il~grDvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTRe  466 (633)
                      +..+...|+-.   ..+-+...+.. +..+++++|+|+||||||..  +-+   +...-..       .-++++|--+.|
T Consensus       137 l~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~--l~a---l~~~i~~-------~~rivtiEd~~E  204 (323)
T d1g6oa_         137 HSFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY--IKS---IMEFIPK-------EERIISIEDTEE  204 (323)
T ss_dssp             HHHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH--HHH---HGGGSCT-------TCCEEEEESSCC
T ss_pred             hHHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH--HHH---Hhhhccc-------ccceeeccchhh
Confidence            34445555433   23444444444 45678999999999999983  222   2222111       124777777777


Q ss_pred             H
Q 006737          467 L  467 (633)
Q Consensus       467 L  467 (633)
                      |
T Consensus       205 l  205 (323)
T d1g6oa_         205 I  205 (323)
T ss_dssp             C
T ss_pred             h
Confidence            6

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.03  E-value=0.33  Score=43.19  Aligned_cols=73  Identities=12%  Similarity=0.123  Sum_probs=53.6

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|+++.-+..+.+.+.+.     ++.+..++|+.+.....   ..+..+.++|||+|.-     +..    .+++.
T Consensus        29 k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~-----~~~----Gid~~   94 (168)
T d1t5ia_          29 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----FGR----GMDIE   94 (168)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-----CST----TCCGG
T ss_pred             eEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeecccc-----ccc----hhhcc
Confidence            5999999999999888777654     77889999998766543   4456678899999942     222    36677


Q ss_pred             CeeEEEEecc
Q 006737          534 GLKMLVLDEA  543 (633)
Q Consensus       534 ~l~~LVIDEA  543 (633)
                      .+.+||+=+.
T Consensus        95 ~~~~vi~~~~  104 (168)
T d1t5ia_          95 RVNIAFNYDM  104 (168)
T ss_dssp             GCSEEEESSC
T ss_pred             cchhhhhhhc
Confidence            7877766543

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=89.96  E-value=0.23  Score=45.88  Aligned_cols=43  Identities=19%  Similarity=0.169  Sum_probs=25.3

Q ss_pred             CCeeEEEEecccccCCcC----hHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          533 MGLKMLVLDEADHLLDLG----FRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       533 s~l~~LVIDEAD~Lld~g----f~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      ..++++|||-++.+....    ....+..+...+.....++++.++.
T Consensus       115 ~~~~~vviDs~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~  161 (242)
T d1tf7a2         115 FKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTS  161 (242)
T ss_dssp             TCCSEEEEECHHHHTSSSCHHHHHHHHHHHHHHHHHTTCEEEEEEEC
T ss_pred             cCCceeeeecchhhhcCCCHHHHHHHHHHHHHHHHHcCCeEEEEEee
Confidence            357899999999887543    2333334444444444566665544

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.47  E-value=0.61  Score=41.45  Aligned_cols=71  Identities=13%  Similarity=0.246  Sum_probs=54.0

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHH---HHHhcCCCcEEEECchhhHHHHhcccCcccccC
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQ---RRLESDPCQILVATPGRLLDHIENKSGLSVRLM  533 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~---~~l~~~~~dILIaTPgrLl~lL~~~~~~~~~Ls  533 (633)
                      ++||.|.++.-|..++..+...     ++.+..++|+.......   ..++.+..+|||||-     .+.+    .+++.
T Consensus        36 k~iiF~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td-----~~~r----GiDi~  101 (168)
T d2j0sa2          36 QAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VWAR----GLDVP  101 (168)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GGSS----SCCCT
T ss_pred             ceEEEeeeHHHHHHHHHHhhhc-----ccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc-----hhcc----ccccc
Confidence            6999999999999988777765     67788899988766543   345567789999994     3333    37788


Q ss_pred             CeeEEEEe
Q 006737          534 GLKMLVLD  541 (633)
Q Consensus       534 ~l~~LVID  541 (633)
                      ++++||.=
T Consensus       102 ~v~~VIn~  109 (168)
T d2j0sa2         102 QVSLIINY  109 (168)
T ss_dssp             TEEEEEES
T ss_pred             CcceEEEe
Confidence            89888753

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=89.18  E-value=0.03  Score=49.53  Aligned_cols=43  Identities=9%  Similarity=0.106  Sum_probs=27.0

Q ss_pred             cCCeeEEEEecccccCCcChHHHHHHHHHHCCCCCcEEEEeccC
Q 006737          532 LMGLKMLVLDEADHLLDLGFRKDVENIVDCLPRRRQSLLFSATM  575 (633)
Q Consensus       532 Ls~l~~LVIDEAD~Lld~gf~~~l~~Il~~lpk~~Q~IlfSATl  575 (633)
                      ....+++++||++..... -...+..+...+.....+++++...
T Consensus        97 ~~~~~vlllDE~~~~~~~-~~~~~~~l~~~l~~~~~~il~~~h~  139 (178)
T d1ye8a1          97 KDRRKVIIIDEIGKMELF-SKKFRDLVRQIMHDPNVNVVATIPI  139 (178)
T ss_dssp             HCTTCEEEECCCSTTGGG-CHHHHHHHHHHHTCTTSEEEEECCS
T ss_pred             hcCCCceeecCCCccchh-hHHHHHHHHHHhccCCCEEEEEEcc
Confidence            457789999999765533 2344445555555555677776543

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=88.47  E-value=1  Score=41.80  Aligned_cols=15  Identities=27%  Similarity=0.388  Sum_probs=8.8

Q ss_pred             EEEEccCCCCchhhh
Q 006737          419 AVVKAKTGTGKSIAF  433 (633)
Q Consensus       419 vLv~ApTGSGKTlay  433 (633)
                      +++++|||+|||.+.
T Consensus        15 i~lvGptGvGKTTTi   29 (211)
T d1j8yf2          15 IMLVGVQGTGKATTA   29 (211)
T ss_dssp             EEEECSCCC----HH
T ss_pred             EEEECCCCCCHHHHH
Confidence            567899999999863

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=86.84  E-value=0.3  Score=42.43  Aligned_cols=50  Identities=28%  Similarity=0.480  Sum_probs=41.2

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECc
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATP  515 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTP  515 (633)
                      ++||.|+|+.-|.++++.+..+     ++.+..++++.....    .+.+..+|||||.
T Consensus        37 k~IVFc~t~~~ae~la~~L~~~-----G~~~~~~H~~~~~~~----~~~~~~~vlvaTd   86 (138)
T d1jr6a_          37 RHLIFCHSKKKCDELAAKLVAL-----GINAVAYYRGLDVSV----IPTNGDVVVVATD   86 (138)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHH-----TCEEEEECTTCCSCC----CTTSSCEEEEESS
T ss_pred             CEEEEeCcHHHHHHHHHHHhcc-----ccchhhhhccchhhh----hhhhhcceeehhH
Confidence            4899999999999999888776     788999999877543    3456689999994

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=84.63  E-value=0.41  Score=46.99  Aligned_cols=53  Identities=19%  Similarity=0.123  Sum_probs=38.3

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccchHHHHHHhcCCCcEEEECc
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFKVDQRRLESDPCQILVATP  515 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~~~~~~l~~~~~dILIaTP  515 (633)
                      ++||+||+..-+.++...+.+.     +..|.+++|.+.... ...++.+..+|||+|.
T Consensus        38 ~~~~F~~s~~~~~~~a~~L~~~-----g~~V~~l~~~~~~~e-~~~~~~~~~~~~~~t~   90 (299)
T d1yksa2          38 PTAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTFERE-YPTIKQKKPDFILATD   90 (299)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSCC---------CCCSEEEESS
T ss_pred             CEEEEeCCHHHHHHHHHHHHhc-----CCeEEEEcCcCcHhH-HhhhhcCCcCEEEEec
Confidence            4899999999999998888764     667889999877554 4556677789999994

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.22  E-value=1.2  Score=42.03  Aligned_cols=16  Identities=25%  Similarity=0.540  Sum_probs=14.3

Q ss_pred             CcEEEEccCCCCchhh
Q 006737          417 KDAVVKAKTGTGKSIA  432 (633)
Q Consensus       417 rDvLv~ApTGSGKTla  432 (633)
                      +.+|+.||+|+|||+.
T Consensus        39 ~giLL~GppGtGKT~l   54 (258)
T d1e32a2          39 RGILLYGPPGTGKTLI   54 (258)
T ss_dssp             CEEEEECCTTSSHHHH
T ss_pred             ceeEEecCCCCCchHH
Confidence            5799999999999973

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=82.78  E-value=0.46  Score=47.86  Aligned_cols=28  Identities=32%  Similarity=0.350  Sum_probs=20.0

Q ss_pred             CCCcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          415 EGKDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       415 ~grDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      ..++++|.|+||||||.+. ..++..+..
T Consensus        49 ~~~H~~I~G~tGsGKT~~l-~~li~~~~~   76 (433)
T d1e9ra_          49 EPRHLLVNGATGTGKSVLL-RELAYTGLL   76 (433)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHH
T ss_pred             ccceEEEEeCCCCcHHHHH-HHHHHHHHh
Confidence            3568999999999999764 334444443

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.61  E-value=0.63  Score=39.92  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=18.5

Q ss_pred             CcEEEEccCCCCchhhhHHHHHHHHHH
Q 006737          417 KDAVVKAKTGTGKSIAFLLPAIEAVLK  443 (633)
Q Consensus       417 rDvLv~ApTGSGKTlaylLPiL~~l~~  443 (633)
                      |++++.||+|+|||.. +--++..+..
T Consensus         2 k~v~ItG~~GtGKTtl-~~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTL-IHKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHH-HHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHH-HHHHHHHHHH
Confidence            6899999999999983 3334444433

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=82.41  E-value=0.78  Score=46.82  Aligned_cols=55  Identities=33%  Similarity=0.492  Sum_probs=39.6

Q ss_pred             HHhCCC-cEEEEccCCCCchhhhHHHHHHHHHHhcCCCCCCCCCCeEEEEEcccHHHHHHHHHHHHHHHh
Q 006737          412 ACLEGK-DAVVKAKTGTGKSIAFLLPAIEAVLKATSSSTTQLVPPIYVLILCPTRELASQIAAEAIALLK  480 (633)
Q Consensus       412 ~il~gr-DvLv~ApTGSGKTlaylLPiL~~l~~~~~~~~~~~~~~~~vLILvPTReLa~Qi~~~l~~l~~  480 (633)
                      .+..|. .+.+.|-|||+|+++  +..+   ......         .+|||+|+...|.++++.+..++.
T Consensus        23 ~L~~g~~~~~L~GlsgS~ka~~--~A~l---~~~~~r---------p~LvVt~~~~~A~~l~~dL~~~l~   78 (408)
T d1c4oa1          23 ALRDGERFVTLLGATGTGKTVT--MAKV---IEALGR---------PALVLAPNKILAAQLAAEFRELFP   78 (408)
T ss_dssp             HHHTTCSEEEEEECTTSCHHHH--HHHH---HHHHTC---------CEEEEESSHHHHHHHHHHHHHHCT
T ss_pred             HHhcCCCcEEEecCCCCHHHHH--HHHH---HHHhCC---------CEEEEeCCHHHHHHHHHHHHHhcC
Confidence            344554 578899999999973  3333   222111         178999999999999999998864

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=81.19  E-value=3.2  Score=39.20  Aligned_cols=70  Identities=21%  Similarity=0.299  Sum_probs=49.7

Q ss_pred             EEEEEcccHHHHHHHHHHHHHHHhcCCCceEEEEECCccch-----------HHHHHHhcCCCcEEEECchhhHHHHhcc
Q 006737          457 YVLILCPTRELASQIAAEAIALLKNHDGIGVLTLVGGTRFK-----------VDQRRLESDPCQILVATPGRLLDHIENK  525 (633)
Q Consensus       457 ~vLILvPTReLa~Qi~~~l~~l~~~~~~i~v~~l~Gg~~~~-----------~~~~~l~~~~~dILIaTPgrLl~lL~~~  525 (633)
                      ++||.+.+++-+..+++.+.+.     ++.+..+.|.....           .....+..+.++|||+|-     .+.. 
T Consensus       163 k~iiF~~~~~~~~~~~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~-----~~~~-  231 (286)
T d1wp9a2         163 KIIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS-----VGEE-  231 (286)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG-----GGGG-
T ss_pred             cEEEEeCcHHhHHHHHHHHHHc-----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcc-----ceec-
Confidence            6999999999999888776653     67777777753322           123455667789999993     2333 


Q ss_pred             cCcccccCCeeEEEE
Q 006737          526 SGLSVRLMGLKMLVL  540 (633)
Q Consensus       526 ~~~~~~Ls~l~~LVI  540 (633)
                         .+++..+.+||+
T Consensus       232 ---Gld~~~~~~Vi~  243 (286)
T d1wp9a2         232 ---GLDVPEVDLVVF  243 (286)
T ss_dssp             ---GGGSTTCCEEEE
T ss_pred             ---cccCCCCCEEEE
Confidence               378889998886

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=81.10  E-value=2.7  Score=38.19  Aligned_cols=30  Identities=30%  Similarity=0.369  Sum_probs=20.2

Q ss_pred             CeeEEEEecccccCCcC---hHHHHHHHHHHCC
Q 006737          534 GLKMLVLDEADHLLDLG---FRKDVENIVDCLP  563 (633)
Q Consensus       534 ~l~~LVIDEAD~Lld~g---f~~~l~~Il~~lp  563 (633)
                      .--++|+||+|.+.+..   +...+..+....+
T Consensus       136 ~~~~i~id~~~~~~~~~~~~~~~~l~~~~~~~~  168 (283)
T d2fnaa2         136 DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLK  168 (283)
T ss_dssp             SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCT
T ss_pred             cccccccchhhhhcccchHHHHHHHHHHHHhhh
Confidence            34578999999987543   5666666665543

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=80.95  E-value=2.1  Score=40.98  Aligned_cols=40  Identities=23%  Similarity=0.373  Sum_probs=24.4

Q ss_pred             EEEEecccccCCcC----hHHHHHHHHH-HCCC-CCcEEEEeccCChh
Q 006737          537 MLVLDEADHLLDLG----FRKDVENIVD-CLPR-RRQSLLFSATMPKE  578 (633)
Q Consensus       537 ~LVIDEAD~Lld~g----f~~~l~~Il~-~lpk-~~Q~IlfSATl~~e  578 (633)
                      +++|||+|.|+..|    -...+..++. .+.. +.|+|+  ||=+.+
T Consensus       113 IlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIg--atT~ee  158 (268)
T d1r6bx2         113 ILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIG--STTYQE  158 (268)
T ss_dssp             EEEETTTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEE--EECHHH
T ss_pred             eEEecchHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEE--eCCHHH
Confidence            68899999998643    2345556655 3332 455555  555555