Citrus Sinensis ID: 010709

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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---
Protein Sequence
MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSDLTTKLSFSSKSLPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccHHHHHHHHHHccccEEEccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHHccccccccccEEEEEcccHHHHHHHHHHHHHHHHccccccEEEEEccccHHHHHHHHHccccEEEEcccHHHHHHHcccccccccEEEEccccccccccccHHHHHHHHHccccccEEEEEcccccHHHHHHHHHHHcccEEEEEcccccccccEEEEEEEEcccHHHHHHHHHHHHHHHHHHccccccccEEEEEcccccHHHHHHHHHHccccEEEcccccccHHHHHHHHHHHcccccEEEEEcccccccccccccEEEccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccHHHHHHHHHHHccccEEEccccccccccccccccccHHHHHHHHHHcccccccHHHHcccHHHcccccEEEEEccccHHHHHHHHHHHHHHHccccccccccccEEEEcccHHHHHHHHHHHHHHccccccccEEEEEccccccHHHHHHHcccEEEEEcHHHHHHHHcccccccccccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcEEcccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHccccccccEEEEEEccccHHHHHHHHHHccccEEEEcccccHHHHHHHHHHHHcccccEEEEHHHHHccccccccEEEEEEcccccHHHHHEEcccccccccccEEEEEcccHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
mmyepphrrtsssnsvskvsssssssssssssssvvtldsdlttklsfsskslpnfsnsnsnttcrrsyashpvpqpvfnnwkpsdrvlrfnpeqIEEVRLRLNVDVTvasgsvpapapiesftdmclhpsimkdiefheytrptsiqaqampvalsgrdllgcaetgsgktaaftipmiqhcvaqtpvgrgdgplalVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNiaeqrselrggvsivvatpgrfldhlqqgntslsrvSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEyltdpvqvkvgkvssptANVIQILEKVSENEKVDRLLALLVEEAFLaekschpfpltIVFVERKTRCDEVSEALVAEGLHAVAlhggrnqsdrESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESlcttsfnittnldgdmKKLEFCLILAITVLLFVIFLSIISWI
Flexible Loop (DISEMBL)
mmyepphrrtsssnsvskvsssssssssssssssvvtlDSDLTTKLsfsskslpnfsnsnsNTTCRRSYAshpvpqpvfnnwkpsDRVLRFNPEQIEEVRLRLNVDVTVAsgsvpapapiESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGtniaeqrselrGGVSIVVATPGRFLDhlqqgntslsrVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFlaekschpfPLTIVFVERKTRCDEVSEALVAEGLHavalhggrnqsdRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
Low Complexity Region (SEG)
MMYEPPHRRTsssnsvskvsssssssssssssssvvtldsdlttklsfsskslpnfsnsnsnTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRllallveeaflaeKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
Disordered region (IsUnstruct)
*****************************************************************************VFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG*************FRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISW*
Disordered Region (DISOPRED)
MMYEPPH******************************************************************VPQPVFNNWKPSDRV****PE*IEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP*GRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLA**SCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
Disordered Region (DISEMBL)
***************************************SDLTTKLSFSSKSLPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG*********ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
Disordered Region (DISPRO)
************************************************************************PVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSDLTTKLSFSSKSLPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELxxxxxxxxxxxxxxxxxxxxxIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMKKLEFCLILAITVLLFVIFLSIISWI
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	503	2.2.26 [Sep-21-2011]
Q6BY27	536	ATP-dependent RNA helicas	yes	no	0.654	0.613	0.451	2e-82
Q6FLF3	544	ATP-dependent RNA helicas	yes	no	0.727	0.672	0.424	2e-81
A5DL80	554	ATP-dependent RNA helicas	N/A	no	0.654	0.593	0.445	3e-81
A3LQW7	530	ATP-dependent RNA helicas	yes	no	0.654	0.620	0.451	7e-81
P24783	546	ATP-dependent RNA helicas	yes	no	0.689	0.635	0.428	1e-80
A6ZRX0	546	ATP-dependent RNA helicas	N/A	no	0.689	0.635	0.428	2e-80
Q501J6	650	Probable ATP-dependent RN	yes	no	0.705	0.546	0.431	2e-80
Q92841	729	Probable ATP-dependent RN	yes	no	0.705	0.486	0.431	2e-80
A5DS77	552	ATP-dependent RNA helicas	N/A	no	0.654	0.596	0.454	5e-80
Q0DB53	602	DEAD-box ATP-dependent RN	yes	no	0.701	0.586	0.448	1e-79

>sp|Q6BY27|DBP2_DEBHA ATP-dependent RNA helicase DBP2 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=DBP2 PE=3 SV=1

 Score =  306 bits (784), Expect = 2e-82,   Method: Compositional matrix adjust.
 Identities = 152/337 (45%), Positives = 221/337 (65%), Gaps = 8/337 (2%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           P PI SF +      ++K+++   + +PTSIQ Q  P+ALSGRD++G A TGSGKT ++ 
Sbjct: 101 PKPITSFDEAGFPDYVLKEVKQQGFPKPTSIQCQGWPMALSGRDMVGIASTGSGKTLSYC 160

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           +P I H  AQ  +  GDGP+ LVLAPTRELA QI++E      S    +   V GG    
Sbjct: 161 LPSIVHINAQPLLSPGDGPIVLVLAPTRELAVQIQQECSKFGSS-SRIRNTCVYGGAPKG 219

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
           +Q  +L  GV I +ATPGR +D L+ G T+L RV++++LDEADRMLDMGFEPQIR+++  
Sbjct: 220 QQIRDLARGVEICIATPGRLIDMLETGKTNLRRVTYLVLDEADRMLDMGFEPQIRKIVDQ 279

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKVSENEKVDR 355
           +    QTL++SAT P E++AL ++YL DP+QV VG +    ++ I Q++E V+E EK DR
Sbjct: 280 IRPDRQTLMWSATWPKEVQALTRDYLNDPIQVTVGSLELAASHTITQLVEVVTEFEKRDR 339

Query: 356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
           L+  L       E  C      ++F   K  CDE++  L A+G  A+A+HG + Q +R+ 
Sbjct: 340 LIKHLETATADPEAKC------LIFASTKRTCDEITNYLRADGWPALAIHGDKQQGERDW 393

Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            L++F+ G + I+VATDVA+RG+DV G+++V+NLD+P
Sbjct: 394 VLKEFKTGKSPIMVATDVAARGIDVKGISYVINLDMP 430

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.
Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)
EC: 3EC: .EC: 6EC: .EC: 4EC: .EC: 1EC: 3

>sp|Q6FLF3|DBP2_CANGA ATP-dependent RNA helicase DBP2 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=DBP2 PE=3 SV=1

 Score =  303 bits (777), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 160/377 (42%), Positives = 237/377 (62%), Gaps = 11/377 (2%)

Query: 77  PVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDI 136
           P   N+     V+R   +Q E  + R   ++T+    +P P  I +F +      ++K++
Sbjct: 69  PFEKNFYVEHEVVRNRSDQ-EVAQFRKESEMTITGHDIPKP--ITTFDEAGFPDYVLKEV 125

Query: 137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPL 196
           +   + +PTSIQ Q  P+ALSGRD++G A TGSGKT ++ +P I H  AQ  +  GDGP+
Sbjct: 126 KAEGFDKPTSIQCQGWPMALSGRDMVGIAATGSGKTLSYCLPGIVHINAQPLLSPGDGPI 185

Query: 197 ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF 256
            LVLAPTRELA QI+KE     +S    +   V GG    +Q  EL  G  IV+ATPGR 
Sbjct: 186 VLVLAPTRELAVQIQKECSKFGKS-SRIRNTCVYGGVPRGQQIRELIRGAEIVIATPGRL 244

Query: 257 LDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEA 316
           +D L+ G T+L RV++++LDEADRMLDMGFEPQIR+++  +    QTL++SAT P E++ 
Sbjct: 245 IDMLEAGKTNLKRVTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVQQ 304

Query: 317 LAQEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFP 375
           LA++YL DP+QV++G +  + + N+ Q++E VSE EK DRL+  L   +   E       
Sbjct: 305 LARDYLNDPIQVQIGSLELAASHNITQLVEVVSEFEKRDRLVKHLDTASQDKESKI---- 360

Query: 376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS 435
             ++F   K  CDE++  L  +G  A+A+HG ++Q +R+  L +FR G++ I+VATDVA+
Sbjct: 361 --LIFASTKRTCDEITSYLRQDGWPALAIHGDKDQRERDWVLNEFRTGNSPIMVATDVAA 418

Query: 436 RGLDVMGVAHVVNLDLP 452
           RG+DV G+  VVN D+P
Sbjct: 419 RGIDVKGINFVVNYDMP 435

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DL80|DBP2_PICGU ATP-dependent RNA helicase DBP2 OS=Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) GN=DBP2 PE=3 SV=3

 Score =  302 bits (774), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 150/337 (44%), Positives = 222/337 (65%), Gaps = 8/337 (2%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           P PI SF +      ++ +++   + +PT+IQ Q  P+ALSGRD++G A TGSGKT ++ 
Sbjct: 121 PKPITSFDEAGFPDYVLNEVKQQGFPKPTAIQCQGWPMALSGRDMIGIAATGSGKTLSYC 180

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           +P I H  AQ  +G GDGP+ LVLAPTRELA QI++E      S    +   + GG    
Sbjct: 181 LPSIVHINAQPLLGPGDGPIVLVLAPTRELAVQIQQECSKFGAS-SRIRNTCIYGGAPKG 239

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
           +Q  +L  GV I +ATPGR +D L+ G T+L RV++++LDEADRMLDMGFEPQIR+++  
Sbjct: 240 QQIRDLARGVEICIATPGRLIDMLETGKTNLRRVTYLVLDEADRMLDMGFEPQIRKIVDQ 299

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKVSENEKVDR 355
           +    QTL++SAT P E++ L ++YL DP+QV +G +    ++ I QI+E +SE EK DR
Sbjct: 300 IRPDRQTLMWSATWPKEVQTLTRDYLNDPIQVTIGSLELAASHTITQIVEVLSEFEKRDR 359

Query: 356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
           L+  L  E   A+K        ++F   K  CDE++  L A+G  A+A+HG + Q++R+ 
Sbjct: 360 LVKHL--ETATADKEAK----VLIFSSTKRACDEITSYLRADGWPALAIHGDKQQNERDW 413

Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            LR+F+ G + I+VATDVA+RG+DV G+++V+N D+P
Sbjct: 414 VLREFKTGKSPIMVATDVAARGIDVKGISYVINYDMP 450

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324) (taxid: 294746)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A3LQW7|DBP2_PICST ATP-dependent RNA helicase DBP2 OS=Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) GN=DBP2 PE=3 SV=1

 Score =  301 bits (771), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 152/337 (45%), Positives = 220/337 (65%), Gaps = 8/337 (2%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           P PI +F +      ++ +++   +  PT+IQ Q  P+ALSGRD++G A TGSGKT ++ 
Sbjct: 93  PHPITTFDEAGFPEYVLNEVKAQGFPSPTAIQCQGWPMALSGRDMVGIAATGSGKTLSYC 152

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           +P I H  AQ  +  GDGP+ LVLAPTRELA QI++E      S    +   V GG    
Sbjct: 153 LPAIVHINAQPLLSPGDGPVVLVLAPTRELAVQIQQECSKFGSS-SRIRNTCVYGGAPKG 211

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
           +Q  +L  GV IV+ATPGR +D L+ G T+L RV++++LDEADRMLDMGFEPQIR+++  
Sbjct: 212 QQIRDLARGVEIVIATPGRLIDMLEMGKTNLKRVTYLVLDEADRMLDMGFEPQIRKIVDQ 271

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKVSENEKVDR 355
           +    QTL++SAT P E++ LA++YL DP+QV++G +    ++ I Q++E +SE EK DR
Sbjct: 272 IRPDRQTLMWSATWPKEVQNLARDYLQDPIQVRIGSLELAASHTITQVVEVISEYEKRDR 331

Query: 356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
           L+  L  E    EK        ++F   K  CDEV+  L A+G  A+A+HG + QS+R+ 
Sbjct: 332 LVKHL--ETATTEKESK----VLIFASTKKTCDEVTSYLRADGWPALAIHGDKQQSERDW 385

Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            LR+F+ G + I+VATDVA+RG+DV G+  V+N D+P
Sbjct: 386 VLREFKTGKSPIMVATDVAARGIDVKGINFVINFDMP 422

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (taxid: 322104)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|P24783|DBP2_YEAST ATP-dependent RNA helicase DBP2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=DBP2 PE=1 SV=1

 Score =  300 bits (769), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 153/357 (42%), Positives = 229/357 (64%), Gaps = 10/357 (2%)

Query: 97  EEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL 156
           E  + R   ++T++   +P P  I +F +      ++ +++   + +PT IQ Q  P+AL
Sbjct: 91  EIAQFRKENEMTISGHDIPKP--ITTFDEAGFPDYVLNEVKAEGFDKPTGIQCQGWPMAL 148

Query: 157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA 216
           SGRD++G A TGSGKT ++ +P I H  AQ  +  GDGP+ LVLAPTRELA QI+ E   
Sbjct: 149 SGRDMVGIAATGSGKTLSYCLPGIVHINAQPLLAPGDGPIVLVLAPTRELAVQIQTECSK 208

Query: 217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD 276
              S    +   V GG   ++Q  +L  G  IV+ATPGR +D L+ G T+L RV++++LD
Sbjct: 209 FGHS-SRIRNTCVYGGVPKSQQIRDLSRGSEIVIATPGRLIDMLEIGKTNLKRVTYLVLD 267

Query: 277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS-S 335
           EADRMLDMGFEPQIR+++  +    QTL++SAT P E++ LA +YL DP+QV+VG +  S
Sbjct: 268 EADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVKQLAADYLNDPIQVQVGSLELS 327

Query: 336 PTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV 395
            + N+ QI+E VS+ EK DRL        +L   S      T++F   K  CD++++ L 
Sbjct: 328 ASHNITQIVEVVSDFEKRDRL------NKYLETASQDNEYKTLIFASTKRMCDDITKYLR 381

Query: 396 AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +G  A+A+HG ++Q +R+  L++FRNG + I+VATDVA+RG+DV G+ +V+N D+P
Sbjct: 382 EDGWPALAIHGDKDQRERDWVLQEFRNGRSPIMVATDVAARGIDVKGINYVINYDMP 438

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A6ZRX0|DBP2_YEAS7 ATP-dependent RNA helicase DBP2 OS=Saccharomyces cerevisiae (strain YJM789) GN=DBP2 PE=3 SV=1

 Score =  300 bits (769), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 153/357 (42%), Positives = 229/357 (64%), Gaps = 10/357 (2%)

Query: 97  EEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL 156
           E  + R   ++T++   +P P  I +F +      ++ +++   + +PT IQ Q  P+AL
Sbjct: 91  EIAQFRKENEMTISGHDIPKP--ITTFDEAGFPDYVLNEVKAEGFDKPTGIQCQGWPMAL 148

Query: 157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA 216
           SGRD++G A TGSGKT ++ +P I H  AQ  +  GDGP+ LVLAPTRELA QI+ E   
Sbjct: 149 SGRDMVGIAATGSGKTLSYCLPGIVHINAQPLLAPGDGPIVLVLAPTRELAVQIQTECSK 208

Query: 217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD 276
              S    +   V GG   ++Q  +L  G  IV+ATPGR +D L+ G T+L RV++++LD
Sbjct: 209 FGHS-SRIRNTCVYGGVPKSQQIRDLSRGSEIVIATPGRLIDMLEIGKTNLKRVTYLVLD 267

Query: 277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS-S 335
           EADRMLDMGFEPQIR+++  +    QTL++SAT P E++ LA +YL DP+QV+VG +  S
Sbjct: 268 EADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVKQLAADYLNDPIQVQVGSLELS 327

Query: 336 PTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV 395
            + N+ QI+E VS+ EK DRL        +L   S      T++F   K  CD++++ L 
Sbjct: 328 ASHNITQIVEVVSDFEKRDRL------NKYLETASQDNEYKTLIFASTKRMCDDITKYLR 381

Query: 396 AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +G  A+A+HG ++Q +R+  L++FRNG + I+VATDVA+RG+DV G+ +V+N D+P
Sbjct: 382 EDGWPALAIHGDKDQRERDWVLQEFRNGRSPIMVATDVAARGIDVKGINYVINYDMP 438

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Saccharomyces cerevisiae (strain YJM789) (taxid: 307796)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q501J6|DDX17_MOUSE Probable ATP-dependent RNA helicase DDX17 OS=Mus musculus GN=Ddx17 PE=2 SV=1

 Score =  300 bits (767), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 158/366 (43%), Positives = 228/366 (62%), Gaps = 11/366 (3%)

Query: 88  VLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSI 147
           V R  P +++E  LR   ++TV  G V  P P+ +F        +M  +    +T PT I
Sbjct: 62  VARLTPYEVDE--LRRKKEITVRGGDV-CPKPVFAFHHANFPQYVMDVLMDQHFTEPTPI 118

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
           Q Q  P+ALSGRD++G A+TGSGKT A+ +P I H   Q  + RGDGP+ LVLAPTRELA
Sbjct: 119 QCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPICLVLAPTRELA 178

Query: 208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL 267
           QQ+++      +     K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L
Sbjct: 179 QQVQQVADDYGK-CSRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNL 237

Query: 268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQ 327
            R ++++LDEADRMLDMGFEPQIR+++  +    QTL++SAT P E+  LA+++L D  Q
Sbjct: 238 RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLRDYTQ 297

Query: 328 VKVGKVS-SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR 386
           + VG +  S   N++QI++   E+EK  +L+ L+  E  +AEK       TI+FVE K R
Sbjct: 298 INVGNLELSANHNILQIVDVCMESEKDHKLIQLM--EEIMAEKENK----TIIFVETKRR 351

Query: 387 CDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHV 446
           CD+++  +  +G  A+ +HG ++Q +R+  L +FR+G   IL+ATDVASRGLDV  V  V
Sbjct: 352 CDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFV 411

Query: 447 VNLDLP 452
           +N D P
Sbjct: 412 INYDYP 417

RNA-dependent ATPase activity. Involved in transcriptional regulation. Transcriptional coactivator for estrogen receptor ESR1. Increases ESR1 AF-1 domain-mediated transactivation (By similarity). Synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and probably involved in skeletal muscle differentiation.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q92841|DDX17_HUMAN Probable ATP-dependent RNA helicase DDX17 OS=Homo sapiens GN=DDX17 PE=1 SV=2

 Score =  300 bits (767), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 158/366 (43%), Positives = 228/366 (62%), Gaps = 11/366 (3%)

Query: 88  VLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSI 147
           V R  P +++E  LR   ++TV  G V  P P+ +F        +M  +    +T PT I
Sbjct: 141 VARLTPYEVDE--LRRKKEITVRGGDV-CPKPVFAFHHANFPQYVMDVLMDQHFTEPTPI 197

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
           Q Q  P+ALSGRD++G A+TGSGKT A+ +P I H   Q  + RGDGP+ LVLAPTRELA
Sbjct: 198 QCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPICLVLAPTRELA 257

Query: 208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL 267
           QQ+++      +     K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L
Sbjct: 258 QQVQQVADDYGK-CSRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNL 316

Query: 268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQ 327
            R ++++LDEADRMLDMGFEPQIR+++  +    QTL++SAT P E+  LA+++L D  Q
Sbjct: 317 RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLRDYTQ 376

Query: 328 VKVGKVS-SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR 386
           + VG +  S   N++QI++   E+EK  +L+ L+  E  +AEK       TI+FVE K R
Sbjct: 377 INVGNLELSANHNILQIVDVCMESEKDHKLIQLM--EEIMAEKENK----TIIFVETKRR 430

Query: 387 CDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHV 446
           CD+++  +  +G  A+ +HG ++Q +R+  L +FR+G   IL+ATDVASRGLDV  V  V
Sbjct: 431 CDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKFV 490

Query: 447 VNLDLP 452
           +N D P
Sbjct: 491 INYDYP 496

RNA-dependent ATPase activity. Involved in transcriptional regulation. Transcriptional coactivator for estrogen receptor ESR1. Increases ESR1 AF-1 domain-mediated transactivation. Synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and probably involved in skeletal muscle differentiation.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A5DS77|DBP2_LODEL ATP-dependent RNA helicase DBP2 OS=Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) GN=DBP2 PE=3 SV=1

 Score =  298 bits (764), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 153/337 (45%), Positives = 220/337 (65%), Gaps = 8/337 (2%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           P PI SF +      ++ +++   + +PT IQ Q  P+ALSGRD++G A TGSGKT ++ 
Sbjct: 112 PHPITSFDEAGFPDYVLNELKNQGFPKPTGIQCQGWPMALSGRDMVGIAATGSGKTLSYC 171

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           +P I H  AQ  + RGDGP+ LVLAPTRELA QI+ E      S    +   V GG    
Sbjct: 172 LPGIVHINAQPLLKRGDGPIVLVLAPTRELACQIQTECSKFGAS-SRIRNTCVYGGAPKG 230

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
            Q  +L  GV I +ATPGR +D L+ G T+L RV++++LDEADRMLDMGFEPQIR+++  
Sbjct: 231 PQIRDLANGVEICIATPGRLIDMLEAGKTNLKRVTYLVLDEADRMLDMGFEPQIRKIVDQ 290

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKVSENEKVDR 355
           +    QTL++SAT P E++ LA++YL +P+QV +G +    ++ I QI++ V+E +K D 
Sbjct: 291 IRPDRQTLMWSATWPKEVQNLARDYLDNPIQVTIGSLELAASHTITQIVQVVTEYQKRDL 350

Query: 356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
           L+  L  E+ LA+ +       +VF   K  CDEV+  L A+G  A+A+HG + Q +R+ 
Sbjct: 351 LVKHL--ESALADSNSK----VLVFASTKRTCDEVTSYLRADGWPALAIHGDKEQHERDW 404

Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            L++FR GS +I+VATDVA+RG+DV G+ HVVN D+P
Sbjct: 405 VLKEFRQGSHSIMVATDVAARGIDVKGITHVVNYDMP 441

ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.

Lodderomyces elongisporus (strain ATCC 11503 / CBS 2605 / JCM 1781 / NBRC 1676 / NRRL YB-4239) (taxid: 379508)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q0DB53|RH52A_ORYSJ DEAD-box ATP-dependent RNA helicase 52A OS=Oryza sativa subsp. japonica GN=Os06g0602400 PE=2 SV=2

 Score =  297 bits (761), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 167/372 (44%), Positives = 232/372 (62%), Gaps = 19/372 (5%)

Query: 98  EVRL-RLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL 156
           E RL + ++ V V+   VP PA  + F    L  ++++++    Y  PT +Q  +MP+AL
Sbjct: 62  ERRLDKYDIPVEVSGEDVPPPA--DGFEAAGLVEAVLRNVARCGYESPTPVQRYSMPIAL 119

Query: 157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGD-----------GPLALVLAPTRE 205
           +GRDL+ CA+TGSGKTAAF +P++   VA    G G             P ALVLAPTRE
Sbjct: 120 AGRDLMACAQTGSGKTAAFCLPVVSGLVAAGGSGIGHRERSSFNRAAAKPRALVLAPTRE 179

Query: 206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT 265
           LA QI +E K  S      +  +  GGT +  Q  +L  G  I+VATPGR +D +++   
Sbjct: 180 LAAQINEEAKKFSFQT-GLRVVVAYGGTPMYNQLRDLERGADILVATPGRLVDMVERSKV 238

Query: 266 SLSRVSFVILDEADRMLDMGFEPQIREVMQ--NLPDK--HQTLLFSATMPVEIEALAQEY 321
           SL  + ++++DEADRMLDMGFEPQIR++++  N+P K   QT+LFSAT P EI+ LA ++
Sbjct: 239 SLEAIKYLVMDEADRMLDMGFEPQIRKIVERMNMPRKSVRQTMLFSATFPPEIQRLASDF 298

Query: 322 LTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFV 381
           L++ + + VG+V S T  ++Q +E +S+ EK   LL LL  ++     S    PLT+VFV
Sbjct: 299 LSNYIFITVGRVGSSTDLIMQKVELLSDGEKRGYLLDLLQRQSVGVANSKLQQPLTLVFV 358

Query: 382 ERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM 441
           E K   D +   L ++G  A A+HG R Q +RESALR F+ G T I+VATDVASRGLDV 
Sbjct: 359 ETKREADSLRYWLYSKGFPATAIHGDRTQQERESALRSFKTGLTPIMVATDVASRGLDVP 418

Query: 442 GVAHVVNLDLPK 453
            VAHV+N DLPK
Sbjct: 419 NVAHVINYDLPK 430

Oryza sativa subsp. japonica (taxid: 39947)

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	503
225434327	568	PREDICTED: ATP-dependent RNA helicase DB	0.878	0.778	0.744	0.0
224124820	559	predicted protein [Populus trichocarpa]	0.884	0.796	0.738	0.0
255565933	564	dead box ATP-dependent RNA helicase, put	0.898	0.801	0.705	0.0
8489871	622	DEAD box protein P68 [Pisum sativum]	0.880	0.712	0.710	0.0
302753758	575	hypothetical protein SELMODRAFT_75384 [S	0.904	0.791	0.667	1e-175
147801232	489	hypothetical protein VITISV_009507 [Viti	0.846	0.871	0.735	1e-174
168034811	582	predicted protein [Physcomitrella patens	0.757	0.654	0.769	1e-174
168067875	538	predicted protein [Physcomitrella patens	0.807	0.754	0.733	1e-173
224146601	530	predicted protein [Populus trichocarpa]	0.705	0.669	0.759	1e-165
303278630	471	predicted protein [Micromonas pusilla CC	0.755	0.806	0.656	1e-145

>gi|225434327|ref|XP_002266157.1| PREDICTED: ATP-dependent RNA helicase DBP2 [Vitis vinifera] gi|297745752|emb|CBI15808.3| unnamed protein product [Vitis vinifera]

 Score =  671 bits (1730), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 350/470 (74%), Positives = 383/470 (81%), Gaps = 28/470 (5%)

Query: 1   MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSD--LTTKLSFSSKS------ 52
           M Y PPH R  SS         S S +S  + +S VTLD     T  LS+SS +      
Sbjct: 1   MSYVPPHLRNPSS---------SISRTSKPTETSAVTLDDTHRTTNNLSYSSTNSHLSHS 51

Query: 53  -------LPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNV 105
                  L  +++SN+    R    +  VP+PVF  WKPSDRV    PEQIEEVRLRLNV
Sbjct: 52  NASSSPSLSRWASSNAAAVPR----TPSVPEPVFPQWKPSDRVFLMKPEQIEEVRLRLNV 107

Query: 106 DVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCA 165
           DVTVA    PAPAPIESFTDM LH SIMKDI FHEYTRPT IQAQAMPVALSGRDLLGCA
Sbjct: 108 DVTVAPDLPPAPAPIESFTDMGLHQSIMKDITFHEYTRPTFIQAQAMPVALSGRDLLGCA 167

Query: 166 ETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFK 225
           ETGSGKTAAF IPMIQHC+AQ PV RGDGPLALVLAPTRELAQQIEKEVKA SRSLDSF+
Sbjct: 168 ETGSGKTAAFAIPMIQHCLAQPPVRRGDGPLALVLAPTRELAQQIEKEVKAFSRSLDSFR 227

Query: 226 TAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG 285
           TAIVVGGTNI+EQRSELR GV+IVVATPGRF+ HLQ+GNTSLSR+SFV+LDEADRMLDMG
Sbjct: 228 TAIVVGGTNISEQRSELRAGVNIVVATPGRFIHHLQEGNTSLSRISFVVLDEADRMLDMG 287

Query: 286 FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILE 345
           FEPQIREVMQNLP KHQTLLFSATMP+EIE LAQEYL +PVQVKVGKVS PTANV QILE
Sbjct: 288 FEPQIREVMQNLPQKHQTLLFSATMPMEIETLAQEYLNNPVQVKVGKVSCPTANVSQILE 347

Query: 346 KVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALH 405
           KVSE+EK+D LLALLVEEA  AE+   PFPLTIVFVERKTRCDEV+EALVA+GL AVALH
Sbjct: 348 KVSESEKIDGLLALLVEEASQAERCGRPFPLTIVFVERKTRCDEVAEALVAQGLRAVALH 407

Query: 406 GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           GGR+Q++RE+ALRDFRNG+TNILVATDVASRGLDV GVAHV+NLDLPK +
Sbjct: 408 GGRSQAEREAALRDFRNGATNILVATDVASRGLDVTGVAHVINLDLPKAM 457

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124820|ref|XP_002319430.1| predicted protein [Populus trichocarpa] gi|222857806|gb|EEE95353.1| predicted protein [Populus trichocarpa]

 Score =  670 bits (1729), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 339/459 (73%), Positives = 381/459 (83%), Gaps = 14/459 (3%)

Query: 1   MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSDLTTKLSFSSKSLPNFSNSN 60
           M Y PPH R SSSN+          + ++S + SV   D++    LS SS +    S++ 
Sbjct: 1   MSYIPPHLRNSSSNA----------TITASRAHSVPPTDTNDHPNLSHSSSNFNTSSSTT 50

Query: 61  SNTTCRRSYASHP----VPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPA 116
             +  RRS  +      VPQPVF NW PSDRVLRFNP+QI E+R RLN+DV+VASGS  A
Sbjct: 51  FASPSRRSSGAFSRTISVPQPVFPNWTPSDRVLRFNPDQIAEIRSRLNIDVSVASGSPLA 110

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           PA IESF DMCLH SIMKDI  HEYTRPTSIQAQAM VALSGRDLLGCAETGSGKTAAFT
Sbjct: 111 PAAIESFEDMCLHQSIMKDIAHHEYTRPTSIQAQAMTVALSGRDLLGCAETGSGKTAAFT 170

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           IPMIQHC+AQ  V RGDGPLALVLAPTRELAQQIEKEVK  SRSL+SF+TAIVVGGTNIA
Sbjct: 171 IPMIQHCLAQPTVRRGDGPLALVLAPTRELAQQIEKEVKGFSRSLESFRTAIVVGGTNIA 230

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
           +QR ELR GV ++VATPGR +DHLQQGNTSLSR+SF++LDEADRMLDMGFEPQIREVM+N
Sbjct: 231 DQRLELRAGVDVIVATPGRLIDHLQQGNTSLSRISFIVLDEADRMLDMGFEPQIREVMRN 290

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRL 356
           LP+KHQTLLFSATMPVEIE L QEYLT PVQV+VGKVSSPTANV QIL KVSE+EK+D L
Sbjct: 291 LPEKHQTLLFSATMPVEIETLTQEYLTSPVQVRVGKVSSPTANVSQILTKVSESEKIDCL 350

Query: 357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESA 416
           LALLVE+A  AE+S  PFPLTIVFVERKTRC+EV+EALVA+ L AVALHGGR+QSDRE+A
Sbjct: 351 LALLVEDASQAERSNQPFPLTIVFVERKTRCNEVAEALVAQALQAVALHGGRSQSDREAA 410

Query: 417 LRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           LRDFR+GST+ILVATDVASRGLDV GVAHV+NLDLPK +
Sbjct: 411 LRDFRSGSTSILVATDVASRGLDVTGVAHVINLDLPKTM 449

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565933|ref|XP_002523955.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223536802|gb|EEF38442.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  645 bits (1664), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/458 (70%), Positives = 390/458 (85%), Gaps = 6/458 (1%)

Query: 1   MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSDLTTKLSFSS-KSLPN-FSN 58
           M Y PPH R   +++ +  ++++++++++++ +S +TL++D +TKLS S+ KSL +  SN
Sbjct: 1   MSYVPPHLR---NSTATTTTTTTTTTTTTTTITSSITLENDHSTKLSTSTWKSLSSTLSN 57

Query: 59  SNSNTTCR-RSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAP 117
            +  TT    S  +  VP PV   W PS+RVLR N +Q+E+VR RLN++VTVASGS PAP
Sbjct: 58  GSRRTTAAFTSPRTLSVPDPVLPQWTPSERVLRLNSQQVEDVRARLNIEVTVASGSPPAP 117

Query: 118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTI 177
           APIESF DMCL+ +IMKDI +H YTRPT IQ QAM V+LSGRDLL CAETGSGKTAAFTI
Sbjct: 118 APIESFEDMCLNQNIMKDIAYHGYTRPTPIQVQAMTVSLSGRDLLACAETGSGKTAAFTI 177

Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
           PMIQHC+AQ+P+ RGDGPLALVLAPTRELAQQIEKEVK  SRSLDSF+TAIVVGGTNIA+
Sbjct: 178 PMIQHCLAQSPIRRGDGPLALVLAPTRELAQQIEKEVKCFSRSLDSFRTAIVVGGTNIAD 237

Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL 297
           QRSELR GV I+VATPGRF+DHLQQGNTSLSR+SF++LDEADRMLDMGFEPQIREV+ NL
Sbjct: 238 QRSELRAGVDIMVATPGRFIDHLQQGNTSLSRISFIVLDEADRMLDMGFEPQIREVLHNL 297

Query: 298 PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL 357
           P++HQTLLFSATMP EIE LAQEYLT PVQVKVGKVS  TANV Q+L+KVSE+EK+D LL
Sbjct: 298 PERHQTLLFSATMPEEIETLAQEYLTTPVQVKVGKVSGLTANVSQVLKKVSESEKIDCLL 357

Query: 358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL 417
            LLVE+A  AE++ HPFPLT+VFV+RK RCDEV+EALVA+GL AVALHGGR+Q++RE+AL
Sbjct: 358 GLLVEDASQAERADHPFPLTVVFVDRKARCDEVAEALVAQGLRAVALHGGRSQNEREAAL 417

Query: 418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
            DFR+GST+ILVATDVASRGLDV GV HV+NLDLPK +
Sbjct: 418 HDFRSGSTDILVATDVASRGLDVTGVTHVINLDLPKTM 455

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8489871|gb|AAF75791.1|AF271892_1 DEAD box protein P68 [Pisum sativum]

 Score =  644 bits (1661), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 327/460 (71%), Positives = 378/460 (82%), Gaps = 17/460 (3%)

Query: 1   MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSDL-TTKLSFSSKSLPNFSNS 59
           M Y PPH R +SS +V+  +  S+SS          TLD     T L+FSS    + S+S
Sbjct: 1   MSYVPPHLRNASSTAVATTTRPSASSG---------TLDHHHHNTNLAFSSSYPHSNSSS 51

Query: 60  NSNTTCRRSYASHP------VPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGS 113
            +N + R S A+        VP  VF NW+PS+RV R NP+QIEEV +RLN+DVTV+S S
Sbjct: 52  LANGSRRTSAATSAISELVTVPDTVFPNWQPSERVSRMNPDQIEEV-VRLNLDVTVSSDS 110

Query: 114 VPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTA 173
             AP PIESF DMCLHPSIMKDI +HEYTRP+SIQAQAMP+ALSGRDLLGCAETGSGKTA
Sbjct: 111 TAAPGPIESFNDMCLHPSIMKDIAYHEYTRPSSIQAQAMPIALSGRDLLGCAETGSGKTA 170

Query: 174 AFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT 233
           AFTIPM+QHC+ Q P+ RGDGPLALVLAPTRELAQQIEKEV+A SRSL+S K  IVVGGT
Sbjct: 171 AFTIPMLQHCLVQPPIRRGDGPLALVLAPTRELAQQIEKEVQAFSRSLESLKNCIVVGGT 230

Query: 234 NIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREV 293
           NI +QRSELR GV I VATPGRF+DHLQQGNTSLSR+S+V+LDEADRMLDMGFEPQIRE+
Sbjct: 231 NIEKQRSELRAGVEIAVATPGRFIDHLQQGNTSLSRISYVVLDEADRMLDMGFEPQIREI 290

Query: 294 MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
           M++LP+KHQTLLFSATMPVEIEALA+EYL +PVQVKVGKVSSPT NV Q L KVS +EK+
Sbjct: 291 MRSLPEKHQTLLFSATMPVEIEALAKEYLANPVQVKVGKVSSPTTNVSQTLVKVSGSEKI 350

Query: 354 DRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR 413
           DRLL LLVEEA  AEK  H FPLTIVFVERKTRCDEV+EALVA+GL AV+LHGG +Q++R
Sbjct: 351 DRLLDLLVEEASQAEKCGHRFPLTIVFVERKTRCDEVAEALVAQGLSAVSLHGGHSQNER 410

Query: 414 ESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           E+AL++FR+ ST+ILVATDVASRGLDV GV+HV+NLDLPK
Sbjct: 411 EAALQNFRSSSTSILVATDVASRGLDVTGVSHVINLDLPK 450

Source: Pisum sativum

Species: Pisum sativum

Genus: Pisum

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302753758|ref|XP_002960303.1| hypothetical protein SELMODRAFT_75384 [Selaginella moellendorffii] gi|302767980|ref|XP_002967410.1| hypothetical protein SELMODRAFT_168957 [Selaginella moellendorffii] gi|300165401|gb|EFJ32009.1| hypothetical protein SELMODRAFT_168957 [Selaginella moellendorffii] gi|300171242|gb|EFJ37842.1| hypothetical protein SELMODRAFT_75384 [Selaginella moellendorffii]

 Score =  620 bits (1599), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 309/463 (66%), Positives = 364/463 (78%), Gaps = 8/463 (1%)

Query: 1   MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSDLTTKLSFSSKSLPN---FS 57
           M Y PPH R+ +S++    + +S S S  SSS    + D D        S++ P+   F+
Sbjct: 1   MPYIPPHLRSGASSNSRAATPASPSPSQRSSSGDFGSRDRDYGGSFGSYSRNRPDANGFA 60

Query: 58  NSNSNTTCRRSYASH-----PVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASG 112
           + N     +  + S      P P+ V++ W+PS+RV R   +QI +VR RLNVDV +  G
Sbjct: 61  SGNGYGREKWPFPSRDTRGLPPPEAVWSRWQPSERVRRMQSDQIADVRARLNVDVEITDG 120

Query: 113 SVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKT 172
           +  A AP+E+F DMCLH +IMKDI FHEYT PT IQAQAMPVALSGRDLLGCAETGSGKT
Sbjct: 121 TPAAQAPVETFEDMCLHANIMKDIAFHEYTNPTPIQAQAMPVALSGRDLLGCAETGSGKT 180

Query: 173 AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGG 232
           AAF IPMIQHC+AQ P+  GDGPLALVLAPTRELAQQIEKEV+A SRS D FKTAIVVGG
Sbjct: 181 AAFAIPMIQHCLAQPPIRHGDGPLALVLAPTRELAQQIEKEVRAFSRSTDGFKTAIVVGG 240

Query: 233 TNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIRE 292
           T+I EQRSELR GV +VVATPGRF+DHLQQGN+SL RVS+V+LDEADRMLDMGF PQI+E
Sbjct: 241 THIGEQRSELRSGVQVVVATPGRFIDHLQQGNSSLLRVSYVVLDEADRMLDMGFLPQIKE 300

Query: 293 VMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEK 352
           VMQNLP KHQTLLFSATMP EIEALAQEYLT PVQVKVGKVSSPT+NV+Q LEKV E +K
Sbjct: 301 VMQNLPKKHQTLLFSATMPEEIEALAQEYLTKPVQVKVGKVSSPTSNVLQSLEKVDEKDK 360

Query: 353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSD 412
           +D LLA+LVE +  +E++  P PLTIVFVERK RCD+V++AL+A+GL A ALHGGR Q +
Sbjct: 361 IDYLLAMLVESSNQSERAGQPPPLTIVFVERKARCDDVADALLAQGLKAAALHGGRTQGE 420

Query: 413 RESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           RE+ALRDFR G+ +ILVATDVASRGLDV GVAHVVNLDLPKV+
Sbjct: 421 REAALRDFRKGAISILVATDVASRGLDVTGVAHVVNLDLPKVM 463

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147801232|emb|CAN75572.1| hypothetical protein VITISV_009507 [Vitis vinifera]

 Score =  619 bits (1595), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 328/446 (73%), Positives = 362/446 (81%), Gaps = 20/446 (4%)

Query: 1   MMYEPPHRRTSSSNSVSKVSSSSSSSSSSSSSSSVVTLDSD--LTTKLSFSSKSLPNFSN 58
           M Y PPH R  SS         S S +S  + +S VTLD     T  LS+SS +     +
Sbjct: 1   MSYVPPHLRNPSS---------SJSRTSKPTETSAVTLDDTHRTTNNLSYSSTNSHLSHS 51

Query: 59  SNSNTTCRR-----SYASHP----VPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTV 109
           + S++         + A+ P    VP+PVF  WKPSDRV    PEQIEEVRLRLNVDVTV
Sbjct: 52  NASSSXSLSRWASSNAAAVPRTPSVPEPVFPQWKPSDRVFXMKPEQIEEVRLRLNVDVTV 111

Query: 110 ASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGS 169
           A    PAPAPIESFTDM LH SIMKDI FHEYTRPT IQAQAMPVALSGRDLLGCAETGS
Sbjct: 112 APDLPPAPAPIESFTDMGLHQSIMKDIXFHEYTRPTFIQAQAMPVALSGRDLLGCAETGS 171

Query: 170 GKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIV 229
           GKTAAF IPMIQHC+AQ PV RGDGPLALVLAPTRELAQQIEKEVKA SRSLDSF+TAIV
Sbjct: 172 GKTAAFAIPMIQHCLAQPPVRRGDGPLALVLAPTRELAQQIEKEVKAFSRSLDSFRTAIV 231

Query: 230 VGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQ 289
           VGGTNI+EQRSELR GV+IVVATPGRF+ HLQ+GNTSLSR+SFV+LDEADRMLDMGFEPQ
Sbjct: 232 VGGTNISEQRSELRAGVNIVVATPGRFIHHLQEGNTSLSRISFVVLDEADRMLDMGFEPQ 291

Query: 290 IREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE 349
           IREVMQNLP KHQTLLFSATMP+EIE LAQEYL +PVQVKVGKVS PTANV QILEKVSE
Sbjct: 292 IREVMQNLPQKHQTLLFSATMPMEIETLAQEYLNNPVQVKVGKVSCPTANVSQILEKVSE 351

Query: 350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRN 409
           +EK+D LLALLVEEA  AE+   PFPLTIVFVERKTRCDEV+EALVA+GL AVALHGGR+
Sbjct: 352 SEKIDGLLALLVEEASQAERCGRPFPLTIVFVERKTRCDEVAEALVAQGLRAVALHGGRS 411

Query: 410 QSDRESALRDFRNGSTNILVATDVAS 435
           Q++RE+ALRDFRNG+TNILV   ++S
Sbjct: 412 QAEREAALRDFRNGATNILVCLCISS 437

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168034811|ref|XP_001769905.1| predicted protein [Physcomitrella patens subsp. patens] gi|168034871|ref|XP_001769935.1| predicted protein [Physcomitrella patens subsp. patens] gi|162678811|gb|EDQ65265.1| predicted protein [Physcomitrella patens subsp. patens] gi|162678841|gb|EDQ65295.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  617 bits (1591), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 293/381 (76%), Positives = 334/381 (87%)

Query: 75  PQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMK 134
           P+ V+  W+PS+RV +  PEQI EVR RLNVDV +A+GS PAPAPIESF DMCLH SIMK
Sbjct: 89  PEVVWATWQPSERVQKLQPEQIAEVRARLNVDVEIATGSEPAPAPIESFEDMCLHLSIMK 148

Query: 135 DIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG 194
           D+ FH YT PT IQAQA+PVALSGRDLLGCAETGSGKTAAF++PMIQHC+AQ P+ RGDG
Sbjct: 149 DVTFHNYTTPTPIQAQALPVALSGRDLLGCAETGSGKTAAFSLPMIQHCLAQPPIRRGDG 208

Query: 195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPG 254
           PLALVLAPTRELAQQIEKEVKA  RS + F+TAIVVGGTNI EQRSELR GV IVVATPG
Sbjct: 209 PLALVLAPTRELAQQIEKEVKAFCRSAEGFRTAIVVGGTNIYEQRSELRAGVEIVVATPG 268

Query: 255 RFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEI 314
           RF+DHLQQGN+SLSRVS+V+LDEADRMLDMGFEPQIREVM++LP KHQTLLFSATMP EI
Sbjct: 269 RFIDHLQQGNSSLSRVSYVVLDEADRMLDMGFEPQIREVMRSLPKKHQTLLFSATMPEEI 328

Query: 315 EALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPF 374
           EALAQEYL +P++VKVG+VSSPTANV Q LEK++E EK++ LLALLV+E   +  +  P 
Sbjct: 329 EALAQEYLDNPIRVKVGRVSSPTANVTQNLEKITEKEKIESLLALLVDEHSQSLDTNQPP 388

Query: 375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA 434
           PLTIVFVERK RCDEV++ALV +GL A ALHGGR+QS+RE+ALRDFR G+TNILVATDVA
Sbjct: 389 PLTIVFVERKARCDEVTDALVEQGLKATALHGGRSQSEREAALRDFRKGTTNILVATDVA 448

Query: 435 SRGLDVMGVAHVVNLDLPKVL 455
           SRGLDV GVAHV+NLDLPK +
Sbjct: 449 SRGLDVTGVAHVINLDLPKTM 469

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168067875|ref|XP_001785829.1| predicted protein [Physcomitrella patens subsp. patens] gi|162662518|gb|EDQ49361.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  614 bits (1583), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 300/409 (73%), Positives = 340/409 (83%), Gaps = 3/409 (0%)

Query: 47  SFSSKSLPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVD 106
           SF + +    S S    +  R       P+ V+ +WKPS+RV +  PEQI EVR RLNVD
Sbjct: 39  SFGASAGARRSASEGEGSAARGVGH---PEVVWPDWKPSERVRKLLPEQIAEVRARLNVD 95

Query: 107 VTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAE 166
           V +   + PAPAPIESF DMCLH SIMKD+ FH YT PT IQAQA+PVALSGRDLLGCAE
Sbjct: 96  VEITPDTEPAPAPIESFEDMCLHLSIMKDVTFHNYTTPTPIQAQALPVALSGRDLLGCAE 155

Query: 167 TGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKT 226
           TGSGKTAAF++PMIQHC+AQ P+ RGDGPLALVLAPTRELAQQIEKEVKA SRS + FKT
Sbjct: 156 TGSGKTAAFSLPMIQHCLAQPPIRRGDGPLALVLAPTRELAQQIEKEVKAFSRSAEGFKT 215

Query: 227 AIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGF 286
           +IVVGGTNI EQRSELR GV IVVATPGRF+DHLQQGN+SLSRVS+V+LDEADRMLDMGF
Sbjct: 216 SIVVGGTNIYEQRSELRAGVEIVVATPGRFIDHLQQGNSSLSRVSYVVLDEADRMLDMGF 275

Query: 287 EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEK 346
           EPQIREVM++LP KHQTLLFSATMP EIEALAQEYL  PV+VKVG+VSSPTANV Q LEK
Sbjct: 276 EPQIREVMRSLPKKHQTLLFSATMPEEIEALAQEYLNKPVRVKVGRVSSPTANVTQNLEK 335

Query: 347 VSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG 406
           ++E EK+D LLALLV+E   +  S  P PLTIVFVERK RCDEV++ALV +GL A ALHG
Sbjct: 336 ITEKEKIDSLLALLVDEHSQSLDSNQPPPLTIVFVERKARCDEVTDALVEQGLKATALHG 395

Query: 407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           GR+QS+RE+ALRDFR G+TNILVATDVASRGLDV GVAHV+NLDLPK +
Sbjct: 396 GRSQSEREAALRDFRKGTTNILVATDVASRGLDVTGVAHVINLDLPKTM 444

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146601|ref|XP_002326066.1| predicted protein [Populus trichocarpa] gi|222862941|gb|EEF00448.1| predicted protein [Populus trichocarpa]

 Score =  588 bits (1515), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 290/382 (75%), Positives = 316/382 (82%), Gaps = 27/382 (7%)

Query: 74  VPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIM 133
           VPQPVF  W PSDRVLRF P+QIEE+R +L ++V+VASGS PAPAPIESF DMCLH SIM
Sbjct: 67  VPQPVFPQWTPSDRVLRFTPDQIEEIRSQLKINVSVASGSPPAPAPIESFEDMCLHQSIM 126

Query: 134 KDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGD 193
           KDI  HEYTRPT IQAQAM VALSGRDLLGCAETGSGKTAAFTIPMIQHC+AQ PV RGD
Sbjct: 127 KDIAHHEYTRPTLIQAQAMTVALSGRDLLGCAETGSGKTAAFTIPMIQHCLAQPPVQRGD 186

Query: 194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATP 253
           GPLA+VLAPTRELAQQIEKEVK  SRSL+SF+TAIVVGGT  A+Q SELR GV ++VATP
Sbjct: 187 GPLAMVLAPTRELAQQIEKEVKRFSRSLESFRTAIVVGGTKSADQGSELRAGVDVIVATP 246

Query: 254 GRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVE 313
           GR +DHLQQGNTSLSR+SF++LDEADRMLDMGFEPQIREVM NLP+KHQTLLFSATMPVE
Sbjct: 247 GRLIDHLQQGNTSLSRISFIVLDEADRMLDMGFEPQIREVMHNLPEKHQTLLFSATMPVE 306

Query: 314 IEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHP 373
           IE LAQEYL  PVQVKVGKVSSPTANV QIL KVS +EK+D LLALLVE+A  AEKS   
Sbjct: 307 IETLAQEYLISPVQVKVGKVSSPTANVSQILTKVSASEKIDCLLALLVEDASQAEKSNQS 366

Query: 374 FPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV 433
           FPLTIVFVERKTRC+EV+EALVA+GL A                           VATDV
Sbjct: 367 FPLTIVFVERKTRCNEVAEALVAQGLQA---------------------------VATDV 399

Query: 434 ASRGLDVMGVAHVVNLDLPKVL 455
           ASRGLDV GVAHV+NLDLPK +
Sbjct: 400 ASRGLDVTGVAHVINLDLPKTM 421

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|303278630|ref|XP_003058608.1| predicted protein [Micromonas pusilla CCMP1545] gi|226459768|gb|EEH57063.1| predicted protein [Micromonas pusilla CCMP1545]

 Score =  522 bits (1344), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 250/381 (65%), Positives = 297/381 (77%), Gaps = 1/381 (0%)

Query: 75  PQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMK 134
           P  +F  WKPS+RV      QIEE+R R++V V    G   AP P+ESF DM L+  I+ 
Sbjct: 1   PPAIFPKWKPSERVQALTVNQIEEIRRRMDVTVECKEGDEAAP-PVESFEDMMLNAKILL 59

Query: 135 DIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG 194
           DI FHEY +PT IQAQA+P+ LSGRD+LGCAETGSGKTAAF+IPMIQHC+ Q P+ RGDG
Sbjct: 60  DIRFHEYDKPTPIQAQAIPIILSGRDVLGCAETGSGKTAAFSIPMIQHCLEQDPIKRGDG 119

Query: 195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPG 254
           P A+V+APTRELAQQIEKE K  SRS   FKT IVVGGTN+++QRS+LR GV + VATPG
Sbjct: 120 PFAIVMAPTRELAQQIEKEAKVFSRSSKGFKTTIVVGGTNMSDQRSDLRQGVEVCVATPG 179

Query: 255 RFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEI 314
           R +DHL QGNT+L RVS VILDEADRMLDMGFEPQIREVMQNLP  HQTLLFSATMP E+
Sbjct: 180 RLIDHLHQGNTNLGRVSLVILDEADRMLDMGFEPQIREVMQNLPTPHQTLLFSATMPAEV 239

Query: 315 EALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPF 374
           E+LA +YL  PV+VKVG VS PTANV Q LEK+ + +KVDRL  LL+EE   AEK     
Sbjct: 240 ESLAADYLNKPVKVKVGAVSVPTANVAQHLEKLVDAQKVDRLCELLLEEKAEAEKFGGSL 299

Query: 375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA 434
           P+T+VFVERK R DEV E L AEG+ A A HGGR+Q +RE+AL D++NG  ++L ATDVA
Sbjct: 300 PMTVVFVERKARADEVMELLNAEGVSAAAFHGGRSQQEREAALSDYKNGKCSVLCATDVA 359

Query: 435 SRGLDVMGVAHVVNLDLPKVL 455
           +RGLDV G+AHVVNLD+P++ 
Sbjct: 360 ARGLDVKGIAHVVNLDMPRMF 380

Source: Micromonas pusilla CCMP1545

Species: Micromonas pusilla

Genus: Micromonas

Order: Mamiellales

Class: Mamiellophyceae

Phylum: Chlorophyta

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	503
FB|FBgn0029979	945	CG10777 [Drosophila melanogast	0.727	0.387	0.421	5e-76
FB|FBgn0035720	818	CG10077 [Drosophila melanogast	0.717	0.441	0.445	7.3e-75
SGD|S000005056	546	DBP2 "ATP-dependent RNA helica	0.687	0.633	0.424	2.5e-72
UNIPROTKB|E1C2R8	496	DDX17 "Uncharacterized protein	0.745	0.756	0.407	1.8e-71
FB|FBgn0003261	719	Rm62 "Rm62" [Drosophila melano	0.721	0.504	0.414	2.9e-71
CGD|CAL0003204	562	DBP2 [Candida albicans (taxid:	0.685	0.613	0.420	6.1e-71
UNIPROTKB|A7E307	650	DDX17 "Uncharacterized protein	0.703	0.544	0.422	6.1e-71
UNIPROTKB|E2RJ60	650	DDX17 "Uncharacterized protein	0.703	0.544	0.422	6.1e-71
UNIPROTKB|F1PID8	736	DDX17 "Uncharacterized protein	0.703	0.480	0.422	6.1e-71
UNIPROTKB|H3BLZ8	731	DDX17 "Probable ATP-dependent	0.703	0.484	0.422	6.1e-71

FB|FBgn0029979 CG10777 [Drosophila melanogaster (taxid:7227)]

 Score = 766 (274.7 bits), Expect = 5.0e-76, P = 5.0e-76
 Identities = 159/377 (42%), Positives = 247/377 (65%)

Query:    79 FNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEF 138
             F N  P+   L  + +Q+ E+R  L  ++TV+   +P P  + SF +  L   ++++++ 
Sbjct:   201 FYNIHPN--TLAKSEQQVAEIRREL--EITVSGNELPHP--VVSFEESSLPAHVIEEMKR 254

Query:   139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL 198
               +T+PT+IQ+Q  P+ALSGRDL+G A+TGSGKT A+ +P I H   Q P+ RG+GP+AL
Sbjct:   255 QGFTKPTAIQSQGWPIALSGRDLVGIAQTGSGKTLAYMLPAIVHIGNQPPIIRGEGPIAL 314

Query:   199 VLAPTRELAQQIEKEVKALSRSLD-SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFL 257
             VLAPTRELAQQI+  V+          +   + GG++   Q  +L  GV +++ATPGR +
Sbjct:   315 VLAPTRELAQQIQSVVRDYGHLCKPEIRHTCIFGGSSKVPQARDLDRGVEVIIATPGRLI 374

Query:   258 DHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEA 316
             D L+  NT+L R ++++LDEADRMLDMGFEPQIR++++ + PD+ Q +++SAT P E++A
Sbjct:   375 DFLENRNTNLQRCTYLVLDEADRMLDMGFEPQIRKIIEQIRPDR-QVVMWSATWPKEVQA 433

Query:   317 LAQEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFP 375
             LA ++L D +Q+ +G ++ S   N+ QI+E  +E EK  R                +   
Sbjct:   434 LAGDFLNDYIQINIGSMNLSANHNIRQIVEICTEIEKPQRLVCLLNEISPIKNSGNNGNK 493

Query:   376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS 435
             + IVFVE K + +++ + + AEG +A ++HG + Q++R+S L+DFRNG +NIL+ATDVAS
Sbjct:   494 I-IVFVETKIKVEDILQIIRAEGYNATSIHGDKTQNERDSVLKDFRNGKSNILIATDVAS 552

Query:   436 RGLDVMGVAHVVNLDLP 452
             RGLDV  + +V+N D P
Sbjct:   553 RGLDVEDLQYVINYDYP 569

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

FB|FBgn0035720 CG10077 [Drosophila melanogaster (taxid:7227)]

 Score = 755 (270.8 bits), Expect = 7.3e-75, P = 7.3e-75
 Identities = 167/375 (44%), Positives = 234/375 (62%)

Query:    80 NNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFH 139
             N +KP D VL     + E   L  N ++T+    VP P+ IE F +      +M +I   
Sbjct:   120 NFYKPCDSVLARTVGETETF-LTSN-EITIKGDQVPTPS-IE-FEEGGFPDYVMNEIRKQ 175

Query:   140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV 199
              + +PT+IQAQ  P+A+SGRDL+G A+TGSGKT A+ +P + H   Q  + RGDGP+ALV
Sbjct:   176 GFAKPTAIQAQGWPIAMSGRDLVGVAQTGSGKTLAYVLPAVVHINNQPRLERGDGPIALV 235

Query:   200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDH 259
             LAPTRELAQQI+ +V     S    +   + GG    +Q  +L  GV IV+ATPGR +D 
Sbjct:   236 LAPTRELAQQIQ-QVAIEFGSNTHVRNTCIFGGAPKGQQARDLERGVEIVIATPGRLIDF 294

Query:   260 LQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALA 318
             L++G TSL R ++++LDEADRMLDMGFEPQIR++MQ + PD+ Q L++SAT P E+  LA
Sbjct:   295 LERGTTSLKRCTYLVLDEADRMLDMGFEPQIRKIMQQIRPDR-QVLMWSATWPKEVRQLA 353

Query:   319 QEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLT 377
             +E+L + +QV +G +S S   N++QI++   ENEK+ +                     T
Sbjct:   354 EEFLNNYIQVNIGSLSLSANHNILQIVDVCDENEKLMKLIKLLTDISAENETK------T 407

Query:   378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG 437
             I+FVE K R DE++  +  +G  A A+HG ++Q +R+  L  FRNG  +ILVATDVA+RG
Sbjct:   408 IIFVETKKRVDEITRNISRQGWRACAIHGDKSQQERDFVLSSFRNGRHSILVATDVAARG 467

Query:   438 LDVMGVAHVVNLDLP 452
             LDV  V  V+N D P
Sbjct:   468 LDVDDVKFVINYDYP 482

GO:0003724 "RNA helicase activity" evidence=ISS

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005875 "microtubule associated complex" evidence=IDA

SGD|S000005056 DBP2 "ATP-dependent RNA helicase of the DEAD-box protein family" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 731 (262.4 bits), Expect = 2.5e-72, P = 2.5e-72
 Identities = 152/358 (42%), Positives = 228/358 (63%)

Query:    97 EEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL 156
             E  + R   ++T++   +P P  I +F +      ++ +++   + +PT IQ Q  P+AL
Sbjct:    91 EIAQFRKENEMTISGHDIPKP--ITTFDEAGFPDYVLNEVKAEGFDKPTGIQCQGWPMAL 148

Query:   157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA 216
             SGRD++G A TGSGKT ++ +P I H  AQ  +  GDGP+ LVLAPTRELA QI+ E   
Sbjct:   149 SGRDMVGIAATGSGKTLSYCLPGIVHINAQPLLAPGDGPIVLVLAPTRELAVQIQTECSK 208

Query:   217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD 276
                S    +   V GG   ++Q  +L  G  IV+ATPGR +D L+ G T+L RV++++LD
Sbjct:   209 FGHS-SRIRNTCVYGGVPKSQQIRDLSRGSEIVIATPGRLIDMLEIGKTNLKRVTYLVLD 267

Query:   277 EADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS- 334
             EADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E++ LA +YL DP+QV+VG +  
Sbjct:   268 EADRMLDMGFEPQIRKIVDQIRPDR-QTLMWSATWPKEVKQLAADYLNDPIQVQVGSLEL 326

Query:   335 SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEAL 394
             S + N+ QI+E VS+ EK DR                     T++F   K  CD++++ L
Sbjct:   327 SASHNITQIVEVVSDFEKRDRLNKYLETASQDNEYK------TLIFASTKRMCDDITKYL 380

Query:   395 VAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
               +G  A+A+HG ++Q +R+  L++FRNG + I+VATDVA+RG+DV G+ +V+N D+P
Sbjct:   381 REDGWPALAIHGDKDQRERDWVLQEFRNGRSPIMVATDVAARGIDVKGINYVINYDMP 438

GO:0071042 "nuclear polyadenylation-dependent mRNA catabolic process" evidence=IGI;IMP

GO:0005739 "mitochondrion" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0008186 "RNA-dependent ATPase activity" evidence=IMP;IDA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA;IPI

GO:0003723 "RNA binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA;IMP

GO:0016787 "hydrolase activity" evidence=IEA

GO:0042254 "ribosome biogenesis" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0003724 "RNA helicase activity" evidence=ISS

UNIPROTKB|E1C2R8 DDX17 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 723 (259.6 bits), Expect = 1.8e-71, P = 1.8e-71
 Identities = 159/390 (40%), Positives = 235/390 (60%)

Query:    66 RRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTD 125
             ++ +  + +P+   N +     V R  P ++EE  LR   ++T+  G    P P+ +F  
Sbjct:    38 KKKWDLNELPKFEKNFYVEHPEVARLTPYEVEE--LRRKKEITIR-GMEGCPKPVFAF-H 93

Query:   126 MCLHPSIMKDIEFHE-YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCV 184
              C  P  + D    + +T PT IQ Q  P+ALSGRD++G A+TGSGKT A+ +P I H  
Sbjct:    94 QCSFPQYVMDALMDQNFTEPTPIQCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHIN 153

Query:   185 AQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRG 244
              Q  + RGDGP+ LVLAPTRELAQQ+++      +     K+  + GG     Q  +L  
Sbjct:   154 HQPYLERGDGPICLVLAPTRELAQQVQQVADDYGKC-SRLKSTCIYGGAPKGPQIRDLER 212

Query:   245 GVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQT 303
             GV I +ATPGR +D L+ G T+L R ++++LDEADRMLDMGFEPQIR+++  + PD+ QT
Sbjct:   213 GVEICIATPGRLIDFLEAGKTNLRRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDR-QT 271

Query:   304 LLFSATMPVEIEALAQEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXX 362
             L++SAT P E+  LA+++L D VQ+ VG +  S   N++QI++   E+EK D        
Sbjct:   272 LMWSATWPKEVRQLAEDFLQDYVQINVGNLELSANHNILQIVDVCMESEK-DHKLIQLME 330

Query:   363 XXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRN 422
                   ++      TI+FVE K RCD+++  +  +G  A+ +HG ++Q +R+  L +FR+
Sbjct:   331 EIMAEKEN-----KTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRS 385

Query:   423 GSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             G   IL+ATDVASRGLDV  V  V+N D P
Sbjct:   386 GKAPILIATDVASRGLDVEDVKFVINYDYP 415

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0072358 "cardiovascular system development" evidence=IEA

FB|FBgn0003261 Rm62 "Rm62" [Drosophila melanogaster (taxid:7227)]

 Score = 721 (258.9 bits), Expect = 2.9e-71, P = 2.9e-71
 Identities = 156/376 (41%), Positives = 235/376 (62%)

Query:    80 NNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFH 139
             N ++    V   +P +++  R R   ++TV  G VP P  I+ F+++ L   +MK+I   
Sbjct:   245 NFYQEHPNVANRSPYEVQ--RYREEQEITVR-GQVPNP--IQDFSEVHLPDYVMKEIRRQ 299

Query:   140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV 199
              Y  PT+IQAQ  P+A+SG + +G A+TGSGKT  + +P I H   Q P+ RGDGP+ALV
Sbjct:   300 GYKAPTAIQAQGWPIAMSGSNFVGIAKTGSGKTLGYILPAIVHINNQQPLQRGDGPIALV 359

Query:   200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDH 259
             LAPTRELAQQI++       S    +   V GG     Q  +L+ G  IV+ATPGR +D 
Sbjct:   360 LAPTRELAQQIQQVATEFGSS-SYVRNTCVFGGAPKGGQMRDLQRGCEIVIATPGRLIDF 418

Query:   260 LQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALA 318
             L  G+T+L R ++++LDEADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E++ LA
Sbjct:   419 LSAGSTNLKRCTYLVLDEADRMLDMGFEPQIRKIVSQIRPDR-QTLMWSATWPKEVKQLA 477

Query:   319 QEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLT 377
             +++L + +Q+ +G +  S   N+ Q+++   E  K ++                 P  + 
Sbjct:   478 EDFLGNYIQINIGSLELSANHNIRQVVDVCDEFSKEEKLKTLLSDIYDTSES---PGKI- 533

Query:   378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG 437
             I+FVE K R D +   + + G+   A+HG ++QS+R+  LR+FR+G +NILVATDVA+RG
Sbjct:   534 IIFVETKRRVDNLVRFIRSFGVRCGAIHGDKSQSERDFVLREFRSGKSNILVATDVAARG 593

Query:   438 LDVMGVAHVVNLDLPK 453
             LDV G+ +V+N D P+
Sbjct:   594 LDVDGIKYVINFDYPQ 609

GO:0004004 "ATP-dependent RNA helicase activity" evidence=ISS;NAS

GO:0003729 "mRNA binding" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0016246 "RNA interference" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0000381 "regulation of alternative mRNA splicing, via spliceosome" evidence=IMP

GO:0005634 "nucleus" evidence=IC;IDA

GO:0019730 "antimicrobial humoral response" evidence=IMP

GO:0005703 "polytene chromosome puff" evidence=IDA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0071013 "catalytic step 2 spliceosome" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=IC

GO:0005700 "polytene chromosome" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

CGD|CAL0003204 DBP2 [Candida albicans (taxid:5476)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 151/359 (42%), Positives = 224/359 (62%)

Query:    96 IEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVA 155
             IE+ R + N ++TV    +P P  I +F +      ++++++   + +PT IQ Q  P+A
Sbjct:   106 IEQFR-KEN-EMTVKGHDIPHP--ITTFDEAGFPDYVLQEVKDQGFPKPTPIQCQGWPMA 161

Query:   156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK 215
             LSGRD++G A TGSGKT ++ +P I H  AQ  +  GDGP+ LVLAPTRELA QI+ E  
Sbjct:   162 LSGRDMIGIAATGSGKTLSYCLPSIVHINAQPQLQYGDGPIVLVLAPTRELAVQIQTECS 221

Query:   216 ALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL 275
                +S    +   V GG     Q  +L  GV I +ATPGR +D L+ G T+L RV++++L
Sbjct:   222 KFGKS-SRIRNTCVYGGAPKGPQIRDLARGVEICIATPGRLIDMLEAGKTNLKRVTYLVL 280

Query:   276 DEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS 334
             DEADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E++ L ++YL DP+QV +G + 
Sbjct:   281 DEADRMLDMGFEPQIRKIVDQIRPDR-QTLMWSATWPKEVQQLTRDYLNDPIQVTIGSLE 339

Query:   335 SPTANVI-QILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEA 393
                ++ I Q++E + E  K DR                      +VF   K  CDE++  
Sbjct:   340 LAASHTITQLVEVIDEFSKRDRLVKHLESALNEKDNKI------LVFASTKRTCDEITTY 393

Query:   394 LVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             L ++G  A+A+HG + Q++R+  L +FR G T+I+VATDVA+RG+DV G+ HV+N D+P
Sbjct:   394 LRSDGWPALAIHGDKEQNERDWVLDEFRKGKTSIMVATDVAARGIDVKGITHVINYDMP 452

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=IEA

GO:0006364 "rRNA processing" evidence=IEA

UNIPROTKB|A7E307 DDX17 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 155/367 (42%), Positives = 224/367 (61%)

Query:    88 VLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSI 147
             V R  P +++E  LR   ++TV  G V  P P+ +F        +M  +    +T PT I
Sbjct:    62 VARLTPYEVDE--LRRKKEITVRGGDV-CPKPVFAFHHANFPQYVMDVLMDQHFTEPTPI 118

Query:   148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
             Q Q  P+ALSGRD++G A+TGSGKT A+ +P I H   Q  + RGDGP+ LVLAPTRELA
Sbjct:   119 QCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPICLVLAPTRELA 178

Query:   208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL 267
             QQ+++      +     K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L
Sbjct:   179 QQVQQVADDYGKC-SRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNL 237

Query:   268 SRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPV 326
              R ++++LDEADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E+  LA+++L D  
Sbjct:   238 RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDR-QTLMWSATWPKEVRQLAEDFLRDYT 296

Query:   327 QVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKT 385
             Q+ VG +  S   N++QI++   E+EK D              ++      TI+FVE K 
Sbjct:   297 QINVGNLELSANHNILQIVDVCMESEK-DHKLIQLMEEIMAEKEN-----KTIIFVETKR 350

Query:   386 RCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAH 445
             RCD+++  +  +G  A+ +HG ++Q +R+  L +FR+G   IL+ATDVASRGLDV  V  
Sbjct:   351 RCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKF 410

Query:   446 VVNLDLP 452
             V+N D P
Sbjct:   411 VINYDYP 417

GO:0072358 "cardiovascular system development" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E2RJ60 DDX17 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 155/367 (42%), Positives = 224/367 (61%)

Query:    88 VLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSI 147
             V R  P +++E  LR   ++TV  G V  P P+ +F        +M  +    +T PT I
Sbjct:    62 VARLTPYEVDE--LRRKKEITVRGGDV-CPKPVFAFHHANFPQYVMDVLMDQHFTEPTPI 118

Query:   148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
             Q Q  P+ALSGRD++G A+TGSGKT A+ +P I H   Q  + RGDGP+ LVLAPTRELA
Sbjct:   119 QCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPICLVLAPTRELA 178

Query:   208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL 267
             QQ+++      +     K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L
Sbjct:   179 QQVQQVADDYGKC-SRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNL 237

Query:   268 SRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPV 326
              R ++++LDEADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E+  LA+++L D  
Sbjct:   238 RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDR-QTLMWSATWPKEVRQLAEDFLRDYT 296

Query:   327 QVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKT 385
             Q+ VG +  S   N++QI++   E+EK D              ++      TI+FVE K 
Sbjct:   297 QINVGNLELSANHNILQIVDVCMESEK-DHKLIQLMEEIMAEKEN-----KTIIFVETKR 350

Query:   386 RCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAH 445
             RCD+++  +  +G  A+ +HG ++Q +R+  L +FR+G   IL+ATDVASRGLDV  V  
Sbjct:   351 RCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKF 410

Query:   446 VVNLDLP 452
             V+N D P
Sbjct:   411 VINYDYP 417

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1PID8 DDX17 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 155/367 (42%), Positives = 224/367 (61%)

Query:    88 VLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSI 147
             V R  P +++E  LR   ++TV  G V  P P+ +F        +M  +    +T PT I
Sbjct:   143 VARLTPYEVDE--LRRKKEITVRGGDV-CPKPVFAFHHANFPQYVMDVLMDQHFTEPTPI 199

Query:   148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
             Q Q  P+ALSGRD++G A+TGSGKT A+ +P I H   Q  + RGDGP+ LVLAPTRELA
Sbjct:   200 QCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPICLVLAPTRELA 259

Query:   208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL 267
             QQ+++      +     K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L
Sbjct:   260 QQVQQVADDYGKC-SRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNL 318

Query:   268 SRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPV 326
              R ++++LDEADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E+  LA+++L D  
Sbjct:   319 RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDR-QTLMWSATWPKEVRQLAEDFLRDYT 377

Query:   327 QVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKT 385
             Q+ VG +  S   N++QI++   E+EK D              ++      TI+FVE K 
Sbjct:   378 QINVGNLELSANHNILQIVDVCMESEK-DHKLIQLMEEIMAEKEN-----KTIIFVETKR 431

Query:   386 RCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAH 445
             RCD+++  +  +G  A+ +HG ++Q +R+  L +FR+G   IL+ATDVASRGLDV  V  
Sbjct:   432 RCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKF 491

Query:   446 VVNLDLP 452
             V+N D P
Sbjct:   492 VINYDYP 498

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|H3BLZ8 DDX17 "Probable ATP-dependent RNA helicase DDX17" [Homo sapiens (taxid:9606)]

 Score = 718 (257.8 bits), Expect = 6.1e-71, P = 6.1e-71
 Identities = 155/367 (42%), Positives = 224/367 (61%)

Query:    88 VLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSI 147
             V R  P +++E  LR   ++TV  G V  P P+ +F        +M  +    +T PT I
Sbjct:   141 VARLTPYEVDE--LRRKKEITVRGGDV-CPKPVFAFHHANFPQYVMDVLMDQHFTEPTPI 197

Query:   148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
             Q Q  P+ALSGRD++G A+TGSGKT A+ +P I H   Q  + RGDGP+ LVLAPTRELA
Sbjct:   198 QCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYLERGDGPICLVLAPTRELA 257

Query:   208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL 267
             QQ+++      +     K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L
Sbjct:   258 QQVQQVADDYGKC-SRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNL 316

Query:   268 SRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPV 326
              R ++++LDEADRMLDMGFEPQIR+++  + PD+ QTL++SAT P E+  LA+++L D  
Sbjct:   317 RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDR-QTLMWSATWPKEVRQLAEDFLRDYT 375

Query:   327 QVKVGKVS-SPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKT 385
             Q+ VG +  S   N++QI++   E+EK D              ++      TI+FVE K 
Sbjct:   376 QINVGNLELSANHNILQIVDVCMESEK-DHKLIQLMEEIMAEKEN-----KTIIFVETKR 429

Query:   386 RCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAH 445
             RCD+++  +  +G  A+ +HG ++Q +R+  L +FR+G   IL+ATDVASRGLDV  V  
Sbjct:   430 RCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKAPILIATDVASRGLDVEDVKF 489

Query:   446 VVNLDLP 452
             V+N D P
Sbjct:   490 VINYDYP 496

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

GO:0009791 "post-embryonic development" evidence=IEA

GO:0072358 "cardiovascular system development" 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

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.4.13	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	503
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-127
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	1e-101
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-101
cd00268	203	cd00268, DEADc, DEAD-box helicases	6e-96
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-94
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-83
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	6e-77
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	1e-74
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	1e-72
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	4e-72
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	9e-65
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	4e-62
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	2e-61
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-57
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	4e-45
cd00079	131	cd00079, HELICc, Helicase superfamily c-terminal d	1e-24
pfam00271	78	pfam00271, Helicase_C, Helicase conserved C-termin	2e-18
smart00490	82	smart00490, HELICc, helicase superfamily c-termina	2e-17
COG1205	851	COG1205, COG1205, Distinct helicase family with a	4e-15
COG0514	590	COG0514, RecQ, Superfamily II DNA helicase [DNA re	5e-14
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	2e-12
COG1061	442	COG1061, SSL2, DNA or RNA helicases of superfamily	1e-10
COG1202	830	COG1202, COG1202, Superfamily II helicase, archaea	6e-10
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	1e-08
TIGR00614	470	TIGR00614, recQ_fam, ATP-dependent DNA helicase, R	1e-08
TIGR01389	591	TIGR01389, recQ, ATP-dependent DNA helicase RecQ	1e-08
TIGR00643	630	TIGR00643, recG, ATP-dependent DNA helicase RecG	5e-07
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	1e-06
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	7e-06
COG1203	733	COG1203, COG1203, CRISPR-associated helicase Cas3	2e-05
PRK11057	607	PRK11057, PRK11057, ATP-dependent DNA helicase Rec	2e-05
PRK13679	168	PRK13679, PRK13679, hypothetical protein; Provisio	3e-05
PRK13766	773	PRK13766, PRK13766, Hef nuclease; Provisional	4e-05
COG1643	845	COG1643, HrpA, HrpA-like helicases [DNA replicatio	9e-05
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	1e-04
COG1111	542	COG1111, MPH1, ERCC4-like helicases [DNA replicati	2e-04
PRK00254	720	PRK00254, PRK00254, ski2-like helicase; Provisiona	2e-04
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	4e-04
PRK09401	1176	PRK09401, PRK09401, reverse gyrase; Reviewed	6e-04
COG4581	1041	COG4581, COG4581, Superfamily II RNA helicase [DNA	0.001
pfam05501	122	pfam05501, DUF755, Domain of unknown function (DUF	0.004

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

 Score =  379 bits (976), Expect = e-127
 Identities = 146/335 (43%), Positives = 206/335 (61%), Gaps = 15/335 (4%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F  + L P +++ ++   +  PT IQ  A+P+ L+GRD+LG A+TG+GKTAAF +P++Q
Sbjct: 30  EFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQ 89

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
             +            AL+LAPTRELA QI +E++ L ++L   + A+V GG +I +Q   
Sbjct: 90  KILKS---VERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEA 146

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L+ GV IVVATPGR LD +++G   LS V  ++LDEADRMLDMGF   I ++++ LP   
Sbjct: 147 LKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDR 206

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVG--KVSSPTANVIQILEKV-SENEKVDRLLA 358
           QTLLFSATMP +I  LA+ YL DPV+++V   K+      + Q   +V SE EK++ LL 
Sbjct: 207 QTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLLK 266

Query: 359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALR 418
           LL                 IVFV  K   +E++E+L   G    ALHG   Q +R+ AL 
Sbjct: 267 LL---------KDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALE 317

Query: 419 DFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            F++G   +LVATDVA+RGLD+  V+HV+N DLP 
Sbjct: 318 KFKDGELRVLVATDVAARGLDIPDVSHVINYDLPL 352

Length = 513

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

 Score =  314 bits (806), Expect = e-101
 Identities = 172/467 (36%), Positives = 251/467 (53%), Gaps = 33/467 (7%)

Query: 7   HRRTSSSNSVSKVSSSSSSSSSSSSS--SSVVTLDSDLTTKLSFSSKSLPNFSNSNSNTT 64
            R T  S+S   VSS  S++ +S      S     +             P + N +    
Sbjct: 1   MRSTDGSSSNGSVSSGPSNNYNSYGPYPDSSNPYGNYQANHQDNYGGFRPGYGNYSGGYG 60

Query: 65  CR--RSYASHPVP---QPVFNNWK-----PSDRVLRFNPEQI-----EEV-RLRLNVDVT 108
                SY S  +    QP+  +WK     P ++       ++     +EV  +R   ++T
Sbjct: 61  GFGMNSYGSSTLGKRLQPI--DWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEIT 118

Query: 109 VASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETG 168
           + +G    P P+ SF        I+K ++   +T PT IQ Q  P+ALSGRD++G AETG
Sbjct: 119 IIAGE-NVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETG 177

Query: 169 SGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAI 228
           SGKT AF +P I H  AQ  +  GDGP+ LVLAPTRELA+QI ++      S    +  +
Sbjct: 178 SGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASS-KIRNTV 236

Query: 229 VVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEP 288
             GG     Q   LR GV I++A PGR +D L+   T+L RV++++LDEADRMLDMGFEP
Sbjct: 237 AYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEP 296

Query: 289 QIRE-VMQNLPDKHQTLLFSATMPVEIEALAQEYLTD-PVQVKVGKVSSPTA-NVIQILE 345
           QIR+ V Q  PD+ QTL++SAT P E+++LA++   + PV V VG +      N+ Q + 
Sbjct: 297 QIRKIVSQIRPDR-QTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVF 355

Query: 346 KVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALH 405
            V E+EK  +L  LL       ++        ++FVE K   D +++ L  +G  A+ +H
Sbjct: 356 VVEEHEKRGKLKMLL-------QRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIH 408

Query: 406 GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           G + Q +R   L +F+ G + I++ATDVASRGLDV  V +V+N D P
Sbjct: 409 GDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFP 455

Length = 545

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

 Score =  311 bits (799), Expect = e-101
 Identities = 136/332 (40%), Positives = 197/332 (59%), Gaps = 17/332 (5%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F+ + L P+++ ++    YT  T IQAQ++P  L+G+D++  A+TGSGKTAAF + ++Q
Sbjct: 5   AFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQ 64

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               +          ALVL PTRELA Q+ KE++ L+R + + K   + GG  +  Q   
Sbjct: 65  KLDVKRF-----RVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDS 119

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  I+V TPGR LDHL++G   L  ++ ++LDEADRMLDMGF+  I  +++  P + 
Sbjct: 120 LEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARR 179

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKVSENEKVDRLLALL 360
           QTLLFSAT P  I A++Q +  DPV+VKV   S+     I Q   +VS +E++  L  LL
Sbjct: 180 QTLLFSATYPEGIAAISQRFQRDPVEVKV--ESTHDLPAIEQRFYEVSPDERLPALQRLL 237

Query: 361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF 420
                      H     +VF   K  C EV++AL A+G  A+ALHG   Q DR+  L  F
Sbjct: 238 ---------LHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRF 288

Query: 421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            N S ++LVATDVA+RGLD+  +  V+N +L 
Sbjct: 289 ANRSCSVLVATDVAARGLDIKALEAVINYELA 320

Length = 460

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

 Score =  288 bits (740), Expect = 6e-96
 Identities = 104/207 (50%), Positives = 147/207 (71%), Gaps = 4/207 (1%)

Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F ++ L P +++ I    + +PT IQA+A+P  LSGRD++G A+TGSGKTAAF IP+++ 
Sbjct: 1   FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60

Query: 183 CVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL 242
                P  + DGP AL+LAPTRELA QI +  + L +  +  K  ++ GGT+I +Q  +L
Sbjct: 61  LD---PSPKKDGPQALILAPTRELALQIAEVARKLGKHTN-LKVVVIYGGTSIDKQIRKL 116

Query: 243 RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ 302
           + G  IVVATPGR LD L++G   LS+V +++LDEADRMLDMGFE QIRE+++ LP   Q
Sbjct: 117 KRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQ 176

Query: 303 TLLFSATMPVEIEALAQEYLTDPVQVK 329
           TLLFSATMP E+  LA+++L +PV++ 
Sbjct: 177 TLLFSATMPKEVRDLARKFLRNPVRIL 203

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

 Score =  292 bits (750), Expect = 4e-94
 Identities = 139/334 (41%), Positives = 209/334 (62%), Gaps = 11/334 (3%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           SF  + L P I++ +    Y  PT IQ QA+P  L GRDL+  A+TG+GKTA FT+P++Q
Sbjct: 2   SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 182 HCVAQTPVGRGDGPL-ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS 240
           H + + P  +G  P+ AL+L PTRELA QI + V+  S+ L+  ++ +V GG +I  Q  
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLN-IRSLVVFGGVSINPQMM 120

Query: 241 ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK 300
           +LRGGV ++VATPGR LD   Q    L +V  ++LDEADRMLDMGF   IR V+  LP K
Sbjct: 121 KLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAK 180

Query: 301 HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALL 360
            Q LLFSAT   +I+ALA++ L +P++++V + ++ +  V Q +  V +  K + LL+ +
Sbjct: 181 RQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRE-LLSQM 239

Query: 361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF 420
           + +    +         +VF   K   + ++E L  +G+ + A+HG ++Q  R  AL DF
Sbjct: 240 IGKGNWQQ--------VLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADF 291

Query: 421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLPKV 454
           ++G   +LVATD+A+RGLD+  + HVVN +LP V
Sbjct: 292 KSGDIRVLVATDIAARGLDIEELPHVVNYELPNV 325

Length = 456

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

 Score =  264 bits (677), Expect = 2e-83
 Identities = 124/333 (37%), Positives = 184/333 (55%), Gaps = 13/333 (3%)

Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F+++ L  S+++ ++   YTRPT+IQA+A+P AL GRD+LG A TG+GKTAAF +P +QH
Sbjct: 3   FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62

Query: 183 CVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL 242
            +   P  +   P  L+L PTRELA Q+  + + L++       A + GG          
Sbjct: 63  LL-DFPRRKSGPPRILILTPTRELAMQVADQARELAKHTH-LDIATITGGVAYMNHAEVF 120

Query: 243 RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ 302
                IVVATPGR L ++++ N     V  +ILDEADRMLDMGF   I  +      + Q
Sbjct: 121 SENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQ 180

Query: 303 TLLFSATMPVE-IEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRLLALL 360
           TLLFSAT+  + ++  A+  L DPV+V+          + Q   +  + E K   L  LL
Sbjct: 181 TLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHLL 240

Query: 361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF 420
            +      +S       IVFV  + R  E++  L   G++   L G   Q+ R  A++  
Sbjct: 241 KQPE--VTRS-------IVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRL 291

Query: 421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            +G  N+LVATDVA+RG+D+  V+HV+N D+P+
Sbjct: 292 TDGRVNVLVATDVAARGIDIDDVSHVINFDMPR 324

Length = 434

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

 Score =  250 bits (639), Expect = 6e-77
 Identities = 134/362 (37%), Positives = 200/362 (55%), Gaps = 16/362 (4%)

Query: 94  EQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMP 153
            Q E +R +L + V    G    P PI SF+   L P ++ ++E   Y  PT IQ QA+P
Sbjct: 98  SQAELLRRKLEIHV---KGEAV-PPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIP 153

Query: 154 VALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGD--GPLALVLAPTRELAQQIE 211
            ALSGR LL  A+TGSGKTA+F +P+I  C         +   PLA+VL PTREL  Q+E
Sbjct: 154 AALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVE 213

Query: 212 KEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVS 271
            + K L + L  FKTA+VVGG  + +Q   ++ GV ++V TPGR +D L + +  L  VS
Sbjct: 214 DQAKVLGKGL-PFKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVS 272

Query: 272 FVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG 331
            ++LDE D ML+ GF  Q+ ++ Q L  + Q LLFSAT+  E+E  A     D + + +G
Sbjct: 273 VLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIG 331

Query: 332 KVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVS 391
             + P   V Q+   V   +K  +L  +L       +   H  P  +VFV  +   D ++
Sbjct: 332 NPNRPNKAVKQLAIWVETKQKKQKLFDIL-------KSKQHFKPPAVVFVSSRLGADLLA 384

Query: 392 EAL-VAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLD 450
            A+ V  GL A+++HG ++  +R   ++ F  G   ++VAT V  RG+D++ V  V+  D
Sbjct: 385 NAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFD 444

Query: 451 LP 452
           +P
Sbjct: 445 MP 446

Length = 518

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

 Score =  247 bits (632), Expect = 1e-74
 Identities = 130/331 (39%), Positives = 191/331 (57%), Gaps = 14/331 (4%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F D+ L   I++ +    Y +P+ IQA+ +P  L+GRD+LG A+TGSGKTAAF++P++ 
Sbjct: 7   TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLH 66

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
           +   +        P  LVLAPTRELA Q+ + +   S+ +       + GG     Q   
Sbjct: 67  NLDPEL-----KAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRA 121

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           LR G  IVV TPGR LDHL++G   LS++S ++LDEAD ML MGF   +  +M  +P+ H
Sbjct: 122 LRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGH 181

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLV 361
           QT LFSATMP  I  + + ++ +P +V++    +   ++ Q    V    K + L+  L 
Sbjct: 182 QTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLE 241

Query: 362 EEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFR 421
            E F A          I+FV  K    EV+EAL   G ++ AL+G  NQ+ RE  L   +
Sbjct: 242 AEDFDA---------AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLK 292

Query: 422 NGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           +G  +IL+ATDVA+RGLDV  ++ VVN D+P
Sbjct: 293 DGRLDILIATDVAARGLDVERISLVVNYDIP 323

Length = 629

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

 Score =  236 bits (603), Expect = 1e-72
 Identities = 123/335 (36%), Positives = 184/335 (54%), Gaps = 16/335 (4%)

Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F+D  LHP +++ +E   +   T IQA A+P+ L+GRD+ G A+TG+GKT AF      +
Sbjct: 10  FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69

Query: 183 CVAQTPVGRG---DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
            +   P       + P AL++APTRELA QI  + + L+++    K  +  GG    +Q 
Sbjct: 70  LL-SHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQA-TGLKLGLAYGGDGYDKQL 127

Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD 299
             L  GV I++ T GR +D+ +Q + +L  +  V+LDEADRM D+GF   IR + + +P 
Sbjct: 128 KVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPP 187

Query: 300 KHQ--TLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL 357
            +Q   +LFSAT+   +  LA E++ +P  V+V         + + L   S  EK+ RLL
Sbjct: 188 ANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKM-RLL 246

Query: 358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL 417
             L+EE +  +++       I+F   K RC+E+   L A+G     L G   Q  R   L
Sbjct: 247 QTLIEEEW-PDRA-------IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRIL 298

Query: 418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +F  G  +ILVATDVA+RGL +  V HV N DLP
Sbjct: 299 EEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLP 333

Length = 423

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

 Score =  236 bits (603), Expect = 4e-72
 Identities = 139/390 (35%), Positives = 199/390 (51%), Gaps = 47/390 (12%)

Query: 73  PVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIES-FTDMCLHPS 131
             P+P  + WK  D V+                           P   ++ F D  L P 
Sbjct: 65  RKPKPA-SLWKLEDFVVE--------------------------PQEGKTRFHDFNLAPE 97

Query: 132 IMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG- 190
           +M  I    +   T IQAQ +   L+G D +G A+TG+GKTAAF I +I   + QTP   
Sbjct: 98  LMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ-LLQTPPPK 156

Query: 191 ---RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGG-V 246
               G+ P AL++APTREL  QI K+  AL++          VGG +  +Q  +L     
Sbjct: 157 ERYMGE-PRALIIAPTRELVVQIAKDAAALTKYTG-LNVMTFVGGMDFDKQLKQLEARFC 214

Query: 247 SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK--HQTL 304
            I+VATPGR LD  Q+G   L  V  ++LDEADRMLDMGF PQ+R++++  P K   QTL
Sbjct: 215 DILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTL 274

Query: 305 LFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEA 364
           LFSAT   ++  LA+++ TDP  V++   +  +  V Q +  V+ ++K   L  L+ +  
Sbjct: 275 LFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYKLLYNLVTQN- 333

Query: 365 FLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS 424
                   P+   +VF  RK     + E LV +G++A  L G   Q  R   L  FR G 
Sbjct: 334 --------PWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGK 385

Query: 425 TNILVATDVASRGLDVMGVAHVVNLDLPKV 454
             +LVATDVA RG+ + G++HV+N  LP+ 
Sbjct: 386 IRVLVATDVAGRGIHIDGISHVINFTLPED 415

Length = 475

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

 Score =  219 bits (559), Expect = 9e-65
 Identities = 130/336 (38%), Positives = 190/336 (56%), Gaps = 15/336 (4%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F+   LHP+++  +E   +TR T IQA  +PVAL G D+ G A+TG+GKT AF + ++ 
Sbjct: 10  TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 182 HCVAQTPVG--RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
             +++  +   + + P AL+LAPTRELA QI K+       L   + A+V GG +  +QR
Sbjct: 70  RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQR 128

Query: 240 SELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
             L+ GV +++ATPGR +D+++Q    SL      +LDEADRM D+GF   IR +++ +P
Sbjct: 129 ELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMP 188

Query: 299 DK--HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRL 356
           ++   QTLLFSAT+   +  LA E++ +P ++ V   +   A V Q +   ++ EK   L
Sbjct: 189 ERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTLL 248

Query: 357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESA 416
           L LL         S      T+VFV  K   + V+  L   G     L G   Q  RES 
Sbjct: 249 LGLL---------SRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESL 299

Query: 417 LRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           L  F+ G   ILVATDVA+RGL + GV +V N DLP
Sbjct: 300 LNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLP 335

Length = 572

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

 Score =  208 bits (530), Expect = 4e-62
 Identities = 118/338 (34%), Positives = 184/338 (54%), Gaps = 24/338 (7%)

Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           ++SF  + L+  +++ I  + + +P++IQ + +   L G D +G A++G+GKTA F I  
Sbjct: 27  VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAA 86

Query: 180 IQHCVAQTPVGRGDGPL----ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI 235
           +Q           D  L    AL+LAPTRELAQQI+K V AL   L   +    VGGT +
Sbjct: 87  LQ---------LIDYDLNACQALILAPTRELAQQIQKVVLALGDYLK-VRCHACVGGTVV 136

Query: 236 AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ 295
            +  ++L+ GV +VV TPGR  D + + +  +  +   ILDEAD ML  GF+ QI +V +
Sbjct: 137 RDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFK 196

Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVD 354
            LP   Q  LFSATMP EI  L  +++ DP ++ V K       + Q    V + E K D
Sbjct: 197 KLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFD 256

Query: 355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRE 414
            L  L   E     ++       I++   + + D +++ +         +HG  +Q DR+
Sbjct: 257 TLCDLY--ETLTITQA-------IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRD 307

Query: 415 SALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             +R+FR+GST +L+ TD+ +RG+DV  V+ V+N DLP
Sbjct: 308 LIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP 345

Length = 401

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

 Score =  198 bits (505), Expect = 2e-61
 Identities = 83/175 (47%), Positives = 115/175 (65%), Gaps = 8/175 (4%)

Query: 145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR 204
           T IQAQA+P  LSG+D+L  A TGSGKT AF +P++Q  + +       GP ALVLAPTR
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKK-----GGPQALVLAPTR 55

Query: 205 ELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL-RGGVSIVVATPGRFLDHLQQG 263
           ELA+QI +E+K L + L   + A++ GGT++ EQ  +L +G   I+V TPGR LD L++G
Sbjct: 56  ELAEQIYEELKKLFKILG-LRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRG 114

Query: 264 NTSLSR-VSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEAL 317
              L + +  ++LDEA R+LDMGF   + E++  LP   Q LL SAT+P  +E L
Sbjct: 115 KLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169

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|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score =  189 bits (481), Expect = 2e-57
 Identities = 87/203 (42%), Positives = 114/203 (56%), Gaps = 9/203 (4%)

Query: 136 IEFHEYTRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG 194
           IE   +      Q +A+   LSG RD++  A TGSGKT A  +P ++       + RG G
Sbjct: 1   IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEA------LKRGKG 54

Query: 195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVS-IVVATP 253
              LVL PTRELA+Q  +E+K L  SL   K   + GG +  EQ  +L  G + I+V TP
Sbjct: 55  GRVLVLVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTP 113

Query: 254 GRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVE 313
           GR LD L+    SLS V  VILDEA R+LD GF  Q+ ++++ LP   Q LL SAT P E
Sbjct: 114 GRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEE 173

Query: 314 IEALAQEYLTDPVQVKVGKVSSP 336
           IE L + +L DPV + VG     
Sbjct: 174 IENLLELFLNDPVFIDVGFTPLE 196

Length = 201

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

 Score =  154 bits (392), Expect = 4e-45
 Identities = 63/152 (41%), Positives = 87/152 (57%), Gaps = 8/152 (5%)

Query: 159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS 218
           RD+L  A TGSGKT A  +P+++       +    G   LVLAPTRELA Q+ + +K L 
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILEL------LDSLKGGQVLVLAPTRELANQVAERLKELF 54

Query: 219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA 278
              +  K   ++GGT+I +Q   L G   IVV TPGR LD L++   SL ++  +ILDEA
Sbjct: 55  --GEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEA 112

Query: 279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATM 310
            R+L+ GF     +++  LP   Q LL SAT 
Sbjct: 113 HRLLNQGFGLLGLKILLKLPKDRQVLLLSATP 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|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process

 Score = 98.5 bits (246), Expect = 1e-24
 Identities = 44/113 (38%), Positives = 62/113 (54%), Gaps = 7/113 (6%)

Query: 341 IQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLH 400
           I+      E+EK++ LL LL E      K        ++F   K   DE++E L   G+ 
Sbjct: 2   IKQYVLPVEDEKLEALLELLKEHLKKGGK-------VLIFCPSKKMLDELAELLRKPGIK 54

Query: 401 AVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
             ALHG  +Q +RE  L+DFR G   +LVATDV +RG+D+  V+ V+N DLP 
Sbjct: 55  VAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPW 107

Length = 131

>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain

 Score = 79.1 bits (196), Expect = 2e-18
 Identities = 31/62 (50%), Positives = 40/62 (64%)

Query: 392 EALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL 451
           + L   G+    LHGG +Q +RE  L DFRNG + +LVATDVA RG+D+  V  V+N DL
Sbjct: 1   KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60

Query: 452 PK 453
           P 
Sbjct: 61  PW 62

The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. Length = 78

>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 32/66 (48%), Positives = 41/66 (62%)

Query: 388 DEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
           +E++E L   G+    LHGG +Q +RE  L  F NG   +LVATDVA RGLD+ GV  V+
Sbjct: 1   EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60

Query: 448 NLDLPK 453
             DLP 
Sbjct: 61  IYDLPW 66

Length = 82

>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 = 77.8 bits (192), Expect = 4e-15
 Identities = 80/348 (22%), Positives = 134/348 (38%), Gaps = 73/348 (20%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
           Q  A+ +   GR+++    TGSGKT +F +P++ H   + P  R     AL+L PT  LA
Sbjct: 75  QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHL-LRDPSAR-----ALLLYPTNALA 128

Query: 208 Q-QIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPG----RFLDHLQQ 262
             Q E+  + +S            G T   E+R+ +R    I++  P       L +   
Sbjct: 129 NDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDA 188

Query: 263 GNTSLSRVSFVILDEA---------------DRMLDMGFEPQIREVMQNLPDKHQTLLFS 307
               L  + ++++DE                 R+L       +R     L    Q +  S
Sbjct: 189 WLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRR-----LRRYGSPL----QIICTS 239

Query: 308 ATM--PVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEK-----VSENEK------VD 354
           AT+  P E    A+E      +V V +  SP      +  +     ++E+ +      + 
Sbjct: 240 ATLANPGE---FAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELA 296

Query: 355 RLLALLVEEAFLAEKSCHPFPLTIVF------VERKTRCDEVSEALVAEG---LHAVALH 405
            L ALLV               T+VF      VE           LV EG   L AV+ +
Sbjct: 297 TLAALLVRNGI----------QTLVFFRSRKQVELLYL--SPRRRLVREGGKLLDAVSTY 344

Query: 406 -GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             G ++ +R     +F+ G    ++AT+    G+D+  +  V+    P
Sbjct: 345 RAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYP 392

Length = 851

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

 Score = 74.3 bits (183), Expect = 5e-14
 Identities = 76/334 (22%), Positives = 125/334 (37%), Gaps = 74/334 (22%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL- 206
           Q + +   LSG+D L    TG GK+  + IP +        +  G   L LV++P   L 
Sbjct: 22  QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL--------LLEG---LTLVVSPLISLM 70

Query: 207 ------AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATP-----GR 255
                  +        L+ +L   +   V+             G + ++  +P      R
Sbjct: 71  KDQVDQLEAAGIRAAYLNSTLSREERQQVL--------NQLKSGQLKLLYISPERLMSPR 122

Query: 256 FLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEP---QIREVMQNLPDKHQTLLFSATM 310
           FL+ L++       +S V +DEA  +   G  F P   ++  +   LP+    L  +AT 
Sbjct: 123 FLELLKRL-----PISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNP-PVLALTATA 176

Query: 311 PVEIEALAQEYL--TDPVQVKVGKVSSPTANVIQILEKVSENEKVDR-LLALLVEEA--- 364
              +    +E L   D    +                        DR  LAL V E    
Sbjct: 177 TPRVRDDIREQLGLQDANIFRGS---------------------FDRPNLALKVVEKGEP 215

Query: 365 -----FLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRD 419
                FLA          I++   + + +E++E L   G+ A A H G +  +RE   + 
Sbjct: 216 SDQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQA 275

Query: 420 FRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           F N    ++VAT+    G+D   V  V++ DLP 
Sbjct: 276 FLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPG 309

Length = 590

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

 Score = 69.2 bits (170), Expect = 2e-12
 Identities = 90/355 (25%), Positives = 152/355 (42%), Gaps = 58/355 (16%)

Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKT-AAFTIPMIQHCVAQ 186
           L P + +  +  ++T  T  Q  A+P   SG ++L  A TGSGKT AAF +P+I   ++ 
Sbjct: 8   LDPRVREWFK-RKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAF-LPVINELLSL 65

Query: 187 TPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGV 246
                 DG  AL ++P + L   I + ++   R L   + A+  G T  +E++  L+   
Sbjct: 66  GKGKLEDGIYALYISPLKALNNDIRRRLEEPLRELG-IEVAVRHGDTPQSEKQKMLKNPP 124

Query: 247 SIVVATP---------GRFLDHLQQGNTSLSRVSFVILDE------ADR--MLDMGFEPQ 289
            I++ TP          +F + L+        V +VI+DE      + R   L +  E +
Sbjct: 125 HILITTPESLAILLNSPKFRELLRD-------VRYVIVDEIHALAESKRGVQLALSLE-R 176

Query: 290 IREVMQNLPDKHQTLLFSATM--PVEIEALAQEYLT-DPVQVKVGKVSSPTANVIQILEK 346
           +RE+  +     Q +  SAT+  P E+     ++L       ++  VS+     I+++  
Sbjct: 177 LRELAGDF----QRIGLSATVGPPEEVA----KFLVGFGDPCEIVDVSAAKKLEIKVISP 228

Query: 347 VSENEKVDRLLALLVEE-AFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE----GLHA 401
           V +    + L A L E  A L +K       T++F    TR    +E L       G   
Sbjct: 229 VEDLIYDEELWAALYERIAELVKKH----RTTLIFT--NTR--SGAERLAFRLKKLGPDI 280

Query: 402 VALHGG---RNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           + +H G   R    R       + G    +VAT     G+D+  +  V+ L  PK
Sbjct: 281 IEVHHGSLSREL--RLEVEERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPK 333

Length = 814

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

 Score = 62.8 bits (153), Expect = 1e-10
 Identities = 66/328 (20%), Positives = 102/328 (31%), Gaps = 91/328 (27%)

Query: 164 CAETGSGKT--AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ-IEKEVKALSRS 220
              TG+GKT  AA  I  +                 LVL PT+EL  Q  E   K L  +
Sbjct: 61  VLPTGAGKTVVAAEAIAEL-------------KRSTLVLVPTKELLDQWAEALKKFLLLN 107

Query: 221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVAT----PGRFLDHLQQGNTSLSRVSFVILD 276
            +      + GG        EL     + VAT      R L     GN        +I D
Sbjct: 108 DEIG----IYGGGEK-----ELEPAK-VTVATVQTLARRQLLDEFLGN----EFGLIIFD 153

Query: 277 EADRMLDMGFEPQIREVMQNL-------------PDKHQTLLFSATMPVEI-----EALA 318
           E   +    +  +I E++                       LF    P+       E + 
Sbjct: 154 EVHHLPAPSYR-RILELLSAAYPRLGLTATPEREDGGRIGDLFDLIGPIVYEVSLKELID 212

Query: 319 QEYLTDP--VQVKVG--------------------KVSSPTANVIQILEKVSENEK---- 352
           + YL     V++KV                     +         +       +E+    
Sbjct: 213 EGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRARGTLRAENEARRIAIASERKIAA 272

Query: 353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSD 412
           V  LL                   T++F        E+++  +A G+   A+ G   + +
Sbjct: 273 VRGLLLKHARGDK-----------TLIFASDVEHAYEIAKLFLAPGIVE-AITGETPKEE 320

Query: 413 RESALRDFRNGSTNILVATDVASRGLDV 440
           RE+ L  FR G   +LV   V   G+D+
Sbjct: 321 REAILERFRTGGIKVLVTVKVLDEGVDI 348

Length = 442

>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific [General function prediction only]

 Score = 61.7 bits (150), Expect = 6e-10
 Identities = 93/369 (25%), Positives = 147/369 (39%), Gaps = 38/369 (10%)

Query: 86  DRVL-----RFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHE 140
           D+VL     RF+P +  E+      D   A        P+    ++ +     + ++   
Sbjct: 160 DKVLEMLDPRFDPLEDPELT---RYDEVTAETDEVERVPV---DELDIPEKFKRMLKREG 213

Query: 141 YTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV 199
                 +Q  A+   L  G +LL  + T SGKT    +  I   +         G   L 
Sbjct: 214 IEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLL-------SGGKKMLF 266

Query: 200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVS----IVVATPGR 255
           L P   LA Q  ++ K     L   K AI VG + I  +   +    S    I+V T   
Sbjct: 267 LVPLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEG 325

Query: 256 FLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREV---MQNLPDKHQTLLFSATM-- 310
             D+L +    L  +  V++DE   + D    P++  +   ++ L    Q +  SAT+  
Sbjct: 326 I-DYLLRTGKDLGDIGTVVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGN 384

Query: 311 PVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKS 370
           P E   LA++     V      V  P    +      +E+EK D ++A LV+  F  E S
Sbjct: 385 PEE---LAKKLGAKLVLYDERPV--PLERHLVFAR--NESEKWD-IIARLVKREFSTESS 436

Query: 371 CHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVA 430
                 TIVF   + RC E+++AL  +GL A   H G    +R+S  R F       +V 
Sbjct: 437 KGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVT 496

Query: 431 TDVASRGLD 439
           T   + G+D
Sbjct: 497 TAALAAGVD 505

Length = 830

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

 Score = 57.4 bits (139), Expect = 1e-08
 Identities = 28/133 (21%), Positives = 51/133 (38%), Gaps = 12/133 (9%)

Query: 146 SIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE 205
             Q       LS  ++L  A TGSGKT    + ++        +  G G   + + P + 
Sbjct: 35  PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILST------LLEGGGK-VVYIVPLKA 87

Query: 206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT 265
           LA++  +E   L       +  I  G     +   E      ++V TP +     ++  +
Sbjct: 88  LAEEKYEEFSRLEELGI--RVGISTGDY---DLDDERLARYDVIVTTPEKLDSLTRKRPS 142

Query: 266 SLSRVSFVILDEA 278
            +  V  V++DE 
Sbjct: 143 WIEEVDLVVIDEI 155

Length = 766

>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family

 Score = 57.1 bits (138), Expect = 1e-08
 Identities = 74/341 (21%), Positives = 134/341 (39%), Gaps = 54/341 (15%)

Query: 131 SIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG 190
           SI+K +      RP  +Q + +   L GRD      TG GK+  + +P +  C       
Sbjct: 1   SILKTVFGLSSFRP--VQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL--CS------ 50

Query: 191 RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGV---- 246
                + LV++P   L   +E +V  L  S      A  +  +   EQ+  +   +    
Sbjct: 51  ---DGITLVISPLISL---MEDQVLQLKASGIP---ATFLNSSQSKEQQKNVLTDLKDGK 101

Query: 247 -SIVVATP------GRFLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEPQIRE---VM 294
             ++  TP       R L  L+        ++ + +DEA  +   G  F P  +    + 
Sbjct: 102 IKLLYVTPEKCSASNRLLQTLE----ERKGITLIAVDEAHCISQWGHDFRPDYKALGSLK 157

Query: 295 QNLPDKH-QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANV-IQILEKVSENEK 352
           Q  P+     L  +A+  V  + L Q  L +P Q+       P  N+  ++  K  +   
Sbjct: 158 QKFPNVPIMALTATASPSVREDILRQLNLKNP-QIFCTSFDRP--NLYYEVRRKTPK--I 212

Query: 353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSD 412
           ++ LL  + +E              I++   + + ++V+ +L   G+ A A H G   S 
Sbjct: 213 LEDLLRFIRKE--------FKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISA 264

Query: 413 RESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           R+     F+     ++VAT     G++   V  V++  LPK
Sbjct: 265 RDDVHHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPK 305

All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 470

>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ

 Score = 57.0 bits (138), Expect = 1e-08
 Identities = 73/324 (22%), Positives = 131/324 (40%), Gaps = 68/324 (20%)

Query: 156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ-QIE--K 212
           L GRD+L    TG GK+  + +P +               L +V++P   L + Q++  +
Sbjct: 26  LDGRDVLVVMPTGGGKSLCYQVPALLL-----------KGLTVVISPLISLMKDQVDQLR 74

Query: 213 EVKALSRSLDSFKTAIVVGGTNIAEQRSE-----LRGGVSIVVATPGR-----FLDHLQQ 262
                +  L+S         T  A+++ +     + G + ++   P R     FL+ LQ+
Sbjct: 75  AAGVAAAYLNS---------TLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQR 125

Query: 263 GNTSLSRVSFVILDEADRMLDMG--FEP------QIREVMQNLPDKHQTLLFSATMPVEI 314
              +L     V +DEA  +   G  F P       + E    +P     +  +AT   E 
Sbjct: 126 IPIAL-----VAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVP----RIALTATADAET 176

Query: 315 EALAQEYL--TDPVQVKVGKVSSPTANVI-QILEKVSENEKVDRLLALLVEEAFLAEKSC 371
               +E L   D  +      S    N+   +++K   N K   LL  L +      +S 
Sbjct: 177 RQDIRELLRLADANEFIT---SFDRPNLRFSVVKK---NNKQKFLLDYLKKHR---GQS- 226

Query: 372 HPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVAT 431
                 I++   + + +E++E L ++G+ A+A H G +   R     DF      ++VAT
Sbjct: 227 -----GIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVAT 281

Query: 432 DVASRGLDVMGVAHVVNLDLPKVL 455
           +    G+D   V  V++ D+P  L
Sbjct: 282 NAFGMGIDKPNVRFVIHYDMPGNL 305

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 591

>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG

 Score = 52.0 bits (125), Expect = 5e-07
 Identities = 82/300 (27%), Positives = 126/300 (42%), Gaps = 64/300 (21%)

Query: 166 ETGSGKT--AAFTI-PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD 222
           + GSGKT  AA  +   I+            G    ++APT  LA+Q    ++ L   L 
Sbjct: 264 DVGSGKTLVAALAMLAAIEA-----------GYQVALMAPTEILAEQHYNSLRNLLAPLG 312

Query: 223 SFKTAIVVGGTNIAEQRSELR-----GGVSIVVATPGRFLDH-LQQGNTSLSRVSFVILD 276
             + A++ G     ++R EL      G + +VV T      H L Q      R++ VI+D
Sbjct: 313 -IEVALLTGSLK-GKRRKELLETIASGQIHLVVGT------HALIQEKVEFKRLALVIID 364

Query: 277 EADRMLDMGFEP--QIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS 334
           E  R    G E   ++RE  Q     H  L+ SAT P+    LA   LT    +    + 
Sbjct: 365 EQHRF---GVEQRKKLREKGQGGFTPHV-LVMSAT-PIP-RTLA---LTVYGDLDTSIID 415

Query: 335 SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL 394
                   I   + ++++ D +   + EE  +A+         +V+       +E SE L
Sbjct: 416 ELPPGRKPITTVLIKHDEKDIVYEFIEEE--IAKGR----QAYVVY----PLIEE-SEKL 464

Query: 395 ---VAEGLH----------AVALHGGRNQSD-RESALRDFRNGSTNILVATDVASRGLDV 440
               AE L+           V L  GR +SD +E+ + +FR G  +ILVAT V   G+DV
Sbjct: 465 DLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDV 524

[DNA metabolism, DNA replication, recombination, and repair]. Length = 630

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

 Score = 50.9 bits (122), Expect = 1e-06
 Identities = 91/355 (25%), Positives = 135/355 (38%), Gaps = 60/355 (16%)

Query: 129 HPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP 188
           HP ++  +E     RP   QA+A  +A +GR ++    T SGK+ A+ +P++      + 
Sbjct: 22  HPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVL------SA 75

Query: 189 VGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSI 248
           +       AL LAPT+ LA    + V+ L  +L   + A   G T   E+R   R     
Sbjct: 76  LADDPRATALYLAPTKALAADQLRAVREL--TLRGVRPATYDGDTP-TEERRWAREHARY 132

Query: 249 VVATP-----GRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQT 303
           V+  P     G    H  +    L R+ +V++DE      + F   +  V++ L      
Sbjct: 133 VLTNPDMLHRGILPSH-ARWARFLRRLRYVVIDECHSYRGV-FGSHVALVLRRLRRLCAR 190

Query: 304 -------LLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQIL------EKVSEN 350
                  +L SAT   +  A A   +  PV   V +  SP       L      E   EN
Sbjct: 191 YGASPVFVLASATT-ADPAAAASRLIGAPVVA-VTEDGSPRGARTVALWEPPLTELTGEN 248

Query: 351 -EKVDR--------LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHA 401
              V R        LLA LV E             T+ FV R  R  E+  A+    L  
Sbjct: 249 GAPVRRSASAEAADLLADLVAEGA----------RTLTFV-RSRRGAELVAAIARRLLGE 297

Query: 402 V---------ALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
           V         A   G    DR    R  R+G    +  T+    G+D+ G+  VV
Sbjct: 298 VDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNALELGVDISGLDAVV 352

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|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 48.3 bits (116), Expect = 7e-06
 Identities = 33/111 (29%), Positives = 55/111 (49%), Gaps = 21/111 (18%)

Query: 349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVE-RKTRCDEVSEALVAEGLHAVALHGG 407
           E+ K+++L  ++ E+  L +   +P    IVF + R T  +++ + L  EG+ AV   G 
Sbjct: 345 EHPKLEKLREIVKEQ--LGK---NPDSRIIVFTQYRDT-AEKIVDLLEKEGIKAVRFVG- 397

Query: 408 RNQSDRES-----------ALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
             Q+ ++             L  FR G  N+LV+T VA  GLD+  V  V+
Sbjct: 398 --QASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI 446

Length = 773

>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]

 Score = 46.7 bits (111), Expect = 2e-05
 Identities = 59/315 (18%), Positives = 97/315 (30%), Gaps = 62/315 (19%)

Query: 164 CAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
            A TG GKT A  I      +A            + + P R + + + +  K      + 
Sbjct: 220 EAPTGYGKTEASLILA----LALLDEKIKLKSRVIYVLPFRTIIEDMYRRAK------EI 269

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDH-------------LQQGNTSLSRV 270
           F    V+G +  +  +  L       +       D              +Q    S+   
Sbjct: 270 FGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGF 329

Query: 271 SF----------VILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF-SATMPV----EIE 315
            F          VILDE     D      +  +++ L +    +L  SAT+P     +++
Sbjct: 330 KFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLK 389

Query: 316 ALAQE----YLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSC 371
               +            K  +            E+V   +     L  L+ E     K  
Sbjct: 390 KALGKGREVVENAKFCPKEDEPGLKRK------ERVDVEDGPQEELIELISEEVKEGKK- 442

Query: 372 HPFPLTIVFVERKTRCD--EVSEALVAEGLHAVALHGGRNQSDRESALRDFRN----GST 425
                  V V   T     E+ E L  +G   + LH      DRE   R+ +        
Sbjct: 443 -------VLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEG 495

Query: 426 NILVATDVASRGLDV 440
            I+VAT V   G+D+
Sbjct: 496 FIVVATQVIEAGVDI 510

Length = 733

>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional

 Score = 46.6 bits (111), Expect = 2e-05
 Identities = 81/324 (25%), Positives = 132/324 (40%), Gaps = 56/324 (17%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
           Q + +   LSGRD L    TG GK+  + IP +        V  G   L LV++P   L 
Sbjct: 30  QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPAL--------VLDG---LTLVVSPLISLM 78

Query: 208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL-----RGGVSIVVATPGR-----FL 257
           +    ++ A   +      A  +  T   EQ+ E+      G + ++   P R     FL
Sbjct: 79  KDQVDQLLANGVA------AACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFL 132

Query: 258 DHLQQGNTSLSRVSFVILDEADRMLDMG--FEP------QIREVMQNLPDKHQTLLFSAT 309
           +HL   N +L  V     DEA  +   G  F P      Q+R+    LP    T     T
Sbjct: 133 EHLAHWNPALLAV-----DEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDT 187

Query: 310 MPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEK 369
              +I  L    L DP  +++     P  N+   L  V + + +D+L+  + E+     K
Sbjct: 188 TRQDIVRLLG--LNDP-LIQISSFDRP--NIRYTL--VEKFKPLDQLMRYVQEQR---GK 237

Query: 370 SCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILV 429
           S       I++   + + ++ +  L + G+ A A H G +   R      F+     I+V
Sbjct: 238 S------GIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVV 291

Query: 430 ATDVASRGLDVMGVAHVVNLDLPK 453
           AT     G++   V  VV+ D+P+
Sbjct: 292 ATVAFGMGINKPNVRFVVHFDIPR 315

Length = 607

>gnl|CDD|184236 PRK13679, PRK13679, hypothetical protein; Provisional

 Score = 44.2 bits (105), Expect = 3e-05
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 9/70 (12%)

Query: 313 EIEALAQEYLTDPVQVKVGKVSS--PTANVIQILEKVSENEKVDRLLALLVEEAFLAEKS 370
           E+ A+A E  T P  + V KVSS  PT NVI    KV + E+++ L   L    F   ++
Sbjct: 54  ELRAIASE--TKPFTLHVTKVSSFAPTNNVIYF--KVEKTEELEELHERLHSGDF-YGEA 108

Query: 371 CHPF-P-LTI 378
            + F P +TI
Sbjct: 109 EYAFVPHITI 118

Length = 168

>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional

 Score = 46.0 bits (110), Expect = 4e-05
 Identities = 44/165 (26%), Positives = 62/165 (37%), Gaps = 51/165 (30%)

Query: 139 HEYTRPTSIQAQAMPVALSGRDL----LGCAETGSGKT--AAFTIPMIQHCVAQTPVGRG 192
           H   +P +I+A+     L+   L    L    TG GKT  A   I    H       G+ 
Sbjct: 6   HPLIKPNTIEARLYQQLLAATALKKNTLVVLPTGLGKTAIALLVIAERLH----KKGGK- 60

Query: 193 DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA--------EQRSELRG 244
                L+LAPT+ L +Q            + F+  + +    I         E+R+EL  
Sbjct: 61  ----VLILAPTKPLVEQ----------HAEFFRKFLNIPEEKIVVFTGEVSPEKRAELWE 106

Query: 245 GVSIVVATP---------GRFLDHLQQGNTSLSRVSFVILDEADR 280
              ++VATP         GR          SL  VS +I DEA R
Sbjct: 107 KAKVIVATPQVIENDLIAGRI---------SLEDVSLLIFDEAHR 142

Length = 773

>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination, and repair]

 Score = 45.0 bits (107), Expect = 9e-05
 Identities = 69/372 (18%), Positives = 140/372 (37%), Gaps = 59/372 (15%)

Query: 97  EEVRLRLNVDVTVASGSVPAPA-PIESFTDMCLHPSIMKDIEFHE-----YTRPTSIQA- 149
           EE   R   + T A+                    ++   +E+         R   ++A 
Sbjct: 3   EERLSRRLREATDAAMQEMKNQVRGSGMDARSRSANVPDILEYRSGLPVTAVRDEILKAI 62

Query: 150 QAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ 209
           +   V      ++   ETGSGKT    +P  Q  + +   G G         P R LA  
Sbjct: 63  EQNQV------VIIVGETGSGKTTQ--LP--QFLLEE---GLGIAGKIGCTQP-RRLA-- 106

Query: 210 IEKEVKALSRSL-DSFKTAI--VVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTS 266
                ++++  + +     +   VG +   E +   R    I V T G  L  +Q     
Sbjct: 107 ----ARSVAERVAEELGEKLGETVGYSIRFESKVSPR--TRIKVMTDGILLREIQNDPL- 159

Query: 267 LSRVSFVILDEA-DRMLD----MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY 321
           LS  S VI+DEA +R L+    +G    +++++    D  + ++ SAT+  E       Y
Sbjct: 160 LSGYSVVIIDEAHERSLNTDILLGL---LKDLLARRRDDLKLIIMSATLDAER---FSAY 213

Query: 322 LTDPVQVKVGKVSSPTANVIQI--LEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIV 379
             +   +++   + P    ++I  L +   +  +   +   V+               +V
Sbjct: 214 FGNAPVIEIEGRTYP----VEIRYLPEAEADYILLDAIVAAVDIHLREGSGS-----ILV 264

Query: 380 FV----ERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS 435
           F+    E +   + + +A + + L  + L+G  +  ++         G   +++AT++A 
Sbjct: 265 FLPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAE 324

Query: 436 RGLDVMGVAHVV 447
             L + G+ +V+
Sbjct: 325 TSLTIPGIRYVI 336

Length = 845

>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 44.3 bits (105), Expect = 1e-04
 Identities = 47/157 (29%), Positives = 63/157 (40%), Gaps = 19/157 (12%)

Query: 126 MCLHPSIMKD-IEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCV 184
              HP I  + IE   Y    +I A+A+      ++ L    TG GKT       I   V
Sbjct: 3   YAAHPLIKPNTIEPRLYQL--NIAAKAL-----FKNTLVVLPTGLGKTF------IAAMV 49

Query: 185 AQTPVGRGDGPLALVLAPTREL-AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR 243
               +    G   L LAPT+ L  Q  E   K     +   + A + G     E+R EL 
Sbjct: 50  IANRLRWFGGK-VLFLAPTKPLVLQHAEFCRKVTG--IPEDEIAALTGEVR-PEEREELW 105

Query: 244 GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR 280
               + VATP    + L+ G   L  VS +I DEA R
Sbjct: 106 AKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHR 142

Length = 542

>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication, recombination, and repair]

 Score = 43.5 bits (103), Expect = 2e-04
 Identities = 32/121 (26%), Positives = 50/121 (41%), Gaps = 18/121 (14%)

Query: 338 ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE 397
             +I+  E   E+ K+++L  + ++E              IVF E +   +E+   L   
Sbjct: 335 RLLIRADESGVEHPKLEKLREI-LKEQLEKNGDSR----VIVFTEYRDTAEEIVNFLKKI 389

Query: 398 GLHAVALHGGRNQSDRESA-----------LRDFRNGSTNILVATDVASRGLDVMGVAHV 446
           G+ A     G  Q+ RE             +  FR G  N+LVAT V   GLD+  V  V
Sbjct: 390 GIKARVRFIG--QASREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLV 447

Query: 447 V 447
           +
Sbjct: 448 I 448

Length = 542

>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional

 Score = 44.0 bits (104), Expect = 2e-04
 Identities = 44/172 (25%), Positives = 76/172 (44%), Gaps = 29/172 (16%)

Query: 148 QAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL 206
           QA+A+    L G++L+    T SGKT    I M+   + +       G  A+ L P + L
Sbjct: 28  QAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE-------GGKAVYLVPLKAL 80

Query: 207 AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTS 266
           A++  +E K   +     + A+  G     +   E  G   I++AT  +F   L+ G++ 
Sbjct: 81  AEEKYREFKDWEKL--GLRVAMTTGDY---DSTDEWLGKYDIIIATAEKFDSLLRHGSSW 135

Query: 267 LSRVSFVILDEA------DR--MLDMGFEPQIREVMQNLPDKHQTLLFSATM 310
           +  V  V+ DE       DR   L+M        ++ ++  + Q L  SAT+
Sbjct: 136 IKDVKLVVADEIHLIGSYDRGATLEM--------ILTHMLGRAQILGLSATV 179

Length = 720

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

 Score = 42.5 bits (101), Expect = 4e-04
 Identities = 33/113 (29%), Positives = 48/113 (42%), Gaps = 5/113 (4%)

Query: 143 RPTSIQAQAMPVALSGRDLLGCAETGSGKT-AAFTIPMIQHCVAQTPVGRGDGPLALVLA 201
            P   Q +    AL GR  L  A TGSGKT A F   +I     + P     G   L + 
Sbjct: 13  TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKP---KKGLHTLYIT 69

Query: 202 PTRELAQQIEKEVKALSRSLD-SFKTAIVVGGTNIAEQRSELRGGVSIVVATP 253
           P R LA  I + ++A    L    +     G T+ +E+  + +    I++ TP
Sbjct: 70  PLRALAVDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTP 122

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|236498 PRK09401, PRK09401, reverse gyrase; Reviewed

 Score = 42.2 bits (100), Expect = 6e-04
 Identities = 57/308 (18%), Positives = 105/308 (34%), Gaps = 84/308 (27%)

Query: 198 LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-----GGVSIVVAT 252
            ++ PTR L +Q+ ++++     +      +    +   +++ E       G   I+V T
Sbjct: 127 YIIFPTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTT 186

Query: 253 PGRFL----DHLQQGNTSLSRVSFVILDEAD----------RMLDM-GFEPQIREVMQNL 297
             +FL    D L +      +  FV +D+ D          ++L + GF  +  E    L
Sbjct: 187 S-QFLSKNFDELPK-----KKFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAMEL 240

Query: 298 PDKHQTLLFSATMPVEIEALAQEYLTDPVQV-----------------------KVGKVS 334
               +          E+E    E       +                       +VG   
Sbjct: 241 IRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRVKLFRELLGFEVGSPV 300

Query: 335 SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPL---TIVFV---ERKTRCD 388
               N++            +  +  LVE   L ++      L    ++FV   + K   +
Sbjct: 301 FYLRNIVDSYIVD------EDSVEKLVE---LVKR------LGDGGLIFVPSDKGKEYAE 345

Query: 389 EVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS-RGLDVMGVAHVV 447
           E++E L   G++A         S  E     F  G  ++LV   VAS  G+ V G     
Sbjct: 346 ELAEYLEDLGINAELAI-----SGFERKFEKFEEGEVDVLVG--VASYYGVLVRG----- 393

Query: 448 NLDLPKVL 455
            +DLP+ +
Sbjct: 394 -IDLPERI 400

Length = 1176

>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication, recombination, and repair]

 Score = 41.2 bits (97), Expect = 0.001
 Identities = 40/169 (23%), Positives = 68/169 (40%), Gaps = 24/169 (14%)

Query: 147 IQAQAMPVALSGRDLLGCAETGSGKT--AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR 204
            Q +A+ +   G  +L CA T SGKT  A + I +     A      G     +  +P +
Sbjct: 123 FQQEAIAILERGESVLVCAPTSSGKTVVAEYAIAL-----ALR---DGQR--VIYTSPIK 172

Query: 205 ELAQQIEKEVKALSRSLDSFKTAIVV--GGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ 262
            L+ Q  +++ A           + +  G  +I             +V T     + L +
Sbjct: 173 ALSNQKYRDLLAK---FGDVADMVGLMTGDVSI-------NPDAPCLVMTTEILRNMLYR 222

Query: 263 GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP 311
           G+ SL  + +V+ DE   + D        EV+  LPD  + +  SAT+P
Sbjct: 223 GSESLRDIEWVVFDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSATVP 271

Length = 1041

>gnl|CDD|218612 pfam05501, DUF755, Domain of unknown function (DUF755)

 Score = 37.0 bits (86), Expect = 0.004
 Identities = 18/30 (60%), Positives = 20/30 (66%), Gaps = 4/30 (13%)

Query: 5   PPHRRTSSSNSVSKVSSSSSSSSSSSSSSS 34
              +R  SS+S    SSSSSSSSSSSS SS
Sbjct: 97  SAKKRRRSSSS----SSSSSSSSSSSSESS 122

This family is predominated by ORFs from Circoviridae. The function of this family remains to be determined. Length = 122

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	503
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
PTZ00110	545	helicase; Provisional	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	100.0
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	100.0
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
PRK13767	876	ATP-dependent helicase; Provisional	100.0
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	100.0
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	100.0
PRK02362	737	ski2-like helicase; Provisional	100.0
COG1201	814	Lhr Lhr-like helicases [General function predictio	100.0
PRK00254	720	ski2-like helicase; Provisional	100.0
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	100.0
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	100.0
PRK10689	1147	transcription-repair coupling factor; Provisional	100.0
PRK01172	674	ski2-like helicase; Provisional	100.0
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	100.0
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	100.0
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	100.0
PHA02653	675	RNA helicase NPH-II; Provisional	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	100.0
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	100.0
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	100.0
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
PHA02558	501	uvsW UvsW helicase; Provisional	100.0
COG1202	830	Superfamily II helicase, archaea-specific [General	100.0
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	100.0
COG1205	851	Distinct helicase family with a unique C-terminal	100.0
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	100.0
KOG0354	746	consensus DEAD-box like helicase [General function	100.0
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	100.0
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	100.0
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	100.0
PRK13766	773	Hef nuclease; Provisional	100.0
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	100.0
COG1204	766	Superfamily II helicase [General function predicti	100.0
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	100.0
PRK09200	790	preprotein translocase subunit SecA; Reviewed	100.0
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	100.0
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	100.0
KOG0353	695	consensus ATP-dependent DNA helicase [General func	100.0
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	100.0
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	100.0
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	100.0
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	100.0
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
PRK05580	679	primosome assembly protein PriA; Validated	99.98
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.98
PRK04914	956	ATP-dependent helicase HepA; Validated	99.97
PRK09694	878	helicase Cas3; Provisional	99.97
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	99.97
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.97
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.97
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.97
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	99.97
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.97
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.97
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.97
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.96
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.96
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.96
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	99.96
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.96
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.95
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.95
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.95
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.95
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.95
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	99.95
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.94
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.93
COG4096	875	HsdR Type I site-specific restriction-modification	99.93
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	99.91
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.9
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.9
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	99.89
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.89
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	99.88
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	99.88
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.88
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.87
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.87
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.87
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	99.85
KOG0387	923	consensus Transcription-coupled repair protein CSB	99.84
PRK05298	652	excinuclease ABC subunit B; Provisional	99.84
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	99.83
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	99.82
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.81
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	99.81
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.81
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	99.8
KOG1123	776	consensus RNA polymerase II transcription initiati	99.8
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.78
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	99.77
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	99.77
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.75
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.75
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	99.75
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	99.74
COG4889	1518	Predicted helicase [General function prediction on	99.73
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.72
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	99.71
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.7
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.69
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	99.68
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.65
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	99.64
smart00490	82	HELICc helicase superfamily c-terminal domain.	99.61
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	99.61
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.6
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	99.58
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.58
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	99.57
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	99.54
KOG1002	791	consensus Nucleotide excision repair protein RAD16	99.54
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.51
PRK14873	665	primosome assembly protein PriA; Provisional	99.49
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	99.45
KOG4439	901	consensus RNA polymerase II transcription terminat	99.41
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.4
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	99.39
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	99.34
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	99.31
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.3
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	99.28
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.16
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.16
COG0610	962	Type I site-specific restriction-modification syst	99.15
KOG2340	698	consensus Uncharacterized conserved protein [Funct	99.13
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	99.1
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	98.98
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	98.79
PRK15483	986	type III restriction-modification system StyLTI en	98.77
COG3587	985	Restriction endonuclease [Defense mechanisms]	98.73
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	98.71
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.58
KOG1016	1387	consensus Predicted DNA helicase, DEAD-box superfa	98.5
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.49
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.47
KOG1803	649	consensus DNA helicase [Replication, recombination	98.31
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	98.27
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	98.27
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	98.26
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.2
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.19
KOG1001	674	consensus Helicase-like transcription factor HLTF/	98.17
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	98.17
PRK10536	262	hypothetical protein; Provisional	98.15
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.09
PF13245	76	AAA_19: Part of AAA domain	98.06
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	98.04
TIGR00376	637	DNA helicase, putative. The gene product may repre	98.0
PF13307	167	Helicase_C_2: Helicase C-terminal domain; PDB: 4A1	97.93
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.79
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.76
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.76
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.7
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.66
PRK04296	190	thymidine kinase; Provisional	97.58
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.56
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.54
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.49
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.46
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.45
PRK06526	254	transposase; Provisional	97.38
PRK08181	269	transposase; Validated	97.34
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.33
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	97.33
PRK14974	336	cell division protein FtsY; Provisional	97.3
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.28
KOG0383	696	consensus Predicted helicase [General function pre	97.27
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.23
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.18
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.17
smart00382	148	AAA ATPases associated with a variety of cellular	97.07
PRK05642	234	DNA replication initiation factor; Validated	97.03
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.01
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.95
PRK08084	235	DNA replication initiation factor; Provisional	96.91
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.91
smart00492	141	HELICc3 helicase superfamily c-terminal domain.	96.9
KOG1131	755	consensus RNA polymerase II transcription initiati	96.9
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.87
KOG0298	1394	consensus DEAD box-containing helicase-like transc	96.85
PRK06893	229	DNA replication initiation factor; Validated	96.85
PRK11054	684	helD DNA helicase IV; Provisional	96.75
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.75
PF13173	128	AAA_14: AAA domain	96.68
PRK06921	266	hypothetical protein; Provisional	96.66
smart00491	142	HELICc2 helicase superfamily c-terminal domain.	96.66
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.62
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.61
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.61
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.61
PRK08727	233	hypothetical protein; Validated	96.6
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	96.58
PRK07952	244	DNA replication protein DnaC; Validated	96.58
PHA02533	534	17 large terminase protein; Provisional	96.57
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.56
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.56
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.55
PRK08116	268	hypothetical protein; Validated	96.53
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.5
PRK08769	319	DNA polymerase III subunit delta'; Validated	96.49
PRK12377	248	putative replication protein; Provisional	96.48
COG1484	254	DnaC DNA replication protein [DNA replication, rec	96.4
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	96.34
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.34
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	96.33
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.32
PRK08903	227	DnaA regulatory inactivator Hda; Validated	96.32
PRK12422	445	chromosomal replication initiation protein; Provis	96.31
PRK06835	329	DNA replication protein DnaC; Validated	96.31
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.27
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.26
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.25
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.24
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.21
PF00004	132	AAA: ATPase family associated with various cellula	96.17
COG2256	436	MGS1 ATPase related to the helicase subunit of the	96.17
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	96.16
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	96.15
PTZ00293	211	thymidine kinase; Provisional	96.14
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.14
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.14
PF13871	278	Helicase_C_4: Helicase_C-like	96.13
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	96.12
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	96.12
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.11
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.1
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.09
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.09
PHA02544	316	44 clamp loader, small subunit; Provisional	96.06
PRK12402	337	replication factor C small subunit 2; Reviewed	96.05
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.05
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.05
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.05
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	96.01
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.0
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.96
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.96
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.95
PLN03025	319	replication factor C subunit; Provisional	95.95
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.85
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	95.84
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.82
PRK05580	679	primosome assembly protein PriA; Validated	95.81
PRK09183	259	transposase/IS protein; Provisional	95.79
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.78
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.78
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	95.78
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	95.77
COG3973	747	Superfamily I DNA and RNA helicases [General funct	95.76
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.75
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	95.74
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	95.74
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.73
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.72
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.72
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	95.7
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	95.68
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	95.67
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.66
PRK07993	334	DNA polymerase III subunit delta'; Validated	95.66
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	95.65
PRK13342	413	recombination factor protein RarA; Reviewed	95.63
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.61
TIGR00595	505	priA primosomal protein N'. All proteins in this f	95.61
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.6
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	95.59
PRK10867	433	signal recognition particle protein; Provisional	95.54
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	95.53
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	95.53
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.52
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.5
PRK08699	325	DNA polymerase III subunit delta'; Validated	95.48
TIGR00959	428	ffh signal recognition particle protein. This mode	95.45
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.45
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	95.43
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	95.42
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	95.41
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	95.4
PF05729	166	NACHT: NACHT domain	95.39
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.37
CHL00181	287	cbbX CbbX; Provisional	95.35
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	95.32
PRK07940	394	DNA polymerase III subunit delta'; Validated	95.32
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.3
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	95.3
PRK09112	351	DNA polymerase III subunit delta'; Validated	95.29
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	95.29
PRK11823	446	DNA repair protein RadA; Provisional	95.28
PRK04195	482	replication factor C large subunit; Provisional	95.24
PHA00729	226	NTP-binding motif containing protein	95.24
PRK07471	365	DNA polymerase III subunit delta'; Validated	95.22
PRK08939	306	primosomal protein DnaI; Reviewed	95.22
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	95.2
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	95.2
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	95.19
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.19
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	95.16
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	95.13
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.12
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	95.08
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.05
PRK13341	725	recombination factor protein RarA/unknown domain f	95.05
COG0593	408	DnaA ATPase involved in DNA replication initiation	95.02
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.97
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	94.94
PHA03368	738	DNA packaging terminase subunit 1; Provisional	94.92
PRK14873	665	primosome assembly protein PriA; Provisional	94.91
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	94.89
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	94.89
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	94.88
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.85
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.82
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	94.82
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	94.81
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.78
COG1198	730	PriA Primosomal protein N' (replication factor Y)	94.78
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	94.76
COG5008	375	PilU Tfp pilus assembly protein, ATPase PilU [Cell	94.68
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	94.68
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	94.68
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	94.67
PRK13851	344	type IV secretion system protein VirB11; Provision	94.67
PRK10416	318	signal recognition particle-docking protein FtsY;	94.67
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	94.66
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	94.64
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	94.61
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	94.59
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	94.58
KOG0701	1606	consensus dsRNA-specific nuclease Dicer and relate	94.53
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	94.49
COG3972	660	Superfamily I DNA and RNA helicases [General funct	94.48
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	94.46
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	94.44
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	94.37
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	94.37
PHA03372	668	DNA packaging terminase subunit 1; Provisional	94.34
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	94.29
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	94.25
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	94.24
cd03115	173	SRP The signal recognition particle (SRP) mediates	94.24
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.24
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	94.21
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	94.2
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	94.17
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	94.16
PRK10865	857	protein disaggregation chaperone; Provisional	94.15
PRK00440	319	rfc replication factor C small subunit; Reviewed	94.14
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	94.12
CHL00095	821	clpC Clp protease ATP binding subunit	94.1
PRK10689	1147	transcription-repair coupling factor; Provisional	94.08
PRK06904	472	replicative DNA helicase; Validated	94.05
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	93.99
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	93.96
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	93.83
PRK06067	234	flagellar accessory protein FlaH; Validated	93.82
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	93.77
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	93.7
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	93.67
KOG2028	554	consensus ATPase related to the helicase subunit o	93.63
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	93.6
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	93.54
PRK13764	602	ATPase; Provisional	93.5
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	93.46
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	93.44
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	93.42
PRK07399	314	DNA polymerase III subunit delta'; Validated	93.37
KOG1513	1300	consensus Nuclear helicase MOP-3/SNO (DEAD-box sup	93.3
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.21
PRK10436	462	hypothetical protein; Provisional	93.2
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	93.19
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	93.0
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	93.0
PF12846	304	AAA_10: AAA-like domain	92.93
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	92.9
PRK07004	460	replicative DNA helicase; Provisional	92.89
PRK08840	464	replicative DNA helicase; Provisional	92.88
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	92.87
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	92.86
PF13555	62	AAA_29: P-loop containing region of AAA domain	92.84
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	92.83
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	92.83
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	92.77
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	92.76
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.75
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	92.68
PRK09087	226	hypothetical protein; Validated	92.66
PRK08006	471	replicative DNA helicase; Provisional	92.61
PRK08058	329	DNA polymerase III subunit delta'; Validated	92.58
PRK08506	472	replicative DNA helicase; Provisional	92.58
PRK03992	389	proteasome-activating nucleotidase; Provisional	92.53
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	92.45
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	92.44
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.42
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.41
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	92.41
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	92.35
PRK04841	903	transcriptional regulator MalT; Provisional	92.33
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	92.32
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	92.29
PRK09376	416	rho transcription termination factor Rho; Provisio	92.22
PRK13897	606	type IV secretion system component VirD4; Provisio	92.21
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	92.2
PHA00012	361	I assembly protein	92.05
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	92.01
PRK05748	448	replicative DNA helicase; Provisional	91.91
PRK05973	237	replicative DNA helicase; Provisional	91.89
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	91.87
cd01128	249	rho_factor Transcription termination factor rho is	91.83
TIGR02533	486	type_II_gspE general secretory pathway protein E.	91.83
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	91.82
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	91.74
COG4185	187	Uncharacterized protein conserved in bacteria [Fun	91.71
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	91.7
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	91.68
TIGR00665	434	DnaB replicative DNA helicase. This model describe	91.66
KOG0347	731	consensus RNA helicase [RNA processing and modific	91.61
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	91.57
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	91.55
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	91.53
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	91.45
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	91.45
PHA00350	399	putative assembly protein	91.45
COG4626	546	Phage terminase-like protein, large subunit [Gener	91.41
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	91.38
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	91.37
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	91.25
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	91.23
TIGR00767	415	rho transcription termination factor Rho. Members	91.13
PRK14701	1638	reverse gyrase; Provisional	91.12
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	91.12
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	91.11
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	91.1
COG1485	367	Predicted ATPase [General function prediction only	91.02
PRK09354	349	recA recombinase A; Provisional	90.92
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	90.91
KOG0060	659	consensus Long-chain acyl-CoA transporter, ABC sup	90.77
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	90.76
PRK13850	670	type IV secretion system protein VirD4; Provisiona	90.69
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	90.63
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	90.58
PRK04328	249	hypothetical protein; Provisional	90.53
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	90.44
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	90.42
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	90.38
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	90.35
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	90.25
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	90.17
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	90.12
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	90.07
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	90.05
PRK05416	288	glmZ(sRNA)-inactivating NTPase; Provisional	90.04
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	90.0
CHL00176	638	ftsH cell division protein; Validated	90.0
cd03239	178	ABC_SMC_head The structural maintenance of chromos	89.79
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	89.71
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	89.53
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	89.52

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

Probab=100.00  E-value=9.8e-71  Score=534.73  Aligned_cols=346  Identities=44%  Similarity=0.722  Sum_probs=326.0

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHh-cCCCCCCCCCeEEEE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVA-QTPVGRGDGPLALVL  200 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~-~~~~~~~~~~~~lil  200 (503)
                      .|.++++++.+...++..||..|+|+|.+.||.++.|+|++..+.||||||++|++|++.++.. .+...++++|.+||+
T Consensus        92 ~f~~~~ls~~~~~~lk~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL  171 (519)
T KOG0331|consen   92 AFQELGLSEELMKALKEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVL  171 (519)
T ss_pred             hhhcccccHHHHHHHHhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEE
Confidence            7899999999999999999999999999999999999999999999999999999999999998 566777889999999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +||||||.|+.+.+.+++..+. +++.|++||.....+.+.+..+.+|+|+|||+|.++++.+...+.+++++|+||||+
T Consensus       172 ~PTRELA~QV~~~~~~~~~~~~-~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVLDEADr  250 (519)
T KOG0331|consen  172 APTRELAVQVQAEAREFGKSLR-LRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVLDEADR  250 (519)
T ss_pred             cCcHHHHHHHHHHHHHHcCCCC-ccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccceeEEEeccHHh
Confidence            9999999999999999998774 889999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCC--CCCCceEEEEEEcChhhHHHHHH
Q 010709          281 MLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS--SPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      |+++||..++++|+..+ ++..|++++|||+|..++.++..|+.+|..+.+....  ....++.|....++...|...+.
T Consensus       251 MldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~~~a~~~i~qive~~~~~~K~~~l~  330 (519)
T KOG0331|consen  251 MLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKELKANHNIRQIVEVCDETAKLRKLG  330 (519)
T ss_pred             hhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhhhhhhcchhhhhhhcCHHHHHHHHH
Confidence            99999999999999999 6666899999999999999999999999999988654  66778999999999989998888


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      .++....      ..+.+|+||||++++.|++|+..|+..++++..+||+.+|.+|..+++.|++|+..||||||+++||
T Consensus       331 ~lL~~~~------~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVAaRG  404 (519)
T KOG0331|consen  331 KLLEDIS------SDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVAARG  404 (519)
T ss_pred             HHHHHHh------ccCCCcEEEEecchhhHHHHHHHHHhcCcceeeecccccHHHHHHHHHhcccCCcceEEEccccccc
Confidence            8887765      2466789999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCccee--------eeeeccC
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSF--------NITTNLD  474 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR--------~~~~~~~  474 (503)
                      ||||+|++|||||+|.++++|+||+||+||        ++++..+
T Consensus       405 LDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~  449 (519)
T KOG0331|consen  405 LDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDN  449 (519)
T ss_pred             CCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHH
Confidence            999999999999999999999999999999        4566665

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

Probab=100.00  E-value=1.1e-68  Score=487.97  Aligned_cols=350  Identities=39%  Similarity=0.583  Sum_probs=328.0

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ...+|.++++.+.+.++++..++..|+++|.++||.++.|+|||+.|+||||||.+|++|++++++..+.     .++++
T Consensus        59 ~~~sf~dLgv~~~L~~ac~~l~~~~PT~IQ~~aiP~~L~g~dvIglAeTGSGKT~afaLPIl~~LL~~p~-----~~~~l  133 (476)
T KOG0330|consen   59 SFKSFADLGVHPELLEACQELGWKKPTKIQSEAIPVALGGRDVIGLAETGSGKTGAFALPILQRLLQEPK-----LFFAL  133 (476)
T ss_pred             hhcchhhcCcCHHHHHHHHHhCcCCCchhhhhhcchhhCCCcEEEEeccCCCchhhhHHHHHHHHHcCCC-----CceEE
Confidence            4567999999999999999999999999999999999999999999999999999999999999998653     48899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-CCCCCCCccEEEecc
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-GNTSLSRVSFVILDE  277 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~~~~vViDE  277 (503)
                      |++||||||.|+.+.+..++... ++++.++.||.+...+...+...++|+|+|||+|++++.+ +.+.+..++++|+||
T Consensus       134 VLtPtRELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDE  212 (476)
T KOG0330|consen  134 VLTPTRELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDE  212 (476)
T ss_pred             EecCcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhhcCCCEEEeCcHHHHHHHHhccCccHHHhHHHhhch
Confidence            99999999999999999999877 6999999999999999999999999999999999999995 568999999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH
Q 010709          278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      ||++++++|...+..|++.+|...|++++|||++..+.++...-+.+|..+...........+.|.+..++...|..+|+
T Consensus       213 ADrlLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~ky~tv~~lkQ~ylfv~~k~K~~yLV  292 (476)
T KOG0330|consen  213 ADRLLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSKYQTVDHLKQTYLFVPGKDKDTYLV  292 (476)
T ss_pred             HHhhhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccchhcchHHhhhheEeccccccchhHH
Confidence            99999999999999999999999999999999999999999999999999999998999999999999999999999999


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      .++.+.         ..+.+||||++...++.++-.|+..|+.+.++||.|++..|.-.+++|++|.+.||||||+++||
T Consensus       293 ~ll~e~---------~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqmsq~~Rlg~l~~Fk~~~r~iLv~TDVaSRG  363 (476)
T KOG0330|consen  293 YLLNEL---------AGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMSQSKRLGALNKFKAGARSILVCTDVASRG  363 (476)
T ss_pred             HHHHhh---------cCCcEEEEEeccchHHHHHHHHHhcCcceecccchhhHHHHHHHHHHHhccCCcEEEecchhccc
Confidence            998864         34579999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCccee--------eeeeccC-chhhhhhHH
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSF--------NITTNLD-GDMKKLEFC  483 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR--------~~~~~~~-~~~~~~~~~  483 (503)
                      +|||.|++|||||+|.+..+|+||+||+||        ++.+..| .-+.+++..
T Consensus       364 LDip~Vd~VVNyDiP~~skDYIHRvGRtaRaGrsG~~ItlVtqyDve~~qrIE~~  418 (476)
T KOG0330|consen  364 LDIPHVDVVVNYDIPTHSKDYIHRVGRTARAGRSGKAITLVTQYDVELVQRIEHA  418 (476)
T ss_pred             CCCCCceEEEecCCCCcHHHHHHHcccccccCCCcceEEEEehhhhHHHHHHHHH
Confidence            999999999999999999999999999777        4666666 555666553

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

Probab=100.00  E-value=2.5e-66  Score=488.56  Aligned_cols=374  Identities=40%  Similarity=0.657  Sum_probs=347.2

Q ss_pred             cccCCCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEcc
Q 010709           87 RVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAE  166 (503)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~  166 (503)
                      .+..+++..+..+++.+++..++.    ..|+|+.+|++.+++.++++.+...||..|+|+|++++|..++++|+|..+.
T Consensus       215 ~l~Em~~rdwri~redynis~kg~----~lpnplrnwEE~~~P~e~l~~I~~~~y~eptpIqR~aipl~lQ~rD~igvaE  290 (673)
T KOG0333|consen  215 VLAEMTERDWRIFREDYNISIKGG----RLPNPLRNWEESGFPLELLSVIKKPGYKEPTPIQRQAIPLGLQNRDPIGVAE  290 (673)
T ss_pred             hHHhcCCccceeeecceeeeecCC----CCCccccChhhcCCCHHHHHHHHhcCCCCCchHHHhhccchhccCCeeeEEe
Confidence            445566677778888888877754    8999999999999999999999999999999999999999999999999999


Q ss_pred             CCCchhHHhHHHHHHHHHhcCCC----CCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh
Q 010709          167 TGSGKTAAFTIPMIQHCVAQTPV----GRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL  242 (503)
Q Consensus       167 TGsGKTl~~~lp~l~~~~~~~~~----~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (503)
                      ||||||++|++|++.++...++.    +...||.++|++|||+|++|+.++-.++++.+ +++++.+.||....++--.+
T Consensus       291 TgsGktaaf~ipLl~~IsslP~~~~~en~~~gpyaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~EEq~fql  369 (673)
T KOG0333|consen  291 TGSGKTAAFLIPLLIWISSLPPMARLENNIEGPYAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSFEEQGFQL  369 (673)
T ss_pred             ccCCccccchhhHHHHHHcCCCcchhhhcccCceeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccchhhhhhhh
Confidence            99999999999999998887743    33568999999999999999999999999887 49999999999999988888


Q ss_pred             hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC-----------------------
Q 010709          243 RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD-----------------------  299 (503)
Q Consensus       243 ~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~-----------------------  299 (503)
                      ..+|+|+|+|||+|.+.+.+..+.+.++.+||+|||++|+++||.+++..++.++|.                       
T Consensus       370 s~gceiviatPgrLid~Lenr~lvl~qctyvvldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~  449 (673)
T KOG0333|consen  370 SMGCEIVIATPGRLIDSLENRYLVLNQCTYVVLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSS  449 (673)
T ss_pred             hccceeeecCchHHHHHHHHHHHHhccCceEeccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccc
Confidence            999999999999999999998899999999999999999999999999999999863                       


Q ss_pred             --CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcE
Q 010709          300 --KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLT  377 (503)
Q Consensus       300 --~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~  377 (503)
                        -+|.++||||+|+.++.+++.|+.+|+.+.++....+...+.|.+..+...+|...|...+.+.         ..+++
T Consensus       450 k~yrqT~mftatm~p~verlar~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~---------~~ppi  520 (673)
T KOG0333|consen  450 KKYRQTVMFTATMPPAVERLARSYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKLIEILESN---------FDPPI  520 (673)
T ss_pred             cceeEEEEEecCCChHHHHHHHHHhhCCeEEEeccCCCCccchheEEEEecchHHHHHHHHHHHhC---------CCCCE
Confidence              1689999999999999999999999999999999999999999999999999988888888764         34579


Q ss_pred             EEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhH
Q 010709          378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLA  457 (503)
Q Consensus       378 lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~  457 (503)
                      |||+|+++.|+.|++.|.+.|+++..|||+-+|++|..+++.|++|..+|||||++++||||||+|.+|||||+++++.+
T Consensus       521 IIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvAgRGIDIpnVSlVinydmaksieD  600 (673)
T KOG0333|consen  521 IIFVNTKKGADALAKILEKAGYKVTTLHGGKSQEQRENALADFREGTGDILVATDVAGRGIDIPNVSLVINYDMAKSIED  600 (673)
T ss_pred             EEEEechhhHHHHHHHHhhccceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEecccccCCCCCccceeeecchhhhHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhCccee--------eeeeccC
Q 010709          458 ASESLCTTSF--------NITTNLD  474 (503)
Q Consensus       458 ~~Qr~GR~gR--------~~~~~~~  474 (503)
                      |+|||||+||        +++|..|
T Consensus       601 YtHRIGRTgRAGk~GtaiSflt~~d  625 (673)
T KOG0333|consen  601 YTHRIGRTGRAGKSGTAISFLTPAD  625 (673)
T ss_pred             HHHHhccccccccCceeEEEeccch
Confidence            9999999999        4667666

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=1.7e-64  Score=518.36  Aligned_cols=385  Identities=39%  Similarity=0.610  Sum_probs=344.4

Q ss_pred             CCCCCccCCCCCCCcccCCCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHH
Q 010709           73 PVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAM  152 (503)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i  152 (503)
                      .++.+.+++|.+++.+..+..++++.++...++.+..   +...|.|+.+|+++++++.+++.|..+||..|+++|.++|
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~---g~~~p~p~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai  161 (545)
T PTZ00110         85 NLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIA---GENVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGW  161 (545)
T ss_pred             cccchhhhcccCChhhhcCCHHHHHHHHHhcCcEEec---CCCCCcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHH
Confidence            4556667888888899999999999999998887631   2367889999999999999999999999999999999999


Q ss_pred             HHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECC
Q 010709          153 PVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGG  232 (503)
Q Consensus       153 ~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~  232 (503)
                      |.++.|+|+|+++|||||||++|++|++.++..++......++.+|||+|||+||.|+.+.+++++... .+++.+++|+
T Consensus       162 p~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg  240 (545)
T PTZ00110        162 PIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGG  240 (545)
T ss_pred             HHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCC
Confidence            999999999999999999999999999999887654444567899999999999999999999998765 5888999999


Q ss_pred             ccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCH
Q 010709          233 TNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPV  312 (503)
Q Consensus       233 ~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  312 (503)
                      .....+...+..+++|+|+||++|.+++.+....+.++++|||||||++++++|...+.+++..++++.|++++|||+|.
T Consensus       241 ~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~v~~lViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~  320 (545)
T PTZ00110        241 VPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPK  320 (545)
T ss_pred             CCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhhCcEEEeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCH
Confidence            99888888888899999999999999999888889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcC-CCeEEEeCCCC-CCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHH
Q 010709          313 EIEALAQEYLT-DPVQVKVGKVS-SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEV  390 (503)
Q Consensus       313 ~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l  390 (503)
                      +++.+++.++. ++..+.+.... .....+.+.+..+....|...+..++....       ...+++||||++++.|+.+
T Consensus       321 ~v~~l~~~l~~~~~v~i~vg~~~l~~~~~i~q~~~~~~~~~k~~~L~~ll~~~~-------~~~~k~LIF~~t~~~a~~l  393 (545)
T PTZ00110        321 EVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIM-------RDGDKILIFVETKKGADFL  393 (545)
T ss_pred             HHHHHHHHHhccCCEEEEECCCccccCCCeeEEEEEEechhHHHHHHHHHHHhc-------ccCCeEEEEecChHHHHHH
Confidence            99999998886 57777766544 334567777777777777777777665432       1345799999999999999


Q ss_pred             HHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          391 SEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       391 ~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++.|+..++.+..+||++++.+|..+++.|++|+.+|||||+++++|||+|+|++||+||+|.++++|+||+||+||.
T Consensus       394 ~~~L~~~g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTdv~~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~  471 (545)
T PTZ00110        394 TKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRA  471 (545)
T ss_pred             HHHHHHcCCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcchhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999994

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

Probab=100.00  E-value=7.7e-67  Score=474.78  Aligned_cols=387  Identities=39%  Similarity=0.660  Sum_probs=363.0

Q ss_pred             CCCCCCCCccCCCCCCCcccCCCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHH
Q 010709           70 ASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQA  149 (503)
Q Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~  149 (503)
                      ....+.+|....|.++-.+..++.++-+..+.++.+.|.+.    ..|+|+.+|.++.++..+++.|++.|+..|||+|.
T Consensus       123 kGi~Y~ePi~T~WkPP~hir~mS~e~~e~vRk~~~I~veGd----~ipPPIksF~eMKFP~~~L~~lk~KGI~~PTpIQv  198 (610)
T KOG0341|consen  123 KGITYEEPIKTAWKPPRHIRKMSEEQRELVRKQLHILVEGD----DIPPPIKSFKEMKFPKPLLRGLKKKGIVHPTPIQV  198 (610)
T ss_pred             CCCcccCcchhccCCcHHHHHhhHHHHHHHHHhheEEeeCC----CCCCchhhhhhccCCHHHHHHHHhcCCCCCCceee
Confidence            34667889999999999999999999999999999988865    88999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcC---CCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc-----C
Q 010709          150 QAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQT---PVGRGDGPLALVLAPTRELAQQIEKEVKALSRS-----L  221 (503)
Q Consensus       150 ~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~---~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~-----~  221 (503)
                      +.+|.++.|+|.|..|-||||||++|.+|++...+.+.   +..++.||..||+||+|+||.|.++.+..+...     .
T Consensus       199 QGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EGP~gLiicPSRELArQt~~iie~~~~~L~e~g~  278 (610)
T KOG0341|consen  199 QGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEGPYGLIICPSRELARQTHDIIEQYVAALQEAGY  278 (610)
T ss_pred             cCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCCCeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence            99999999999999999999999999999998877654   456778999999999999999999999888753     3


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                      +.++..++.||....++...++.+.+|+|+|||+|.+++.+....++-++++.+||||+|+++||...++.++..+...+
T Consensus       279 P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~KK~~sLd~CRyL~lDEADRmiDmGFEddir~iF~~FK~QR  358 (610)
T KOG0341|consen  279 PELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAKKIMSLDACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQR  358 (610)
T ss_pred             hhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHHhhccHHHHHHhhhhhHHHHhhccchhhHHHHHHHHhhhh
Confidence            45788899999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             cEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEE
Q 010709          302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFV  381 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~  381 (503)
                      |+++||||+|..++.+++.-+..|+.+.++.......++.|.+.+++.+.|+-+++.-+.+          ..+++||||
T Consensus       359 QTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGAAsldViQevEyVkqEaKiVylLeCLQK----------T~PpVLIFa  428 (610)
T KOG0341|consen  359 QTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGAASLDVIQEVEYVKQEAKIVYLLECLQK----------TSPPVLIFA  428 (610)
T ss_pred             heeeeeccccHHHHHHHHhhcccceEEecccccccchhHHHHHHHHHhhhhhhhHHHHhcc----------CCCceEEEe
Confidence            9999999999999999999999999999999999999999999999999999888877654          345799999


Q ss_pred             cchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHh
Q 010709          382 ERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASES  461 (503)
Q Consensus       382 ~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr  461 (503)
                      ..+..++.++++|.-.|+.++.+|||-.|++|...++.|+.|+.+|||||++++.|+|+|++.||||||+|..+++|.||
T Consensus       429 EkK~DVD~IhEYLLlKGVEavaIHGGKDQedR~~ai~afr~gkKDVLVATDVASKGLDFp~iqHVINyDMP~eIENYVHR  508 (610)
T KOG0341|consen  429 EKKADVDDIHEYLLLKGVEAVAIHGGKDQEDRHYAIEAFRAGKKDVLVATDVASKGLDFPDIQHVINYDMPEEIENYVHR  508 (610)
T ss_pred             ccccChHHHHHHHHHccceeEEeecCcchhHHHHHHHHHhcCCCceEEEecchhccCCCccchhhccCCChHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCcceeeee
Q 010709          462 LCTTSFNIT  470 (503)
Q Consensus       462 ~GR~gR~~~  470 (503)
                      |||+||+-.
T Consensus       509 IGRTGRsg~  517 (610)
T KOG0341|consen  509 IGRTGRSGK  517 (610)
T ss_pred             hcccCCCCC
Confidence            999999643

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

Probab=100.00  E-value=4.8e-63  Score=502.71  Aligned_cols=337  Identities=43%  Similarity=0.673  Sum_probs=311.8

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      ..|.++++++.+++.+...||..|+|+|.++||.++.|+|+++.++||+|||++|.+|++..+....  .....+ +||+
T Consensus        29 ~~F~~l~l~~~ll~~l~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~--~~~~~~-aLil  105 (513)
T COG0513          29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSV--ERKYVS-ALIL  105 (513)
T ss_pred             CCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhccc--ccCCCc-eEEE
Confidence            6799999999999999999999999999999999999999999999999999999999999966421  111112 9999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +||||||.|+++.+..++.....+.+..++||.....+...+..+++|+|+|||+|++++.+..+.+.+++++|+||||+
T Consensus       106 ~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEADr  185 (513)
T COG0513         106 APTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADR  185 (513)
T ss_pred             CCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhhcCEEEeccHhh
Confidence            99999999999999999987645889999999999999988888899999999999999999999999999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCC--CCCceEEEEEEcChhh-HHHHHH
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS--PTANVIQILEKVSENE-KVDRLL  357 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~-k~~~l~  357 (503)
                      |+++||...+..++..++++.|+++||||+|..+..+++.++.+|..+.+.....  ....+.|.+..+.... |...|.
T Consensus       186 mLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i~q~~~~v~~~~~k~~~L~  265 (513)
T COG0513         186 MLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLELLL  265 (513)
T ss_pred             hhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCceEEEEEeCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999888885554  7888999999999876 888888


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      .++...         ...++||||+++..++.++..|...|+.+..+||+++|.+|.++++.|++|+.+||||||+++||
T Consensus       266 ~ll~~~---------~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDvaaRG  336 (513)
T COG0513         266 KLLKDE---------DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARG  336 (513)
T ss_pred             HHHhcC---------CCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechhhcc
Confidence            888653         33369999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      ||||+|++|||||+|.+.+.|+||+||+||.-
T Consensus       337 iDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG  368 (513)
T COG0513         337 LDIPDVSHVINYDLPLDPEDYVHRIGRTGRAG  368 (513)
T ss_pred             CCccccceeEEccCCCCHHHheeccCccccCC
Confidence            99999999999999999999999999999964

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

Probab=100.00  E-value=3.8e-62  Score=499.84  Aligned_cols=380  Identities=35%  Similarity=0.574  Sum_probs=334.9

Q ss_pred             CCccCCCCCCCccc-CCCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH
Q 010709           76 QPVFNNWKPSDRVL-RFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV  154 (503)
Q Consensus        76 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~  154 (503)
                      ...+.+|....... .+..++++.+++..++.+.+.    ..|.|+.+|+++++++.+++.|...||..|+|+|.++|+.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~i~~~g~----~~p~pi~~f~~~~l~~~l~~~L~~~g~~~ptpiQ~~aip~  154 (518)
T PLN00206         79 ATDECFYVRDPGSTSGLSSSQAELLRRKLEIHVKGE----AVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPA  154 (518)
T ss_pred             CcCCcCCccCcchhccCCHHHHHHHHHHCCCEecCC----CCCchhcCHHhCCCCHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            34445555544443 488899999999999887643    7789999999999999999999999999999999999999


Q ss_pred             HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCC--CCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECC
Q 010709          155 ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP--VGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGG  232 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~--~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~  232 (503)
                      ++.|+|+++++|||+|||++|++|++.++.....  .....++++|||+|||+||.|+.+.++.+.... ++.+..++||
T Consensus       155 il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG  233 (518)
T PLN00206        155 ALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGG  233 (518)
T ss_pred             HhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECC
Confidence            9999999999999999999999999988765321  122357899999999999999999999988765 4788889999


Q ss_pred             ccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCH
Q 010709          233 TNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPV  312 (503)
Q Consensus       233 ~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  312 (503)
                      .....+...+..+++|+|+||++|.+++.+....+.++++|||||||+|++++|...+.+++..++ ..|++++|||+++
T Consensus       234 ~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~v~~lViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~  312 (518)
T PLN00206        234 DAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSP  312 (518)
T ss_pred             cchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchheeEEEeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCH
Confidence            988888888888899999999999999998888899999999999999999999999999998885 5799999999999


Q ss_pred             HHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHH
Q 010709          313 EIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSE  392 (503)
Q Consensus       313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~  392 (503)
                      .++.++..++.++..+...........+.+.+..+....+...+...+....       ...+++||||+++..++.+++
T Consensus       313 ~v~~l~~~~~~~~~~i~~~~~~~~~~~v~q~~~~~~~~~k~~~l~~~l~~~~-------~~~~~~iVFv~s~~~a~~l~~  385 (518)
T PLN00206        313 EVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQ-------HFKPPAVVFVSSRLGADLLAN  385 (518)
T ss_pred             HHHHHHHHhCCCCEEEEeCCCCCCCcceeEEEEeccchhHHHHHHHHHHhhc-------ccCCCEEEEcCCchhHHHHHH
Confidence            9999999999999998887777667777888888887777777776665422       123469999999999999999


Q ss_pred             HHHH-CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          393 ALVA-EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       393 ~L~~-~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .|.. .++.+..+||++++.+|..+++.|++|+.+|||||+++++|||+|++++||+||+|.++.+|+||+||+||.
T Consensus       386 ~L~~~~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTdvl~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~  462 (518)
T PLN00206        386 AITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRM  462 (518)
T ss_pred             HHhhccCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEecHhhccCCcccCCEEEEeCCCCCHHHHHHhccccccC
Confidence            9975 589999999999999999999999999999999999999999999999999999999999999999999995

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

Probab=100.00  E-value=9.2e-64  Score=457.64  Aligned_cols=393  Identities=40%  Similarity=0.597  Sum_probs=347.0

Q ss_pred             CCCCCccCCCCCCCcccCCCHHHHHHHHHHcC-ceEEec--CCCCCCCCCcCCcccC-CCCHHHHHHHHHCCCCCCcHHH
Q 010709           73 PVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLN-VDVTVA--SGSVPAPAPIESFTDM-CLHPSIMKDIEFHEYTRPTSIQ  148 (503)
Q Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~v~~~--~~~~~~~~~~~~~~~~-~l~~~l~~~l~~~~~~~~~~~Q  148 (503)
                      .+|...+++|+++.....++++++.++++... +.+...  ....+.|+|.-+|++. .-.+++++++.+.||.+|+|+|
T Consensus       168 ~lpPi~knfYke~~e~s~ls~~q~~~~r~en~~it~dd~K~gekrpIPnP~ctFddAFq~~pevmenIkK~GFqKPtPIq  247 (629)
T KOG0336|consen  168 KLPPIKKNFYKESNETSNLSKEQLQEWRKENFNITCDDLKEGEKRPIPNPVCTFDDAFQCYPEVMENIKKTGFQKPTPIQ  247 (629)
T ss_pred             cCCchhhhhhhcCchhccCCHHHHHHHHHcCCcEEecccccCCcccCCCCcCcHHHHHhhhHHHHHHHHhccCCCCCcch
Confidence            34555678899999999999999999887754 444321  2234789999999886 6889999999999999999999


Q ss_pred             HHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCC-CCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEE
Q 010709          149 AQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP-VGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA  227 (503)
Q Consensus       149 ~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~-~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~  227 (503)
                      .++||.+++|.|++.+|.||+|||++|++|.+.++..++. .+...++.+|+++|||+|+.|+.-+++++..  ++.+..
T Consensus       248 SQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalqie~e~~kysy--ng~ksv  325 (629)
T KOG0336|consen  248 SQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQIEGEVKKYSY--NGLKSV  325 (629)
T ss_pred             hcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCCCceEEEeccHHHHHHHHhHHhHhhh--cCcceE
Confidence            9999999999999999999999999999999988877764 2344678999999999999999999988863  478899


Q ss_pred             EEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      +++||.+..++...+..+.+|+++||++|.++...+.+++..+.++|+||||+|++++|.+++++++--++|++|+++.|
T Consensus       326 c~ygggnR~eqie~lkrgveiiiatPgrlndL~~~n~i~l~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRqtvmTS  405 (629)
T KOG0336|consen  326 CVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINLASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTS  405 (629)
T ss_pred             EEecCCCchhHHHHHhcCceEEeeCCchHhhhhhcCeeeeeeeEEEEecchhhhhcccccHHHHHHhhhcCCcceeeeec
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCHHHHHHHHHhcCCCeEEEeCCCCCC-CCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhh
Q 010709          308 ATMPVEIEALAQEYLTDPVQVKVGKVSSP-TANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR  386 (503)
Q Consensus       308 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~  386 (503)
                      ||+|+.+..++..|+.+|..+.++..... ...+.|.+......+|. .+.+.+.+..       .+..|+||||.++..
T Consensus       406 ATWP~~VrrLa~sY~Kep~~v~vGsLdL~a~~sVkQ~i~v~~d~~k~-~~~~~f~~~m-------s~ndKvIiFv~~K~~  477 (629)
T KOG0336|consen  406 ATWPEGVRRLAQSYLKEPMIVYVGSLDLVAVKSVKQNIIVTTDSEKL-EIVQFFVANM-------SSNDKVIIFVSRKVM  477 (629)
T ss_pred             ccCchHHHHHHHHhhhCceEEEecccceeeeeeeeeeEEecccHHHH-HHHHHHHHhc-------CCCceEEEEEechhh
Confidence            99999999999999999999999887744 45577877555556665 4444443333       456689999999999


Q ss_pred             HHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcce
Q 010709          387 CDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTS  466 (503)
Q Consensus       387 ~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~g  466 (503)
                      |+.|...|.-.|+..-.+||+-.|.+|+..++.|++|+++|||||++++||||+|++.||+|||+|.+++.|+||+||+|
T Consensus       478 AD~LSSd~~l~gi~~q~lHG~r~Q~DrE~al~~~ksG~vrILvaTDlaSRGlDv~DiTHV~NyDFP~nIeeYVHRvGrtG  557 (629)
T KOG0336|consen  478 ADHLSSDFCLKGISSQSLHGNREQSDREMALEDFKSGEVRILVATDLASRGLDVPDITHVYNYDFPRNIEEYVHRVGRTG  557 (629)
T ss_pred             hhhccchhhhcccchhhccCChhhhhHHHHHHhhhcCceEEEEEechhhcCCCchhcceeeccCCCccHHHHHHHhcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             e--------eeeeccCc
Q 010709          467 F--------NITTNLDG  475 (503)
Q Consensus       467 R--------~~~~~~~~  475 (503)
                      |        ++++.+|.
T Consensus       558 RaGr~G~sis~lt~~D~  574 (629)
T KOG0336|consen  558 RAGRTGTSISFLTRNDW  574 (629)
T ss_pred             cCCCCcceEEEEehhhH
Confidence            7        46677763

>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=2.7e-63  Score=433.93  Aligned_cols=356  Identities=32%  Similarity=0.513  Sum_probs=323.1

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      ..-.++.+|+++++.+++++.+..+||.+|..+|+.|++.++.|+|||+.+..|+|||.+|.+.+++.+.-.     ...
T Consensus        21 ~~~~v~~~F~~Mgl~edlLrgiY~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~-----~r~   95 (400)
T KOG0328|consen   21 EKVKVIPTFDDMGLKEDLLRGIYAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS-----VRE   95 (400)
T ss_pred             cCcccccchhhcCchHHHHHHHHHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccc-----cce
Confidence            334567789999999999999999999999999999999999999999999999999999888777654332     224


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      ..+||+.||||||.|+.+.+..++.++ ++.+..+.||.+..+..+.+..+.+++.+|||++++++.+..+.-+.++++|
T Consensus        96 tQ~lilsPTRELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlV  174 (400)
T KOG0328|consen   96 TQALILSPTRELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLV  174 (400)
T ss_pred             eeEEEecChHHHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHhccccccceeEEE
Confidence            679999999999999999999999887 4889999999999998899999999999999999999999999999999999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh-HH
Q 010709          275 LDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KV  353 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~  353 (503)
                      +||||.|++.+|..++..+++++|+..|++++|||+|.++.+...+|+.+|+.+.+.+...+...+.+++..+..++ |.
T Consensus       175 LDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrdeltlEgIKqf~v~ve~EewKf  254 (400)
T KOG0328|consen  175 LDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRDELTLEGIKQFFVAVEKEEWKF  254 (400)
T ss_pred             eccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecCCCchhhhhhheeeechhhhhH
Confidence            99999999999999999999999999999999999999999999999999999999999998888999999998887 99


Q ss_pred             HHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc
Q 010709          354 DRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV  433 (503)
Q Consensus       354 ~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~  433 (503)
                      +.|+.+.....         -..++|||+++..++.|.+.++..++.|..+||+|++++|.++++.|++|+-+|||+|++
T Consensus       255 dtLcdLYd~Lt---------ItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDV  325 (400)
T KOG0328|consen  255 DTLCDLYDTLT---------ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDV  325 (400)
T ss_pred             hHHHHHhhhhe---------hheEEEEecccchhhHHHHHHHhhCceeeeccCCcchhHHHHHHHHhhcCCceEEEEech
Confidence            88888775432         224899999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCEEEEccCCCChhHHHHhhCcceee--------eeeccC-chhhhhhHHHH
Q 010709          434 ASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN--------ITTNLD-GDMKKLEFCLI  485 (503)
Q Consensus       434 ~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~--------~~~~~~-~~~~~~~~~~~  485 (503)
                      -+||+|+|.|++|||||+|.+.+.|+|||||.||.        +...+| ..++.++.+|.
T Consensus       326 waRGiDv~qVslviNYDLP~nre~YIHRIGRSGRFGRkGvainFVk~~d~~~lrdieq~ys  386 (400)
T KOG0328|consen  326 WARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAINFVKSDDLRILRDIEQYYS  386 (400)
T ss_pred             hhccCCcceeEEEEecCCCccHHHHhhhhccccccCCcceEEEEecHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999984        344444 44555555554

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

Probab=100.00  E-value=1.7e-61  Score=453.58  Aligned_cols=379  Identities=40%  Similarity=0.642  Sum_probs=356.1

Q ss_pred             CCccCCCCCCCcccCCCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHH
Q 010709           76 QPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVA  155 (503)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i  155 (503)
                      .+.+++|.+++.+..+...+.-.++..++..|...    ..|.|+.+|+++++++.|...+++..|.+||++|.+++|..
T Consensus       182 p~~kdfy~e~esI~gl~~~d~~~~r~~Lnlrv~g~----s~~rpvtsfeh~gfDkqLm~airk~Ey~kptpiq~qalpta  257 (731)
T KOG0339|consen  182 PFNKDFYEEHESIEGLTKMDVIDLRLTLNLRVSGS----SPPRPVTSFEHFGFDKQLMTAIRKSEYEKPTPIQCQALPTA  257 (731)
T ss_pred             ccccccccChhhhhccccccchhhHhhhcceeccC----CCCCCcchhhhcCchHHHHHHHhhhhcccCCcccccccccc
Confidence            44567888899999999999999999999988865    78899999999999999999999999999999999999999


Q ss_pred             hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccH
Q 010709          156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI  235 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (503)
                      +.|++|+-.|.||||||.+|+.|++.+++.++....+++|..||++|||+||.|++.++++|++.. +++++++|||...
T Consensus       258 lsgrdvigIAktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk  336 (731)
T KOG0339|consen  258 LSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSK  336 (731)
T ss_pred             cccccchheeeccCcchhHHHHHHHHHhcchhhhcCCCCCeEEEEeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcH
Confidence            999999999999999999999999999999999888999999999999999999999999999887 5999999999999


Q ss_pred             HHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHH
Q 010709          236 AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       236 ~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~  315 (503)
                      .++...+..++.|+|||||+|++++.-+..++.+++++|||||++|.++||.++++.|...+++++|.|+||||++..++
T Consensus       337 ~eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe  416 (731)
T KOG0339|consen  337 WEQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIE  416 (731)
T ss_pred             HHHHHhhhcCCeEEEechHHHHHHHHhhcccceeeeEEEEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHH
Confidence            99999999999999999999999999989999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChh-hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHH
Q 010709          316 ALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSEN-EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL  394 (503)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L  394 (503)
                      .+++.++.+|+.+...........+.|.+..+... .|+.-++..|...        ...+++|||+..+..++.++..|
T Consensus       417 ~lard~L~dpVrvVqg~vgean~dITQ~V~V~~s~~~Kl~wl~~~L~~f--------~S~gkvlifVTKk~~~e~i~a~L  488 (731)
T KOG0339|consen  417 KLARDILSDPVRVVQGEVGEANEDITQTVSVCPSEEKKLNWLLRHLVEF--------SSEGKVLIFVTKKADAEEIAANL  488 (731)
T ss_pred             HHHHHHhcCCeeEEEeehhccccchhheeeeccCcHHHHHHHHHHhhhh--------ccCCcEEEEEeccCCHHHHHHHh
Confidence            99999999999998888888888899988888764 5666665555443        34568999999999999999999


Q ss_pred             HHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          395 VAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       395 ~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      ...+++|..+||++.|.+|.+++.+|+.+...|||+|+++++|+|||++++|||||+.++++.+.||+||+||
T Consensus       489 klk~~~v~llhgdkdqa~rn~~ls~fKkk~~~VlvatDvaargldI~~ikTVvnyD~ardIdththrigrtgR  561 (731)
T KOG0339|consen  489 KLKGFNVSLLHGDKDQAERNEVLSKFKKKRKPVLVATDVAARGLDIPSIKTVVNYDFARDIDTHTHRIGRTGR  561 (731)
T ss_pred             ccccceeeeecCchhhHHHHHHHHHHhhcCCceEEEeeHhhcCCCccccceeecccccchhHHHHHHhhhccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999

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

Probab=100.00  E-value=2.3e-62  Score=460.02  Aligned_cols=334  Identities=37%  Similarity=0.570  Sum_probs=304.5

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      ..+|.+++|+..+++++...||..|+|+|..+||..+.|+|++.||.||+|||.+|.+|+|.+++..+..  -...+|||
T Consensus       180 ~~sF~~mNLSRPlLka~~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~--~~~TRVLV  257 (691)
T KOG0338|consen  180 NESFQSMNLSRPLLKACSTLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK--VAATRVLV  257 (691)
T ss_pred             hhhHHhcccchHHHHHHHhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc--CcceeEEE
Confidence            4479999999999999999999999999999999999999999999999999999999999999887632  34578999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecch
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDEA  278 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDEa  278 (503)
                      ++|||+|+.|++...++++... ++.++++.||.+.+.+-..++..++|+|+|||+|.+++.+. .+.++++.++|+|||
T Consensus       258 L~PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDEA  336 (691)
T KOG0338|consen  258 LVPTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDEA  336 (691)
T ss_pred             EeccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEechH
Confidence            9999999999999999999877 59999999999999999999999999999999999999885 678999999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh---HHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE---KVDR  355 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---k~~~  355 (503)
                      |+|++.+|..++..|+..+++.+|.++||||++..+.+++.--+.+|+.+.++........+.|.++.+....   +-..
T Consensus       337 DRMLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiRIR~~re~dRea~  416 (691)
T KOG0338|consen  337 DRMLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIRIRPKREGDREAM  416 (691)
T ss_pred             HHHHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhHHHheeccccccccHHH
Confidence            9999999999999999999999999999999999999999999999999999998888888888877665322   2222


Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccc
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS  435 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  435 (503)
                      +..++....         ...+|||+.+++.|..+.-.|.-.|+++.-+||.++|.+|.+.++.|++++++|||||++++
T Consensus       417 l~~l~~rtf---------~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGsLtQ~QRlesL~kFk~~eidvLiaTDvAs  487 (691)
T KOG0338|consen  417 LASLITRTF---------QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGSLTQEQRLESLEKFKKEEIDVLIATDVAS  487 (691)
T ss_pred             HHHHHHHhc---------ccceEEEEehHHHHHHHHHHHHHhhchhhhhcccccHHHHHHHHHHHHhccCCEEEEechhh
Confidence            333333221         12499999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCCChhHHHHhhCcc
Q 010709          436 RGLDVMGVAHVVNLDLPKVLLAASESLCTT  465 (503)
Q Consensus       436 ~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~  465 (503)
                      |||||++|.+||||.+|+++..|+||+||+
T Consensus       488 RGLDI~gV~tVINy~mP~t~e~Y~HRVGRT  517 (691)
T KOG0338|consen  488 RGLDIEGVQTVINYAMPKTIEHYLHRVGRT  517 (691)
T ss_pred             ccCCccceeEEEeccCchhHHHHHHHhhhh
Confidence            999999999999999999999999999873

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=3.2e-60  Score=477.37  Aligned_cols=338  Identities=36%  Similarity=0.545  Sum_probs=304.1

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCC--CCCCCeEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG--RGDGPLAL  198 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~--~~~~~~~l  198 (503)
                      .+|+++++++.+++.|..+||..|+++|.++||.+++|+|++++||||+|||++|++|++..+...+...  ...++++|
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~l   87 (423)
T PRK04837          8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRAL   87 (423)
T ss_pred             CCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            5799999999999999999999999999999999999999999999999999999999999887654321  23468899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      ||+||++||.|+++.+..+.... ++.+..++||.....+...+..+++|+|+||++|.+++.+..+.+.++++||||||
T Consensus        88 il~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l~~v~~lViDEa  166 (423)
T PRK04837         88 IMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEA  166 (423)
T ss_pred             EECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccccEEEEecH
Confidence            99999999999999999998766 58899999999888887888888999999999999999988888999999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCC--CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPD--KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRL  356 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l  356 (503)
                      |++++++|...+..++..++.  ..+.+++|||++..+..+...++.+|..+.+.........+.+.+.......|...+
T Consensus       167 d~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~~~~~i~~~~~~~~~~~k~~~l  246 (423)
T PRK04837        167 DRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRLL  246 (423)
T ss_pred             HHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCcCCCceeEEEEeCCHHHHHHHH
Confidence            999999999999999999874  566899999999999999999999998888776665556677777777777777766


Q ss_pred             HHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccccc
Q 010709          357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR  436 (503)
Q Consensus       357 ~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~  436 (503)
                      ..++...         ...++||||+++..|+.+++.|...|+.+..+||++++.+|..+++.|++|+.+|||||+++++
T Consensus       247 ~~ll~~~---------~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTdv~~r  317 (423)
T PRK04837        247 QTLIEEE---------WPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAAR  317 (423)
T ss_pred             HHHHHhc---------CCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEechhhc
Confidence            6665431         3457999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          437 GLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       437 Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |||+|+|++||+||+|.+...|+||+||+||.
T Consensus       318 GiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~  349 (423)
T PRK04837        318 GLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRA  349 (423)
T ss_pred             CCCccccCEEEEeCCCCchhheEeccccccCC
Confidence            99999999999999999999999999999995

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

Probab=100.00  E-value=1.7e-60  Score=447.08  Aligned_cols=340  Identities=34%  Similarity=0.491  Sum_probs=311.0

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      ...|+...|++..++++..+||..+|++|...++.++.|+|+++.|.||+|||++|++|++..+...+...+ ++-.+||
T Consensus        81 ~~~f~~~~LS~~t~kAi~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r-~~~~vlI  159 (543)
T KOG0342|consen   81 TFRFEEGSLSPLTLKAIKEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPR-NGTGVLI  159 (543)
T ss_pred             hhHhhccccCHHHHHHHHhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCC-CCeeEEE
Confidence            345888899999999999999999999999999999999999999999999999999999999887654333 6788999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecch
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDEA  278 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDEa  278 (503)
                      ++|||+||.|++.+++++..+...+.++.+.||.......+.+..+++|+|+|||+|.+++++. .+..++++++|+|||
T Consensus       160 i~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlDEA  239 (543)
T KOG0342|consen  160 ICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLDEA  239 (543)
T ss_pred             ecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhccceeEeecc
Confidence            9999999999999999999888779999999999998888888889999999999999999985 456777899999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcC-CCeEEEeCCCC--CCCCceEEEEEEcChhhHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLT-DPVQVKVGKVS--SPTANVIQILEKVSENEKVDR  355 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~~~~~~~k~~~  355 (503)
                      |++++.||...+.+|+..++..+|.++||||.+..++++++..+. +|..+......  .....+.|.+..++...+...
T Consensus       240 DrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~~~The~l~Qgyvv~~~~~~f~l  319 (543)
T KOG0342|consen  240 DRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGERETHERLEQGYVVAPSDSRFSL  319 (543)
T ss_pred             hhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCCcchhhcccceEEeccccchHHH
Confidence            999999999999999999999999999999999999999987776 47777765544  455668888888888888888


Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccc
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS  435 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  435 (503)
                      ++.+++++...        .|+||||++......+++.|+...++|..+||+++|..|..++.+|++.+.-||||||+++
T Consensus       320 l~~~LKk~~~~--------~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~Q~kRT~~~~~F~kaesgIL~cTDVaA  391 (543)
T KOG0342|consen  320 LYTFLKKNIKR--------YKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQKQNKRTSTFFEFCKAESGILVCTDVAA  391 (543)
T ss_pred             HHHHHHHhcCC--------ceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCcccccchHHHHHhhcccceEEecchhh
Confidence            88888876422        5799999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          436 RGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       436 ~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ||+|+|+|+|||+||+|.+.++|+||+||+||.
T Consensus       392 RGlD~P~V~~VvQ~~~P~d~~~YIHRvGRTaR~  424 (543)
T KOG0342|consen  392 RGLDIPDVDWVVQYDPPSDPEQYIHRVGRTARE  424 (543)
T ss_pred             ccCCCCCceEEEEeCCCCCHHHHHHHhcccccc
Confidence            999999999999999999999999999999993

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=3e-59  Score=473.12  Aligned_cols=337  Identities=41%  Similarity=0.675  Sum_probs=302.5

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCC-CCCCCCeEEEE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPV-GRGDGPLALVL  200 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~-~~~~~~~~lil  200 (503)
                      +|++++|++.+.+.|..+||..|+++|.++|+.+++++|+++++|||+|||++|++|++..+...... .....+++|||
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil   81 (456)
T PRK10590          2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALIL   81 (456)
T ss_pred             CHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEE
Confidence            58999999999999999999999999999999999999999999999999999999999987654321 12234689999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +||++||.|+.+.++.+.... ++.+..++|+.....+...+..+++|+|+||++|++++....+.+.++++|||||||+
T Consensus        82 ~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~~v~~lViDEah~  160 (456)
T PRK10590         82 TPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADR  160 (456)
T ss_pred             eCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHcCCcccccceEEEeecHHH
Confidence            999999999999999998765 4888889999988888777888899999999999999988888899999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHH
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALL  360 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l  360 (503)
                      +++++|...+..++..++...|++++|||+++.+..++..++.+|..+.+.........+.+.+..+....+...+..++
T Consensus       161 ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~l~  240 (456)
T PRK10590        161 MLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQMI  240 (456)
T ss_pred             HhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEEEEEcCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999988877666666667777777777666655444443


Q ss_pred             HHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCC
Q 010709          361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDV  440 (503)
Q Consensus       361 ~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi  440 (503)
                      ..         ....++||||+++..++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||+++++|||+
T Consensus       241 ~~---------~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTdv~~rGiDi  311 (456)
T PRK10590        241 GK---------GNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDI  311 (456)
T ss_pred             Hc---------CCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEccHHhcCCCc
Confidence            32         234579999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          441 MGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       441 p~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|++||+||+|.+..+|+||+||+||.
T Consensus       312 p~v~~VI~~~~P~~~~~yvqR~GRaGR~  339 (456)
T PRK10590        312 EELPHVVNYELPNVPEDYVHRIGRTGRA  339 (456)
T ss_pred             ccCCEEEEeCCCCCHHHhhhhccccccC
Confidence            9999999999999999999999999994

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.4e-60  Score=451.87  Aligned_cols=358  Identities=34%  Similarity=0.516  Sum_probs=321.3

Q ss_pred             CCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCc
Q 010709           91 FNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSG  170 (503)
Q Consensus        91 ~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsG  170 (503)
                      ...+.++++...+..-.         ...+..|.+++++....++|+..+|..++.+|+.+||..+.|+||+..|.||||
T Consensus        48 ~Eee~i~~l~~ky~ei~---------~~~~~kF~dlpls~~t~kgLke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSG  118 (758)
T KOG0343|consen   48 QEEEEIEELKQKYAEID---------STTIKKFADLPLSQKTLKGLKEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSG  118 (758)
T ss_pred             hhHHHHHHHHHHHHHhh---------hhhhhhHHhCCCchHHHHhHhhcCCccHHHHHHhhcchhccCcccccccccCCC
Confidence            34455666666553211         234567999999999999999999999999999999999999999999999999


Q ss_pred             hhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEE
Q 010709          171 KTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVV  250 (503)
Q Consensus       171 KTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv  250 (503)
                      ||++|++|+|..+.... .....|-.+|||.|||+||.|+++.+.+.+.+. ++..+++.||.........+ ++.+|+|
T Consensus       119 KTLAFlvPvlE~L~r~k-Ws~~DGlGalIISPTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi-~~mNILV  195 (758)
T KOG0343|consen  119 KTLAFLVPVLEALYRLK-WSPTDGLGALIISPTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERI-SQMNILV  195 (758)
T ss_pred             ceeeehHHHHHHHHHcC-CCCCCCceeEEecchHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhh-hcCCeEE
Confidence            99999999999876532 334567889999999999999999999999876 69999999999988877766 4599999


Q ss_pred             ECcHHHHHHHHcC-CCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEE
Q 010709          251 ATPGRFLDHLQQG-NTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVK  329 (503)
Q Consensus       251 ~Tp~~l~~~l~~~-~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~  329 (503)
                      ||||+|++++... .+...++.++|+||||+++++||...+..|+..+|+.+|+++||||.+..+.++++-.+.+|..+.
T Consensus       196 CTPGRLLQHmde~~~f~t~~lQmLvLDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vs  275 (758)
T KOG0343|consen  196 CTPGRLLQHMDENPNFSTSNLQMLVLDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVS  275 (758)
T ss_pred             echHHHHHHhhhcCCCCCCcceEEEeccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEE
Confidence            9999999999875 567789999999999999999999999999999999999999999999999999999999999987


Q ss_pred             eCC--CCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEc
Q 010709          330 VGK--VSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALH  405 (503)
Q Consensus       330 ~~~--~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh  405 (503)
                      +..  ....+.++.|.+..++...|+..|+.++..+         ...+.|||+.+.+++..+++.|++.  |+.+..+|
T Consensus       276 vhe~a~~atP~~L~Q~y~~v~l~~Ki~~L~sFI~sh---------lk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~  346 (758)
T KOG0343|consen  276 VHENAVAATPSNLQQSYVIVPLEDKIDMLWSFIKSH---------LKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALH  346 (758)
T ss_pred             EeccccccChhhhhheEEEEehhhHHHHHHHHHHhc---------cccceEEEEehhhHHHHHHHHHHhcCCCCceeeec
Confidence            763  3466778999999999999999999999874         5568999999999999999999876  88999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          406 GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       406 ~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      |.|.|..|.+++.+|.+...-||+||++++||+|+|.|+|||++|+|.++..|+||+||+.|.-
T Consensus       347 G~~~Q~~R~ev~~~F~~~~~~vLF~TDv~aRGLDFpaVdwViQ~DCPedv~tYIHRvGRtAR~~  410 (758)
T KOG0343|consen  347 GTMSQKKRIEVYKKFVRKRAVVLFCTDVAARGLDFPAVDWVIQVDCPEDVDTYIHRVGRTARYK  410 (758)
T ss_pred             cchhHHHHHHHHHHHHHhcceEEEeehhhhccCCCcccceEEEecCchhHHHHHHHhhhhhccc
Confidence            9999999999999999999999999999999999999999999999999999999999999953

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=3.5e-59  Score=474.87  Aligned_cols=333  Identities=40%  Similarity=0.625  Sum_probs=304.7

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .+|+++++++.+.+.|...||..|+|+|.++|+.+++|+|++++||||+|||++|++|++..+...     ..++++||+
T Consensus         4 ~~f~~l~l~~~l~~~l~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~-----~~~~~~lil   78 (460)
T PRK11776          4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK-----RFRVQALVL   78 (460)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhc-----cCCceEEEE
Confidence            469999999999999999999999999999999999999999999999999999999999886432     124679999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +||++||.|+.+.++.++....++.+..++||.....+...+..+++|+|+||++|.+++.+..+.+.++++||+||||+
T Consensus        79 ~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~l~~lViDEad~  158 (460)
T PRK11776         79 CPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADR  158 (460)
T ss_pred             eCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHcCCccHHHCCEEEEECHHH
Confidence            99999999999999999876656889999999999888888888999999999999999998888899999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHH
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALL  360 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l  360 (503)
                      +++++|...+..++..+++..|++++|||+++.+..+...++.+|..+.+.... ....+.+.+..+....|...+..++
T Consensus       159 ~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~-~~~~i~~~~~~~~~~~k~~~l~~ll  237 (460)
T PRK11776        159 MLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH-DLPAIEQRFYEVSPDERLPALQRLL  237 (460)
T ss_pred             HhCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC-CCCCeeEEEEEeCcHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999988776544 3445778888888777877777766


Q ss_pred             HHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCC
Q 010709          361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDV  440 (503)
Q Consensus       361 ~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi  440 (503)
                      ...         ...++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|||+
T Consensus       238 ~~~---------~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTdv~~rGiDi  308 (460)
T PRK11776        238 LHH---------QPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDI  308 (460)
T ss_pred             Hhc---------CCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEecccccccch
Confidence            432         34579999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          441 MGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       441 p~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |++++||+||+|.+...|+||+||+||.
T Consensus       309 ~~v~~VI~~d~p~~~~~yiqR~GRtGR~  336 (460)
T PRK11776        309 KALEAVINYELARDPEVHVHRIGRTGRA  336 (460)
T ss_pred             hcCCeEEEecCCCCHhHhhhhcccccCC
Confidence            9999999999999999999999999994

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

Probab=100.00  E-value=1.2e-59  Score=438.27  Aligned_cols=338  Identities=33%  Similarity=0.491  Sum_probs=304.3

Q ss_pred             CcccCC--CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          122 SFTDMC--LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       122 ~~~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      .|++++  |++++++++...||...||+|..+||.++.++||++.++||||||++|++|++..+..+.....+..-.+||
T Consensus         5 ~~~~l~~~L~~~l~~~l~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalI   84 (567)
T KOG0345|consen    5 SFSSLAPPLSPWLLEALDESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALI   84 (567)
T ss_pred             chhhcCCCccHHHHHHHHhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCccceeEEE
Confidence            466664  669999999999999999999999999999999999999999999999999999875543221111246899


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCC--CCCCCccEEEec
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGN--TSLSRVSFVILD  276 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~--~~l~~~~~vViD  276 (503)
                      |+|||||+.|+.+.+..+..++..+.+.++.||....+....+. .+++|+|+|||+|.+++.+..  +.++.+.++|+|
T Consensus        85 IsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLD  164 (567)
T KOG0345|consen   85 ISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLD  164 (567)
T ss_pred             ecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceEEec
Confidence            99999999999999999998888899999999998887766665 678899999999999999843  456699999999


Q ss_pred             chhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCC--CCCceEEEEEEcChhhHHH
Q 010709          277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS--PTANVIQILEKVSENEKVD  354 (503)
Q Consensus       277 EaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~k~~  354 (503)
                      |||+++++||...++.|+..+|+.+++=+||||....+.++....++||+.+.+.....  ....+...+..+...+|..
T Consensus       165 EADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~tPS~L~~~Y~v~~a~eK~~  244 (567)
T KOG0345|consen  165 EADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSATPSSLALEYLVCEADEKLS  244 (567)
T ss_pred             chHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeecccccccCchhhcceeeEecHHHHHH
Confidence            99999999999999999999999999999999999999999999999999998877664  5666888899999999999


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      .++.++.+.         ..+|+|||+++-..++.....|...  +..++.+||.|.+..|..+++.|.+..-.+|+|||
T Consensus       245 ~lv~~L~~~---------~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~q~~R~k~~~~F~~~~~~vl~~TD  315 (567)
T KOG0345|consen  245 QLVHLLNNN---------KDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMSQKARAKVLEAFRKLSNGVLFCTD  315 (567)
T ss_pred             HHHHHHhcc---------ccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhcchhHHHHHHHHHhccCceEEeeh
Confidence            999999773         4568999999999999999988765  67899999999999999999999998899999999


Q ss_pred             ccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          433 VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +++||||||+|++||+||+|++...|.||+||+||.
T Consensus       316 VaARGlDip~iD~VvQ~DpP~~~~~FvHR~GRTaR~  351 (567)
T KOG0345|consen  316 VAARGLDIPGIDLVVQFDPPKDPSSFVHRCGRTARA  351 (567)
T ss_pred             hhhccCCCCCceEEEecCCCCChhHHHhhcchhhhc
Confidence            999999999999999999999999999999998884

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=1.1e-58  Score=478.99  Aligned_cols=334  Identities=39%  Similarity=0.617  Sum_probs=307.5

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .+|.+++|++.+++.|..+||..|+++|.++|+.+++++|+|++||||+|||++|++|++..+...     ..++++||+
T Consensus         6 ~~f~~l~L~~~ll~al~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~-----~~~~~~LIL   80 (629)
T PRK11634          6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE-----LKAPQILVL   80 (629)
T ss_pred             CCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc-----cCCCeEEEE
Confidence            459999999999999999999999999999999999999999999999999999999999876542     235789999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +||++||.|+++.++.+.....++.+..++||.....+...+..+++|+|+||++|.+++.+..+.+.++++|||||||+
T Consensus        81 ~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~l~~lVlDEAd~  160 (629)
T PRK11634         81 APTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADE  160 (629)
T ss_pred             eCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcchhhceEEEeccHHH
Confidence            99999999999999999877767899999999998888888888899999999999999998888899999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHH
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALL  360 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l  360 (503)
                      |++++|...+..++..++...|+++||||+|..+..+...|+.+|..+.+.........+.+.+..+....|...+..++
T Consensus       161 ml~~gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q~~~~v~~~~k~~~L~~~L  240 (629)
T PRK11634        161 MLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFL  240 (629)
T ss_pred             HhhcccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEEEEEEechhhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998887766666677888888888778887777776


Q ss_pred             HHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCC
Q 010709          361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDV  440 (503)
Q Consensus       361 ~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi  440 (503)
                      ...         ...++||||+++..++.+++.|...|+.+..+||++++.+|.++++.|++|+.+|||||+++++|||+
T Consensus       241 ~~~---------~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATdv~arGIDi  311 (629)
T PRK11634        241 EAE---------DFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDV  311 (629)
T ss_pred             Hhc---------CCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcchHhcCCCc
Confidence            442         33469999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          441 MGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       441 p~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|++||+||+|.+...|+||+||+||.
T Consensus       312 p~V~~VI~~d~P~~~e~yvqRiGRtGRa  339 (629)
T PRK11634        312 ERISLVVNYDIPMDSESYVHRIGRTGRA  339 (629)
T ss_pred             ccCCEEEEeCCCCCHHHHHHHhccccCC
Confidence            9999999999999999999999999984

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

Probab=100.00  E-value=9.7e-60  Score=424.44  Aligned_cols=352  Identities=36%  Similarity=0.496  Sum_probs=309.6

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ....|..+|+++|+.+.++.+|+..|||+|..|||.+++|+|+|.+|.||||||++|.+|+|+++...+     .+-.++
T Consensus         5 t~~~F~~LGl~~Wlve~l~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLsedP-----~giFal   79 (442)
T KOG0340|consen    5 TAKPFSILGLSPWLVEQLKALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSEDP-----YGIFAL   79 (442)
T ss_pred             ccCchhhcCccHHHHHHHHHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhccCC-----CcceEE
Confidence            345799999999999999999999999999999999999999999999999999999999999987753     477899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC----CCCCCCccEEE
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG----NTSLSRVSFVI  274 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~----~~~l~~~~~vV  274 (503)
                      |++|||+||.|+.+.|..+++.. .+++.+++||+..-.+...+...+|++|+|||++.+++..+    .+.+++++++|
T Consensus        80 vlTPTrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkflV  158 (442)
T KOG0340|consen   80 VLTPTRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKFLV  158 (442)
T ss_pred             EecchHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceeeEE
Confidence            99999999999999999999877 59999999999999988999999999999999999999875    34688999999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCC--eEEEeCCCCCCCCceEEEEEEcChhhH
Q 010709          275 LDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDP--VQVKVGKVSSPTANVIQILEKVSENEK  352 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~k  352 (503)
                      +|||+++++..|...+..+...+|+.+|.++||||+++.+..+......++  ..............+.+.+..++...|
T Consensus       159 lDEADrvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vstvetL~q~yI~~~~~vk  238 (442)
T KOG0340|consen  159 LDEADRVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVSTVETLYQGYILVSIDVK  238 (442)
T ss_pred             ecchhhhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCCchhhhhhheeecchhhh
Confidence            999999999999999999999999999999999999888776554444432  222333334556667888999999999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      -.+++..+......      +.+.++||+++..+|+.|+..|...++.++.+||.|+|++|...+.+|+++..+||||||
T Consensus       239 daYLv~~Lr~~~~~------~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~Q~eR~~aLsrFrs~~~~iliaTD  312 (442)
T KOG0340|consen  239 DAYLVHLLRDFENK------ENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMPQKERLAALSRFRSNAARILIATD  312 (442)
T ss_pred             HHHHHHHHhhhhhc------cCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcchHHHHHHHHHHHhhcCccEEEEec
Confidence            99999888765432      345699999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCEEEEccCCCChhHHHHhhCccee--------eeeeccC-chhhhhhH
Q 010709          433 VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF--------NITTNLD-GDMKKLEF  482 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR--------~~~~~~~-~~~~~~~~  482 (503)
                      +++||+|||.|++|||||+|+++..|+||+||+.|        +++++.| .-+..++.
T Consensus       313 VAsRGLDIP~V~LVvN~diPr~P~~yiHRvGRtARAGR~G~aiSivt~rDv~l~~aiE~  371 (442)
T KOG0340|consen  313 VASRGLDIPTVELVVNHDIPRDPKDYIHRVGRTARAGRKGMAISIVTQRDVELLQAIEE  371 (442)
T ss_pred             hhhcCCCCCceeEEEecCCCCCHHHHHHhhcchhcccCCcceEEEechhhHHHHHHHHH
Confidence            99999999999999999999999999999998544        4666666 44444443

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.6e-58  Score=475.58  Aligned_cols=338  Identities=38%  Similarity=0.564  Sum_probs=302.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCC--CCCCCeEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG--RGDGPLAL  198 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~--~~~~~~~l  198 (503)
                      .+|++++|++.+++.|...||..|+++|.++||.+++|+|+++++|||+|||++|++|++..+...+...  ...++++|
T Consensus         9 ~~f~~l~l~~~l~~~L~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raL   88 (572)
T PRK04537          9 LTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRAL   88 (572)
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEE
Confidence            4699999999999999999999999999999999999999999999999999999999999887543211  12357899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecc
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDE  277 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDE  277 (503)
                      ||+||++|+.|+++.+.+++... ++.+..++|+.....+...+..+++|+|+||++|++++.+. .+.+..+++|||||
T Consensus        89 Il~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViDE  167 (572)
T PRK04537         89 ILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDE  167 (572)
T ss_pred             EEeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEecC
Confidence            99999999999999999998765 58899999999988887778888999999999999998765 46788999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCC--CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHH
Q 010709          278 ADRMLDMGFEPQIREVMQNLPD--KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDR  355 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~  355 (503)
                      ||++++++|...+..++..++.  ..|+++||||++..+..+...++.+|..+.+.........+.+.+.......|...
T Consensus       168 Ah~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~~i~q~~~~~~~~~k~~~  247 (572)
T PRK04537        168 ADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFPADEEKQTL  247 (572)
T ss_pred             HHHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccccccccceeEEEEecCHHHHHHH
Confidence            9999999999999999999876  68999999999999999999999988777666555555667777777777777777


Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccc
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS  435 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  435 (503)
                      +..++..         ....++||||+++..|+.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||++++
T Consensus       248 L~~ll~~---------~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTdv~a  318 (572)
T PRK04537        248 LLGLLSR---------SEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAA  318 (572)
T ss_pred             HHHHHhc---------ccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEehhhh
Confidence            6666543         2345799999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          436 RGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       436 ~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|||+|+|++||+||+|.+..+|+||+||+||.
T Consensus       319 rGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~  351 (572)
T PRK04537        319 RGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARL  351 (572)
T ss_pred             cCCCccCCCEEEEcCCCCCHHHHhhhhcccccC
Confidence            999999999999999999999999999999994

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

Probab=100.00  E-value=6e-60  Score=451.34  Aligned_cols=356  Identities=43%  Similarity=0.666  Sum_probs=324.3

Q ss_pred             CCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCC
Q 010709          112 GSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGR  191 (503)
Q Consensus       112 ~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~  191 (503)
                      .+...|.++..|.+..+.+.+..+++..++..|+|+|+.+||.+..|+++++||+||+|||.+|++|++.+++.......
T Consensus        65 ~G~~~p~~i~~f~~~~l~~~l~~ni~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~  144 (482)
T KOG0335|consen   65 SGRDVPPHIPTFDEAILGEALAGNIKRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDR  144 (482)
T ss_pred             cCCccCCCcccccccchhHHHhhccccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccC
Confidence            34467777889999999999999999999999999999999999999999999999999999999999999988754222


Q ss_pred             -----CCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCC
Q 010709          192 -----GDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTS  266 (503)
Q Consensus       192 -----~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~  266 (503)
                           ...|.+||++|||+||.|++.+.+++.... .+.....||+.+...+.+.+..+|+|+|+|||+|.+++..+.+.
T Consensus       145 ~~~~~~~~P~~lIlapTReL~~Qi~nea~k~~~~s-~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~  223 (482)
T KOG0335|consen  145 GESGGGVYPRALILAPTRELVDQIYNEARKFSYLS-GMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIERGKIS  223 (482)
T ss_pred             cccCCCCCCceEEEeCcHHHhhHHHHHHHhhcccc-cceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhcceee
Confidence                 135899999999999999999999998554 68999999999999998999999999999999999999999999


Q ss_pred             CCCccEEEecchhHHhh-CCCHHHHHHHHHhCC----CCCcEEEEEeeCCHHHHHHHHHhcCC-CeEEEeCCCCCCCCce
Q 010709          267 LSRVSFVILDEADRMLD-MGFEPQIREVMQNLP----DKHQTLLFSATMPVEIEALAQEYLTD-PVQVKVGKVSSPTANV  340 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~-~~~~~~~~~il~~~~----~~~q~i~~SAT~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  340 (503)
                      |++++++|+||||+|++ ++|.+.+++++.+..    ...|.++||||.|.+++.++..|+.+ ...+.+........++
T Consensus       224 l~~~k~~vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~~~ni  303 (482)
T KOG0335|consen  224 LDNCKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGSTSENI  303 (482)
T ss_pred             hhhCcEEEecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccccccc
Confidence            99999999999999999 899999999998874    37899999999999999999999886 8889999999999999


Q ss_pred             EEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHH
Q 010709          341 IQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF  420 (503)
Q Consensus       341 ~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f  420 (503)
                      .|.+..+....|...|+.++...............+++|||.+++.|.+++..|...++.+..+||..++.+|.+.++.|
T Consensus       304 ~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~tq~er~~al~~F  383 (482)
T KOG0335|consen  304 TQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRTQIEREQALNDF  383 (482)
T ss_pred             eeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhhhhHHHHHHHHh
Confidence            99999999999999999998765422111112234799999999999999999999999999999999999999999999


Q ss_pred             hcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       421 ~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|...|||||++++||||||+|++||+||+|.+..+|+|||||+||.
T Consensus       384 r~g~~pvlVaT~VaaRGlDi~~V~hVInyDmP~d~d~YvHRIGRTGR~  431 (482)
T KOG0335|consen  384 RNGKAPVLVATNVAARGLDIPNVKHVINYDMPADIDDYVHRIGRTGRV  431 (482)
T ss_pred             hcCCcceEEEehhhhcCCCCCCCceeEEeecCcchhhHHHhccccccC
Confidence            999999999999999999999999999999999999999999999994

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=3.2e-57  Score=457.81  Aligned_cols=336  Identities=36%  Similarity=0.572  Sum_probs=299.8

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      +|+++++++.+++.|...||..|+++|.++++.+++|+|+++++|||+|||++|++|++.++...+.. ...++++||++
T Consensus         2 ~f~~l~l~~~l~~~l~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~lil~   80 (434)
T PRK11192          2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRR-KSGPPRILILT   80 (434)
T ss_pred             CHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhcccc-CCCCceEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999999988764321 22357899999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                      ||++||.|+++.+..++... ++.+..++|+.....+...+..+++|+|+||++|.+++.+..+.+.++++|||||||++
T Consensus        81 Pt~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~~~~~~~~v~~lViDEah~~  159 (434)
T PRK11192         81 PTRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRM  159 (434)
T ss_pred             CcHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCcCcccCCEEEEECHHHH
Confidence            99999999999999998766 58999999999988887778888999999999999999988888999999999999999


Q ss_pred             hhCCCHHHHHHHHHhCCCCCcEEEEEeeCCH-HHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcCh-hhHHHHHHHH
Q 010709          282 LDMGFEPQIREVMQNLPDKHQTLLFSATMPV-EIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE-NEKVDRLLAL  359 (503)
Q Consensus       282 ~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~k~~~l~~~  359 (503)
                      ++++|...+..+...++...|+++||||++. .+..+...++.+|..+...........+.+.+..... ..+...+..+
T Consensus       160 l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~~~~~~~~~~~k~~~l~~l  239 (434)
T PRK11192        160 LDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLEHKTALLCHL  239 (434)
T ss_pred             hCCCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCcccccCceEEEEEeCCHHHHHHHHHHH
Confidence            9999999999999999888999999999985 5788888889999888877666666667777766654 4454444444


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCC
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLD  439 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gld  439 (503)
                      +..         ....++||||++++.|+.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|||
T Consensus       240 ~~~---------~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd~~~~GiD  310 (434)
T PRK11192        240 LKQ---------PEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGID  310 (434)
T ss_pred             Hhc---------CCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEccccccCcc
Confidence            322         23457999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          440 VMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       440 ip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|++++||+||+|.+...|+||+||+||.
T Consensus       311 ip~v~~VI~~d~p~s~~~yiqr~GR~gR~  339 (434)
T PRK11192        311 IDDVSHVINFDMPRSADTYLHRIGRTGRA  339 (434)
T ss_pred             CCCCCEEEEECCCCCHHHHhhcccccccC
Confidence            99999999999999999999999999994

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

Probab=100.00  E-value=1.4e-59  Score=417.37  Aligned_cols=350  Identities=31%  Similarity=0.525  Sum_probs=320.9

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      -..|+++.|..+++..+...||.+|.|+|.++||.++.|+|++.-|..|+|||.+|.+|++..+...     .+.-.++|
T Consensus        84 G~efEd~~Lkr~LLmgIfe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~-----~~~IQ~~i  158 (459)
T KOG0326|consen   84 GNEFEDYCLKRELLMGIFEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPK-----KNVIQAII  158 (459)
T ss_pred             CccHHHhhhhHHHHHHHHHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCcc-----ccceeEEE
Confidence            3469999999999999999999999999999999999999999999999999999999999886543     23567899


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++|||+||.|+.+.++++++++. +.+...+||++..+..-.+....+++|+|||++++++.++.-.++++.++|+||||
T Consensus       159 lVPtrelALQtSqvc~~lskh~~-i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~KgVa~ls~c~~lV~DEAD  237 (459)
T KOG0326|consen  159 LVPTRELALQTSQVCKELSKHLG-IKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKKGVADLSDCVILVMDEAD  237 (459)
T ss_pred             EeecchhhHHHHHHHHHHhcccC-eEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhcccccchhceEEEechhh
Confidence            99999999999999999999884 99999999999999888888999999999999999999988899999999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLAL  359 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~  359 (503)
                      .++...|...+.+++..+|+..|++++|||.|-.+..+..+++.+|..+..-. ......+.|++-.+...+|+..|-.+
T Consensus       238 KlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~-eLtl~GvtQyYafV~e~qKvhCLntL  316 (459)
T KOG0326|consen  238 KLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLME-ELTLKGVTQYYAFVEERQKVHCLNTL  316 (459)
T ss_pred             hhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhh-hhhhcchhhheeeechhhhhhhHHHH
Confidence            99999999999999999999999999999999999999999999998886543 34566788999999999999888877


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCC
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLD  439 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gld  439 (503)
                      +....         -...|||||+.+.++.+++.+.+.|+.+..+|+.|.|+.|.+++..|++|.++.||||+++.||||
T Consensus       317 fskLq---------INQsIIFCNS~~rVELLAkKITelGyscyyiHakM~Q~hRNrVFHdFr~G~crnLVctDL~TRGID  387 (459)
T KOG0326|consen  317 FSKLQ---------INQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMAQEHRNRVFHDFRNGKCRNLVCTDLFTRGID  387 (459)
T ss_pred             HHHhc---------ccceEEEeccchHhHHHHHHHHhccchhhHHHHHHHHhhhhhhhhhhhccccceeeehhhhhcccc
Confidence            76532         235899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEccCCCChhHHHHhhCccee--------eeeeccC-chhhhhhHHHH
Q 010709          440 VMGVAHVVNLDLPKVLLAASESLCTTSF--------NITTNLD-GDMKKLEFCLI  485 (503)
Q Consensus       440 ip~v~~VI~~~~p~s~~~~~Qr~GR~gR--------~~~~~~~-~~~~~~~~~~~  485 (503)
                      +++|++|||||+|++.+.|.||+||.||        ++.+++| -++.+++.-+.
T Consensus       388 iqavNvVINFDfpk~aEtYLHRIGRsGRFGhlGlAInLityedrf~L~~IE~eLG  442 (459)
T KOG0326|consen  388 IQAVNVVINFDFPKNAETYLHRIGRSGRFGHLGLAINLITYEDRFNLYRIEQELG  442 (459)
T ss_pred             cceeeEEEecCCCCCHHHHHHHccCCccCCCcceEEEEEehhhhhhHHHHHHHhc
Confidence            9999999999999999999999999999        5677777 66666665543

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1e-55  Score=450.53  Aligned_cols=341  Identities=38%  Similarity=0.581  Sum_probs=300.7

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCC--CCCCC
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG--RGDGP  195 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~--~~~~~  195 (503)
                      .....|.++++++.+.+.|..+||..|+++|.++|+.+++|+|+|+++|||+|||++|++|++..+...+...  ....+
T Consensus        84 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~  163 (475)
T PRK01297         84 EGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEP  163 (475)
T ss_pred             cCCCCHhHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCc
Confidence            3445688999999999999999999999999999999999999999999999999999999999887653211  11257


Q ss_pred             eEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          196 LALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       196 ~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      ++|||+||++||.|+.+.++.+.... ++.+..++||.....+...+. ..++|+|+||++|++++.+....++++++||
T Consensus       164 ~aLil~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~~l~~l~~lV  242 (475)
T PRK01297        164 RALIIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMV  242 (475)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCcccccCceEE
Confidence            89999999999999999999998665 588888999887766655554 5689999999999999888888899999999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhCCC--CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhH
Q 010709          275 LDEADRMLDMGFEPQIREVMQNLPD--KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEK  352 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k  352 (503)
                      |||||++.+++|...+..++..++.  +.|++++|||++.++..++..++.+|..+.+.........+.+.+..+....+
T Consensus       243 iDEah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~k  322 (475)
T PRK01297        243 LDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDK  322 (475)
T ss_pred             echHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCCCcccEEEEEecchhH
Confidence            9999999999999999999998854  57999999999999999999999999888776666555667777777777777


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      ...+..++..         ....++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||+
T Consensus       323 ~~~l~~ll~~---------~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~  393 (475)
T PRK01297        323 YKLLYNLVTQ---------NPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATD  393 (475)
T ss_pred             HHHHHHHHHh---------cCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEcc
Confidence            6666665543         2345799999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          433 VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++++|||+|++++||+||+|.+..+|+||+||+||.
T Consensus       394 ~l~~GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~  429 (475)
T PRK01297        394 VAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRA  429 (475)
T ss_pred             ccccCCcccCCCEEEEeCCCCCHHHHHHhhCccCCC
Confidence            999999999999999999999999999999999994

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

Probab=100.00  E-value=6.9e-58  Score=432.25  Aligned_cols=349  Identities=34%  Similarity=0.542  Sum_probs=306.9

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHH-HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcC-CCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIE-FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQT-PVGRG  192 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~-~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~-~~~~~  192 (503)
                      ..|-....|..++|++.+...|+ .+++..||.+|.++||.+++|+|++|.++||||||++|++|+++.+.... ...+.
T Consensus       130 e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs  209 (708)
T KOG0348|consen  130 EAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRS  209 (708)
T ss_pred             ccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccccc
Confidence            33444567999999999999996 47999999999999999999999999999999999999999999988765 56788


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCcc
Q 010709          193 DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVS  271 (503)
Q Consensus       193 ~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~  271 (503)
                      .|+.+||++||||||.|+++.+.++.+.+..+.-+.+.||...+.+...++++++|+|+|||+|++++.+. .+.+.+++
T Consensus       210 ~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LR  289 (708)
T KOG0348|consen  210 DGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLR  289 (708)
T ss_pred             CCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeee
Confidence            89999999999999999999999999888778888899999999999999999999999999999999985 56888999


Q ss_pred             EEEecchhHHhhCCCHHHHHHHHHhC-------------CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCC-----
Q 010709          272 FVILDEADRMLDMGFEPQIREVMQNL-------------PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKV-----  333 (503)
Q Consensus       272 ~vViDEaH~l~~~~~~~~~~~il~~~-------------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-----  333 (503)
                      +||+||+|++++.||...+..|++.+             ++..|.+++|||++..+..++.--+.||+.+..+..     
T Consensus       290 wlVlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~  369 (708)
T KOG0348|consen  290 WLVLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLN  369 (708)
T ss_pred             EEEecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcC
Confidence            99999999999999999999998776             224788999999999999999999999988862111     


Q ss_pred             --------------------CCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHH
Q 010709          334 --------------------SSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEA  393 (503)
Q Consensus       334 --------------------~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~  393 (503)
                                          ......+.|.+..++..-++-.|..++.+......     ..++|||+.+.+.++.-+..
T Consensus       370 p~~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~-----~qk~iVF~S~~d~VeFHy~l  444 (708)
T KOG0348|consen  370 PKDKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEE-----KQKMIVFFSCSDSVEFHYSL  444 (708)
T ss_pred             cchhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhh-----hceeEEEEechhHHHHHHHH
Confidence                                12234466778888888888888888877654432     23799999999999999988


Q ss_pred             HHH----------------------CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC
Q 010709          394 LVA----------------------EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL  451 (503)
Q Consensus       394 L~~----------------------~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~  451 (503)
                      |..                      .+.++..+||+|+|++|..+++.|...+..||+|||+++||+|+|+|++||.||+
T Consensus       445 f~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~QeeRts~f~~Fs~~~~~VLLcTDVAaRGLDlP~V~~vVQYd~  524 (708)
T KOG0348|consen  445 FSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSMEQEERTSVFQEFSHSRRAVLLCTDVAARGLDLPHVGLVVQYDP  524 (708)
T ss_pred             HHhhhhcccccccCCcccCCChhhhhcceEEEecCchhHHHHHHHHHhhccccceEEEehhhhhccCCCCCcCeEEEeCC
Confidence            864                      2357899999999999999999999999999999999999999999999999999


Q ss_pred             CCChhHHHHhhCcceee
Q 010709          452 PKVLLAASESLCTTSFN  468 (503)
Q Consensus       452 p~s~~~~~Qr~GR~gR~  468 (503)
                      |.+.++|+||+||+.|.
T Consensus       525 P~s~adylHRvGRTARa  541 (708)
T KOG0348|consen  525 PFSTADYLHRVGRTARA  541 (708)
T ss_pred             CCCHHHHHHHhhhhhhc
Confidence            99999999999997774

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.1e-56  Score=457.63  Aligned_cols=381  Identities=43%  Similarity=0.662  Sum_probs=356.2

Q ss_pred             CCccCCCCCCCcccCCCHHHHHHHHHHcC-ceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH
Q 010709           76 QPVFNNWKPSDRVLRFNPEQIEEVRLRLN-VDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV  154 (503)
Q Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~  154 (503)
                      .+...+|.+...+..+..++++.++.... +.++..    ..|.|+.+|...+++..++..++++||..|+++|.+|||+
T Consensus       323 pFRknfy~e~~di~~ms~~eV~~yr~~l~~i~v~g~----~~pkpv~sW~q~gl~~~il~tlkkl~y~k~~~IQ~qAiP~  398 (997)
T KOG0334|consen  323 PFRKNFYIEVRDIKRMSAAEVDEYRCELDGIKVKGK----ECPKPVTSWTQCGLSSKILETLKKLGYEKPTPIQAQAIPA  398 (997)
T ss_pred             hhhhcccccchhHHHHHHHHHHHhhcCccceeeccC----CCCcccchHhhCCchHHHHHHHHHhcCCCCcchhhhhcch
Confidence            44456777888889998899999988776 777655    8899999999999999999999999999999999999999


Q ss_pred             HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCcc
Q 010709          155 ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN  234 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~  234 (503)
                      ++.|+|||.+|.||||||++|++|++.+...++....++||.+||++|||+|+.|+.+.++.|...+ ++.+.+++|+..
T Consensus       399 ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~  477 (997)
T KOG0334|consen  399 IMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSG  477 (997)
T ss_pred             hccCcceEEeeccCCccchhhhcchhhhhhcCCChhhCCCceEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCcc
Confidence            9999999999999999999999999999999999888899999999999999999999999999886 699999999999


Q ss_pred             HHHHHHHhhCCCcEEEECcHHHHHHHHcCCC---CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNT---SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       235 ~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~---~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      ..++...++.++.|+|||||+.++.+..+..   ++.++.++|+||||+|.+++|.++...|+..+++.+|++++|||+|
T Consensus       478 ~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfp  557 (997)
T KOG0334|consen  478 ISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFP  557 (997)
T ss_pred             HHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhh
Confidence            9999999999999999999999999887654   4555669999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC-hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHH
Q 010709          312 VEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS-ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEV  390 (503)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l  390 (503)
                      ..+..++...+..|+.+.++........+.+.+..+. ..+|...|..++.....        .+++||||..++.|+.+
T Consensus       558 r~m~~la~~vl~~Pveiiv~~~svV~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e--------~~~tiiFv~~qe~~d~l  629 (997)
T KOG0334|consen  558 RSMEALARKVLKKPVEIIVGGRSVVCKEVTQVVRVCAIENEKFLKLLELLGERYE--------DGKTIIFVDKQEKADAL  629 (997)
T ss_pred             HHHHHHHHHhhcCCeeEEEccceeEeccceEEEEEecCchHHHHHHHHHHHHHhh--------cCCEEEEEcCchHHHHH
Confidence            9999999999999999999988889999999999998 88999999999988754        45799999999999999


Q ss_pred             HHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          391 SEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       391 ~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      .+.|.+.|+.+..+||+.++.+|..+++.|++|.+.+||||+++++|+|++.+.+|||||+|...++|+||.||+||+-
T Consensus       630 ~~~L~~ag~~~~slHGgv~q~dR~sti~dfK~~~~~LLvaTsvvarGLdv~~l~Lvvnyd~pnh~edyvhR~gRTgrag  708 (997)
T KOG0334|consen  630 LRDLQKAGYNCDSLHGGVDQHDRSSTIEDFKNGVVNLLVATSVVARGLDVKELILVVNYDFPNHYEDYVHRVGRTGRAG  708 (997)
T ss_pred             HHHHHhcCcchhhhcCCCchHHHHhHHHHHhccCceEEEehhhhhcccccccceEEEEcccchhHHHHHHHhcccccCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998853

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=1.4e-54  Score=435.58  Aligned_cols=335  Identities=34%  Similarity=0.531  Sum_probs=294.2

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ...+|+++++++.+.+.+..+||..|+++|.++|+.+++|+|+++++|||+|||++|++|++..+...     ..++++|
T Consensus        26 ~~~~~~~l~l~~~~~~~l~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~-----~~~~~~l  100 (401)
T PTZ00424         26 IVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD-----LNACQAL  100 (401)
T ss_pred             ccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC-----CCCceEE
Confidence            35679999999999999999999999999999999999999999999999999999999999876432     2357899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      |++|+++|+.|+.+.+..++... .+.+..+.|+....+....+..+++|+|+||+++.+++.+....++++++||||||
T Consensus       101 il~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l~~i~lvViDEa  179 (401)
T PTZ00424        101 ILAPTRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEA  179 (401)
T ss_pred             EECCCHHHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCcccccccEEEEecH
Confidence            99999999999999999988654 46777888988887777777788999999999999999887788999999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChh-hHHHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSEN-EKVDRLL  357 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~k~~~l~  357 (503)
                      |++.+.++...+..++..+++..|++++|||+++.+..+...++.+|..+.+.........+.+.+..+... .+...+.
T Consensus       180 h~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  259 (401)
T PTZ00424        180 DEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLC  259 (401)
T ss_pred             HHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCcccCCceEEEEecChHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999988876665555555666666665543 2333333


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      ..+..         ....++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|
T Consensus       260 ~~~~~---------~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~~l~~G  330 (401)
T PTZ00424        260 DLYET---------LTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG  330 (401)
T ss_pred             HHHHh---------cCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcccccCC
Confidence            33321         234579999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|+|++++||++|+|.+...|+||+||+||.
T Consensus       331 iDip~v~~VI~~~~p~s~~~y~qr~GRagR~  361 (401)
T PTZ00424        331 IDVQQVSLVINYDLPASPENYIHRIGRSGRF  361 (401)
T ss_pred             cCcccCCEEEEECCCCCHHHEeecccccccC
Confidence            9999999999999999999999999999994

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.4e-56  Score=410.40  Aligned_cols=341  Identities=32%  Similarity=0.494  Sum_probs=310.6

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCC-CCCCCCeEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPV-GRGDGPLALV  199 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~-~~~~~~~~li  199 (503)
                      .+|++++|++.+++++...||.+||-+|..+||.+++|+|++..|.||||||.+|++|+++.++..... ....++.++|
T Consensus        19 ktFe~~gLD~RllkAi~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~i   98 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAITKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVI   98 (569)
T ss_pred             ccHHHhCCCHHHHHHHHHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeEE
Confidence            579999999999999999999999999999999999999999999999999999999999999988765 4557899999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCC-CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC-CCCCCccEEEecc
Q 010709          200 LAPTRELAQQIEKEVKALSRSLD-SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDE  277 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~-~~l~~~~~vViDE  277 (503)
                      ++||+|||+|++..+.++...+. .+++.-+..+.+.......+...++|+|+||++++.++..+. ..+..++++|+||
T Consensus        99 LvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvDE  178 (569)
T KOG0346|consen   99 LVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVDE  178 (569)
T ss_pred             EechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEech
Confidence            99999999999999998876654 466666666666666667778889999999999999999876 5788999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCC-CCceEEEEEEcChhhHHHHH
Q 010709          278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSP-TANVIQILEKVSENEKVDRL  356 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~l  356 (503)
                      ||-++..||...+..+...+|+..|.++||||+..++..+-+.++++|+.+.+.....+ ...+.|++..+...+|...+
T Consensus       179 ADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL~Qy~v~cse~DKflll  258 (569)
T KOG0346|consen  179 ADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQLTQYQVKCSEEDKFLLL  258 (569)
T ss_pred             hhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccceEEEEEeccchhHHHH
Confidence            99999999999999999999999999999999999999999999999999888766644 45688999999999999998


Q ss_pred             HHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc----
Q 010709          357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD----  432 (503)
Q Consensus       357 ~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~----  432 (503)
                      +.+++.....        +|.|||+|+.+.|..+.-+|.+.|++.+.+.|.||...|..++++|..|-.+|+||||    
T Consensus       259 yallKL~LI~--------gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP~NSR~Hii~QFNkG~YdivIAtD~s~~  330 (569)
T KOG0346|consen  259 YALLKLRLIR--------GKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELPANSRCHIIEQFNKGLYDIVIATDDSAD  330 (569)
T ss_pred             HHHHHHHHhc--------CceEEEEechhhhHHHHHHHHHhCcHhhhhcccccccchhhHHHHhhCcceeEEEEccCccc
Confidence            8888776544        5799999999999999999999999999999999999999999999999999999999    


Q ss_pred             -------------------------------ccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          433 -------------------------------VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       433 -------------------------------~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                                                     -.+||||+..|.+|+|||+|.+...|+||+||++|..
T Consensus       331 ~~~~eee~kgk~~e~~~kndkkskkK~D~E~GVsRGIDF~~V~~VlNFD~P~t~~sYIHRvGRTaRg~  398 (569)
T KOG0346|consen  331 GDKLEEEVKGKSDEKNPKNDKKSKKKLDKESGVSRGIDFHHVSNVLNFDFPETVTSYIHRVGRTARGN  398 (569)
T ss_pred             hhhhhccccccccccCCCCccccccccCchhchhccccchheeeeeecCCCCchHHHHHhccccccCC
Confidence                                           2468999999999999999999999999999999954

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.3e-55  Score=413.94  Aligned_cols=341  Identities=30%  Similarity=0.494  Sum_probs=285.4

Q ss_pred             CCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCC------
Q 010709          117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPV------  189 (503)
Q Consensus       117 ~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~------  189 (503)
                      +..+..|..++++..++++|...||..|+++|...+|++..| .|++..|.||||||++|-+|++..+......      
T Consensus       177 ~~DvsAW~~l~lp~~iL~aL~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~  256 (731)
T KOG0347|consen  177 KVDVSAWKNLFLPMEILRALSNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSN  256 (731)
T ss_pred             ccChHHHhcCCCCHHHHHHHHhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhh
Confidence            445667999999999999999999999999999999999999 6899999999999999999999954432211      


Q ss_pred             --CCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC--
Q 010709          190 --GRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT--  265 (503)
Q Consensus       190 --~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--  265 (503)
                        .....+..||++|||+||.|+.+-+..+.... ++++..++||.....+.+.+...++|+|+|||+|+.++.....  
T Consensus       257 ~~~k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~t-~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l  335 (731)
T KOG0347|consen  257 TSAKYVKPIALVVTPTRELAHQVKQHLKAIAEKT-QIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHL  335 (731)
T ss_pred             HHhccCcceeEEecChHHHHHHHHHHHHHhcccc-CeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhh
Confidence              11123349999999999999999999998765 6999999999999999999999999999999999999988654  


Q ss_pred             -CCCCccEEEecchhHHhhCCCHHHHHHHHHhCC-----CCCcEEEEEeeCCHHH---------------------HHHH
Q 010709          266 -SLSRVSFVILDEADRMLDMGFEPQIREVMQNLP-----DKHQTLLFSATMPVEI---------------------EALA  318 (503)
Q Consensus       266 -~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~-----~~~q~i~~SAT~~~~~---------------------~~~~  318 (503)
                       .+.+++++|+||+|+|++.|.-..+..++..+.     ..+|.+.||||++-..                     +.++
T Consensus       336 ~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lm  415 (731)
T KOG0347|consen  336 GNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLM  415 (731)
T ss_pred             hhhhhceEEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHH
Confidence             577889999999999999998888888887764     4689999999994221                     1122


Q ss_pred             H--HhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHH
Q 010709          319 Q--EYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA  396 (503)
Q Consensus       319 ~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~  396 (503)
                      +  .+..+|..+...........+....+.|+..+|-.+++.++..          -+|++|||||+...+.+|+-+|..
T Consensus       416 k~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~r----------yPGrTlVF~NsId~vKRLt~~L~~  485 (731)
T KOG0347|consen  416 KKIGFRGKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTR----------YPGRTLVFCNSIDCVKRLTVLLNN  485 (731)
T ss_pred             HHhCccCCCeeEecCcchhHHHHHHHHhhcCCccccceeEEEEEee----------cCCceEEEechHHHHHHHHHHHhh
Confidence            2  2345666665555444444444455555555555555444433          357799999999999999999999


Q ss_pred             CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          397 EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       397 ~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .++....+|+.|.|++|.+.+++|++..-.||||||+++||+|||+|.|||||-.|++.+.|+||.||+.|.
T Consensus       486 L~i~p~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHYqVPrtseiYVHRSGRTARA  557 (731)
T KOG0347|consen  486 LDIPPLPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHYQVPRTSEIYVHRSGRTARA  557 (731)
T ss_pred             cCCCCchhhHHHHHHHHHHhHHHHhcCCCeEEEeehhhhccCCCCCcceEEEeecCCccceeEecccccccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999884

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

Probab=100.00  E-value=3.9e-52  Score=377.48  Aligned_cols=339  Identities=28%  Similarity=0.437  Sum_probs=296.5

Q ss_pred             CCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCC
Q 010709          113 SVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG  190 (503)
Q Consensus       113 ~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~  190 (503)
                      +..+-....+|+++.|.|++++.+..++|.+|+.+|..++|.++..  ++.|..+..|+|||.||.+.+|.++...    
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            3355567789999999999999999999999999999999999976  6799999999999999999999875442    


Q ss_pred             CCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-CCCCCCC
Q 010709          191 RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-GNTSLSR  269 (503)
Q Consensus       191 ~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~  269 (503)
                       ...|.++.|+|+|+||.|+-+.+.+.++.. ++.......+....+..   .-..+|+++|||.+.+++.+ ..+.+.+
T Consensus       158 -~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~rG~---~i~eqIviGTPGtv~Dlm~klk~id~~k  232 (477)
T KOG0332|consen  158 -VVVPQCICLAPTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKRGN---KLTEQIVIGTPGTVLDLMLKLKCIDLEK  232 (477)
T ss_pred             -ccCCCceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccccCC---cchhheeeCCCccHHHHHHHHHhhChhh
Confidence             235889999999999999999999999876 56666665554211110   01257999999999999987 6678899


Q ss_pred             ccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC
Q 010709          270 VSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS  348 (503)
Q Consensus       270 ~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  348 (503)
                      ++++|+|||+.|++. ||.++-.+|...+++..|++++|||....+..++.....++..+.+........++.|++..|.
T Consensus       233 ikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~eel~L~~IkQlyv~C~  312 (477)
T KOG0332|consen  233 IKVFVLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKREELALDNIKQLYVLCA  312 (477)
T ss_pred             ceEEEecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehhhccccchhhheeecc
Confidence            999999999999887 7999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             h-hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          349 E-NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       349 ~-~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                      . ..|...+..+....         .-+..||||.++..+..++..+...|..|..+||+|...+|..+++.|++|..+|
T Consensus       313 ~~~~K~~~l~~lyg~~---------tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kV  383 (477)
T KOG0332|consen  313 CRDDKYQALVNLYGLL---------TIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLTVEQRAAIIDRFREGKEKV  383 (477)
T ss_pred             chhhHHHHHHHHHhhh---------hhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccchhHHHHHHHHHHhcCcceE
Confidence            5 45666666644332         2345899999999999999999999999999999999999999999999999999


Q ss_pred             EEEccccccCCCCCCCCEEEEccCCC------ChhHHHHhhCcceeee
Q 010709          428 LVATDVASRGLDVMGVAHVVNLDLPK------VLLAASESLCTTSFNI  469 (503)
Q Consensus       428 LvaT~~~~~Gldip~v~~VI~~~~p~------s~~~~~Qr~GR~gR~~  469 (503)
                      ||+|++.+||||++.|+.|||||+|.      +.+.|+|||||+||.-
T Consensus       384 LitTnV~ARGiDv~qVs~VvNydlP~~~~~~pD~etYlHRiGRtGRFG  431 (477)
T KOG0332|consen  384 LITTNVCARGIDVAQVSVVVNYDLPVKYTGEPDYETYLHRIGRTGRFG  431 (477)
T ss_pred             EEEechhhcccccceEEEEEecCCccccCCCCCHHHHHHHhccccccc
Confidence            99999999999999999999999995      5699999999999953

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

Probab=100.00  E-value=1.2e-52  Score=384.28  Aligned_cols=349  Identities=35%  Similarity=0.583  Sum_probs=316.1

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      +.+|++++|.+.|++.++.+||.+|+.+|+.||..+..|.|+++.+++|+|||.+|.+++++.+...     .....+++
T Consensus        25 vdsfddm~L~e~LLrgiy~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~-----~ke~qali   99 (397)
T KOG0327|consen   25 VDSFDDMNLKESLLRGIYAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS-----VKETQALI   99 (397)
T ss_pred             hhhhhhcCCCHHHHhHHHhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcc-----hHHHHHHH
Confidence            4479999999999999999999999999999999999999999999999999999999999875332     23466899


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh-hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL-RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      ++|+|+||.|+.+....++... ++.+..+.||.....+...+ ...++|+++|||++.+++....+....+++.|+|||
T Consensus       100 laPtreLa~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~~l~~~~iKmfvlDEa  178 (397)
T KOG0327|consen  100 LAPTRELAQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRGSLSTDGIKMFVLDEA  178 (397)
T ss_pred             hcchHHHHHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccccccccceeEEeecch
Confidence            9999999999999999998776 58888888888776444434 456899999999999999998888888999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      +.++..+|..++..++..++++.|++++|||.|.++....+.|+.+|+.+.+.........+.+++..+...+|+..++.
T Consensus       179 DEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq~~i~v~k~~k~~~l~d  258 (397)
T KOG0327|consen  179 DEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQFYINVEKEEKLDTLCD  258 (397)
T ss_pred             HhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheeeeeeeccccccccHHHH
Confidence            99999999999999999999999999999999999999999999999999999988888889999999999999999988


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCC
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGL  438 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl  438 (503)
                      +.. ...          ..+||||+++.+..+...|...++.+..+|+.+.+.+|..+++.|+.|..+|||+|+.+++|+
T Consensus       259 l~~-~~~----------q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttdl~argi  327 (397)
T KOG0327|consen  259 LYR-RVT----------QAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTDLLARGI  327 (397)
T ss_pred             HHH-hhh----------cceEEecchhhHHHHHHHHhhCCceEEEeecccchhhhhHHHHHhhcCCceEEeecccccccc
Confidence            887 222          389999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCChhHHHHhhCccee--------eeeeccC-chhhhhhHHHH
Q 010709          439 DVMGVAHVVNLDLPKVLLAASESLCTTSF--------NITTNLD-GDMKKLEFCLI  485 (503)
Q Consensus       439 dip~v~~VI~~~~p~s~~~~~Qr~GR~gR--------~~~~~~~-~~~~~~~~~~~  485 (503)
                      |+..+..||||++|....+|+||+||+||        ++.+..+ .++..++.+|.
T Consensus       328 dv~~~slvinydlP~~~~~yihR~gr~gr~grkg~~in~v~~~d~~~lk~ie~~y~  383 (397)
T KOG0327|consen  328 DVQQVSLVVNYDLPARKENYIHRIGRAGRFGRKGVAINFVTEEDVRDLKDIEKFYN  383 (397)
T ss_pred             chhhcceeeeeccccchhhhhhhcccccccCCCceeeeeehHhhHHHHHhHHHhcC
Confidence            99999999999999999999999999999        3455555 77777776653

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

Probab=100.00  E-value=1.3e-50  Score=427.17  Aligned_cols=319  Identities=24%  Similarity=0.300  Sum_probs=253.1

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          127 CLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       127 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      .+++.+.+.|+..||..|+++|.++++.+++|+|+++++|||||||++|++|++..+...      .+.++|||+|||+|
T Consensus        20 ~l~~~l~~~L~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~------~~~~aL~l~PtraL   93 (742)
T TIGR03817        20 WAHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD------PRATALYLAPTKAL   93 (742)
T ss_pred             cCCHHHHHHHHHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC------CCcEEEEEcChHHH
Confidence            378999999999999999999999999999999999999999999999999999988653      25789999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC----CCCCCCccEEEecchhHHh
Q 010709          207 AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG----NTSLSRVSFVILDEADRML  282 (503)
Q Consensus       207 a~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~----~~~l~~~~~vViDEaH~l~  282 (503)
                      +.|+.+.++++.  ..++++..+.|++.. ++...+..+++|+|+||++|...+...    ...++++++|||||||++.
T Consensus        94 a~q~~~~l~~l~--~~~i~v~~~~Gdt~~-~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~~~  170 (742)
T TIGR03817        94 AADQLRAVRELT--LRGVRPATYDGDTPT-EERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYR  170 (742)
T ss_pred             HHHHHHHHHHhc--cCCeEEEEEeCCCCH-HHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhhcc
Confidence            999999999987  235778777777764 444566677999999999997544321    1237889999999999987


Q ss_pred             hCCCHHHHHHHHHh-------CCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC-------
Q 010709          283 DMGFEPQIREVMQN-------LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS-------  348 (503)
Q Consensus       283 ~~~~~~~~~~il~~-------~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------  348 (503)
                      +. |+..+..++.+       .+.++|++++|||+++..+ .+..+++.+..+ +.....+.......+....       
T Consensus       171 g~-fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~-i~~~~~~~~~~~~~~~~p~~~~~~~~  247 (742)
T TIGR03817       171 GV-FGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA-VTEDGSPRGARTVALWEPPLTELTGE  247 (742)
T ss_pred             Cc-cHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE-ECCCCCCcCceEEEEecCCccccccc
Confidence            63 66665554443       4567899999999988765 677788877654 3332222222222111111       


Q ss_pred             ---------hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--------CCeEEEEcCCCCHH
Q 010709          349 ---------ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--------GLHAVALHGGRNQS  411 (503)
Q Consensus       349 ---------~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--------~~~v~~lh~~~~~~  411 (503)
                               ...+...+..++.           ...++||||++++.++.++..|+..        +..+..+||+++++
T Consensus       248 ~~~~~r~~~~~~~~~~l~~l~~-----------~~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~  316 (742)
T TIGR03817       248 NGAPVRRSASAEAADLLADLVA-----------EGARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPE  316 (742)
T ss_pred             cccccccchHHHHHHHHHHHHH-----------CCCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHH
Confidence                     0112222222221           1246999999999999999998763        56788999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          412 DRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       412 ~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|.++++.|++|++++||||+++++|||||++++||++|+|.+..+|+||+||+||.
T Consensus       317 eR~~ie~~f~~G~i~vLVaTd~lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~  373 (742)
T TIGR03817       317 DRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRR  373 (742)
T ss_pred             HHHHHHHHHHcCCceEEEECchHhccCCcccccEEEEeCCCCCHHHHHHhccccCCC
Confidence            999999999999999999999999999999999999999999999999999999994

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.

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=2.9e-51  Score=394.72  Aligned_cols=339  Identities=27%  Similarity=0.443  Sum_probs=306.1

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      ..+.....|+.+.+...++..|+..+|..|+++|..|||.++.+-|+||.+..|+|||++|.+.++..+.-.     ...
T Consensus        19 V~~~~~~~fe~l~l~r~vl~glrrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~~-----~~~   93 (980)
T KOG4284|consen   19 VQSNCTPGFEQLALWREVLLGLRRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDSR-----SSH   93 (980)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHHhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCcc-----cCc
Confidence            345566789999999999999999999999999999999999999999999999999999988777665432     346


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      +.++|++|||++|.|+.+.+.+++..+.++++..+.||+........+. .++|+|+|||++.+++..+.+++..++++|
T Consensus        94 ~q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk-~~rIvIGtPGRi~qL~el~~~n~s~vrlfV  172 (980)
T KOG4284|consen   94 IQKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLK-QTRIVIGTPGRIAQLVELGAMNMSHVRLFV  172 (980)
T ss_pred             ceeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhh-hceEEecCchHHHHHHHhcCCCccceeEEE
Confidence            7899999999999999999999999888999999999999887766664 489999999999999999999999999999


Q ss_pred             ecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh--
Q 010709          275 LDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE--  351 (503)
Q Consensus       275 iDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  351 (503)
                      +||||.+++. .|...+..|+..+|..+|++++|||.|.++.+.+.+|+++|..+...........+.|++.......  
T Consensus       173 LDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~GikQyv~~~~s~nns  252 (980)
T KOG4284|consen  173 LDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFGIKQYVVAKCSPNNS  252 (980)
T ss_pred             eccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccCCceeechhheeeeccCCcch
Confidence            9999999985 6999999999999999999999999999999999999999999999888888888899888776432  


Q ss_pred             ------HHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q 010709          352 ------KVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGST  425 (503)
Q Consensus       352 ------k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~  425 (503)
                            |++.|-+++..         -|....||||+....|+.++.+|...|+.|.++.|.|+|.+|..+++.++.-.+
T Consensus       253 veemrlklq~L~~vf~~---------ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~Q~~Rl~a~~~lr~f~~  323 (980)
T KOG4284|consen  253 VEEMRLKLQKLTHVFKS---------IPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMSQKDRLLAVDQLRAFRV  323 (980)
T ss_pred             HHHHHHHHHHHHHHHhh---------CchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccchhHHHHHHHHhhhceE
Confidence                  33333332222         355569999999999999999999999999999999999999999999999999


Q ss_pred             cEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          426 NILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       426 ~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|||+|++.+||||-++|++|||.|+|.+...|.||||||||.
T Consensus       324 rILVsTDLtaRGIDa~~vNLVVNiD~p~d~eTY~HRIGRAgRF  366 (980)
T KOG4284|consen  324 RILVSTDLTARGIDADNVNLVVNIDAPADEETYFHRIGRAGRF  366 (980)
T ss_pred             EEEEecchhhccCCccccceEEecCCCcchHHHHHHhhhcccc
Confidence            9999999999999999999999999999999999999999994

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

Probab=100.00  E-value=4.2e-51  Score=376.17  Aligned_cols=337  Identities=37%  Similarity=0.519  Sum_probs=315.1

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      ...|..++|+..+++++.+.||+.|+|+|+..+|.++++++++..+-||+|||.||++|+++++....    ..|-++++
T Consensus        20 ~g~fqsmgL~~~v~raI~kkg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s----~~g~Rali   95 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHKKGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS----QTGLRALI   95 (529)
T ss_pred             CCCccccCCCHHHHHHHHHhhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc----ccccceee
Confidence            45699999999999999999999999999999999999999999999999999999999999987652    34678999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      +.|||+|+.|..+.++.+++.. +++..+++||....+++..+..++||+++||+++..+.-...+.++.+.|||+||++
T Consensus        96 lsptreLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~vem~l~l~sveyVVfdEad  174 (529)
T KOG0337|consen   96 LSPTRELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEAD  174 (529)
T ss_pred             ccCcHHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehheeccccceeeeeehhhh
Confidence            9999999999999999999877 599999999999999999999999999999999988877777889999999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLAL  359 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~  359 (503)
                      ++..+||..++.+++.+++...|.++||||+|..+.++++.-+.+|+.+.++-.......+...+..+...+|...|+.+
T Consensus       175 rlfemgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk~~f~~~~~a~K~aaLl~i  254 (529)
T KOG0337|consen  175 RLFEMGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLSI  254 (529)
T ss_pred             HHHhhhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhhhheeeeccHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999888888888888889999999999999988


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCC
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLD  439 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gld  439 (503)
                      +.....        ...++|||.++..++.+...|+..|+.+..++|.+.+..|...+..|..++..+||.|++++||+|
T Consensus       255 l~~~~~--------~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD~~aRk~~~~~F~~~k~~~lvvTdvaaRG~d  326 (529)
T KOG0337|consen  255 LGGRIK--------DKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLDQEARKINGRDFRGRKTSILVVTDVAARGLD  326 (529)
T ss_pred             Hhcccc--------ccceeEEecccchHHHHHHHHHhcCCCccccccccChHhhhhccccccCCccceEEEehhhhccCC
Confidence            876542        335999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          440 VMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       440 ip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      ||..+.|||||+|.+..-|.||+||+.|..
T Consensus       327 iplldnvinyd~p~~~klFvhRVgr~arag  356 (529)
T KOG0337|consen  327 IPLLDNVINYDFPPDDKLFVHRVGRVARAG  356 (529)
T ss_pred             CccccccccccCCCCCceEEEEecchhhcc
Confidence            999999999999999999999999966644

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

Probab=100.00  E-value=2.1e-48  Score=407.24  Aligned_cols=315  Identities=19%  Similarity=0.247  Sum_probs=242.8

Q ss_pred             CCCCHHHHHHHH-HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          126 MCLHPSIMKDIE-FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       126 ~~l~~~l~~~l~-~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      ++....+...++ .+|+..++++|.++|+.++.|+|+++++|||+|||+||++|++..           ++.+|||+|++
T Consensus       442 fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~-----------~GiTLVISPLi  510 (1195)
T PLN03137        442 FPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC-----------PGITLVISPLV  510 (1195)
T ss_pred             CCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc-----------CCcEEEEeCHH
Confidence            455555655554 479999999999999999999999999999999999999999864           45699999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh------CCCcEEEECcHHHHH--HHHcC---CCCCCCccEE
Q 010709          205 ELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR------GGVSIVVATPGRFLD--HLQQG---NTSLSRVSFV  273 (503)
Q Consensus       205 ~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~Ilv~Tp~~l~~--~l~~~---~~~l~~~~~v  273 (503)
                      +|+.++...+...     ++....+.++....++...+.      ...+|+|+||++|..  .+.+.   ......+.+|
T Consensus       511 SLmqDQV~~L~~~-----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L~~~~~LslI  585 (1195)
T PLN03137        511 SLIQDQIMNLLQA-----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARF  585 (1195)
T ss_pred             HHHHHHHHHHHhC-----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhhhhcccccee
Confidence            9998655555443     477888888887766544332      468999999999852  12211   1123458899


Q ss_pred             EecchhHHhhCC--CHHHHHHH--HHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcCh
Q 010709          274 ILDEADRMLDMG--FEPQIREV--MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE  349 (503)
Q Consensus       274 ViDEaH~l~~~~--~~~~~~~i--l~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  349 (503)
                      ||||||++.+||  |++.+..+  +....+..+++++|||++..+...+...+.....+.+. ......++...+  +..
T Consensus       586 VIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr-~Sf~RpNL~y~V--v~k  662 (1195)
T PLN03137        586 VIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFR-QSFNRPNLWYSV--VPK  662 (1195)
T ss_pred             ccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEee-cccCccceEEEE--ecc
Confidence            999999999987  88887764  44444578899999999999887666665432211111 112223332222  222


Q ss_pred             hhH-HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          350 NEK-VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       350 ~~k-~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      ..+ ...+..++...        ......||||.+++.|+.+++.|...|+.+..+||+|++.+|..+++.|..|+++||
T Consensus       663 ~kk~le~L~~~I~~~--------~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs~eeR~~vqe~F~~Gei~VL  734 (1195)
T PLN03137        663 TKKCLEDIDKFIKEN--------HFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINII  734 (1195)
T ss_pred             chhHHHHHHHHHHhc--------ccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCCHHHHHHHHHHHhcCCCcEE
Confidence            222 23333333321        223468999999999999999999999999999999999999999999999999999


Q ss_pred             EEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          429 VATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |||+++++|||+|+|++||+|++|++++.|+||+|||||
T Consensus       735 VATdAFGMGIDkPDVR~VIHydlPkSiEsYyQriGRAGR  773 (1195)
T PLN03137        735 CATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGR  773 (1195)
T ss_pred             EEechhhcCCCccCCcEEEEcCCCCCHHHHHhhhcccCC
Confidence            999999999999999999999999999999999999999

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

Probab=100.00  E-value=3.2e-49  Score=379.88  Aligned_cols=355  Identities=31%  Similarity=0.465  Sum_probs=297.3

Q ss_pred             HHHHcCceEEecCCCCCCCCCcCCcccC----CCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHH
Q 010709           99 VRLRLNVDVTVASGSVPAPAPIESFTDM----CLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus        99 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~----~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~  174 (503)
                      .|..+.+.+.+    ...|.++.+|.++    ..++.+++++...+|..|+++|.+++|.++++++++.|+|||+|||++
T Consensus       114 ~Rk~~k~~v~G----~~~~~~l~~f~~lt~~~~~~~~ll~nl~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtla  189 (593)
T KOG0344|consen  114 IRKSNKINVDG----FHLPPPLLSFSDLTYDYSMNKRLLENLQELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLA  189 (593)
T ss_pred             chhcceeeccC----CCCCCccccccccchhhhhcHHHHHhHhhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhh
Confidence            34444444443    3778999999984    689999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh--ccCCCceEEEEECC-ccHHHHHHHhhCCCcEEEE
Q 010709          175 FTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS--RSLDSFKTAIVVGG-TNIAEQRSELRGGVSIVVA  251 (503)
Q Consensus       175 ~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~--~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~Ilv~  251 (503)
                      |.+|++.++..........|-+++|+.|+|+||.|+++++.++.  .... ..+..+... .............++|++.
T Consensus       190 f~~Pil~~L~~~~~~~~~~gl~a~Il~ptreLa~Qi~re~~k~~~~~~t~-~~a~~~~~~~~~~qk~a~~~~~k~dili~  268 (593)
T KOG0344|consen  190 FNLPILQHLKDLSQEKHKVGLRALILSPTRELAAQIYREMRKYSIDEGTS-LRAAQFSKPAYPSQKPAFLSDEKYDILIS  268 (593)
T ss_pred             hhhHHHHHHHHhhcccCccceEEEEecchHHHHHHHHHHHHhcCCCCCCc-hhhhhcccccchhhccchhHHHHHHHHhc
Confidence            99999999887654344567889999999999999999999998  3332 222222222 1111111222245899999


Q ss_pred             CcHHHHHHHHcCC--CCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCC-CCCcEEEEEeeCCHHHHHHHHHhcCCCeE
Q 010709          252 TPGRFLDHLQQGN--TSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLP-DKHQTLLFSATMPVEIEALAQEYLTDPVQ  327 (503)
Q Consensus       252 Tp~~l~~~l~~~~--~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~~  327 (503)
                      ||-++...+..+.  ..+..+.++|+||||++.+. .|..++..|+..+. ++..+-+||||.+..++++++....++..
T Consensus       269 TP~ri~~~~~~~~~~idl~~V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~  348 (593)
T KOG0344|consen  269 TPMRIVGLLGLGKLNIDLSKVEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKR  348 (593)
T ss_pred             CHHHHHHHhcCCCccchhheeeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhcccee
Confidence            9999999998765  67899999999999999998 89999999988775 46677789999999999999999999999


Q ss_pred             EEeCCCCCCCCceEEEEEEcC-hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHH-HHCCCeEEEEc
Q 010709          328 VKVGKVSSPTANVIQILEKVS-ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL-VAEGLHAVALH  405 (503)
Q Consensus       328 ~~~~~~~~~~~~~~~~~~~~~-~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L-~~~~~~v~~lh  405 (503)
                      +.++........+.|....+. ...|+..+.+++...         -.+++|||+.+.+.|.+|.+.| .-.++++..+|
T Consensus       349 vivg~~~sa~~~V~QelvF~gse~~K~lA~rq~v~~g---------~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh  419 (593)
T KOG0344|consen  349 VIVGLRNSANETVDQELVFCGSEKGKLLALRQLVASG---------FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIH  419 (593)
T ss_pred             EEEecchhHhhhhhhhheeeecchhHHHHHHHHHhcc---------CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEe
Confidence            999888777777777766664 445666666666542         4567999999999999999999 66789999999


Q ss_pred             CCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          406 GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       406 ~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |+.++.+|.+.++.|+.|+++|||||++++||+|+.++++|||||+|.+..+|+||+||+||
T Consensus       420 ~e~~~~qrde~~~~FR~g~IwvLicTdll~RGiDf~gvn~VInyD~p~s~~syihrIGRtgR  481 (593)
T KOG0344|consen  420 GERSQKQRDETMERFRIGKIWVLICTDLLARGIDFKGVNLVINYDFPQSDLSYIHRIGRTGR  481 (593)
T ss_pred             cccchhHHHHHHHHHhccCeeEEEehhhhhccccccCcceEEecCCCchhHHHHHHhhccCC
Confidence            99999999999999999999999999999999999999999999999999999999999988

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=100.00  E-value=6.3e-48  Score=391.60  Aligned_cols=304  Identities=18%  Similarity=0.284  Sum_probs=236.5

Q ss_pred             HHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       137 ~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      ..+||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..           ++.+||++|+++|+.|+.+.++.
T Consensus         5 ~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~-----------~~~~lVi~P~~~L~~dq~~~l~~   73 (470)
T TIGR00614         5 TVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS-----------DGITLVISPLISLMEDQVLQLKA   73 (470)
T ss_pred             hhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc-----------CCcEEEEecHHHHHHHHHHHHHH
Confidence            3579999999999999999999999999999999999999998853           45689999999999999888876


Q ss_pred             HhccCCCceEEEEECCccHHHHHHH----hhCCCcEEEECcHHHHHHH-HcCCC-CCCCccEEEecchhHHhhCC--CHH
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSE----LRGGVSIVVATPGRFLDHL-QQGNT-SLSRVSFVILDEADRMLDMG--FEP  288 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~Tp~~l~~~l-~~~~~-~l~~~~~vViDEaH~l~~~~--~~~  288 (503)
                      +     ++.+..+.++....+....    ..+..+|+++||+++.... ....+ ...++++|||||||++.++|  |..
T Consensus        74 ~-----gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~fr~  148 (470)
T TIGR00614        74 S-----GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRP  148 (470)
T ss_pred             c-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccccHH
Confidence            5     3667777777665533221    2345899999999975322 11112 46789999999999998876  677


Q ss_pred             HHHHH--HHhCCCCCcEEEEEeeCCHHHHHHHHHhc--CCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHH
Q 010709          289 QIREV--MQNLPDKHQTLLFSATMPVEIEALAQEYL--TDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEA  364 (503)
Q Consensus       289 ~~~~i--l~~~~~~~q~i~~SAT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~  364 (503)
                      .+..+  +....++.+++++|||+++.+...+...+  .+|..+...   ....++...+.. ........+...+... 
T Consensus       149 ~~~~l~~l~~~~~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s---~~r~nl~~~v~~-~~~~~~~~l~~~l~~~-  223 (470)
T TIGR00614       149 DYKALGSLKQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCTS---FDRPNLYYEVRR-KTPKILEDLLRFIRKE-  223 (470)
T ss_pred             HHHHHHHHHHHcCCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCC---CCCCCcEEEEEe-CCccHHHHHHHHHHHh-
Confidence            76654  33333577899999999998776665554  344443322   122223222222 1123344444444331 


Q ss_pred             HhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCC
Q 010709          365 FLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVA  444 (503)
Q Consensus       365 ~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~  444 (503)
                             .+...+||||++++.|+.+++.|...|+.+..+||+|++++|..+++.|++|+.+|||||+++++|||+|+|+
T Consensus       224 -------~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~~~~~GID~p~V~  296 (470)
T TIGR00614       224 -------FKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVR  296 (470)
T ss_pred             -------cCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEechhhccCCcccce
Confidence                   2334579999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccCCCChhHHHHhhCcceee
Q 010709          445 HVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       445 ~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +||++++|++++.|+||+||+||.
T Consensus       297 ~VI~~~~P~s~~~y~Qr~GRaGR~  320 (470)
T TIGR00614       297 FVIHYSLPKSMESYYQESGRAGRD  320 (470)
T ss_pred             EEEEeCCCCCHHHHHhhhcCcCCC
Confidence            999999999999999999999993

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

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

Probab=100.00  E-value=9.1e-48  Score=361.26  Aligned_cols=336  Identities=27%  Similarity=0.377  Sum_probs=273.2

Q ss_pred             CcCCcccCCCCHHHH----------HHHHHCCCCCCcHHHHHHHHHHhc---------CCCeEEEccCCCchhHHhHHHH
Q 010709          119 PIESFTDMCLHPSIM----------KDIEFHEYTRPTSIQAQAMPVALS---------GRDLLGCAETGSGKTAAFTIPM  179 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~----------~~l~~~~~~~~~~~Q~~~i~~i~~---------~~~vii~~~TGsGKTl~~~lp~  179 (503)
                      ....|+.+++++...          ..+.++++.+..|+|...+|+++.         .+|++|.||||||||++|.+|+
T Consensus       125 slq~~s~l~~se~k~~~d~lea~~~q~l~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPI  204 (620)
T KOG0350|consen  125 SLQIFSVLGKSEMKNLEDTLEATIDQLLVKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPI  204 (620)
T ss_pred             ceeeeeccchhHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHH
Confidence            333455555555444          448899999999999999999862         5799999999999999999999


Q ss_pred             HHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCC-----CcEEEECcH
Q 010709          180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGG-----VSIVVATPG  254 (503)
Q Consensus       180 l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~Ilv~Tp~  254 (503)
                      ++.+..++    -+.-++|||+|+++|+.|+++.|.++.... ++.++...|.....++...+.+.     .+|+|+|||
T Consensus       205 VQ~L~~R~----v~~LRavVivPtr~L~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPG  279 (620)
T KOG0350|consen  205 VQLLSSRP----VKRLRAVVIVPTRELALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPG  279 (620)
T ss_pred             HHHHccCC----ccceEEEEEeeHHHHHHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCch
Confidence            99876653    123679999999999999999999999776 58899999998888877777643     489999999


Q ss_pred             HHHHHHHc-CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC----------------------------------C
Q 010709          255 RFLDHLQQ-GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP----------------------------------D  299 (503)
Q Consensus       255 ~l~~~l~~-~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~----------------------------------~  299 (503)
                      +|.+++.+ ..+.+++++++||||||||++..|..++-.++..+.                                  +
T Consensus       280 RLVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~  359 (620)
T KOG0350|consen  280 RLVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYP  359 (620)
T ss_pred             HHHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCc
Confidence            99999995 468999999999999999998877777665543331                                  2


Q ss_pred             CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCC----CCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCC
Q 010709          300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK----VSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFP  375 (503)
Q Consensus       300 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~  375 (503)
                      +.+.+.+|||+......+..--+..|..+.+..    .......+.+....+....+...++.++....         ..
T Consensus       360 ~l~kL~~satLsqdP~Kl~~l~l~~Prl~~v~~~~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~k---------~~  430 (620)
T KOG0350|consen  360 PLWKLVFSATLSQDPSKLKDLTLHIPRLFHVSKPLIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSNK---------LN  430 (620)
T ss_pred             hhHhhhcchhhhcChHHHhhhhcCCCceEEeecccceeeecChhhhhceeecccccchHhHHHHHHHhh---------cc
Confidence            345788899998777777777778886665543    22334444555555566566677777776543         33


Q ss_pred             cEEEEEcchhhHHHHHHHHH----HCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC
Q 010709          376 LTIVFVERKTRCDEVSEALV----AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL  451 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~----~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~  451 (503)
                      ++|+|+++.+.+.++++.|.    ....++-.+.|++.++.|.+.++.|..|++++|||+|+++||+|+.+++.|||||+
T Consensus       431 r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~l~~k~r~k~l~~f~~g~i~vLIcSD~laRGiDv~~v~~VINYd~  510 (620)
T KOG0350|consen  431 RTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQLNGKRRYKMLEKFAKGDINVLICSDALARGIDVNDVDNVINYDP  510 (620)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhccccchhhhhhhhhhHHHHHHHHHHHhcCCceEEEehhhhhcCCcccccceEeecCC
Confidence            69999999999999999887    33567777999999999999999999999999999999999999999999999999


Q ss_pred             CCChhHHHHhhCcceee
Q 010709          452 PKVLLAASESLCTTSFN  468 (503)
Q Consensus       452 p~s~~~~~Qr~GR~gR~  468 (503)
                      |.+...|+||+||++|.
T Consensus       511 P~~~ktyVHR~GRTARA  527 (620)
T KOG0350|consen  511 PASDKTYVHRAGRTARA  527 (620)
T ss_pred             CchhhHHHHhhcccccc
Confidence            99999999999998874

>PRK13767 ATP-dependent helicase; Provisional

Probab=100.00  E-value=1.7e-46  Score=403.66  Aligned_cols=331  Identities=20%  Similarity=0.244  Sum_probs=245.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCC-CCCCeEEEEcccHHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGR-GDGPLALVLAPTREL  206 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~-~~~~~~lil~Ptr~L  206 (503)
                      +++.+.+.+. .+|..|+++|.++++.+++|+|+++++|||+|||++|++|++..+........ ..+.++||++|+++|
T Consensus        18 l~~~v~~~~~-~~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraL   96 (876)
T PRK13767         18 LRPYVREWFK-EKFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRAL   96 (876)
T ss_pred             cCHHHHHHHH-HccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHH
Confidence            4555555544 47899999999999999999999999999999999999999998875432211 346789999999999


Q ss_pred             HHHHHHHHHHH-------h----ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC--CCCCccEE
Q 010709          207 AQQIEKEVKAL-------S----RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT--SLSRVSFV  273 (503)
Q Consensus       207 a~q~~~~~~~~-------~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--~l~~~~~v  273 (503)
                      ++|+++.+.+.       .    ....++.+.+.+|+....+....+...++|+|+||++|..++....+  .+.++++|
T Consensus        97 a~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~V  176 (876)
T PRK13767         97 NNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKWV  176 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCEE
Confidence            99998866532       2    22235788999999988877777778899999999999877765433  47889999


Q ss_pred             EecchhHHhhCCCHHHHHHHH----HhCCCCCcEEEEEeeCCHHHHHHHHHhcC-------CCeEEEeCCCCCCCCceEE
Q 010709          274 ILDEADRMLDMGFEPQIREVM----QNLPDKHQTLLFSATMPVEIEALAQEYLT-------DPVQVKVGKVSSPTANVIQ  342 (503)
Q Consensus       274 ViDEaH~l~~~~~~~~~~~il----~~~~~~~q~i~~SAT~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~  342 (503)
                      ||||+|.+.+..++..+...+    ...+++.|+|++|||+++. ..+......       .+..+ +.........+..
T Consensus       177 VIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~-~~va~~L~~~~~~~~~r~~~i-v~~~~~k~~~i~v  254 (876)
T PRK13767        177 IVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-EEVAKFLVGYEDDGEPRDCEI-VDARFVKPFDIKV  254 (876)
T ss_pred             EEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-HHHHHHhcCccccCCCCceEE-EccCCCccceEEE
Confidence            999999998776665554443    3344678999999999652 223322211       12222 1111111111110


Q ss_pred             EE-----EEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC------CCeEEEEcCCCCHH
Q 010709          343 IL-----EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE------GLHAVALHGGRNQS  411 (503)
Q Consensus       343 ~~-----~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~------~~~v~~lh~~~~~~  411 (503)
                      ..     ...........+...+.....       ..+++||||+++..|+.++..|+..      +..+..+||+++++
T Consensus       255 ~~p~~~l~~~~~~~~~~~l~~~L~~~i~-------~~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~  327 (876)
T PRK13767        255 ISPVDDLIHTPAEEISEALYETLHELIK-------EHRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSRE  327 (876)
T ss_pred             eccCccccccccchhHHHHHHHHHHHHh-------cCCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHH
Confidence            00     001111122233333332221       2346999999999999999999873      46799999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          412 DRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       412 ~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|..+++.|++|+.+|||||+++++|||+|++++||+++.|.++.+|+||+||+||.
T Consensus       328 ~R~~ve~~fk~G~i~vLVaTs~Le~GIDip~Vd~VI~~~~P~sv~~ylQRiGRaGR~  384 (876)
T PRK13767        328 VRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAGHR  384 (876)
T ss_pred             HHHHHHHHHHcCCCeEEEECChHHhcCCCCCCcEEEEeCCCCCHHHHHHhcccCCCC
Confidence            999999999999999999999999999999999999999999999999999999985

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=100.00  E-value=2.7e-46  Score=389.12  Aligned_cols=309  Identities=19%  Similarity=0.281  Sum_probs=237.3

Q ss_pred             HHHHHHHH-HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          130 PSIMKDIE-FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       130 ~~l~~~l~-~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      +...+.|+ .+||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..           ++.+||++|+++|+.
T Consensus        11 ~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~-----------~g~tlVisPl~sL~~   79 (607)
T PRK11057         11 SLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVL-----------DGLTLVVSPLISLMK   79 (607)
T ss_pred             hHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHc-----------CCCEEEEecHHHHHH
Confidence            33334443 379999999999999999999999999999999999999999854           356899999999999


Q ss_pred             HHHHHHHHHhccCCCceEEEEECCccHHHHHHH----hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC
Q 010709          209 QIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE----LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM  284 (503)
Q Consensus       209 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~  284 (503)
                      |+.+.++.++     +...++.++....+....    ..+..+++++||+++........+...++++|||||||++.++
T Consensus        80 dqv~~l~~~g-----i~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~~~l~~~~l~~iVIDEaH~i~~~  154 (607)
T PRK11057         80 DQVDQLLANG-----VAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFLEHLAHWNPALLAVDEAHCISQW  154 (607)
T ss_pred             HHHHHHHHcC-----CcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHHHHHhhCCCCEEEEeCccccccc
Confidence            9998888753     566666666655443222    2245789999999986432222344567899999999999987


Q ss_pred             C--CHHHHHHH--HHhCCCCCcEEEEEeeCCHHHHHHHHHhc--CCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          285 G--FEPQIREV--MQNLPDKHQTLLFSATMPVEIEALAQEYL--TDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       285 ~--~~~~~~~i--l~~~~~~~q~i~~SAT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      +  |.+.+..+  +....+..+++++|||+++.....+...+  .+|... .....  ..++..  ..+....+...+..
T Consensus       155 G~~fr~~y~~L~~l~~~~p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~-~~~~~--r~nl~~--~v~~~~~~~~~l~~  229 (607)
T PRK11057        155 GHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISSFD--RPNIRY--TLVEKFKPLDQLMR  229 (607)
T ss_pred             cCcccHHHHHHHHHHHhCCCCcEEEEecCCChhHHHHHHHHhCCCCeEEE-ECCCC--CCccee--eeeeccchHHHHHH
Confidence            6  67666544  22233568899999999988766544443  344433 22211  222221  12222233344444


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCC
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGL  438 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl  438 (503)
                      .+..         ....++||||+++++|+.+++.|...|+.+..+||+|++++|.++++.|++|+.+|||||+++++||
T Consensus       230 ~l~~---------~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~a~~~GI  300 (607)
T PRK11057        230 YVQE---------QRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGI  300 (607)
T ss_pred             HHHh---------cCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEechhhccC
Confidence            4332         2345799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          439 DVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       439 dip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|+|++||+||+|++.++|+||+|||||.
T Consensus       301 Dip~V~~VI~~d~P~s~~~y~Qr~GRaGR~  330 (607)
T PRK11057        301 NKPNVRFVVHFDIPRNIESYYQETGRAGRD  330 (607)
T ss_pred             CCCCcCEEEEeCCCCCHHHHHHHhhhccCC
Confidence            999999999999999999999999999993

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=100.00  E-value=4.5e-45  Score=381.47  Aligned_cols=300  Identities=22%  Similarity=0.333  Sum_probs=238.9

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .+||..++++|.++++.+++|+|+++++|||+|||++|++|++..           ++.++|++|+++|+.|+.+.++.+
T Consensus         8 ~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~-----------~g~~lVisPl~sL~~dq~~~l~~~   76 (591)
T TIGR01389         8 TFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL-----------KGLTVVISPLISLMKDQVDQLRAA   76 (591)
T ss_pred             hcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc-----------CCcEEEEcCCHHHHHHHHHHHHHc
Confidence            479999999999999999999999999999999999999998853           356899999999999999988875


Q ss_pred             hccCCCceEEEEECCccHHHHHHH----hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC--CHHHHH
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSE----LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEPQIR  291 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~--~~~~~~  291 (503)
                      +     +.+..+.++....+....    ..+..+|+++||+++........+...++++|||||||++.++|  |.+.+.
T Consensus        77 g-----i~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~~~l~~~~l~~iViDEaH~i~~~g~~frp~y~  151 (591)
T TIGR01389        77 G-----VAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFLNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQ  151 (591)
T ss_pred             C-----CcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHHHHHhcCCCCEEEEeCCcccccccCccHHHHH
Confidence            3     667777777665543322    23568999999999965433334456789999999999998875  777766


Q ss_pred             HHH---HhCCCCCcEEEEEeeCCHHHHHHHHHhcC--CCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHh
Q 010709          292 EVM---QNLPDKHQTLLFSATMPVEIEALAQEYLT--DPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFL  366 (503)
Q Consensus       292 ~il---~~~~~~~q~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~  366 (503)
                      ++.   ..++ ..+++++|||+++.+...+...+.  ++..+ ..  .....++...  ......+...+...+...   
T Consensus       152 ~l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~-~~--~~~r~nl~~~--v~~~~~~~~~l~~~l~~~---  222 (591)
T TIGR01389       152 RLGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEF-IT--SFDRPNLRFS--VVKKNNKQKFLLDYLKKH---  222 (591)
T ss_pred             HHHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeE-ec--CCCCCCcEEE--EEeCCCHHHHHHHHHHhc---
Confidence            553   3343 445999999999988877766664  33322 21  1122233222  222334445555555432   


Q ss_pred             hhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEE
Q 010709          367 AEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHV  446 (503)
Q Consensus       367 ~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~V  446 (503)
                            ...++||||++++.|+.+++.|...|+.+..+||+|++++|..+++.|.+|+.+|||||+++++|||+|+|++|
T Consensus       223 ------~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~a~~~GID~p~v~~V  296 (591)
T TIGR01389       223 ------RGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFV  296 (591)
T ss_pred             ------CCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechhhccCcCCCCCEE
Confidence                  24569999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCChhHHHHhhCcceee
Q 010709          447 VNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       447 I~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|++|++++.|+||+||+||.
T Consensus       297 I~~~~p~s~~~y~Q~~GRaGR~  318 (591)
T TIGR01389       297 IHYDMPGNLESYYQEAGRAGRD  318 (591)
T ss_pred             EEcCCCCCHHHHhhhhccccCC
Confidence            9999999999999999999993

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.

>PRK02362 ski2-like helicase; Provisional

Probab=100.00  E-value=1.5e-45  Score=393.33  Aligned_cols=324  Identities=21%  Similarity=0.296  Sum_probs=247.0

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH-HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~-i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .|+++++++.+.+.+...|+..|+|+|.++++. +.+|+|+++++|||+|||++|.+|++..+..        ++++||+
T Consensus         2 ~~~~l~lp~~~~~~l~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~--------~~kal~i   73 (737)
T PRK02362          2 KIAELPLPEGVIEFYEAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR--------GGKALYI   73 (737)
T ss_pred             ChhhcCCCHHHHHHHHhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc--------CCcEEEE
Confidence            478899999999999999999999999999998 6789999999999999999999999988742        5779999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++||.|+++.++++.. . ++++..++|+......   .....+|+|+||+++..++.+....++++++|||||+|.
T Consensus        74 ~P~raLa~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~~~~l~~v~lvViDE~H~  148 (737)
T PRK02362         74 VPLRALASEKFEEFERFEE-L-GVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNGAPWLDDITCVVVDEVHL  148 (737)
T ss_pred             eChHHHHHHHHHHHHHhhc-C-CCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcChhhhhhcCEEEEECccc
Confidence            9999999999999998753 2 5788888887654332   224589999999999888877555678999999999999


Q ss_pred             HhhCCCHHHHHHHHHhC---CCCCcEEEEEeeCCHHHHHHHHHhcCC--------CeEEEeCCCCCCCCceEEEEEEcCh
Q 010709          281 MLDMGFEPQIREVMQNL---PDKHQTLLFSATMPVEIEALAQEYLTD--------PVQVKVGKVSSPTANVIQILEKVSE  349 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~---~~~~q~i~~SAT~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~  349 (503)
                      +.+.+++..++.++.++   .+..|+|++|||+++. .++. .|+..        |+.+..................+..
T Consensus       149 l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~la-~wl~~~~~~~~~rpv~l~~~v~~~~~~~~~~~~~~~~~  226 (737)
T PRK02362        149 IDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELA-DWLDAELVDSEWRPIDLREGVFYGGAIHFDDSQREVEV  226 (737)
T ss_pred             cCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHH-HHhCCCcccCCCCCCCCeeeEecCCeeccccccccCCC
Confidence            88888888888776554   5688999999999752 3233 33321        1111100000000000000000111


Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC-------------------------------
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG-------------------------------  398 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~-------------------------------  398 (503)
                      ..+ ......+....       ...+++||||++++.|+.+++.|....                               
T Consensus       227 ~~~-~~~~~~~~~~~-------~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L  298 (737)
T PRK02362        227 PSK-DDTLNLVLDTL-------EEGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDL  298 (737)
T ss_pred             ccc-hHHHHHHHHHH-------HcCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHH
Confidence            111 12222222211       134579999999999999988886431                               


Q ss_pred             -----CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE----cc-----CCCChhHHHHhhCc
Q 010709          399 -----LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN----LD-----LPKVLLAASESLCT  464 (503)
Q Consensus       399 -----~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~----~~-----~p~s~~~~~Qr~GR  464 (503)
                           ..+..+|++|++.+|..+++.|++|.++|||||+++++|+|+|++++||+    ||     .|.+..+|.||+||
T Consensus       299 ~~~l~~gva~hHagl~~~eR~~ve~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GR  378 (737)
T PRK02362        299 ADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGR  378 (737)
T ss_pred             HHHHHhCEEeecCCCCHHHHHHHHHHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhc
Confidence                 36889999999999999999999999999999999999999999999997    66     58899999999999


Q ss_pred             ceee
Q 010709          465 TSFN  468 (503)
Q Consensus       465 ~gR~  468 (503)
                      |||.
T Consensus       379 AGR~  382 (737)
T PRK02362        379 AGRP  382 (737)
T ss_pred             CCCC
Confidence            9994

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

Probab=100.00  E-value=5.7e-45  Score=374.43  Aligned_cols=361  Identities=21%  Similarity=0.256  Sum_probs=279.6

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      +++.+.+.+... |..||+.|.+||+.+.+|+|++|+||||||||+++++|++..+...+......+-.+|||+|.|+|.
T Consensus         8 l~~~v~~~~~~~-~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn   86 (814)
T COG1201           8 LDPRVREWFKRK-FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKALN   86 (814)
T ss_pred             cCHHHHHHHHHh-cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHH
Confidence            678888888877 9999999999999999999999999999999999999999999887533334567899999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC--CCCCccEEEecchhHHhhCC
Q 010709          208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT--SLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       208 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--~l~~~~~vViDEaH~l~~~~  285 (503)
                      +.+.+.+..++... ++.+...+|++...+..+...+.+||+++||+.|.-++....+  .+.++++|||||.|.+.+..
T Consensus        87 ~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~sK  165 (814)
T COG1201          87 NDIRRRLEEPLREL-GIEVAVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAESK  165 (814)
T ss_pred             HHHHHHHHHHHHHc-CCccceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhccc
Confidence            99999999999876 6888999999999888888889999999999999777765433  58899999999999998776


Q ss_pred             CHHHHHHHHHh---CCCCCcEEEEEeeCCHHHHHHHHHhcCC--CeEEEeCCCCCCCCceEEEEEEcC--h-hhHHHHHH
Q 010709          286 FEPQIREVMQN---LPDKHQTLLFSATMPVEIEALAQEYLTD--PVQVKVGKVSSPTANVIQILEKVS--E-NEKVDRLL  357 (503)
Q Consensus       286 ~~~~~~~il~~---~~~~~q~i~~SAT~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~--~-~~k~~~l~  357 (503)
                      .+.++.--+.+   +.++.|.|++|||..+ ....++...+.  +..+.... ......+........  . ..-...++
T Consensus       166 RG~~Lsl~LeRL~~l~~~~qRIGLSATV~~-~~~varfL~g~~~~~~Iv~~~-~~k~~~i~v~~p~~~~~~~~~~~~~~~  243 (814)
T COG1201         166 RGVQLALSLERLRELAGDFQRIGLSATVGP-PEEVAKFLVGFGDPCEIVDVS-AAKKLEIKVISPVEDLIYDEELWAALY  243 (814)
T ss_pred             cchhhhhhHHHHHhhCcccEEEeehhccCC-HHHHHHHhcCCCCceEEEEcc-cCCcceEEEEecCCccccccchhHHHH
Confidence            55555433332   3338999999999963 33344444433  33432221 111111111111111  0 11112233


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC-CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccccc
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG-LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR  436 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~-~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~  436 (503)
                      ..+.+....       ...+|||+|++..++.++..|++.+ ..+..+||.++.++|..+.+.|++|+.+++|||..++-
T Consensus       244 ~~i~~~v~~-------~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgSlSre~R~~vE~~lk~G~lravV~TSSLEL  316 (814)
T COG1201         244 ERIAELVKK-------HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSLEL  316 (814)
T ss_pred             HHHHHHHhh-------cCcEEEEEeChHHHHHHHHHHHHhcCCceeeecccccHHHHHHHHHHHhcCCceEEEEccchhh
Confidence            333222211       1249999999999999999999886 89999999999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhHHHHhhCcceeeeee-----------------------ccCchhhhhhHHHHHHHHHHHH
Q 010709          437 GLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITT-----------------------NLDGDMKKLEFCLILAITVLLF  493 (503)
Q Consensus       437 Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~~-----------------------~~~~~~~~~~~~~~~~~~~~~~  493 (503)
                      |||+.+++.||+++.|+++..+.||+||+|+.+..                       ..++.+..++......|.++|+
T Consensus       317 GIDiG~vdlVIq~~SP~sV~r~lQRiGRsgHr~~~~Skg~ii~~~r~dllE~~vi~~~a~~g~le~~~i~~~~LDVLaq~  396 (814)
T COG1201         317 GIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGIIIAEDRDDLLECLVLADLALEGKLERIKIPKNPLDVLAQQ  396 (814)
T ss_pred             ccccCCceEEEEeCCcHHHHHHhHhccccccccCCcccEEEEecCHHHHHHHHHHHHHHHhCCcccCCCCCcchhHHHHH
Confidence            99999999999999999999999999999985421                       1124444555667788888888


Q ss_pred             HHHHhh
Q 010709          494 VIFLSI  499 (503)
Q Consensus       494 ~~~~~~  499 (503)
                      +.||-+
T Consensus       397 ivg~~~  402 (814)
T COG1201         397 IVGMAL  402 (814)
T ss_pred             HHHHHh
Confidence            888754

>PRK00254 ski2-like helicase; Provisional

Probab=100.00  E-value=2.5e-44  Score=382.92  Aligned_cols=325  Identities=20%  Similarity=0.273  Sum_probs=248.8

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH-HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~-i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .|+++++++.+.+.++..|+..|+++|.++++. +++|+|+++++|||+|||++|.+|++..+...       ++++||+
T Consensus         2 ~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~~-------~~~~l~l   74 (720)
T PRK00254          2 KVDELRVDERIKRVLKERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLRE-------GGKAVYL   74 (720)
T ss_pred             cHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHhc-------CCeEEEE
Confidence            477889999999999999999999999999986 78999999999999999999999999887643       5789999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++|+.|+++.++.+.. . ++++..++|+......   ....++|+|+||+++..++.+....++++++||+||+|.
T Consensus        75 ~P~~aLa~q~~~~~~~~~~-~-g~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~~~~~l~~l~lvViDE~H~  149 (720)
T PRK00254         75 VPLKALAEEKYREFKDWEK-L-GLRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVVADEIHL  149 (720)
T ss_pred             eChHHHHHHHHHHHHHHhh-c-CCEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhCCchhhhcCCEEEEcCcCc
Confidence            9999999999999988643 3 5788888888765432   225689999999999888876666788999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCC-ce-EEEEEEcChh--hHH-HH
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTA-NV-IQILEKVSEN--EKV-DR  355 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~--~k~-~~  355 (503)
                      +.+.+++..+..++.++....|+|++|||+++ ..++.. |+...... ......+.. .+ .+........  .+. ..
T Consensus       150 l~~~~rg~~le~il~~l~~~~qiI~lSATl~n-~~~la~-wl~~~~~~-~~~rpv~l~~~~~~~~~~~~~~~~~~~~~~~  226 (720)
T PRK00254        150 IGSYDRGATLEMILTHMLGRAQILGLSATVGN-AEELAE-WLNAELVV-SDWRPVKLRKGVFYQGFLFWEDGKIERFPNS  226 (720)
T ss_pred             cCCccchHHHHHHHHhcCcCCcEEEEEccCCC-HHHHHH-HhCCcccc-CCCCCCcceeeEecCCeeeccCcchhcchHH
Confidence            98888999999999999889999999999975 344443 55432211 111110100 00 0111111111  110 11


Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC---------------------------------CCeEE
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE---------------------------------GLHAV  402 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~---------------------------------~~~v~  402 (503)
                      ....+.+...       ..+++||||++++.|+.++..|...                                 ...+.
T Consensus       227 ~~~~~~~~i~-------~~~~vLVF~~sr~~~~~~a~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~  299 (720)
T PRK00254        227 WESLVYDAVK-------KGKGALVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLKKALRGGVA  299 (720)
T ss_pred             HHHHHHHHHH-------hCCCEEEEEcChHHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHhcCCCcHHHHHHHhhCEE
Confidence            1112211111       2346999999999998877666321                                 23589


Q ss_pred             EEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE-------ccCCC-ChhHHHHhhCcceee
Q 010709          403 ALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN-------LDLPK-VLLAASESLCTTSFN  468 (503)
Q Consensus       403 ~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~-------~~~p~-s~~~~~Qr~GR~gR~  468 (503)
                      ++|++|++++|..+++.|++|.++|||||+++++|+|+|++++||.       ++.|. ...+|.||+|||||.
T Consensus       300 ~hHagl~~~eR~~ve~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~~~~~~~~~~~~~Qm~GRAGR~  373 (720)
T PRK00254        300 FHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFGWEDIPVLEIQQMMGRAGRP  373 (720)
T ss_pred             EeCCCCCHHHHHHHHHHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCCCCceeCCHHHHHHhhhccCCC
Confidence            9999999999999999999999999999999999999999999994       55544 567999999999994

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

Probab=100.00  E-value=1.5e-43  Score=365.89  Aligned_cols=305  Identities=17%  Similarity=0.193  Sum_probs=239.1

Q ss_pred             CCCCCCcHHHHHHHHHHhcCC-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCC-eEEEEcccHHHHHHHHHHHHH
Q 010709          139 HEYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGP-LALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~-~~lil~Ptr~La~q~~~~~~~  216 (503)
                      .||. |+|||.++++.++.|+ ++++.+|||+|||.++.++++.. ..     ....+ ++++++|||+||.|+++.+.+
T Consensus        12 ~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~-----~~~~~~rLv~~vPtReLa~Qi~~~~~~   84 (844)
T TIGR02621        12 HGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EI-----GAKVPRRLVYVVNRRTVVDQVTEEAEK   84 (844)
T ss_pred             hCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cc-----cccccceEEEeCchHHHHHHHHHHHHH
Confidence            4787 9999999999999998 58888999999998765444422 11     11234 455577999999999999999


Q ss_pred             HhccCC----------------------CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC---------
Q 010709          217 LSRSLD----------------------SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT---------  265 (503)
Q Consensus       217 ~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~---------  265 (503)
                      +++.+.                      .+++..++||.....+...+..+++|+|+|++.+    .+..+         
T Consensus        85 ~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D~i----~sr~L~~gYg~~~~  160 (844)
T TIGR02621        85 IGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVDMI----GSRLLFSGYGCGFK  160 (844)
T ss_pred             HHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHHHH----cCCccccccccccc
Confidence            987552                      3888999999999999999999999999996444    33332         


Q ss_pred             -------CCCCccEEEecchhHHhhCCCHHHHHHHHHhC--CC---CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCC
Q 010709          266 -------SLSRVSFVILDEADRMLDMGFEPQIREVMQNL--PD---KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKV  333 (503)
Q Consensus       266 -------~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~--~~---~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~  333 (503)
                             .+.+++++|+||||  ++++|...+.+|++.+  ++   ++|+++||||++.++......++.++..+.+...
T Consensus       161 ~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~p~ei~~l~~~~~~~p~~i~V~~~  238 (844)
T TIGR02621       161 SRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATSRTDGPDRTTLLSAEDYKHPVLKK  238 (844)
T ss_pred             cccchhhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCCCccHHHHHHHHccCCceeecccc
Confidence                   26889999999999  5789999999999964  33   2699999999999888888888877766655443


Q ss_pred             CCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHH
Q 010709          334 SSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR  413 (503)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r  413 (503)
                      ......+.+. ..++...|...++..+.....      ...+++||||++++.|+.+++.|.+.++  ..+||+|++.+|
T Consensus       239 ~l~a~ki~q~-v~v~~e~Kl~~lv~~L~~ll~------e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~q~dR  309 (844)
T TIGR02621       239 RLAAKKIVKL-VPPSDEKFLSTMVKELNLLMK------DSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLRGAER  309 (844)
T ss_pred             cccccceEEE-EecChHHHHHHHHHHHHHHHh------hCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCCHHHH
Confidence            3333444443 334444455554444332221      1345799999999999999999998877  899999999999


Q ss_pred             H-----HHHHHHhc----CC-------CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          414 E-----SALRDFRN----GS-------TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       414 ~-----~~~~~f~~----g~-------~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .     ++++.|+.    |+       ..|||||+++++||||+. ++||++..|  .++|+||+||+||.
T Consensus       310 ~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATdVaerGLDId~-d~VI~d~aP--~esyIQRiGRtgR~  377 (844)
T TIGR02621       310 DDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTSAGEVGVNISA-DHLVCDLAP--FESMQQRFGRVNRF  377 (844)
T ss_pred             hhHHHHHHHHHHhccccccccccccccceEEeccchhhhcccCCc-ceEEECCCC--HHHHHHHhcccCCC
Confidence            9     78999987    44       689999999999999996 899987776  68999999999995

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.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=100.00  E-value=3.7e-42  Score=366.03  Aligned_cols=339  Identities=18%  Similarity=0.186  Sum_probs=254.7

Q ss_pred             CCHHHHHHHH-HCCCCCCcHHHHHHHHHHhcC------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          128 LHPSIMKDIE-FHEYTRPTSIQAQAMPVALSG------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       128 l~~~l~~~l~-~~~~~~~~~~Q~~~i~~i~~~------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .+..+.+.+. .++| .||++|.++|+.++++      .|++++|+||+|||.+|++|++..+..        +++++|+
T Consensus       436 ~~~~~~~~~~~~~~f-~~T~~Q~~aI~~I~~d~~~~~~~d~Ll~adTGsGKT~val~a~l~al~~--------g~qvlvL  506 (926)
T TIGR00580       436 PDLEWQQEFEDSFPF-EETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD--------GKQVAVL  506 (926)
T ss_pred             CCHHHHHHHHHhCCC-CCCHHHHHHHHHHHhhhcccCcCCEEEECCCCccHHHHHHHHHHHHHHh--------CCeEEEE
Confidence            3345555554 4677 5999999999999874      689999999999999999999877644        5789999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHH---Hhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEec
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS---ELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD  276 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViD  276 (503)
                      +||++||.|+++.+++++... ++++..+.++....+...   .+. +.++|+|+||..+     ...+.+.++++||||
T Consensus       507 vPT~~LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll-----~~~v~f~~L~llVID  580 (926)
T TIGR00580       507 VPTTLLAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLL-----QKDVKFKDLGLLIID  580 (926)
T ss_pred             eCcHHHHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHh-----hCCCCcccCCEEEee
Confidence            999999999999999988765 478888888776544332   233 3589999999433     335678999999999


Q ss_pred             chhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHH
Q 010709          277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRL  356 (503)
Q Consensus       277 EaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l  356 (503)
                      |+|++     +......+..+++..++++||||+.+....+......++..+......  ...+...+.....    ..+
T Consensus       581 Eahrf-----gv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~~--R~~V~t~v~~~~~----~~i  649 (926)
T TIGR00580       581 EEQRF-----GVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED--RLPVRTFVMEYDP----ELV  649 (926)
T ss_pred             ccccc-----chhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCCC--ccceEEEEEecCH----HHH
Confidence            99984     334566677777889999999998776655555556666665543222  2234443332221    111


Q ss_pred             HHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccc
Q 010709          357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA  434 (503)
Q Consensus       357 ~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~  434 (503)
                      ...+....       ...++++|||++++.++.+++.|++.  ++++..+||+|++.+|.+++++|++|+.+|||||+++
T Consensus       650 ~~~i~~el-------~~g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~ii  722 (926)
T TIGR00580       650 REAIRREL-------LRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTII  722 (926)
T ss_pred             HHHHHHHH-------HcCCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECChh
Confidence            22222221       12357999999999999999999985  7899999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee-------eee-cc----Cchhhh---hhHHHHHHHHHHHHHHHHh
Q 010709          435 SRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN-------ITT-NL----DGDMKK---LEFCLILAITVLLFVIFLS  498 (503)
Q Consensus       435 ~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~-------~~~-~~----~~~~~~---~~~~~~~~~~~~~~~~~~~  498 (503)
                      ++|||+|++++||+++.|. ...+|.||+||+||.       ++. ..    +...++   +.....+.+.+.+++..|-
T Consensus       723 e~GIDIp~v~~VIi~~a~~~gls~l~Qr~GRvGR~g~~g~aill~~~~~~l~~~~~~RL~~~~~~~~~g~gf~ia~~Dl~  802 (926)
T TIGR00580       723 ETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLE  802 (926)
T ss_pred             hcccccccCCEEEEecCCCCCHHHHHHHhcCCCCCCCCeEEEEEECCcccCCHHHHHHHHHHHHhhcchhhHHHHHHHHH
Confidence            9999999999999999976 678999999999993       122 11    233344   4444455568888888876


Q ss_pred             h
Q 010709          499 I  499 (503)
Q Consensus       499 ~  499 (503)
                      |
T Consensus       803 ~  803 (926)
T TIGR00580       803 I  803 (926)
T ss_pred             h
Confidence            5

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.

>PRK10689 transcription-repair coupling factor; Provisional

Probab=100.00  E-value=1.8e-41  Score=368.40  Aligned_cols=337  Identities=18%  Similarity=0.158  Sum_probs=255.3

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHHHHhcC------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          130 PSIMKDIEFHEYTRPTSIQAQAMPVALSG------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       130 ~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      .+..+....+.| .||+.|.++|+.++.+      .|++++|+||+|||.+|+.+++..+.        .+++++|++||
T Consensus       588 ~~~~~~~~~~~~-~~T~~Q~~aI~~il~d~~~~~~~d~Ll~a~TGsGKT~val~aa~~~~~--------~g~qvlvLvPT  658 (1147)
T PRK10689        588 EQYQLFCDSFPF-ETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVE--------NHKQVAVLVPT  658 (1147)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHHhhcCCCCCEEEEcCCCcCHHHHHHHHHHHHHH--------cCCeEEEEeCc
Confidence            344455566777 7999999999999976      79999999999999999888776543        26789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh----CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          204 RELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR----GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       204 r~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++||.|+++.+++.+... ++++.++.++....++...+.    +.++|+|+||+.+.     ..+.+.++++|||||+|
T Consensus       659 ~eLA~Q~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~-----~~v~~~~L~lLVIDEah  732 (1147)
T PRK10689        659 TLLAQQHYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQ-----SDVKWKDLGLLIVDEEH  732 (1147)
T ss_pred             HHHHHHHHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHh-----CCCCHhhCCEEEEechh
Confidence            999999999999877554 477888888877766554432    46899999997442     34567899999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLAL  359 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~  359 (503)
                      ++.   +.  ....++.++++.|+++||||+.+....+....+.++..+......  ...+...+...........+...
T Consensus       733 rfG---~~--~~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~--r~~v~~~~~~~~~~~~k~~il~e  805 (1147)
T PRK10689        733 RFG---VR--HKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR--RLAVKTFVREYDSLVVREAILRE  805 (1147)
T ss_pred             hcc---hh--HHHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC--CCCceEEEEecCcHHHHHHHHHH
Confidence            962   22  345567788899999999999888777777788888777543322  22333333332221111111111


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      +           ...++++|||++++.++.+++.|.+.  +.++..+||+|++.+|.+++..|++|+.+|||||+++++|
T Consensus       806 l-----------~r~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTdIierG  874 (1147)
T PRK10689        806 I-----------LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETG  874 (1147)
T ss_pred             H-----------hcCCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECchhhcc
Confidence            1           12356999999999999999999987  7899999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCC-CChhHHHHhhCcceee-------eeecc-----CchhhhhhHHHHHHH---HHHHHHHHHhh
Q 010709          438 LDVMGVAHVVNLDLP-KVLLAASESLCTTSFN-------ITTNL-----DGDMKKLEFCLILAI---TVLLFVIFLSI  499 (503)
Q Consensus       438 ldip~v~~VI~~~~p-~s~~~~~Qr~GR~gR~-------~~~~~-----~~~~~~~~~~~~~~~---~~~~~~~~~~~  499 (503)
                      ||+|++++||..+.. .+..+|.||+||+||.       ++++.     +....++.....+.+   .+.++|..|.|
T Consensus       875 IDIP~v~~VIi~~ad~fglaq~~Qr~GRvGR~g~~g~a~ll~~~~~~~~~~~~~rl~~~~~~~~lg~gf~~a~~dl~~  952 (1147)
T PRK10689        875 IDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEI  952 (1147)
T ss_pred             cccccCCEEEEecCCCCCHHHHHHHhhccCCCCCceEEEEEeCCCcccCHHHHHHHHHHHHhcCCcchHHHHHHHHHh
Confidence            999999999954432 2456799999999994       33322     133445554444444   88999988865

>PRK01172 ski2-like helicase; Provisional

Probab=100.00  E-value=1.9e-42  Score=367.03  Aligned_cols=319  Identities=18%  Similarity=0.228  Sum_probs=240.3

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|+++++++.+.+.+...++. ++++|.++++.+.+|+++++++|||+|||+++.++++..+..        ++++||++
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~--------~~k~v~i~   72 (674)
T PRK01172          2 KISDLGYDDEFLNLFTGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA--------GLKSIYIV   72 (674)
T ss_pred             cHhhcCCCHHHHHHHhhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh--------CCcEEEEe
Confidence            467889999999999999987 999999999999999999999999999999999998877643        46799999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                      |+++||.|+++.++++.. . +..+...+|+......   ....++|+|+||+++..++.+....+.++++||+||+|++
T Consensus        73 P~raLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~~~~l~~v~lvViDEaH~l  147 (674)
T PRK01172         73 PLRSLAMEKYEELSRLRS-L-GMRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHDPYIINDVGLIVADEIHII  147 (674)
T ss_pred             chHHHHHHHHHHHHHHhh-c-CCeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCChhHHhhcCEEEEecchhc
Confidence            999999999999988653 2 4777778877654322   2245899999999998888776666889999999999999


Q ss_pred             hhCCCHHHHHHHHHh---CCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEE-----EcChhhH-
Q 010709          282 LDMGFEPQIREVMQN---LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILE-----KVSENEK-  352 (503)
Q Consensus       282 ~~~~~~~~~~~il~~---~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~k-  352 (503)
                      .+.+++..++.++..   ++++.|+|++|||+++ ..++.+ |+.... +......   ..+...+.     ......+ 
T Consensus       148 ~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n-~~~la~-wl~~~~-~~~~~r~---vpl~~~i~~~~~~~~~~~~~~  221 (674)
T PRK01172        148 GDEDRGPTLETVLSSARYVNPDARILALSATVSN-ANELAQ-WLNASL-IKSNFRP---VPLKLGILYRKRLILDGYERS  221 (674)
T ss_pred             cCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCC-HHHHHH-HhCCCc-cCCCCCC---CCeEEEEEecCeeeecccccc
Confidence            887788777777554   4578899999999975 344443 443221 1111111   11111000     0111111 


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-------------------------CCeEEEEcCC
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-------------------------GLHAVALHGG  407 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-------------------------~~~v~~lh~~  407 (503)
                      ...+...+.+..       ...+++||||++++.|+.+++.|...                         ...+..+||+
T Consensus       222 ~~~~~~~i~~~~-------~~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hag  294 (674)
T PRK01172        222 QVDINSLIKETV-------NDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAG  294 (674)
T ss_pred             cccHHHHHHHHH-------hCCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCC
Confidence            111222222211       23457999999999999999988653                         1247889999


Q ss_pred             CCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC---------CCChhHHHHhhCcceee
Q 010709          408 RNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL---------PKVLLAASESLCTTSFN  468 (503)
Q Consensus       408 ~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~---------p~s~~~~~Qr~GR~gR~  468 (503)
                      +++++|..+++.|++|.++|||||+++++|+|+|+. .||..|.         |-+..+|.||+|||||.
T Consensus       295 l~~~eR~~ve~~f~~g~i~VLvaT~~la~Gvnipa~-~VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~  363 (674)
T PRK01172        295 LSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPAR-LVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRP  363 (674)
T ss_pred             CCHHHHHHHHHHHHcCCCeEEEecchhhccCCCcce-EEEEcCceEeCCCCceeCCHHHHHHHhhcCCCC
Confidence            999999999999999999999999999999999975 5555553         45788999999999995

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

Probab=100.00  E-value=3.7e-42  Score=341.56  Aligned_cols=301  Identities=22%  Similarity=0.316  Sum_probs=236.9

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .+|+..+++-|.++|..+++|+|+++.+|||.||++||++|++..           .+.+|||.|..+|...+.+.++..
T Consensus        12 ~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~-----------~G~TLVVSPLiSLM~DQV~~l~~~   80 (590)
T COG0514          12 VFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLL-----------EGLTLVVSPLISLMKDQVDQLEAA   80 (590)
T ss_pred             HhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhc-----------CCCEEEECchHHHHHHHHHHHHHc
Confidence            468999999999999999999999999999999999999999875           346899999999998888888776


Q ss_pred             hccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC--CHHHHH
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEPQIR  291 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~--~~~~~~  291 (503)
                      +     +.+..+.+..+..+.....    ....++++.+|++|..-.....+....+.++||||||++.+||  |++.+.
T Consensus        81 G-----i~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~~~L~~~~i~l~vIDEAHCiSqWGhdFRP~Y~  155 (590)
T COG0514          81 G-----IRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLELLKRLPISLVAIDEAHCISQWGHDFRPDYR  155 (590)
T ss_pred             C-----ceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHHHHHHhCCCceEEechHHHHhhcCCccCHhHH
Confidence            4     6677776665555443322    2458999999999954333323345678999999999999997  999988


Q ss_pred             HHHH---hCCCCCcEEEEEeeCCHHHHHHHHHhcCCCe-EEEeCCCCCCCCceEEEEEEcC-hhhHHHHHHHHHHHHHHh
Q 010709          292 EVMQ---NLPDKHQTLLFSATMPVEIEALAQEYLTDPV-QVKVGKVSSPTANVIQILEKVS-ENEKVDRLLALLVEEAFL  366 (503)
Q Consensus       292 ~il~---~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~-~~~k~~~l~~~l~~~~~~  366 (503)
                      ++-.   .++ +..++++|||.++.+...+...+.--. .+.....  ..+++...+.... ...+..    ++.+    
T Consensus       156 ~lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sf--dRpNi~~~v~~~~~~~~q~~----fi~~----  224 (590)
T COG0514         156 RLGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRGSF--DRPNLALKVVEKGEPSDQLA----FLAT----  224 (590)
T ss_pred             HHHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecC--CCchhhhhhhhcccHHHHHH----HHHh----
Confidence            7744   344 677999999999998887776654221 2222222  2223222222211 122222    2222    


Q ss_pred             hhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEE
Q 010709          367 AEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHV  446 (503)
Q Consensus       367 ~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~V  446 (503)
                        ......+..||||.|++.++.+++.|...|+.+..||+||+.++|..+.+.|..++.+|+|||.++++|||.|+|++|
T Consensus       225 --~~~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdVRfV  302 (590)
T COG0514         225 --VLPQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFV  302 (590)
T ss_pred             --hccccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCceEE
Confidence              111344568999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEccCCCChhHHHHhhCccee
Q 010709          447 VNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       447 I~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      ||||+|.++++|.|.+|||||
T Consensus       303 iH~~lP~s~EsYyQE~GRAGR  323 (590)
T COG0514         303 IHYDLPGSIESYYQETGRAGR  323 (590)
T ss_pred             EEecCCCCHHHHHHHHhhccC
Confidence            999999999999999999999

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=100.00  E-value=2e-41  Score=356.91  Aligned_cols=294  Identities=19%  Similarity=0.224  Sum_probs=224.6

Q ss_pred             HHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEE
Q 010709          148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA  227 (503)
Q Consensus       148 Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~  227 (503)
                      -.+.+..+.+++++|++|+||||||++|.++++....        .+++++|++|||++|.|+++++.+......+..++
T Consensus         7 ~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~--------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VG   78 (819)
T TIGR01970         7 LPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG--------IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTVG   78 (819)
T ss_pred             HHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc--------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEE
Confidence            3456666778889999999999999999999887642        24689999999999999999986544322234455


Q ss_pred             EEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh-HHhhCCCHHHH-HHHHHhCCCCCcEEE
Q 010709          228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD-RMLDMGFEPQI-REVMQNLPDKHQTLL  305 (503)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH-~l~~~~~~~~~-~~il~~~~~~~q~i~  305 (503)
                      ....+..      ....+++|+|+|+|+|++++.+ ...+.++++|||||+| ++++.++...+ ..+...++++.|+|+
T Consensus        79 y~vr~~~------~~s~~t~I~v~T~G~Llr~l~~-d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIl  151 (819)
T TIGR01970        79 YRVRGEN------KVSRRTRLEVVTEGILTRMIQD-DPELDGVGALIFDEFHERSLDADLGLALALDVQSSLREDLKILA  151 (819)
T ss_pred             EEEcccc------ccCCCCcEEEECCcHHHHHHhh-CcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCCCceEEE
Confidence            4444432      2345689999999999999876 5679999999999999 57776665443 456666788999999


Q ss_pred             EEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH-HHHHHHHHhhhccCCCCCcEEEEEcch
Q 010709          306 FSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL-ALLVEEAFLAEKSCHPFPLTIVFVERK  384 (503)
Q Consensus       306 ~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~-~~l~~~~~~~~~~~~~~~~~lIF~~~~  384 (503)
                      ||||++...   ...|+.++..+......   ..+.+.+.......+..... ..+.... .     ...+.+||||+++
T Consensus       152 mSATl~~~~---l~~~l~~~~vI~~~gr~---~pVe~~y~~~~~~~~~~~~v~~~l~~~l-~-----~~~g~iLVFlpg~  219 (819)
T TIGR01970       152 MSATLDGER---LSSLLPDAPVVESEGRS---FPVEIRYLPLRGDQRLEDAVSRAVEHAL-A-----SETGSILVFLPGQ  219 (819)
T ss_pred             EeCCCCHHH---HHHHcCCCcEEEecCcc---eeeeeEEeecchhhhHHHHHHHHHHHHH-H-----hcCCcEEEEECCH
Confidence            999998653   45677766555544332   23455555444443332211 1221111 1     1246799999999


Q ss_pred             hhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCC-------
Q 010709          385 TRCDEVSEALVA---EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKV-------  454 (503)
Q Consensus       385 ~~~~~l~~~L~~---~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s-------  454 (503)
                      ++++.+++.|.+   .++.+.++||++++++|.++++.|++|+.+|||||+++++|||||+|++|||+|+|+.       
T Consensus       220 ~eI~~l~~~L~~~~~~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~  299 (819)
T TIGR01970       220 AEIRRVQEQLAERLDSDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKT  299 (819)
T ss_pred             HHHHHHHHHHHhhcCCCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecchHhhcccccCceEEEEcCccccccccccc
Confidence            999999999987   4789999999999999999999999999999999999999999999999999999863       


Q ss_pred             -----------hhHHHHhhCcceee
Q 010709          455 -----------LLAASESLCTTSFN  468 (503)
Q Consensus       455 -----------~~~~~Qr~GR~gR~  468 (503)
                                 .++|.||.|||||.
T Consensus       300 g~~~L~~~~iSkasa~QR~GRAGR~  324 (819)
T TIGR01970       300 GITRLETVRISQASATQRAGRAGRL  324 (819)
T ss_pred             CCceeeEEEECHHHHHhhhhhcCCC
Confidence                       35799999999995

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=100.00  E-value=3.3e-41  Score=367.78  Aligned_cols=299  Identities=18%  Similarity=0.226  Sum_probs=221.6

Q ss_pred             EEccCCCchhHHhHHHHHHHHHhcCCC-----CCCCCCeEEEEcccHHHHHHHHHHHHHHhc-----------cCCCceE
Q 010709          163 GCAETGSGKTAAFTIPMIQHCVAQTPV-----GRGDGPLALVLAPTRELAQQIEKEVKALSR-----------SLDSFKT  226 (503)
Q Consensus       163 i~~~TGsGKTl~~~lp~l~~~~~~~~~-----~~~~~~~~lil~Ptr~La~q~~~~~~~~~~-----------~~~~~~~  226 (503)
                      |++|||||||++|.+|++..+......     ...++.++|||+|+++|++|+.+.++....           ...++++
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            579999999999999999998865321     113468899999999999999998875221           1125889


Q ss_pred             EEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecchhHHhhCCCH----HHHHHHHHhCCCCC
Q 010709          227 AIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDEADRMLDMGFE----PQIREVMQNLPDKH  301 (503)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDEaH~l~~~~~~----~~~~~il~~~~~~~  301 (503)
                      ..++|++...+..+.+.+.++|+|+||++|..++.+. ...++++++|||||+|.+.+..++    ..+.++...++.+.
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~  160 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSA  160 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCC
Confidence            9999999988877777788999999999998887643 346899999999999999876444    44556656667789


Q ss_pred             cEEEEEeeCCHHHHHHHHHhcC--CCeEEEeCCCCCCCCceEEEEEEcChhhH----------------HHHHHHHHHHH
Q 010709          302 QTLLFSATMPVEIEALAQEYLT--DPVQVKVGKVSSPTANVIQILEKVSENEK----------------VDRLLALLVEE  363 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~k----------------~~~l~~~l~~~  363 (503)
                      |+|++|||+++ .+++++ |+.  .++.+. .........+.. +.......+                ...++..+...
T Consensus       161 QrIgLSATI~n-~eevA~-~L~g~~pv~Iv-~~~~~r~~~l~v-~vp~~d~~~~~~~~~~~~~~~~~~r~~~i~~~v~~~  236 (1490)
T PRK09751        161 QRIGLSATVRS-ASDVAA-FLGGDRPVTVV-NPPAMRHPQIRI-VVPVANMDDVSSVASGTGEDSHAGREGSIWPYIETG  236 (1490)
T ss_pred             eEEEEEeeCCC-HHHHHH-HhcCCCCEEEE-CCCCCcccceEE-EEecCchhhccccccccccccchhhhhhhhHHHHHH
Confidence            99999999976 455554 543  355543 222222222222 122111110                11111111111


Q ss_pred             HHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC---------------------------------CeEEEEcCCCCH
Q 010709          364 AFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG---------------------------------LHAVALHGGRNQ  410 (503)
Q Consensus       364 ~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~---------------------------------~~v~~lh~~~~~  410 (503)
                      .....   ....++|||||++..|+.++..|++..                                 ..+..+||++++
T Consensus       237 il~~i---~~~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSk  313 (1490)
T PRK09751        237 ILDEV---LRHRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSK  313 (1490)
T ss_pred             HHHHH---hcCCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCH
Confidence            11100   123469999999999999999997641                                 125689999999


Q ss_pred             HHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          411 SDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       411 ~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++|..+++.|++|++++||||+.+++||||+++++||+++.|.++.+|+||+||+||.
T Consensus       314 eeR~~IE~~fK~G~LrvLVATssLELGIDIg~VDlVIq~gsP~sVas~LQRiGRAGR~  371 (1490)
T PRK09751        314 EQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAGHQ  371 (1490)
T ss_pred             HHHHHHHHHHHhCCceEEEeCcHHHccCCcccCCEEEEeCCCCCHHHHHHHhCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999995

>PHA02653 RNA helicase NPH-II; Provisional

Probab=100.00  E-value=1.1e-40  Score=343.33  Aligned_cols=301  Identities=15%  Similarity=0.139  Sum_probs=217.8

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHHh---------HHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAF---------TIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK  215 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~---------~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~  215 (503)
                      ..+|.++++.+++|+++|++|+||+|||++.         +.|.+..+....  ....++++++++|||+||.|+...+.
T Consensus       166 ~~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~--~~~~~~~ilvt~PrreLa~qi~~~i~  243 (675)
T PHA02653        166 PDVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKID--PNFIERPIVLSLPRVALVRLHSITLL  243 (675)
T ss_pred             HHHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhcc--cccCCcEEEEECcHHHHHHHHHHHHH
Confidence            3569999999999999999999999999862         222222221100  02235689999999999999999987


Q ss_pred             HHhcc--CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHH
Q 010709          216 ALSRS--LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREV  293 (503)
Q Consensus       216 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~i  293 (503)
                      +....  ..+..+.+.+|+.... .........+|+|+|++..       ...+.++++|||||||++...+  ..+..+
T Consensus       244 ~~vg~~~~~g~~v~v~~Gg~~~~-~~~t~~k~~~Ilv~T~~L~-------l~~L~~v~~VVIDEaHEr~~~~--DllL~l  313 (675)
T PHA02653        244 KSLGFDEIDGSPISLKYGSIPDE-LINTNPKPYGLVFSTHKLT-------LNKLFDYGTVIIDEVHEHDQIG--DIIIAV  313 (675)
T ss_pred             HHhCccccCCceEEEEECCcchH-HhhcccCCCCEEEEeCccc-------ccccccCCEEEccccccCccch--hHHHHH
Confidence            76533  2356788899998732 1122223579999997531       2357889999999999876553  445555


Q ss_pred             HHhCC-CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcCh---------hhHHHHHHHHHHHH
Q 010709          294 MQNLP-DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE---------NEKVDRLLALLVEE  363 (503)
Q Consensus       294 l~~~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~k~~~l~~~l~~~  363 (503)
                      ++... ...|+++||||++.+++.+ ..++.+|..+.+...  ....+.+.+.....         ......+...+...
T Consensus       314 lk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr--t~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~  390 (675)
T PHA02653        314 ARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG--TLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKY  390 (675)
T ss_pred             HHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC--cCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHh
Confidence            55443 3358999999999888776 678888888877532  23445555443221         01111122222111


Q ss_pred             HHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHH-hcCCCcEEEEccccccCCCC
Q 010709          364 AFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDF-RNGSTNILVATDVASRGLDV  440 (503)
Q Consensus       364 ~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f-~~g~~~vLvaT~~~~~Gldi  440 (503)
                      .      ....+.+||||+++.+|+.+++.|.+.  ++.+.++||++++.  .+.++.| ++|+.+|||||+++++||||
T Consensus       391 ~------~~~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Lsq~--eq~l~~ff~~gk~kILVATdIAERGIDI  462 (675)
T PHA02653        391 T------PPKGSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVPNI--DEILEKVYSSKNPSIIISTPYLESSVTI  462 (675)
T ss_pred             h------cccCCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcCHH--HHHHHHHhccCceeEEeccChhhccccc
Confidence            0      012357999999999999999999987  79999999999975  4666777 68999999999999999999


Q ss_pred             CCCCEEEEcc---CCC---------ChhHHHHhhCcceee
Q 010709          441 MGVAHVVNLD---LPK---------VLLAASESLCTTSFN  468 (503)
Q Consensus       441 p~v~~VI~~~---~p~---------s~~~~~Qr~GR~gR~  468 (503)
                      |+|++||++|   .|.         |.++|.||+||+||.
T Consensus       463 p~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~  502 (675)
T PHA02653        463 RNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV  502 (675)
T ss_pred             cCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC
Confidence            9999999999   565         778999999999995

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

Probab=100.00  E-value=2e-42  Score=298.86  Aligned_cols=301  Identities=31%  Similarity=0.478  Sum_probs=263.5

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|.++-|.|++++++...||..|..+|.++||....|-|+++.|..|.|||.+|.+.-++.+---     ...-.+|++|
T Consensus        43 gfrdfllkpellraivdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiepv-----~g~vsvlvmc  117 (387)
T KOG0329|consen   43 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPV-----DGQVSVLVMC  117 (387)
T ss_pred             chhhhhcCHHHHHHHHhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCCC-----CCeEEEEEEe
Confidence            48888899999999999999999999999999999999999999999999999988777664221     1235689999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                      +||+||-|+..+..++.+.++++++.+.+||.........+.+-++|+|+|||+++.+..+..+.+++++..|+|||+.|
T Consensus       118 htrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~k~l~lk~vkhFvlDEcdkm  197 (387)
T KOG0329|consen  118 HTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRNRSLNLKNVKHFVLDECDKM  197 (387)
T ss_pred             ccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHhccCchhhcceeehhhHHHH
Confidence            99999999999999999999999999999999988887888888999999999999999999999999999999999998


Q ss_pred             hhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCC-CCCCceEEEEEEcChhhHHHHHHHH
Q 010709          282 LDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRLLAL  359 (503)
Q Consensus       282 ~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~~l~~~  359 (503)
                      ++. +.+..+.++.+.-|...|++.+|||++++++...++|+.+|..+.++... .....+.|++...+..+|...+.++
T Consensus       198 le~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtLHGLqQ~YvkLke~eKNrkl~dL  277 (387)
T KOG0329|consen  198 LEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTLHGLQQYYVKLKENEKNRKLNDL  277 (387)
T ss_pred             HHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhhhhHHHHHHhhhhhhhhhhhhhh
Confidence            876 67888999999999999999999999999999999999999999887654 4455577888888888888888877


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCC
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLD  439 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gld  439 (503)
                      +...         .++.++||+.+...                     +         . |   ..+ +|||++++||+|
T Consensus       278 Ld~L---------eFNQVvIFvKsv~R---------------------l---------~-f---~kr-~vat~lfgrgmd  313 (387)
T KOG0329|consen  278 LDVL---------EFNQVVIFVKSVQR---------------------L---------S-F---QKR-LVATDLFGRGMD  313 (387)
T ss_pred             hhhh---------hhcceeEeeehhhh---------------------h---------h-h---hhh-hHHhhhhccccC
Confidence            7543         33469999987654                     0         0 3   223 899999999999


Q ss_pred             CCCCCEEEEccCCCChhHHHHhhCcceeeeee
Q 010709          440 VMGVAHVVNLDLPKVLLAASESLCTTSFNITT  471 (503)
Q Consensus       440 ip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~~  471 (503)
                      |..++.|+|||+|.+...|.||+|||||.-+.
T Consensus       314 iervNi~~NYdmp~~~DtYlHrv~rAgrfGtk  345 (387)
T KOG0329|consen  314 IERVNIVFNYDMPEDSDTYLHRVARAGRFGTK  345 (387)
T ss_pred             cccceeeeccCCCCCchHHHHHhhhhhccccc
Confidence            99999999999999999999999999996433

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=100.00  E-value=1e-39  Score=343.44  Aligned_cols=335  Identities=20%  Similarity=0.239  Sum_probs=242.0

Q ss_pred             HHHHHH-HHCCCCCCcHHHHHHHHHHhcC------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          131 SIMKDI-EFHEYTRPTSIQAQAMPVALSG------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       131 ~l~~~l-~~~~~~~~~~~Q~~~i~~i~~~------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      .+.+.+ ...+| .||++|.++++.+..+      .+++++|+||||||++|++|++..+..        +.+++|++||
T Consensus       249 ~~~~~~~~~l~f-~lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~--------g~q~lilaPT  319 (681)
T PRK10917        249 ELLKKFLASLPF-ELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA--------GYQAALMAPT  319 (681)
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc--------CCeEEEEecc
Confidence            444444 44566 6999999999999876      379999999999999999999887543        6789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH---HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          204 RELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR---SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       204 r~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++||.|+++.+++++... ++++.+++|+....+..   ..+. +.++|+|+||+.+.+     ...+.++++|||||+|
T Consensus       320 ~~LA~Q~~~~l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~v~~~~l~lvVIDE~H  393 (681)
T PRK10917        320 EILAEQHYENLKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD-----DVEFHNLGLVIIDEQH  393 (681)
T ss_pred             HHHHHHHHHHHHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc-----cchhcccceEEEechh
Confidence            999999999999998765 58899999998854433   2333 359999999987743     3457889999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLAL  359 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~  359 (503)
                      ++..     ..+..+.......++++||||+.+....+..  +.+.....+.........+...+...   .+...++..
T Consensus       394 rfg~-----~qr~~l~~~~~~~~iL~~SATp~prtl~~~~--~g~~~~s~i~~~p~~r~~i~~~~~~~---~~~~~~~~~  463 (681)
T PRK10917        394 RFGV-----EQRLALREKGENPHVLVMTATPIPRTLAMTA--YGDLDVSVIDELPPGRKPITTVVIPD---SRRDEVYER  463 (681)
T ss_pred             hhhH-----HHHHHHHhcCCCCCEEEEeCCCCHHHHHHHH--cCCCceEEEecCCCCCCCcEEEEeCc---ccHHHHHHH
Confidence            8632     2333444445568899999998665443332  33222222222222222333333322   223344444


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchh--------hHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEE
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKT--------RCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILV  429 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~--------~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLv  429 (503)
                      +.....       ...+++|||+..+        .++.+++.|...  ++++..+||+|++.+|.++++.|++|+.+|||
T Consensus       464 i~~~~~-------~g~q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILV  536 (681)
T PRK10917        464 IREEIA-------KGRQAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILV  536 (681)
T ss_pred             HHHHHH-------cCCcEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEE
Confidence            444331       2346999999643        456677777765  57899999999999999999999999999999


Q ss_pred             EccccccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee-------eeec-c--CchhhhhhHHHHHHHHHHHHHHHH
Q 010709          430 ATDVASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN-------ITTN-L--DGDMKKLEFCLILAITVLLFVIFL  497 (503)
Q Consensus       430 aT~~~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~-------~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~  497 (503)
                      ||+++++|+|+|++++||+++.|+ ....+.||+||+||.       ++.. .  +...+++..+....|.+.+.-..|
T Consensus       537 aT~vie~GiDip~v~~VIi~~~~r~gls~lhQ~~GRvGR~g~~g~~ill~~~~~~~~~~~rl~~~~~~~dgf~iae~dl  615 (681)
T PRK10917        537 ATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDL  615 (681)
T ss_pred             ECcceeeCcccCCCcEEEEeCCCCCCHHHHHHHhhcccCCCCceEEEEEECCCCChhHHHHHHHHHHhcchHHHHHHhH
Confidence            999999999999999999999998 578888999999994       2221 1  145556666555555555555544

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=100.00  E-value=1.2e-40  Score=352.04  Aligned_cols=294  Identities=19%  Similarity=0.240  Sum_probs=223.8

Q ss_pred             HHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEE
Q 010709          148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA  227 (503)
Q Consensus       148 Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~  227 (503)
                      -.+.+..+.++++++++|+||||||++|.++++....        .+++++|++|||++|.|+++.+.+......+..++
T Consensus        10 ~~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~--------~~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VG   81 (812)
T PRK11664         10 LPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGG--------INGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVG   81 (812)
T ss_pred             HHHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCC--------cCCeEEEECChHHHHHHHHHHHHHHhCcccCceEE
Confidence            3456666778899999999999999999888886521        13579999999999999999986554332245666


Q ss_pred             EEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-HhhCCCH-HHHHHHHHhCCCCCcEEE
Q 010709          228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-MLDMGFE-PQIREVMQNLPDKHQTLL  305 (503)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-l~~~~~~-~~~~~il~~~~~~~q~i~  305 (503)
                      ...++...      ....++|+|+|||+|.+++.. ...+.++++|||||+|+ .++.++. ..+.+++..++++.|+|+
T Consensus        82 y~vr~~~~------~~~~t~I~v~T~G~Llr~l~~-d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlil  154 (812)
T PRK11664         82 YRMRAESK------VGPNTRLEVVTEGILTRMIQR-DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLI  154 (812)
T ss_pred             EEecCccc------cCCCCcEEEEChhHHHHHHhh-CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCccceEEE
Confidence            66655432      224578999999999998876 56799999999999996 4444432 234556677888999999


Q ss_pred             EEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH-HHHHHHHHhhhccCCCCCcEEEEEcch
Q 010709          306 FSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL-ALLVEEAFLAEKSCHPFPLTIVFVERK  384 (503)
Q Consensus       306 ~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~-~~l~~~~~~~~~~~~~~~~~lIF~~~~  384 (503)
                      ||||++..   ....|+.++..+......   ..+.+.+.......+..... ..+.... .     ...+.+||||+++
T Consensus       155 mSATl~~~---~l~~~~~~~~~I~~~gr~---~pV~~~y~~~~~~~~~~~~v~~~l~~~l-~-----~~~g~iLVFlpg~  222 (812)
T PRK11664        155 MSATLDND---RLQQLLPDAPVIVSEGRS---FPVERRYQPLPAHQRFDEAVARATAELL-R-----QESGSLLLFLPGV  222 (812)
T ss_pred             EecCCCHH---HHHHhcCCCCEEEecCcc---ccceEEeccCchhhhHHHHHHHHHHHHH-H-----hCCCCEEEEcCCH
Confidence            99999865   245677766555544322   23555555555444443221 1222111 1     1246799999999


Q ss_pred             hhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCC-------
Q 010709          385 TRCDEVSEALVA---EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKV-------  454 (503)
Q Consensus       385 ~~~~~l~~~L~~---~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s-------  454 (503)
                      ++++.+++.|..   .++.+..+||++++++|.++++.|++|+.+|||||+++++|||||+|++|||+|+++.       
T Consensus       223 ~ei~~l~~~L~~~~~~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~  302 (812)
T PRK11664        223 GEIQRVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKT  302 (812)
T ss_pred             HHHHHHHHHHHHhccCCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccC
Confidence            999999999987   5789999999999999999999999999999999999999999999999999998864       


Q ss_pred             -----------hhHHHHhhCcceee
Q 010709          455 -----------LLAASESLCTTSFN  468 (503)
Q Consensus       455 -----------~~~~~Qr~GR~gR~  468 (503)
                                 .++|.||.||+||.
T Consensus       303 g~~~L~~~~iSkasa~QR~GRaGR~  327 (812)
T PRK11664        303 GLTRLVTQRISQASMTQRAGRAGRL  327 (812)
T ss_pred             CcceeEEEeechhhhhhhccccCCC
Confidence                       26899999999995

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

Probab=100.00  E-value=2.5e-39  Score=307.10  Aligned_cols=349  Identities=23%  Similarity=0.213  Sum_probs=251.1

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      +..+++.+|.......+.+ |++|+.|||.|||+++.+-+..++.+.       ++++|+++||+-|+.|.++.+++...
T Consensus        12 ~~ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~-------~~kvlfLAPTKPLV~Qh~~~~~~v~~   83 (542)
T COG1111          12 NTIEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWF-------GGKVLFLAPTKPLVLQHAEFCRKVTG   83 (542)
T ss_pred             ccccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhc-------CCeEEEecCCchHHHHHHHHHHHHhC
Confidence            3457888999988887766 999999999999999887777776665       34899999999999999999999884


Q ss_pred             cCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC
Q 010709          220 SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD  299 (503)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~  299 (503)
                      - +.-.+..++|.... +.+...+...+|+|+||+++.+-+..+.+++.++.+||+||||+..+..-...+.+......+
T Consensus        84 i-p~~~i~~ltGev~p-~~R~~~w~~~kVfvaTPQvveNDl~~Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k  161 (542)
T COG1111          84 I-PEDEIAALTGEVRP-EEREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAK  161 (542)
T ss_pred             C-ChhheeeecCCCCh-HHHHHHHhhCCEEEeccHHHHhHHhcCccChHHceEEEechhhhccCcchHHHHHHHHHHhcc
Confidence            3 23455566665554 445667788999999999999999999999999999999999998877555555555555566


Q ss_pred             CCcEEEEEeeCCHHHH---HHHHHhcCCCeEEEeCCCCCCC---CceEEEEEEcChhh----------------------
Q 010709          300 KHQTLLFSATMPVEIE---ALAQEYLTDPVQVKVGKVSSPT---ANVIQILEKVSENE----------------------  351 (503)
Q Consensus       300 ~~q~i~~SAT~~~~~~---~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~----------------------  351 (503)
                      ++.++++||||..+.+   +.++......+.+.........   ..+...+..+....                      
T Consensus       162 ~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~l~~~l~~~Lk~L~~  241 (542)
T COG1111         162 NPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDLLRDALKPRLKPLKE  241 (542)
T ss_pred             CceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            7779999999965544   4444444444444333222111   11111221110000                      


Q ss_pred             --------------------------------------------HHHHHHHHH------------HHHHHhhhc------
Q 010709          352 --------------------------------------------KVDRLLALL------------VEEAFLAEK------  369 (503)
Q Consensus       352 --------------------------------------------k~~~l~~~l------------~~~~~~~~~------  369 (503)
                                                                  ++.....++            .+.......      
T Consensus       242 ~g~~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~elletqGi~~~~~Yl~~l~e~~~~~~sk~a  321 (542)
T COG1111         242 LGVIESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHALELLETQGIRPFYQYLEKLEEEATKGGSKAA  321 (542)
T ss_pred             cCceeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHhcccchHHH
Confidence                                                        000000000            000000000      


Q ss_pred             ----------------------------------------cCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEE-EEc---
Q 010709          370 ----------------------------------------SCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV-ALH---  405 (503)
Q Consensus       370 ----------------------------------------~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~-~lh---  405 (503)
                                                              ..++..++|||++.+..++.+.++|.+.+..+. .+-   
T Consensus       322 ~~l~~d~~~~~al~~~~~~~~~~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa  401 (542)
T COG1111         322 KSLLADPYFKRALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQA  401 (542)
T ss_pred             HHHhcChhhHHHHHHHHHhccccCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeecc
Confidence                                                    011225799999999999999999999988774 333   


Q ss_pred             -----CCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee-------eeecc
Q 010709          406 -----GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN-------ITTNL  473 (503)
Q Consensus       406 -----~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~-------~~~~~  473 (503)
                           .||+|++|.+++++|+.|+.+|||||+++++|||||+++.||+|++..|.-.++||.||+||.       +++..
T Consensus       402 ~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTSVgEEGLDIp~vDlVifYEpvpSeIR~IQR~GRTGR~r~Grv~vLvt~g  481 (542)
T COG1111         402 SREGDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGRVVVLVTEG  481 (542)
T ss_pred             ccccccccCHHHHHHHHHHHhcCCceEEEEcccccccCCCCcccEEEEecCCcHHHHHHHhhCccccCCCCeEEEEEecC
Confidence                 479999999999999999999999999999999999999999999999999999999999995       45555


Q ss_pred             CchhhhhhHHHHHHHHHHHHHHHHh
Q 010709          474 DGDMKKLEFCLILAITVLLFVIFLS  498 (503)
Q Consensus       474 ~~~~~~~~~~~~~~~~~~~~~~~~~  498 (503)
                      ..+-+.....+.-+..|...+.++.
T Consensus       482 trdeayy~~s~rke~~m~e~i~~~~  506 (542)
T COG1111         482 TRDEAYYYSSRRKEQKMIESIRGLS  506 (542)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4565666666666666666665554

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=100.00  E-value=3.1e-39  Score=337.70  Aligned_cols=307  Identities=22%  Similarity=0.256  Sum_probs=225.0

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHHHHhcC------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          131 SIMKDIEFHEYTRPTSIQAQAMPVALSG------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       131 ~l~~~l~~~~~~~~~~~Q~~~i~~i~~~------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      .+.+.+...+| .||++|.++++.++.+      .+.+++|+||||||++|++|++..+..        +.+++|++||+
T Consensus       224 ~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~--------g~qvlilaPT~  294 (630)
T TIGR00643       224 LLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA--------GYQVALMAPTE  294 (630)
T ss_pred             HHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc--------CCcEEEECCHH
Confidence            34455667788 7999999999999865      258999999999999999998877543        57899999999


Q ss_pred             HHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH---HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          205 ELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR---SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       205 ~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +||.|+++.+++++... ++++.+++|+....+..   ..+. +.++|+|+||+.+.+     ...+.++++|||||+|+
T Consensus       295 ~LA~Q~~~~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~-----~~~~~~l~lvVIDEaH~  368 (630)
T TIGR00643       295 ILAEQHYNSLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE-----KVEFKRLALVIIDEQHR  368 (630)
T ss_pred             HHHHHHHHHHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc-----cccccccceEEEechhh
Confidence            99999999999998765 58999999998765432   2232 458999999987753     45678999999999998


Q ss_pred             HhhCCCHHHHHHHHHhCC--CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          281 MLDMGFEPQIREVMQNLP--DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~--~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      +...    +...+.....  ...++++||||+.+....+.  .+.+.....+.........+...+...  . ....++.
T Consensus       369 fg~~----qr~~l~~~~~~~~~~~~l~~SATp~prtl~l~--~~~~l~~~~i~~~p~~r~~i~~~~~~~--~-~~~~~~~  439 (630)
T TIGR00643       369 FGVE----QRKKLREKGQGGFTPHVLVMSATPIPRTLALT--VYGDLDTSIIDELPPGRKPITTVLIKH--D-EKDIVYE  439 (630)
T ss_pred             ccHH----HHHHHHHhcccCCCCCEEEEeCCCCcHHHHHH--hcCCcceeeeccCCCCCCceEEEEeCc--c-hHHHHHH
Confidence            5322    1222333332  25789999999865433322  222211111111111122233333222  2 2244454


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcch--------hhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERK--------TRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~--------~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      .+.+...       ...+++|||+..        ..++.+++.|.+.  ++.+..+||+|++++|..+++.|++|+.+||
T Consensus       440 ~i~~~l~-------~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~IL  512 (630)
T TIGR00643       440 FIEEEIA-------KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDIL  512 (630)
T ss_pred             HHHHHHH-------hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEE
Confidence            4444322       234699999876        3456777777653  7889999999999999999999999999999


Q ss_pred             EEccccccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee
Q 010709          429 VATDVASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN  468 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~  468 (503)
                      |||+++++|||+|++++||+++.|+ ....+.||+||+||.
T Consensus       513 VaT~vie~GvDiP~v~~VIi~~~~r~gls~lhQ~~GRvGR~  553 (630)
T TIGR00643       513 VATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRG  553 (630)
T ss_pred             EECceeecCcccCCCcEEEEeCCCcCCHHHHHHHhhhcccC
Confidence            9999999999999999999999997 678899999999993

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=6e-40  Score=357.23  Aligned_cols=298  Identities=22%  Similarity=0.289  Sum_probs=234.3

Q ss_pred             CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|+ .|+++|..+++.++.|+|++++||||+|||+ |.++++.++..       .+++++||+||++|+.|+++.++.++
T Consensus        77 ~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~-------~g~~alIL~PTreLa~Qi~~~l~~l~  147 (1176)
T PRK09401         77 TGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK-------KGKKSYIIFPTRLLVEQVVEKLEKFG  147 (1176)
T ss_pred             cCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh-------cCCeEEEEeccHHHHHHHHHHHHHHh
Confidence            466 8999999999999999999999999999997 44565555433       26889999999999999999999998


Q ss_pred             ccCCCceEEEEECCcc-----HHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhh---------
Q 010709          219 RSLDSFKTAIVVGGTN-----IAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD---------  283 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~-----~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~---------  283 (503)
                      ... ++.+..++++..     ..+....+. +.++|+|+||++|.+++.  .+...++++|||||||++++         
T Consensus       148 ~~~-~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~--~l~~~~~~~lVvDEaD~~L~~~k~id~~l  224 (1176)
T PRK09401        148 EKV-GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD--ELPKKKFDFVFVDDVDAVLKSSKNIDKLL  224 (1176)
T ss_pred             hhc-CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH--hccccccCEEEEEChHHhhhcccchhhHH
Confidence            765 466666666653     222233333 468999999999998876  35566799999999999986         


Q ss_pred             --CCCH-HHHHHHHHhCCC------------------------CCcEEEEEeeCCHH-HHHHHHHhcCCCeEEEeCCCCC
Q 010709          284 --MGFE-PQIREVMQNLPD------------------------KHQTLLFSATMPVE-IEALAQEYLTDPVQVKVGKVSS  335 (503)
Q Consensus       284 --~~~~-~~~~~il~~~~~------------------------~~q~i~~SAT~~~~-~~~~~~~~~~~~~~~~~~~~~~  335 (503)
                        .||. ..+..++..++.                        ..|++++|||+++. +..   .++.++..+.+.....
T Consensus       225 ~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~ll~~~v~~~~~  301 (1176)
T PRK09401        225 YLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRELLGFEVGSPVF  301 (1176)
T ss_pred             HhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhccceEEecCccc
Confidence              5774 567777776654                        68999999999764 332   2344555566666655


Q ss_pred             CCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhh---HHHHHHHHHHCCCeEEEEcCCCCHHH
Q 010709          336 PTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR---CDEVSEALVAEGLHAVALHGGRNQSD  412 (503)
Q Consensus       336 ~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~---~~~l~~~L~~~~~~v~~lh~~~~~~~  412 (503)
                      ...++.+.+..+.  .+...+..++...          ..++||||+++..   ++.+++.|+..|+.+..+||++    
T Consensus       302 ~~rnI~~~yi~~~--~k~~~L~~ll~~l----------~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~l----  365 (1176)
T PRK09401        302 YLRNIVDSYIVDE--DSVEKLVELVKRL----------GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISGF----  365 (1176)
T ss_pred             ccCCceEEEEEcc--cHHHHHHHHHHhc----------CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCcH----
Confidence            6667777777654  4555555554321          1359999999877   9999999999999999999999    


Q ss_pred             HHHHHHHHhcCCCcEEEE----ccccccCCCCCC-CCEEEEccCCC------ChhHHHHhhCcceee
Q 010709          413 RESALRDFRNGSTNILVA----TDVASRGLDVMG-VAHVVNLDLPK------VLLAASESLCTTSFN  468 (503)
Q Consensus       413 r~~~~~~f~~g~~~vLva----T~~~~~Gldip~-v~~VI~~~~p~------s~~~~~Qr~GR~gR~  468 (503)
                       .+.++.|++|+.+||||    |++++||||+|+ |++|||||+|+      ....+.||+||+-..
T Consensus       366 -~~~l~~F~~G~~~VLVatas~tdv~aRGIDiP~~IryVI~y~vP~~~~~~~~~~~~~~~~~r~~~~  431 (1176)
T PRK09401        366 -ERKFEKFEEGEVDVLVGVASYYGVLVRGIDLPERIRYAIFYGVPKFKFSLEEELAPPFLLLRLLSL  431 (1176)
T ss_pred             -HHHHHHHHCCCCCEEEEecCCCCceeecCCCCcceeEEEEeCCCCEEEeccccccCHHHHHHHHhh
Confidence             23459999999999999    699999999999 89999999998      668899999997533

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=1.8e-38  Score=352.54  Aligned_cols=311  Identities=18%  Similarity=0.235  Sum_probs=239.8

Q ss_pred             HHHHHHHH-CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH
Q 010709          131 SIMKDIEF-HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ  209 (503)
Q Consensus       131 ~l~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q  209 (503)
                      +..+.++. .|| .|+++|.++++.++.|+|++++||||+|||++++++++... .       .++++|||+||++|+.|
T Consensus        67 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~-~-------~g~~aLVl~PTreLa~Q  137 (1638)
T PRK14701         67 EFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLA-L-------KGKKCYIILPTTLLVKQ  137 (1638)
T ss_pred             HHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHH-h-------cCCeEEEEECHHHHHHH
Confidence            44455554 799 69999999999999999999999999999997665554332 1       25789999999999999


Q ss_pred             HHHHHHHHhccCC-CceEEEEECCccHHHHHH---Hhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhh-
Q 010709          210 IEKEVKALSRSLD-SFKTAIVVGGTNIAEQRS---ELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-  283 (503)
Q Consensus       210 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~---~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~-  283 (503)
                      +.+.++.++.... ++.+..++|+....++..   .+. +.++|+|+||++|.+.+...  ...+++++||||||+|++ 
T Consensus       138 i~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~~~i~~iVVDEAD~ml~~  215 (1638)
T PRK14701        138 TVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KHLKFDFIFVDDVDAFLKA  215 (1638)
T ss_pred             HHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hhCCCCEEEEECceecccc
Confidence            9999999886542 467778888887665432   333 35899999999998776542  226799999999999976 


Q ss_pred             ----------CCCHHHHHH----HHH----------------------hCCCCCc-EEEEEeeCCHHHHHHHHHhcCCCe
Q 010709          284 ----------MGFEPQIRE----VMQ----------------------NLPDKHQ-TLLFSATMPVEIEALAQEYLTDPV  326 (503)
Q Consensus       284 ----------~~~~~~~~~----il~----------------------~~~~~~q-~i~~SAT~~~~~~~~~~~~~~~~~  326 (503)
                                .||.+.+..    ++.                      .+++..| ++++|||+++.-  ....++.++.
T Consensus       216 ~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~--~~~~l~~~~l  293 (1638)
T PRK14701        216 SKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKG--DRVKLYRELL  293 (1638)
T ss_pred             ccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchh--HHHHHhhcCe
Confidence                      478877764    332                      2344455 577999998531  1223456777


Q ss_pred             EEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhh---HHHHHHHHHHCCCeEEE
Q 010709          327 QVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR---CDEVSEALVAEGLHAVA  403 (503)
Q Consensus       327 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~---~~~l~~~L~~~~~~v~~  403 (503)
                      .+.++.......++.+.+.......+ ..+..++...          ..++||||++++.   |+.+++.|...|+++..
T Consensus       294 ~f~v~~~~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~----------g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~  362 (1638)
T PRK14701        294 GFEVGSGRSALRNIVDVYLNPEKIIK-EHVRELLKKL----------GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIEL  362 (1638)
T ss_pred             EEEecCCCCCCCCcEEEEEECCHHHH-HHHHHHHHhC----------CCCeEEEEeccccchHHHHHHHHHHHCCCeEEE
Confidence            77777766666778888776655544 3455444321          1358999999875   58999999999999999


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCcEEEEc----cccccCCCCCC-CCEEEEccCCC---ChhHHHHhh-------------
Q 010709          404 LHGGRNQSDRESALRDFRNGSTNILVAT----DVASRGLDVMG-VAHVVNLDLPK---VLLAASESL-------------  462 (503)
Q Consensus       404 lh~~~~~~~r~~~~~~f~~g~~~vLvaT----~~~~~Gldip~-v~~VI~~~~p~---s~~~~~Qr~-------------  462 (503)
                      +||+     |..+++.|++|+.+|||||    ++++||||+|+ |++|||||+|+   ++..|.|..             
T Consensus       363 ~h~~-----R~~~l~~F~~G~~~VLVaT~s~~gvaaRGIDiP~~Vryvi~~~~Pk~~~~~e~~~~~~~~~~~~~~~~~~~  437 (1638)
T PRK14701        363 VSAK-----NKKGFDLFEEGEIDYLIGVATYYGTLVRGLDLPERIRFAVFYGVPKFRFRVDLEDPTIYRILGLLSEILKI  437 (1638)
T ss_pred             ecch-----HHHHHHHHHcCCCCEEEEecCCCCeeEecCccCCccCEEEEeCCCCCCcchhhcccchhhhhcchHHHHHh
Confidence            9995     8899999999999999999    58999999999 99999999999   887777765             


Q ss_pred             Ccceeeee
Q 010709          463 CTTSFNIT  470 (503)
Q Consensus       463 GR~gR~~~  470 (503)
                      ||+||.-.
T Consensus       438 ~~a~~~g~  445 (1638)
T PRK14701        438 EEELKEGI  445 (1638)
T ss_pred             hhhcccCC
Confidence            77777654

>PHA02558 uvsW UvsW helicase; Provisional

Probab=100.00  E-value=4.1e-38  Score=321.31  Aligned_cols=298  Identities=16%  Similarity=0.141  Sum_probs=214.5

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ...|+++|.++++.++.+++.++++|||+|||+++.. +.......      ...++||++||++|+.||.+.+++++..
T Consensus       112 ~~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~-l~~~~~~~------~~~~vLilvpt~eL~~Q~~~~l~~~~~~  184 (501)
T PHA02558        112 KIEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYL-LSRYYLEN------YEGKVLIIVPTTSLVTQMIDDFVDYRLF  184 (501)
T ss_pred             cCCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHH-HHHHHHhc------CCCeEEEEECcHHHHHHHHHHHHHhccc
Confidence            3589999999999999999999999999999987643 33332332      1347999999999999999999998743


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCC
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK  300 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~  300 (503)
                      . ...+..+.+|....       .+.+|+|+|++++.+...   ..++++++||+||||++..    ..+..++..+++.
T Consensus       185 ~-~~~~~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~---~~~~~~~~iIvDEaH~~~~----~~~~~il~~~~~~  249 (501)
T PHA02558        185 P-REAMHKIYSGTAKD-------TDAPIVVSTWQSAVKQPK---EWFDQFGMVIVDECHLFTG----KSLTSIITKLDNC  249 (501)
T ss_pred             c-ccceeEEecCcccC-------CCCCEEEeeHHHHhhchh---hhccccCEEEEEchhcccc----hhHHHHHHhhhcc
Confidence            2 23454566665321       347999999999976442   2467899999999999864    4567777777777


Q ss_pred             CcEEEEEeeCCHHHHHH--HHHhcCCCeEEEeCCCC-----C-CCCceEEEEEEc---------------------Chhh
Q 010709          301 HQTLLFSATMPVEIEAL--AQEYLTDPVQVKVGKVS-----S-PTANVIQILEKV---------------------SENE  351 (503)
Q Consensus       301 ~q~i~~SAT~~~~~~~~--~~~~~~~~~~~~~~~~~-----~-~~~~~~~~~~~~---------------------~~~~  351 (503)
                      .++++||||+.+.....  ...++++ ....+....     . ....+.......                     ....
T Consensus       250 ~~~lGLTATp~~~~~~~~~~~~~fG~-i~~~v~~~~li~~g~l~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  328 (501)
T PHA02558        250 KFKFGLTGSLRDGKANILQYVGLFGD-IFKPVTTSQLMEEGQVTDLKINSIFLRYPDEDRVKLKGEDYQEEIKYITSHTK  328 (501)
T ss_pred             ceEEEEeccCCCccccHHHHHHhhCC-ceEEecHHHHHhCCCcCCceEEEEeccCCHHHhhhhcccchHHHHHHHhccHH
Confidence            88999999996532211  1122221 111111000     0 000000000000                     0111


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc
Q 010709          352 KVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVAT  431 (503)
Q Consensus       352 k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT  431 (503)
                      +...+........       ..+.++||||.+.++++.+++.|++.+.++..+||++++++|..+++.|++|+..|||||
T Consensus       329 Rn~~I~~~~~~~~-------~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT  401 (501)
T PHA02558        329 RNKWIANLALKLA-------KKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVAS  401 (501)
T ss_pred             HHHHHHHHHHHHH-------hcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEE
Confidence            1111111111111       233568999999999999999999999999999999999999999999999999999998


Q ss_pred             -cccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          432 -DVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       432 -~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                       +++++|+|+|++++||+++++++...|+||+||++|.
T Consensus       402 ~~~l~eG~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~  439 (501)
T PHA02558        402 YGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRK  439 (501)
T ss_pred             cceeccccccccccEEEEecCCcchhhhhhhhhccccC
Confidence             8999999999999999999999999999999999995

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

Probab=100.00  E-value=2.2e-38  Score=302.69  Aligned_cols=330  Identities=24%  Similarity=0.269  Sum_probs=258.6

Q ss_pred             cccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH-HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       123 ~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~-i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .+++.+++...+.|+..|++.+.|+|.-++.+ +++|.|.+|+++|+||||++..++-+..++..       |+++|+++
T Consensus       196 vdeLdipe~fk~~lk~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~~-------g~KmlfLv  268 (830)
T COG1202         196 VDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLSG-------GKKMLFLV  268 (830)
T ss_pred             ccccCCcHHHHHHHHhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHhC-------CCeEEEEe
Confidence            56788999999999999999999999999987 67999999999999999999998888887764       68899999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH----HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecc
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR----SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE  277 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDE  277 (503)
                      |..+||+|-++.|++--..+ ++.+.+..|........    ......+||+|+|++-+-.++..+ ..+.+++.|||||
T Consensus       269 PLVALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg-~~lgdiGtVVIDE  346 (830)
T COG1202         269 PLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG-KDLGDIGTVVIDE  346 (830)
T ss_pred             hhHHhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC-CcccccceEEeee
Confidence            99999999999998655555 57787777765443321    112345899999999997777664 6789999999999


Q ss_pred             hhHHhhCCCHH---HHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC-hhhHH
Q 010709          278 ADRMLDMGFEP---QIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS-ENEKV  353 (503)
Q Consensus       278 aH~l~~~~~~~---~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~k~  353 (503)
                      +|.+-+...+.   .+..-++.+-+..|+|.+|||+.+. +.+++.+--+.+..  +..+   ..+..+...+. ..+|.
T Consensus       347 iHtL~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y--~~RP---VplErHlvf~~~e~eK~  420 (830)
T COG1202         347 IHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLY--DERP---VPLERHLVFARNESEKW  420 (830)
T ss_pred             eeeccchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEee--cCCC---CChhHeeeeecCchHHH
Confidence            99877654444   4444456666789999999999654 44677665554333  2222   22334444444 44555


Q ss_pred             HHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc
Q 010709          354 DRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV  433 (503)
Q Consensus       354 ~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~  433 (503)
                      +.+..+.+ ..........-.+++|||.+++..|..++++|..+|+++.++|+|++..+|..+...|.++++.++|+|.+
T Consensus       421 ~ii~~L~k-~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~y~eRk~vE~~F~~q~l~~VVTTAA  499 (830)
T COG1202         421 DIIARLVK-REFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAA  499 (830)
T ss_pred             HHHHHHHH-HHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCcHHHHHHHHHHHhcCCcceEeehhh
Confidence            44444444 44444444456688999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCEEEE----ccCC-CChhHHHHhhCcceeee
Q 010709          434 ASRGLDVMGVAHVVN----LDLP-KVLLAASESLCTTSFNI  469 (503)
Q Consensus       434 ~~~Gldip~v~~VI~----~~~p-~s~~~~~Qr~GR~gR~~  469 (503)
                      ++.|+|+| ++.||+    ++.- -++.+|.|+.|||||-.
T Consensus       500 L~AGVDFP-ASQVIFEsLaMG~~WLs~~EF~QM~GRAGRp~  539 (830)
T COG1202         500 LAAGVDFP-ASQVIFESLAMGIEWLSVREFQQMLGRAGRPD  539 (830)
T ss_pred             hhcCCCCc-hHHHHHHHHHcccccCCHHHHHHHhcccCCCC
Confidence            99999999 455664    2332 37899999999999943

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

Probab=100.00  E-value=1.4e-38  Score=294.16  Aligned_cols=275  Identities=27%  Similarity=0.481  Sum_probs=219.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCC--CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCcc
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLD--SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVS  271 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~  271 (503)
                      .+.++|+-|.|+|+.|....++++-.+..  .++..++.||...+++...+..+++|+|+||+++.+.+..+.+.+..++
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~g~~~lt~cr  365 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISKGLVTLTHCR  365 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhccceeeeeeE
Confidence            35589999999999999998887765543  3555688899999999999999999999999999999999999999999


Q ss_pred             EEEecchhHHhhCCCHHHHHHHHHhCCC------CCcEEEEEeeCCH-HHHHHHHHhcCCCeEEEeCCCCCCCCceEEEE
Q 010709          272 FVILDEADRMLDMGFEPQIREVMQNLPD------KHQTLLFSATMPV-EIEALAQEYLTDPVQVKVGKVSSPTANVIQIL  344 (503)
Q Consensus       272 ~vViDEaH~l~~~~~~~~~~~il~~~~~------~~q~i~~SAT~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (503)
                      ++|+|||+-++..++...+.++...++.      ..|.+++|||+.. ++..+.++.+.-|.-+...........+.+.+
T Consensus       366 FlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD~vpetvHhvv  445 (725)
T KOG0349|consen  366 FLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGEDLVPETVHHVV  445 (725)
T ss_pred             EEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccccccchhhccce
Confidence            9999999999998888888888777653      6789999999842 44555666666777777666665555555444


Q ss_pred             EEcChh------------------------------hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHH
Q 010709          345 EKVSEN------------------------------EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL  394 (503)
Q Consensus       345 ~~~~~~------------------------------~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L  394 (503)
                      ..+...                              +......++++..........+.-.++||||.++..|+.|.+++
T Consensus       446 ~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaiifcrtk~dcDnLer~~  525 (725)
T KOG0349|consen  446 KLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAIIFCRTKQDCDNLERMM  525 (725)
T ss_pred             eecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEEEEeccccchHHHHHH
Confidence            333211                              01111122222211111112233467999999999999999999


Q ss_pred             HHCC---CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          395 VAEG---LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       395 ~~~~---~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +++|   +.++++||+..+.+|.+.++.|+.+.++.||||++++||+||.++-++||+.+|.+..+|.|||||+||.
T Consensus       526 ~qkgg~~~scvclhgDrkP~Erk~nle~Fkk~dvkflictdvaargldi~g~p~~invtlpd~k~nyvhrigrvgra  602 (725)
T KOG0349|consen  526 NQKGGKHYSCVCLHGDRKPDERKANLESFKKFDVKFLICTDVAARGLDITGLPFMINVTLPDDKTNYVHRIGRVGRA  602 (725)
T ss_pred             HHcCCccceeEEEecCCChhHHHHHHHhhhhcCeEEEEEehhhhccccccCCceEEEEecCcccchhhhhhhccchh
Confidence            9874   6899999999999999999999999999999999999999999999999999999999999999999994

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

Probab=100.00  E-value=1.4e-37  Score=329.14  Aligned_cols=326  Identities=20%  Similarity=0.271  Sum_probs=254.6

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          129 HPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       129 ~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      ...+...+.+.|+..|+.+|.+|+..+.+|+|+||+.+||||||.+|++|++.+++..+      ..++|+|.||++||+
T Consensus        56 ~~~l~~~l~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~------~a~AL~lYPtnALa~  129 (851)
T COG1205          56 DESLKSALVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDP------SARALLLYPTNALAN  129 (851)
T ss_pred             hhHHHHHHHHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCc------CccEEEEechhhhHh
Confidence            34457888889999999999999999999999999999999999999999999998864      347899999999999


Q ss_pred             HHHHHHHHHhccCC-CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC----CCCCCccEEEecchhHHhh
Q 010709          209 QIEKEVKALSRSLD-SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN----TSLSRVSFVILDEADRMLD  283 (503)
Q Consensus       209 q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~----~~l~~~~~vViDEaH~l~~  283 (503)
                      .+.++++++..... ++....+.|++...+......+.++|+++||++|..++.+..    +.+.++++||+||+|..-+
T Consensus       130 DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~Lk~lVvDElHtYrG  209 (851)
T COG1205         130 DQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYLVVDELHTYRG  209 (851)
T ss_pred             hHHHHHHHHHHhCCCcceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhcCcEEEEecceeccc
Confidence            99999999998775 577777888887777667788999999999999988666542    3567899999999996433


Q ss_pred             CCCHHHHH----HHHH---hCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC--------
Q 010709          284 MGFEPQIR----EVMQ---NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS--------  348 (503)
Q Consensus       284 ~~~~~~~~----~il~---~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------  348 (503)
                      - |+..+.    +++.   ..+.+.|+|++|||+... ..++..+++......+.....+............        
T Consensus       210 v-~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~~~g~~~~~~~~~~~~p~~~~~~~~~  287 (851)
T COG1205         210 V-QGSEVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESI  287 (851)
T ss_pred             c-chhHHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceeeccCCCCCCCceEEEEeCCcchhhhhhc
Confidence            2 444443    3333   334588999999999644 4477777776655544444444333333322220        


Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHH----HHHHHCC----CeEEEEcCCCCHHHHHHHHHHH
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVS----EALVAEG----LHAVALHGGRNQSDRESALRDF  420 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~----~~L~~~~----~~v~~lh~~~~~~~r~~~~~~f  420 (503)
                      ...+...+-.+.......       .-++|+|+.++..++.+.    ..+...+    ..+..+++++...+|.++...|
T Consensus       288 r~s~~~~~~~~~~~~~~~-------~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~~~er~~ie~~~  360 (851)
T COG1205         288 RRSALAELATLAALLVRN-------GIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEF  360 (851)
T ss_pred             ccchHHHHHHHHHHHHHc-------CceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCCHHHHHHHHHHH
Confidence            112222222222222211       235999999999999987    4444555    5788999999999999999999


Q ss_pred             hcCCCcEEEEccccccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceeee
Q 010709          421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFNI  469 (503)
Q Consensus       421 ~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~~  469 (503)
                      ++|+..++++|++++-|+||.+++.||.++.|. ++.++.||.||+||..
T Consensus       361 ~~g~~~~~~st~AlelgidiG~ldavi~~g~P~~s~~~~~Q~~GRaGR~~  410 (851)
T COG1205         361 KEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRG  410 (851)
T ss_pred             hcCCccEEecchhhhhceeehhhhhHhhcCCCCchHHHHHHhhhhccCCC
Confidence            999999999999999999999999999999999 9999999999999965

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=100.00  E-value=1.1e-37  Score=308.15  Aligned_cols=287  Identities=19%  Similarity=0.153  Sum_probs=198.1

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH---
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA---  236 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~---  236 (503)
                      ++++++|||+|||++|++|++..+...      .+.+++|++|+++|+.|+++.++.++..    .++..+++....   
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~~------~~~~ii~v~P~~~L~~q~~~~l~~~f~~----~~~~~~~~~~~~~~~   70 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKSQ------KADRVIIALPTRATINAMYRRAKELFGS----NLGLLHSSSSFKRIK   70 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhhC------CCCeEEEEeehHHHHHHHHHHHHHHhCc----ccEEeeccHHHHHHh
Confidence            589999999999999999999775432      3578999999999999999999997532    334444433210   


Q ss_pred             ---------HHHHHh-h-----CCCcEEEECcHHHHHHHHcCC----CCC--CCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          237 ---------EQRSEL-R-----GGVSIVVATPGRFLDHLQQGN----TSL--SRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       237 ---------~~~~~~-~-----~~~~Ilv~Tp~~l~~~l~~~~----~~l--~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                               ...... .     ...+|+|+||+++...+....    ..+  -..++|||||+|.+.+.++.. +..++.
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~  149 (358)
T TIGR01587        71 EMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLE  149 (358)
T ss_pred             ccCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHH
Confidence                     000001 0     136799999999988776521    111  123799999999987654333 555554


Q ss_pred             hCC-CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEc--ChhhHHHHHHHHHHHHHHhhhccCC
Q 010709          296 NLP-DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKV--SENEKVDRLLALLVEEAFLAEKSCH  372 (503)
Q Consensus       296 ~~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~k~~~l~~~l~~~~~~~~~~~~  372 (503)
                      .+. .+.|+++||||+|+.+..+...+...+........... ....+.+...  ....+...+..++...        .
T Consensus       150 ~l~~~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~l~~~~--------~  220 (358)
T TIGR01587       150 VLKDNDVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEER-RFERHRFIKIESDKVGEISSLERLLEFI--------K  220 (358)
T ss_pred             HHHHcCCCEEEEecCchHHHHHHHhcCCCcccccCCCCcccc-ccccccceeeccccccCHHHHHHHHHHh--------h
Confidence            443 46899999999998777766655433211111100000 0011111111  1122333333333211        2


Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHCCC--eEEEEcCCCCHHHHHH----HHHHHhcCCCcEEEEccccccCCCCCCCCEE
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAEGL--HAVALHGGRNQSDRES----ALRDFRNGSTNILVATDVASRGLDVMGVAHV  446 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~~~--~v~~lh~~~~~~~r~~----~~~~f~~g~~~vLvaT~~~~~Gldip~v~~V  446 (503)
                      .++++||||++++.|+.+++.|++.+.  .+..+||++++.+|.+    +++.|++|+.+|||||+++++|+|++ +++|
T Consensus       221 ~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~~~~~GiDi~-~~~v  299 (358)
T TIGR01587       221 KGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDIS-ADVM  299 (358)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECcchhceeccC-CCEE
Confidence            345799999999999999999988765  5999999999999976    48899999999999999999999996 8999


Q ss_pred             EEccCCCChhHHHHhhCcceeee
Q 010709          447 VNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       447 I~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      |++..|  ..+|+||+||+||.-
T Consensus       300 i~~~~~--~~~~iqr~GR~gR~g  320 (358)
T TIGR01587       300 ITELAP--IDSLIQRLGRLHRYG  320 (358)
T ss_pred             EEcCCC--HHHHHHHhccccCCC
Confidence            998877  789999999999953

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.

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=9.3e-37  Score=332.85  Aligned_cols=290  Identities=23%  Similarity=0.359  Sum_probs=219.7

Q ss_pred             HHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          134 KDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       134 ~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      +.+.......|+++|..+++.++.|+|++++||||+|||+ |.+|+..++...       +++++|++||++||.|+++.
T Consensus        69 ~~f~~~~g~~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~~-------g~~vLIL~PTreLa~Qi~~~  140 (1171)
T TIGR01054        69 EFFKKAVGSEPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAKK-------GKRCYIILPTTLLVIQVAEK  140 (1171)
T ss_pred             HHHHHhcCCCCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHhc-------CCeEEEEeCHHHHHHHHHHH
Confidence            3334444458999999999999999999999999999997 557776665432       68899999999999999999


Q ss_pred             HHHHhccCCCce---EEEEECCccHHHHH---HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhh---
Q 010709          214 VKALSRSLDSFK---TAIVVGGTNIAEQR---SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD---  283 (503)
Q Consensus       214 ~~~~~~~~~~~~---~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~---  283 (503)
                      ++.++...+ +.   +..++|+....++.   ..+. ++++|+|+||++|.+.+.+  +.. +++++|+||||+|++   
T Consensus       141 l~~l~~~~~-i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~--l~~-~~~~iVvDEaD~~L~~~k  216 (1171)
T TIGR01054       141 ISSLAEKAG-VGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE--LGP-KFDFIFVDDVDALLKASK  216 (1171)
T ss_pred             HHHHHHhcC-CceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH--hcC-CCCEEEEeChHhhhhccc
Confidence            999986542 33   33567887765432   2333 4599999999999987765  222 899999999999987   


Q ss_pred             --------CCCHHH-HHHHH----------------------HhCCCCCc--EEEEEee-CCHHHHHHHHHhcCCCeEEE
Q 010709          284 --------MGFEPQ-IREVM----------------------QNLPDKHQ--TLLFSAT-MPVEIEALAQEYLTDPVQVK  329 (503)
Q Consensus       284 --------~~~~~~-~~~il----------------------~~~~~~~q--~i~~SAT-~~~~~~~~~~~~~~~~~~~~  329 (503)
                              +||... +..++                      ..+++..|  ++++||| .|..+..   .++.++..+.
T Consensus       217 ~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~r~ll~~~  293 (1171)
T TIGR01054       217 NVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLFRELLGFE  293 (1171)
T ss_pred             cHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHcccccceE
Confidence                    577653 44432                      23444445  5678999 5554432   3455666666


Q ss_pred             eCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcch---hhHHHHHHHHHHCCCeEEEEcC
Q 010709          330 VGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERK---TRCDEVSEALVAEGLHAVALHG  406 (503)
Q Consensus       330 ~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~---~~~~~l~~~L~~~~~~v~~lh~  406 (503)
                      ++.......++.+.+.....  +...+..++...          ..++||||+++   +.|+.+++.|.+.|+++..+||
T Consensus       294 v~~~~~~~r~I~~~~~~~~~--~~~~L~~ll~~l----------~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg  361 (1171)
T TIGR01054       294 VGGGSDTLRNVVDVYVEDED--LKETLLEIVKKL----------GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHA  361 (1171)
T ss_pred             ecCccccccceEEEEEeccc--HHHHHHHHHHHc----------CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeC
Confidence            66665566677777665443  233344444321          13589999999   9999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEE----ccccccCCCCCC-CCEEEEccCCCC
Q 010709          407 GRNQSDRESALRDFRNGSTNILVA----TDVASRGLDVMG-VAHVVNLDLPKV  454 (503)
Q Consensus       407 ~~~~~~r~~~~~~f~~g~~~vLva----T~~~~~Gldip~-v~~VI~~~~p~s  454 (503)
                      ++++    .+++.|++|+++||||    |++++||||+|+ |++|||||+|+.
T Consensus       362 ~~~~----~~l~~Fr~G~~~vLVata~~tdv~aRGIDip~~V~~vI~~~~P~~  410 (1171)
T TIGR01054       362 TKPK----EDYEKFAEGEIDVLIGVASYYGTLVRGLDLPERVRYAVFLGVPKF  410 (1171)
T ss_pred             CCCH----HHHHHHHcCCCCEEEEeccccCcccccCCCCccccEEEEECCCCE
Confidence            9973    6899999999999999    599999999999 899999999974

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.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=100.00  E-value=2.7e-36  Score=294.77  Aligned_cols=297  Identities=19%  Similarity=0.153  Sum_probs=204.3

Q ss_pred             HHHHHHHHHhcCCC--eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC---
Q 010709          147 IQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL---  221 (503)
Q Consensus       147 ~Q~~~i~~i~~~~~--vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~---  221 (503)
                      +|.++++.+.++++  +++++|||+|||.+|++|++..           +.++++++|+++|++|+++.++.+...+   
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~-----------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~~   69 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG-----------ENDTIALYPTNALIEDQTEAIKEFVDVFKPE   69 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc-----------CCCEEEEeChHHHHHHHHHHHHHHHHhcCCC
Confidence            49999999998875  8899999999999999988842           3458999999999999999999887533   


Q ss_pred             CCceEEEEECCccHH--HH-----------------HH-HhhCCCcEEEECcHHHHHHHHcCC--------CCCCCccEE
Q 010709          222 DSFKTAIVVGGTNIA--EQ-----------------RS-ELRGGVSIVVATPGRFLDHLQQGN--------TSLSRVSFV  273 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~--~~-----------------~~-~~~~~~~Ilv~Tp~~l~~~l~~~~--------~~l~~~~~v  273 (503)
                      .+..+..+.|.+...  ..                 +. .....+.|+++||+.|..++....        ..+..+++|
T Consensus        70 ~~~~v~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~~i  149 (357)
T TIGR03158        70 RDVNLLHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFSTV  149 (357)
T ss_pred             CCceEEEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCCEE
Confidence            235555555542211  00                 00 112467899999999976554311        125789999


Q ss_pred             EecchhHHhhCC-----CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh--cCCCeEEEeCCC-----------CC
Q 010709          274 ILDEADRMLDMG-----FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY--LTDPVQVKVGKV-----------SS  335 (503)
Q Consensus       274 ViDEaH~l~~~~-----~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~--~~~~~~~~~~~~-----------~~  335 (503)
                      |+||+|.+....     +......++.......+++++|||+++.+...+...  ++.+..+..+..           ..
T Consensus       150 V~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~v~g~~~~~~~~~~~~~~~  229 (357)
T TIGR03158       150 IFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQNAKQAGVKIAPIDGEKYQFPDNPELEADN  229 (357)
T ss_pred             EEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHhccccCceeeeecCcccccCCChhhhccc
Confidence            999999865432     122334444444445789999999999888777765  555543322220           00


Q ss_pred             -------CCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC--CeEEEEcC
Q 010709          336 -------PTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG--LHAVALHG  406 (503)
Q Consensus       336 -------~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~--~~v~~lh~  406 (503)
                             ....+.+.+.. ....+...+..++.. ..... ...+.+++||||++++.++.+++.|++.+  +.+..+||
T Consensus       230 ~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~-i~~~~-~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g  306 (357)
T TIGR03158       230 KTQSFRPVLPPVELELIP-APDFKEEELSELAEE-VIERF-RQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITG  306 (357)
T ss_pred             cccccceeccceEEEEEe-CCchhHHHHHHHHHH-HHHHH-hccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeec
Confidence                   00133333333 222333322222221 11111 01245679999999999999999999864  57889999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcce
Q 010709          407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTS  466 (503)
Q Consensus       407 ~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~g  466 (503)
                      .+++.+|.+.      ++..|||||+++++|||+|.+ +|| ++ |.+.+.|+||+||+|
T Consensus       307 ~~~~~~R~~~------~~~~iLVaTdv~~rGiDi~~~-~vi-~~-p~~~~~yiqR~GR~g  357 (357)
T TIGR03158       307 FAPKKDRERA------MQFDILLGTSTVDVGVDFKRD-WLI-FS-ARDAAAFWQRLGRLG  357 (357)
T ss_pred             CCCHHHHHHh------ccCCEEEEecHHhcccCCCCc-eEE-EC-CCCHHHHhhhcccCC
Confidence            9999988754      478999999999999999976 666 45 899999999999997

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.

>KOG0354 consensus DEAD-box like helicase [General function prediction only]

Probab=100.00  E-value=3.3e-36  Score=302.44  Aligned_cols=351  Identities=23%  Similarity=0.241  Sum_probs=241.0

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      +++.....+..-....++.+|.+....++ |+|+||++|||+|||+++...++.++.+.+      ..++|+++|++-|+
T Consensus        47 ~~~s~~~~~~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p------~~KiVF~aP~~pLv  119 (746)
T KOG0354|consen   47 LDESAAQRWIYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRP------KGKVVFLAPTRPLV  119 (746)
T ss_pred             CChhhhccccccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCC------cceEEEeeCCchHH
Confidence            34444444444566689999999999999 999999999999999999888888877764      47899999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCC-CCCccEEEecchhHHhhCCC
Q 010709          208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTS-LSRVSFVILDEADRMLDMGF  286 (503)
Q Consensus       208 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~-l~~~~~vViDEaH~l~~~~~  286 (503)
                      .|+...+..++.+   ..+....||.........+....+|+|+||+.+.+.+...... +..+.++||||||+..+..-
T Consensus       120 ~QQ~a~~~~~~~~---~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn~~  196 (746)
T KOG0354|consen  120 NQQIACFSIYLIP---YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKNHP  196 (746)
T ss_pred             HHHHHHHhhccCc---ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEccccccccccc
Confidence            9998888777643   5566666665554445567778999999999999988876543 58899999999999877654


Q ss_pred             HHHHH-HHHHhCCCCCcEEEEEeeCCHHHHHHHH----------------------------------------------
Q 010709          287 EPQIR-EVMQNLPDKHQTLLFSATMPVEIEALAQ----------------------------------------------  319 (503)
Q Consensus       287 ~~~~~-~il~~~~~~~q~i~~SAT~~~~~~~~~~----------------------------------------------  319 (503)
                      ...+. ..+.......|+|++|||+.........                                              
T Consensus       197 Y~~Vmr~~l~~k~~~~qILgLTASpG~~~~~v~~~I~~L~asldvr~~ssi~~~y~~lr~~~~i~v~~~~~~~~~~~~f~  276 (746)
T KOG0354|consen  197 YNNIMREYLDLKNQGNQILGLTASPGSKLEQVQNVIDNLCASLDVRTESSIKSNYEELREHVQIPVDLSLCERDIEDPFG  276 (746)
T ss_pred             HHHHHHHHHHhhhccccEEEEecCCCccHHHHHHHHHhhheecccchhhhhhhhHHHHhccCcccCcHHHhhhhhhhhHH
Confidence            44444 5555444455999999999544332110                                              


Q ss_pred             ----Hhc-----------CCCeEEEe----CCCCCCCCce--EEE--------------------EE-------------
Q 010709          320 ----EYL-----------TDPVQVKV----GKVSSPTANV--IQI--------------------LE-------------  345 (503)
Q Consensus       320 ----~~~-----------~~~~~~~~----~~~~~~~~~~--~~~--------------------~~-------------  345 (503)
                          .++           .+......    ........+.  .+.                    +.             
T Consensus       277 ~~i~p~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~f~~~~~~~~~~~ll~~~gir~~~~l~~~~~f~~  356 (746)
T KOG0354|consen  277 MIIEPLLQQLQEEGLIEISDKSTSYEQWVVQAEKAAAPNGPENQRNCFYALHLRKYNLALLISDGIRFVDALDYLEDFYE  356 (746)
T ss_pred             HHHHHHHHHHHhcCccccccccccccchhhhhhhhhccCCCccchhhHHHHHHHHHHHHHHhhcchhhHHHHhhhhhhcc
Confidence                000           00000000    0000000000  000                    00             


Q ss_pred             -------------------------------Ec--ChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHH
Q 010709          346 -------------------------------KV--SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSE  392 (503)
Q Consensus       346 -------------------------------~~--~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~  392 (503)
                                                     ..  ....|+..+.+.+.+...     ..+..++|||+.+++.|..|.+
T Consensus       357 e~~~~k~~~~~~e~~~~~~~~~~m~~~~~l~~~~~~~npkle~l~~~l~e~f~-----~~~dsR~IIFve~R~sa~~l~~  431 (746)
T KOG0354|consen  357 EVALKKYLKLELEARLIRNFTENMNELEHLSLDPPKENPKLEKLVEILVEQFE-----QNPDSRTIIFVETRESALALKK  431 (746)
T ss_pred             ccchhHHHHHHhcchhhHHHHHHHHhhhhhhcCCCccChhHHHHHHHHHHHhh-----cCCCccEEEEEehHHHHHHHHH
Confidence                                           00  012233334444433332     2455679999999999999999


Q ss_pred             HHHHC---CCeEEEEc--------CCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHh
Q 010709          393 ALVAE---GLHAVALH--------GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASES  461 (503)
Q Consensus       393 ~L~~~---~~~v~~lh--------~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr  461 (503)
                      .|.+.   +++...+-        .+|++.+|.+++++|++|+.+|||||+++++||||+.|+.||.||...++..++||
T Consensus       432 ~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATSV~EEGLDI~ec~lVIcYd~~snpIrmIQr  511 (746)
T KOG0354|consen  432 WLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATSVAEEGLDIGECNLVICYDYSSNPIRMVQR  511 (746)
T ss_pred             HHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEecchhccCCcccccEEEEecCCccHHHHHHH
Confidence            99832   33433333        38999999999999999999999999999999999999999999999999999999


Q ss_pred             hCcceee------eeeccCchhhhhhHHHHHHHHHHHHH
Q 010709          462 LCTTSFN------ITTNLDGDMKKLEFCLILAITVLLFV  494 (503)
Q Consensus       462 ~GR~gR~------~~~~~~~~~~~~~~~~~~~~~~~~~~  494 (503)
                      .|| ||.      +++-..+..+....-...+..+-+.+
T Consensus       512 rGR-gRa~ns~~vll~t~~~~~~~E~~~~~~e~lm~~~i  549 (746)
T KOG0354|consen  512 RGR-GRARNSKCVLLTTGSEVIEFERNNLAKEKLMNQTI  549 (746)
T ss_pred             hcc-ccccCCeEEEEEcchhHHHHHHHHHhHHHHHHHHH
Confidence            999 994      22323344444444344444443333

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=8.6e-36  Score=302.13  Aligned_cols=303  Identities=22%  Similarity=0.203  Sum_probs=229.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|+++|..+++.++.|+  |..+.||+|||++|.+|++.....        |+.++|++||++||.|.++.+..+...+
T Consensus       102 ~~p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~--------G~~v~VvTptreLA~qdae~~~~l~~~l  171 (656)
T PRK12898        102 QRHFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA--------GLPVHVITVNDYLAERDAELMRPLYEAL  171 (656)
T ss_pred             CCCChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc--------CCeEEEEcCcHHHHHHHHHHHHHHHhhc
Confidence            379999999999999998  999999999999999999987543        6789999999999999999999998876


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC-------------------------CCCCCCccEEEe
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG-------------------------NTSLSRVSFVIL  275 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~-------------------------~~~l~~~~~vVi  275 (503)
                       ++.+.+++|+....  .+....+++|+|+|..-| .+.+..+                         ......+.++||
T Consensus       172 -Glsv~~i~gg~~~~--~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~r~~~~aIv  248 (656)
T PRK12898        172 -GLTVGCVVEDQSPD--ERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQLLLRGLHFAIV  248 (656)
T ss_pred             -CCEEEEEeCCCCHH--HHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhhcccccceeEe
Confidence             69999999997643  344556799999999887 3333321                         112356789999


Q ss_pred             cchhHHh-h----------C-------CCHHHH--------------------------------HHHHHh---------
Q 010709          276 DEADRML-D----------M-------GFEPQI--------------------------------REVMQN---------  296 (503)
Q Consensus       276 DEaH~l~-~----------~-------~~~~~~--------------------------------~~il~~---------  296 (503)
                      ||+|.++ +          .       .+....                                ++++..         
T Consensus       249 DEvDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~~~v~lt~~g~~~~e~~~~~l~~~~~~~~  328 (656)
T PRK12898        249 DEADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAEKRIELTEAGRARIAELAESLPPAWRGAV  328 (656)
T ss_pred             ecccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCCCeEEEcHHHHHHHHHHhCcchhhcccch
Confidence            9999522 1          0       000000                                000000         


Q ss_pred             ---------------CCC-------------------------------------------------------------C
Q 010709          297 ---------------LPD-------------------------------------------------------------K  300 (503)
Q Consensus       297 ---------------~~~-------------------------------------------------------------~  300 (503)
                                     +..                                                             -
T Consensus       329 ~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQaieaKE~v~i~~e~~t~a~It~q~~Fr~Y  408 (656)
T PRK12898        329 RREELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQMIEAKEGCELTDPRETLARITYQRFFRRY  408 (656)
T ss_pred             HHHHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHHHHHhcCCCCCcCceeeeeehHHHHHHhh
Confidence                           000                                                             0


Q ss_pred             CcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEE
Q 010709          301 HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVF  380 (503)
Q Consensus       301 ~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF  380 (503)
                      .++.+||||.+....++...|..+++.+......  .....+.+..+....|...+.+.+.....       ...++|||
T Consensus       409 ~kl~GmTGTa~~~~~El~~~y~l~vv~IPt~kp~--~r~~~~~~v~~t~~~K~~aL~~~i~~~~~-------~~~pvLIf  479 (656)
T PRK12898        409 LRLAGMTGTAREVAGELWSVYGLPVVRIPTNRPS--QRRHLPDEVFLTAAAKWAAVAARVRELHA-------QGRPVLVG  479 (656)
T ss_pred             HHHhcccCcChHHHHHHHHHHCCCeEEeCCCCCc--cceecCCEEEeCHHHHHHHHHHHHHHHHh-------cCCCEEEE
Confidence            1577999999988888888887777665443322  22233445566777888888887765321       22469999


Q ss_pred             EcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCC---CCC-----EEEEccCC
Q 010709          381 VERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM---GVA-----HVVNLDLP  452 (503)
Q Consensus       381 ~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip---~v~-----~VI~~~~p  452 (503)
                      |++++.++.+++.|.+.|+.+..+||++.+.  +..+..|..+...|+|||++++||+||+   +|.     +||++++|
T Consensus       480 t~t~~~se~L~~~L~~~gi~~~~Lhg~~~~r--E~~ii~~ag~~g~VlVATdmAgRGtDI~l~~~V~~~GGLhVI~~d~P  557 (656)
T PRK12898        480 TRSVAASERLSALLREAGLPHQVLNAKQDAE--EAAIVARAGQRGRITVATNMAGRGTDIKLEPGVAARGGLHVILTERH  557 (656)
T ss_pred             eCcHHHHHHHHHHHHHCCCCEEEeeCCcHHH--HHHHHHHcCCCCcEEEEccchhcccCcCCccchhhcCCCEEEEcCCC
Confidence            9999999999999999999999999986644  4555556666668999999999999999   676     99999999


Q ss_pred             CChhHHHHhhCcceee
Q 010709          453 KVLLAASESLCTTSFN  468 (503)
Q Consensus       453 ~s~~~~~Qr~GR~gR~  468 (503)
                      .+...|.||+||+||.
T Consensus       558 ~s~r~y~hr~GRTGRq  573 (656)
T PRK12898        558 DSARIDRQLAGRCGRQ  573 (656)
T ss_pred             CCHHHHHHhcccccCC
Confidence            9999999999999994

>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]

Probab=100.00  E-value=2e-36  Score=317.69  Aligned_cols=310  Identities=19%  Similarity=0.235  Sum_probs=240.7

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q 010709          133 MKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEK  212 (503)
Q Consensus       133 ~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~  212 (503)
                      ......+|...+++-|.++|...+.|+|++|.+|||.||++||++|++..           ++..|||.|...|.+.+..
T Consensus       254 ~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~-----------~gitvVISPL~SLm~DQv~  322 (941)
T KOG0351|consen  254 LLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL-----------GGVTVVISPLISLMQDQVT  322 (941)
T ss_pred             HHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc-----------CCceEEeccHHHHHHHHHH
Confidence            33446689999999999999999999999999999999999999999865           5678999999999776555


Q ss_pred             HHHHHhccCCCceEEEEECCccHHHHH---HHhhC---CCcEEEECcHHHHHHHH--cCCCCCCC---ccEEEecchhHH
Q 010709          213 EVKALSRSLDSFKTAIVVGGTNIAEQR---SELRG---GVSIVVATPGRFLDHLQ--QGNTSLSR---VSFVILDEADRM  281 (503)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~---~~~Ilv~Tp~~l~~~l~--~~~~~l~~---~~~vViDEaH~l  281 (503)
                      .+...     ++....+.++....++.   ..+..   ..+|++.||+++...-.  .....+..   +.++||||||+.
T Consensus       323 ~L~~~-----~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDEAHCV  397 (941)
T KOG0351|consen  323 HLSKK-----GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDEAHCV  397 (941)
T ss_pred             hhhhc-----CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecHHHHh
Confidence            44322     47788888887765332   33332   58999999999843221  11223333   889999999999


Q ss_pred             hhCC--CHHHHHHHHHh--CCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH
Q 010709          282 LDMG--FEPQIREVMQN--LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       282 ~~~~--~~~~~~~il~~--~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      .+|+  |++.+.++...  ..+...+|++|||.+..++..+-..++-.... +........++...+..-........+.
T Consensus       398 SqWgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~-~~~~sfnR~NL~yeV~~k~~~~~~~~~~  476 (941)
T KOG0351|consen  398 SQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPE-LFKSSFNRPNLKYEVSPKTDKDALLDIL  476 (941)
T ss_pred             hhhcccccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcc-eecccCCCCCceEEEEeccCccchHHHH
Confidence            9996  99988876432  23347799999999999888777666532222 2233344445544444433222222222


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      .....        .++....||||.++.+|+.++..|+..|+.+..||+||+..+|..|.+.|..++++|+|||=++++|
T Consensus       477 ~~~~~--------~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~~~~R~~Vq~~w~~~~~~VivATVAFGMG  548 (941)
T KOG0351|consen  477 EESKL--------RHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLPPKERETVQKAWMSDKIRVIVATVAFGMG  548 (941)
T ss_pred             HHhhh--------cCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCCHHHHHHHHHHHhcCCCeEEEEEeeccCC
Confidence            22222        2566779999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      ||.|+|+.||+|.+|++++.|.|-+|||||
T Consensus       549 IdK~DVR~ViH~~lPks~E~YYQE~GRAGR  578 (941)
T KOG0351|consen  549 IDKPDVRFVIHYSLPKSFEGYYQEAGRAGR  578 (941)
T ss_pred             CCCCceeEEEECCCchhHHHHHHhccccCc
Confidence            999999999999999999999999999999

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=100.00  E-value=1e-35  Score=319.43  Aligned_cols=287  Identities=20%  Similarity=0.286  Sum_probs=199.5

Q ss_pred             HHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH----HHHHHHHHHHHH-HhccCC
Q 010709          148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR----ELAQQIEKEVKA-LSRSLD  222 (503)
Q Consensus       148 Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr----~La~q~~~~~~~-~~~~~~  222 (503)
                      ..+.+..+..++.++|+|+||||||+  ++|.+......     +..+.+++..|+|    +||.++++++.. ++..  
T Consensus        79 r~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g~-----g~~g~I~~TQPRRlAArsLA~RVA~El~~~lG~~--  149 (1294)
T PRK11131         79 KQDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELGR-----GVKGLIGHTQPRRLAARTVANRIAEELETELGGC--  149 (1294)
T ss_pred             HHHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcCC-----CCCCceeeCCCcHHHHHHHHHHHHHHHhhhhcce--
Confidence            44555566667779999999999999  58876654432     1224566677976    555555555543 2211  


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh-HHhhCCCHHH-HHHHHHhCCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD-RMLDMGFEPQ-IREVMQNLPDK  300 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH-~l~~~~~~~~-~~~il~~~~~~  300 (503)
                       +.+.+.+..        ....+++|+|||||+|++++... ..+.++++||||||| ++++.+|... +.+++.. +++
T Consensus       150 -VGY~vrf~~--------~~s~~t~I~v~TpG~LL~~l~~d-~~Ls~~~~IIIDEAHERsLn~DfLLg~Lk~lL~~-rpd  218 (1294)
T PRK11131        150 -VGYKVRFND--------QVSDNTMVKLMTDGILLAEIQQD-RLLMQYDTIIIDEAHERSLNIDFILGYLKELLPR-RPD  218 (1294)
T ss_pred             -eceeecCcc--------ccCCCCCEEEEChHHHHHHHhcC-CccccCcEEEecCccccccccchHHHHHHHhhhc-CCC
Confidence             111111111        12356899999999999999864 458999999999999 5888887754 3344333 357


Q ss_pred             CcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChh------hHHHHHHHHHHHHHHhhhccCCCC
Q 010709          301 HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSEN------EKVDRLLALLVEEAFLAEKSCHPF  374 (503)
Q Consensus       301 ~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~k~~~l~~~l~~~~~~~~~~~~~~  374 (503)
                      .|+|+||||++.  +.+.+.|...| .+.+....   ..+...+......      ..+..++..+....      ..+.
T Consensus       219 lKvILmSATid~--e~fs~~F~~ap-vI~V~Gr~---~pVei~y~p~~~~~~~~~~d~l~~ll~~V~~l~------~~~~  286 (1294)
T PRK11131        219 LKVIITSATIDP--ERFSRHFNNAP-IIEVSGRT---YPVEVRYRPIVEEADDTERDQLQAIFDAVDELG------REGP  286 (1294)
T ss_pred             ceEEEeeCCCCH--HHHHHHcCCCC-EEEEcCcc---ccceEEEeecccccchhhHHHHHHHHHHHHHHh------cCCC
Confidence            899999999964  45555555455 34454332   2344444443221      12222222222111      1345


Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCe---EEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLH---AVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL  451 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~---v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~  451 (503)
                      +.+||||+++++++.+++.|.+.++.   +.++||++++.+|..+++.  .|..+|||||+++++|||||+|++||++|+
T Consensus       287 GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls~~eQ~~Vf~~--~g~rkIIVATNIAEtSITIpgI~yVID~Gl  364 (1294)
T PRK11131        287 GDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLSNSEQNRVFQS--HSGRRIVLATNVAETSLTVPGIKYVIDPGT  364 (1294)
T ss_pred             CCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCCHHHHHHHhcc--cCCeeEEEeccHHhhccccCcceEEEECCC
Confidence            77999999999999999999987654   7899999999999999986  578999999999999999999999999974


Q ss_pred             ---------------C---CChhHHHHhhCcceee
Q 010709          452 ---------------P---KVLLAASESLCTTSFN  468 (503)
Q Consensus       452 ---------------p---~s~~~~~Qr~GR~gR~  468 (503)
                                     |   -|.++|.||+||+||.
T Consensus       365 ~k~~~Yd~~~~~~~Lp~~~iSkasa~QRaGRAGR~  399 (1294)
T PRK11131        365 ARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV  399 (1294)
T ss_pred             ccccccccccCcccCCeeecCHhhHhhhccccCCC
Confidence                           3   3558999999999995

>PRK13766 Hef nuclease; Provisional

Probab=100.00  E-value=6.7e-35  Score=315.34  Aligned_cols=313  Identities=24%  Similarity=0.296  Sum_probs=227.6

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      +...|+++|.+++..++.+ ++++++|||+|||+++++++...+..       .++++||++|+++|+.|+.+.++++..
T Consensus        12 ~~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~-------~~~~vLvl~Pt~~L~~Q~~~~~~~~~~   83 (773)
T PRK13766         12 NTIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK-------KGGKVLILAPTKPLVEQHAEFFRKFLN   83 (773)
T ss_pred             CcCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh-------CCCeEEEEeCcHHHHHHHHHHHHHHhC
Confidence            3457899999999988877 99999999999999998877766532       257899999999999999999998864


Q ss_pred             cCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC
Q 010709          220 SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD  299 (503)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~  299 (503)
                      .. ...+..+.|+....+ ...+..+.+|+|+||+.+...+..+.+.+.++++|||||||++.+......+...+....+
T Consensus        84 ~~-~~~v~~~~g~~~~~~-r~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~~  161 (773)
T PRK13766         84 IP-EEKIVVFTGEVSPEK-RAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDAK  161 (773)
T ss_pred             CC-CceEEEEeCCCCHHH-HHHHHhCCCEEEECHHHHHHHHHcCCCChhhCcEEEEECCccccccccHHHHHHHHHhcCC
Confidence            32 346777777766543 4455667899999999998888777788899999999999998766444444444444455


Q ss_pred             CCcEEEEEeeCCHH---HHHHHHHhcCCCeEEEeCCCCC-----CCCceEEEEEEcCh----------------------
Q 010709          300 KHQTLLFSATMPVE---IEALAQEYLTDPVQVKVGKVSS-----PTANVIQILEKVSE----------------------  349 (503)
Q Consensus       300 ~~q~i~~SAT~~~~---~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~----------------------  349 (503)
                      ..++++||||+...   +.............+.......     ....+.......+.                      
T Consensus       162 ~~~il~lTaTP~~~~~~i~~~~~~L~i~~v~~~~~~~~~v~~~~~~~~v~~~~v~l~~~~~~i~~~l~~~~~~~l~~l~~  241 (773)
T PRK13766        162 NPLVLGLTASPGSDEEKIKEVCENLGIEHVEVRTEDDPDVKPYVHKVKIEWVRVELPEELKEIRDLLNEALKDRLKKLKE  241 (773)
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHhCCceEEEEcCCCChhHHhhhccceeEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67799999998533   2333333322221111100000     00000000000000                      


Q ss_pred             --------------------------------------------------------------------------------
Q 010709          350 --------------------------------------------------------------------------------  349 (503)
Q Consensus       350 --------------------------------------------------------------------------------  349 (503)
                                                                                                      
T Consensus       242 ~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~y~~~l~~~~~~~~~~~  321 (773)
T PRK13766        242 LGVIVSISPDVSKKELLGLQKKLQQEIANDDSEGYEAISILAEAMKLRHAVELLETQGVEALRRYLERLREEARSSGGSK  321 (773)
T ss_pred             CCCcccCCCCcCHHHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHhhccccCCcH
Confidence                                                                                            


Q ss_pred             ------------------------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEc
Q 010709          350 ------------------------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALH  405 (503)
Q Consensus       350 ------------------------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh  405 (503)
                                              ..|...+..++.+.     ....+..++||||+++..|+.+++.|...++.+..+|
T Consensus       322 ~~~~l~~~~~~~~~~~~~~~~~~~~pK~~~L~~il~~~-----~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~  396 (773)
T PRK13766        322 ASKRLVEDPRFRKAVRKAKELDIEHPKLEKLREIVKEQ-----LGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFV  396 (773)
T ss_pred             HHHHHHhCHHHHHHHHHHHhcccCChHHHHHHHHHHHH-----HhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEE
Confidence                                    00000000000000     0013567899999999999999999999999999998


Q ss_pred             CC--------CCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          406 GG--------RNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       406 ~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |.        +++.+|.++++.|++|+.+|||||+++++|+|+|++++||+||+|++...|+||+||+||
T Consensus       397 g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~~~~eGldi~~~~~VI~yd~~~s~~r~iQR~GR~gR  466 (773)
T PRK13766        397 GQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGR  466 (773)
T ss_pred             ccccccccCCCCHHHHHHHHHHHHcCCCCEEEECChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccCc
Confidence            86        999999999999999999999999999999999999999999999999999999999999

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

Probab=100.00  E-value=1.1e-36  Score=281.26  Aligned_cols=313  Identities=17%  Similarity=0.247  Sum_probs=227.4

Q ss_pred             HHHHH-CCCCC-CcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q 010709          134 KDIEF-HEYTR-PTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI  210 (503)
Q Consensus       134 ~~l~~-~~~~~-~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~  210 (503)
                      +.|++ +|+.. -++.|.+|+..+..+ +||.|++|||+||++||++|.|.+           +...||+.|..+|...+
T Consensus         9 eaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~-----------~gITIV~SPLiALIkDQ   77 (641)
T KOG0352|consen    9 EALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVH-----------GGITIVISPLIALIKDQ   77 (641)
T ss_pred             HHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHh-----------CCeEEEehHHHHHHHHH
Confidence            44433 45544 377899999998865 589999999999999999999976           45789999999998888


Q ss_pred             HHHHHHHhccCCCceEEEEECCccHHHHHHH------hhCCCcEEEECcHHHH----HHHHcCCCCCCCccEEEecchhH
Q 010709          211 EKEVKALSRSLDSFKTAIVVGGTNIAEQRSE------LRGGVSIVVATPGRFL----DHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~Ilv~Tp~~l~----~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      .+.+..+-     +.+..+....+..+..+.      .+....+++.||+...    +-+.+....-..+.++|+||||+
T Consensus        78 iDHL~~LK-----Vp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHC  152 (641)
T KOG0352|consen   78 IDHLKRLK-----VPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHC  152 (641)
T ss_pred             HHHHHhcC-----CchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHHHhhhceeeeEEechhhh
Confidence            88777763     444444444333332222      2356789999998752    22223333456689999999999


Q ss_pred             HhhCC--CHHHHHHH--HHhCCCCCcEEEEEeeCCHHHHHHHH--HhcCCCeEEEeCCCCCCCCceEEEEEEcChhh---
Q 010709          281 MLDMG--FEPQIREV--MQNLPDKHQTLLFSATMPVEIEALAQ--EYLTDPVQVKVGKVSSPTANVIQILEKVSENE---  351 (503)
Q Consensus       281 l~~~~--~~~~~~~i--l~~~~~~~q~i~~SAT~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---  351 (503)
                      ..+||  |++.+.++  ++..-+....++++||..+.+++.+-  -.+.+|+.+.-....  ..++   +..+...+   
T Consensus       153 VSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~F--R~NL---FYD~~~K~~I~  227 (641)
T KOG0352|consen  153 VSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTF--RDNL---FYDNHMKSFIT  227 (641)
T ss_pred             HhhhccccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcch--hhhh---hHHHHHHHHhh
Confidence            99996  88888766  33334567799999999998887543  345677665322111  1111   11111111   


Q ss_pred             -HHHHHHHHHHH----HHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q 010709          352 -KVDRLLALLVE----EAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTN  426 (503)
Q Consensus       352 -k~~~l~~~l~~----~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~  426 (503)
                       -...|.++...    ............+-.||||.++++|++++-.|...|+++..+|.|+...+|.++.+.|.+++..
T Consensus       228 D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq~AI~l~~~Gi~A~AYHAGLK~~ERTeVQe~WM~~~~P  307 (641)
T KOG0352|consen  228 DCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQVAIMLEIAGIPAMAYHAGLKKKERTEVQEKWMNNEIP  307 (641)
T ss_pred             hHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHHHHHHhhhcCcchHHHhcccccchhHHHHHHHhcCCCC
Confidence             11122222111    1111111222335589999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          427 ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       427 vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |++||..+++|+|-|+|++||++++|++++-|.|..|||||
T Consensus       308 vI~AT~SFGMGVDKp~VRFViHW~~~qn~AgYYQESGRAGR  348 (641)
T KOG0352|consen  308 VIAATVSFGMGVDKPDVRFVIHWSPSQNLAGYYQESGRAGR  348 (641)
T ss_pred             EEEEEeccccccCCcceeEEEecCchhhhHHHHHhcccccc
Confidence            99999999999999999999999999999999999999999

>COG1204 Superfamily II helicase [General function prediction only]

Probab=100.00  E-value=4e-36  Score=313.67  Aligned_cols=323  Identities=19%  Similarity=0.237  Sum_probs=240.1

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHHHh-cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          127 CLHPSIMKDIEFHEYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       127 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      .+++.+.+-+...++..+.+.|+.++...+ .++|++||+|||+|||+.+++.++..+...       +.+++||+|+++
T Consensus        15 ~~~~~v~~i~~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~-------~~k~vYivPlkA   87 (766)
T COG1204          15 KLDDRVLEILKGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG-------GGKVVYIVPLKA   87 (766)
T ss_pred             cccHHHHHHhccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc-------CCcEEEEeChHH
Confidence            366777788888888888888988888765 558999999999999999999999887764       577999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       206 La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      ||.+.+++++++-. + ++++...+|+......   .-.+++|+|+||+++...+.+......++++|||||+|.+.+..
T Consensus        88 La~Ek~~~~~~~~~-~-GirV~~~TgD~~~~~~---~l~~~~ViVtT~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~  162 (766)
T COG1204          88 LAEEKYEEFSRLEE-L-GIRVGISTGDYDLDDE---RLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRT  162 (766)
T ss_pred             HHHHHHHHhhhHHh-c-CCEEEEecCCcccchh---hhccCCEEEEchHHhhHhhhcCcchhhcccEEEEeeeeecCCcc
Confidence            99999999994433 2 6999999999875542   23569999999999988888776678899999999999777666


Q ss_pred             CHHHHHHHHHhCC---CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCC-CCceEEEEEEcChhh------HHHH
Q 010709          286 FEPQIREVMQNLP---DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSP-TANVIQILEKVSENE------KVDR  355 (503)
Q Consensus       286 ~~~~~~~il~~~~---~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~------k~~~  355 (503)
                      .++.++.++.+.+   ...|++++|||+|+. .+++...-.++..-.+...... .....+.+.......      +...
T Consensus       163 RG~~lE~iv~r~~~~~~~~rivgLSATlpN~-~evA~wL~a~~~~~~~rp~~l~~~v~~~~~~~~~~~~~k~~~~~~~~~  241 (766)
T COG1204         163 RGPVLESIVARMRRLNELIRIVGLSATLPNA-EEVADWLNAKLVESDWRPVPLRRGVPYVGAFLGADGKKKTWPLLIDNL  241 (766)
T ss_pred             cCceehhHHHHHHhhCcceEEEEEeeecCCH-HHHHHHhCCcccccCCCCcccccCCccceEEEEecCccccccccchHH
Confidence            7777777766543   447999999999754 4455544444332122221111 111122222222111      2222


Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-------------------------------------C
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-------------------------------------G  398 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-------------------------------------~  398 (503)
                      .+..+....       ...+++||||++++.+...++.++..                                     .
T Consensus       242 ~~~~v~~~~-------~~~~qvLvFv~sR~~a~~~A~~l~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~l~e~v~  314 (766)
T COG1204         242 ALELVLESL-------AEGGQVLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVL  314 (766)
T ss_pred             HHHHHHHHH-------hcCCeEEEEEecCchHHHHHHHHHHHHhhcCChhhhhhccccccccccccccccchHHHHHHHH
Confidence            333333222       24567999999999999999998730                                     0


Q ss_pred             CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE-----cc-----CCCChhHHHHhhCcceee
Q 010709          399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN-----LD-----LPKVLLAASESLCTTSFN  468 (503)
Q Consensus       399 ~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~-----~~-----~p~s~~~~~Qr~GR~gR~  468 (503)
                      ..+..+|+|++.++|..+.+.|++|.++||+||..++.|+|+|. +.||.     |+     .+-+..+++|++|||||-
T Consensus       315 ~GvafHhAGL~~~~R~~vE~~Fr~g~ikVlv~TpTLA~GVNLPA-~~VIIk~~~~y~~~~g~~~i~~~dv~QM~GRAGRP  393 (766)
T COG1204         315 RGVAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPA-RTVIIKDTRRYDPKGGIVDIPVLDVLQMAGRAGRP  393 (766)
T ss_pred             hCccccccCCCHHHHHHHHHHHhcCCceEEEechHHhhhcCCcc-eEEEEeeeEEEcCCCCeEECchhhHhhccCcCCCC
Confidence            24778999999999999999999999999999999999999995 55553     55     344678999999999995


Q ss_pred             ee
Q 010709          469 IT  470 (503)
Q Consensus       469 ~~  470 (503)
                      .+
T Consensus       394 g~  395 (766)
T COG1204         394 GY  395 (766)
T ss_pred             Cc
Confidence            43

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=100.00  E-value=1.1e-34  Score=312.68  Aligned_cols=290  Identities=19%  Similarity=0.240  Sum_probs=206.3

Q ss_pred             HHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEE
Q 010709          150 QAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIV  229 (503)
Q Consensus       150 ~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~  229 (503)
                      +.+..+.+++.+||+|+||||||+  ++|.+......     +..++++++.|+|..|..+++.+.+...    ..++..
T Consensus        74 ~Il~~l~~~~vvii~g~TGSGKTT--qlPq~lle~~~-----~~~~~I~~tQPRRlAA~svA~RvA~elg----~~lG~~  142 (1283)
T TIGR01967        74 DIAEAIAENQVVIIAGETGSGKTT--QLPKICLELGR-----GSHGLIGHTQPRRLAARTVAQRIAEELG----TPLGEK  142 (1283)
T ss_pred             HHHHHHHhCceEEEeCCCCCCcHH--HHHHHHHHcCC-----CCCceEecCCccHHHHHHHHHHHHHHhC----CCcceE
Confidence            455555566779999999999999  57877654332     1234677788999999888888776552    333333


Q ss_pred             ECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh-HHhhCCCHHH-HHHHHHhCCCCCcEEEEE
Q 010709          230 VGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD-RMLDMGFEPQ-IREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       230 ~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH-~l~~~~~~~~-~~~il~~~~~~~q~i~~S  307 (503)
                      +|.....+  .....+++|+|+|+|+|++++... ..+.++++||||||| ++++.+|... +.+++.. +++.|+|+||
T Consensus       143 VGY~vR~~--~~~s~~T~I~~~TdGiLLr~l~~d-~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~-rpdLKlIlmS  218 (1283)
T TIGR01967       143 VGYKVRFH--DQVSSNTLVKLMTDGILLAETQQD-RFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPR-RPDLKIIITS  218 (1283)
T ss_pred             EeeEEcCC--cccCCCceeeeccccHHHHHhhhC-cccccCcEEEEcCcchhhccchhHHHHHHHHHhh-CCCCeEEEEe
Confidence            34321111  112456899999999999998764 458999999999999 5888887765 4555444 4688999999


Q ss_pred             eeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcCh------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEE
Q 010709          308 ATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFV  381 (503)
Q Consensus       308 AT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~  381 (503)
                      ||++.  ..+.+.|...|+ +.+.....   .+...+.....      ..+...+...+.....      ...+.+|||+
T Consensus       219 ATld~--~~fa~~F~~apv-I~V~Gr~~---PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~------~~~GdILVFL  286 (1283)
T TIGR01967       219 ATIDP--ERFSRHFNNAPI-IEVSGRTY---PVEVRYRPLVEEQEDDDLDQLEAILDAVDELFA------EGPGDILIFL  286 (1283)
T ss_pred             CCcCH--HHHHHHhcCCCE-EEECCCcc---cceeEEecccccccchhhhHHHHHHHHHHHHHh------hCCCCEEEeC
Confidence            99964  455555544453 44443322   23333333221      1233333333332211      1346799999


Q ss_pred             cchhhHHHHHHHHHHCC---CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC-----
Q 010709          382 ERKTRCDEVSEALVAEG---LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK-----  453 (503)
Q Consensus       382 ~~~~~~~~l~~~L~~~~---~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~-----  453 (503)
                      +++.+++.+++.|.+.+   +.+.++||++++++|.++++.+  +..+|||||+++++|||||+|++||++|+++     
T Consensus       287 pg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls~~eQ~~vf~~~--~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd  364 (1283)
T TIGR01967       287 PGEREIRDAAEILRKRNLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYS  364 (1283)
T ss_pred             CCHHHHHHHHHHHHhcCCCCcEEEeccCCCCHHHHHHHhCCC--CCceEEEeccHHHhccccCCeeEEEeCCCccccccc
Confidence            99999999999998764   4689999999999999997754  3479999999999999999999999999654     


Q ss_pred             -------------ChhHHHHhhCcceee
Q 010709          454 -------------VLLAASESLCTTSFN  468 (503)
Q Consensus       454 -------------s~~~~~Qr~GR~gR~  468 (503)
                                   |.++|.||.||+||.
T Consensus       365 ~~~~~~~L~~~~ISkasa~QRaGRAGR~  392 (1283)
T TIGR01967       365 YRTKVQRLPIEPISQASANQRKGRCGRV  392 (1283)
T ss_pred             cccCccccCCccCCHHHHHHHhhhhCCC
Confidence                         458999999999995

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.

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=100.00  E-value=4.6e-34  Score=295.74  Aligned_cols=306  Identities=17%  Similarity=0.177  Sum_probs=226.1

Q ss_pred             CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|. .|+++|..+.+.+++|+  |+.+.||+|||+++.+|++...+.        |+.++|++||++||.|.++.+..+.
T Consensus        75 ~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~--------G~~v~VvTpt~~LA~qd~e~~~~l~  143 (790)
T PRK09200         75 LGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE--------GKGVHLITVNDYLAKRDAEEMGQVY  143 (790)
T ss_pred             hCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc--------CCCeEEEeCCHHHHHHHHHHHHHHH
Confidence            354 89999999999888876  999999999999999999866554        6789999999999999999999999


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hCC-----
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DMG-----  285 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~~-----  285 (503)
                      ..+ ++.++++.|+.....+.+ ...+++|+++||+.| .+++..+      ...++.+.++||||||.++ +..     
T Consensus       144 ~~l-Gl~v~~i~g~~~~~~~r~-~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiLiDea~tpli  221 (790)
T PRK09200        144 EFL-GLTVGLNFSDIDDASEKK-AIYEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSILLDEAQTPLI  221 (790)
T ss_pred             hhc-CCeEEEEeCCCCcHHHHH-HhcCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccceeccCCCcee
Confidence            887 699999999988433333 335699999999999 4544432      1356789999999999732 100     


Q ss_pred             ----------CHHHHHHHHHhCCC--------------------------------------------------------
Q 010709          286 ----------FEPQIREVMQNLPD--------------------------------------------------------  299 (503)
Q Consensus       286 ----------~~~~~~~il~~~~~--------------------------------------------------------  299 (503)
                                .......+...+..                                                        
T Consensus       222 isg~~~~~~~~y~~~~~~~~~l~~~~dy~~d~~~~~~~lt~~g~~~~e~~~~i~~l~~~~~~~~~~~i~~Al~A~~~~~~  301 (790)
T PRK09200        222 ISGKPRVQSNLYHIAAKFVKTLEEDVDYEFDEEKKEVWLTDQGIEKAESYFGIDNLYSLEHQVLYRHIILALRAHVLFKR  301 (790)
T ss_pred             eeCCCccccHHHHHHHHHHHhcccCCCeEEecCCCeEEecHhHHHHHHHhcCCccccChhhhHHHHHHHHHHHHHHHhhc
Confidence                      00011111111100                                                        


Q ss_pred             C-------------------------------------------------------------CcEEEEEeeCCHHHHHHH
Q 010709          300 K-------------------------------------------------------------HQTLLFSATMPVEIEALA  318 (503)
Q Consensus       300 ~-------------------------------------------------------------~q~i~~SAT~~~~~~~~~  318 (503)
                      +                                                             .++.+||+|....-.++.
T Consensus       302 d~dYiV~~~~v~ivD~~TGr~~~gr~~s~GlhQaieaKe~v~i~~e~~t~a~It~q~~fr~Y~kl~GmTGTa~t~~~e~~  381 (790)
T PRK09200        302 DVDYIVYDGEIVLVDRFTGRVLPGRKLQDGLHQAIEAKEGVEITEENRTMASITIQNLFRMFPKLSGMTGTAKTEEKEFF  381 (790)
T ss_pred             CCcEEEECCEEEEEECCCCcCCCCCccChHHHHHHHHhcCCCcCCCceehhhhhHHHHHHHhHHHhccCCCChHHHHHHH
Confidence            0                                                             146677888755444444


Q ss_pred             HHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC
Q 010709          319 QEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG  398 (503)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~  398 (503)
                      +.| +-.+.......+.... -..-........|...+...+.....       ...++||||++++.++.+++.|.+.|
T Consensus       382 ~~Y-~l~v~~IPt~kp~~r~-d~~~~i~~~~~~K~~al~~~i~~~~~-------~~~pvLIf~~t~~~se~l~~~L~~~g  452 (790)
T PRK09200        382 EVY-NMEVVQIPTNRPIIRI-DYPDKVFVTLDEKYKAVIEEVKERHE-------TGRPVLIGTGSIEQSETFSKLLDEAG  452 (790)
T ss_pred             HHh-CCcEEECCCCCCcccc-cCCCeEEcCHHHHHHHHHHHHHHHHh-------cCCCEEEEeCcHHHHHHHHHHHHHCC
Confidence            433 3333221111111111 11123344667788888887765321       34579999999999999999999999


Q ss_pred             CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCC---CCCC-----EEEEccCCCChhHHHHhhCcceee
Q 010709          399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDV---MGVA-----HVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       399 ~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldi---p~v~-----~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.+..+||.+.+.++..+...++.|  .|+|||++++||+||   |+|.     +||++++|.+...|.||+||+||.
T Consensus       453 i~~~~L~~~~~~~e~~~i~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~  528 (790)
T PRK09200        453 IPHNLLNAKNAAKEAQIIAEAGQKG--AVTVATNMAGRGTDIKLGEGVHELGGLAVIGTERMESRRVDLQLRGRSGRQ  528 (790)
T ss_pred             CCEEEecCCccHHHHHHHHHcCCCC--eEEEEccchhcCcCCCcccccccccCcEEEeccCCCCHHHHHHhhccccCC
Confidence            9999999999999988888777766  799999999999999   6998     999999999999999999999994

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

Probab=100.00  E-value=1e-33  Score=279.45  Aligned_cols=299  Identities=20%  Similarity=0.227  Sum_probs=216.1

Q ss_pred             HHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-HHhccCCCceEEE
Q 010709          150 QAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK-ALSRSLDSFKTAI  228 (503)
Q Consensus       150 ~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~-~~~~~~~~~~~~~  228 (503)
                      +.+++|.++..+||||+||||||+  ++|.+.+...+.......++.+-|..|+|..|..+++++. +++.....+.+++
T Consensus       263 ~IMEaIn~n~vvIIcGeTGsGKTT--QvPQFLYEAGf~s~~~~~~gmIGITqPRRVAaiamAkRVa~EL~~~~~eVsYqI  340 (1172)
T KOG0926|consen  263 RIMEAINENPVVIICGETGSGKTT--QVPQFLYEAGFASEQSSSPGMIGITQPRRVAAIAMAKRVAFELGVLGSEVSYQI  340 (1172)
T ss_pred             HHHHHhhcCCeEEEecCCCCCccc--cchHHHHHcccCCccCCCCCeeeecCchHHHHHHHHHHHHHHhccCccceeEEE
Confidence            344555556669999999999998  6999999888876656666678888899988888877665 5555345678889


Q ss_pred             EECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-HhhCC-CHHHHHHHHH---hCC-----
Q 010709          229 VVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-MLDMG-FEPQIREVMQ---NLP-----  298 (503)
Q Consensus       229 ~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-l~~~~-~~~~~~~il~---~~~-----  298 (503)
                      .+.++..        ..+.|.|||.|.|++.+.+ ++.|.+++.|||||||. -++.+ ..--+.+|+.   ...     
T Consensus       341 Rfd~ti~--------e~T~IkFMTDGVLLrEi~~-DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~  411 (1172)
T KOG0926|consen  341 RFDGTIG--------EDTSIKFMTDGVLLREIEN-DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQ  411 (1172)
T ss_pred             EeccccC--------CCceeEEecchHHHHHHHH-hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcc
Confidence            9988743        4589999999999999987 78899999999999994 11111 0111222221   111     


Q ss_pred             -CCCcEEEEEeeCCHHHHHHH--HHhcC-CCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCC
Q 010709          299 -DKHQTLLFSATMPVEIEALA--QEYLT-DPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPF  374 (503)
Q Consensus       299 -~~~q~i~~SAT~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~  374 (503)
                       ++.++|+||||+  .+.++.  +..+. -|..+.+..   ....+..++........+...+.....     .+...|.
T Consensus       412 ~kpLKLIIMSATL--RVsDFtenk~LFpi~pPlikVdA---RQfPVsIHF~krT~~DYi~eAfrKtc~-----IH~kLP~  481 (1172)
T KOG0926|consen  412 IKPLKLIIMSATL--RVSDFTENKRLFPIPPPLIKVDA---RQFPVSIHFNKRTPDDYIAEAFRKTCK-----IHKKLPP  481 (1172)
T ss_pred             cCceeEEEEeeeE--EecccccCceecCCCCceeeeec---ccCceEEEeccCCCchHHHHHHHHHHH-----HhhcCCC
Confidence             267899999999  222222  11111 122333322   222333444443333444443333222     2333688


Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC---------------------------------------------------------
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE---------------------------------------------------------  397 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~---------------------------------------------------------  397 (503)
                      |.+|||+.++.++++|++.|++.                                                         
T Consensus       482 G~ILVFvTGQqEV~qL~~kLRK~~p~~f~~~k~~k~~k~~~e~k~~~s~~~~~~k~~dfe~Ed~~~~~ed~d~~~~~~~~  561 (1172)
T KOG0926|consen  482 GGILVFVTGQQEVDQLCEKLRKRFPESFGGVKMKKNVKAFKELKENPSDIGDSNKTDDFEEEDMYESDEDIDQELVDSGF  561 (1172)
T ss_pred             CcEEEEEeChHHHHHHHHHHHhhCccccccchhhhhhhhccccccchhhhccCcccccchhcccccchhhhhhhhhcccc
Confidence            99999999999999999999761                                                         


Q ss_pred             ------------------------------------------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccc
Q 010709          398 ------------------------------------------GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS  435 (503)
Q Consensus       398 ------------------------------------------~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  435 (503)
                                                                .+.|+++|+-++.++|+++++.-..|.+-|+|||++++
T Consensus       562 ~~~raa~~~~~De~~~~nge~e~d~~e~~~E~~~~~~~~~~~pLyvLPLYSLLs~~~Q~RVF~~~p~g~RLcVVaTNVAE  641 (1172)
T KOG0926|consen  562 ASLRAAFNALADENGSVNGEPEKDESEEGQEAEQGKGKFSPGPLYVLPLYSLLSTEKQMRVFDEVPKGERLCVVATNVAE  641 (1172)
T ss_pred             hhhhhhhhccccccccccCCcccchhhhchhhhhccCCCCCCceEEeehhhhcCHHHhhhhccCCCCCceEEEEeccchh
Confidence                                                      14589999999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCCC------------------hhHHHHhhCcceeee
Q 010709          436 RGLDVMGVAHVVNLDLPKV------------------LLAASESLCTTSFNI  469 (503)
Q Consensus       436 ~Gldip~v~~VI~~~~p~s------------------~~~~~Qr~GR~gR~~  469 (503)
                      ++++||++++||++|..+.                  -++.-||.|||||+-
T Consensus       642 TSLTIPgIkYVVD~Gr~K~R~Yd~~TGV~~FeV~wiSkASadQRAGRAGRtg  693 (1172)
T KOG0926|consen  642 TSLTIPGIKYVVDCGRVKERLYDSKTGVSSFEVDWISKASADQRAGRAGRTG  693 (1172)
T ss_pred             cccccCCeeEEEeccchhhhccccccCceeEEEEeeeccccchhccccCCCC
Confidence            9999999999999997653                  377889999999974

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=100.00  E-value=2.6e-33  Score=285.49  Aligned_cols=303  Identities=19%  Similarity=0.192  Sum_probs=225.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|+++|..+...++.|+  |..++||+|||++|.+|++...+.        |..+.|++||++||.|.++.+..+...+
T Consensus        55 ~~p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~--------G~~V~VvTpt~~LA~qdae~~~~l~~~L  124 (745)
T TIGR00963        55 MRPFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT--------GKGVHVVTVNDYLAQRDAEWMGQVYRFL  124 (745)
T ss_pred             CCccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh--------CCCEEEEcCCHHHHHHHHHHHHHHhccC
Confidence            378999999998887776  999999999999999999655443        4569999999999999999999999887


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHhh-CCCH------
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRMLD-MGFE------  287 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~~-~~~~------  287 (503)
                       ++++.++.|+....+...  ...++|+|+||++| .+++..+      ...+..+.++||||+|+++- ....      
T Consensus       125 -GLsv~~i~g~~~~~~r~~--~y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~LIDeaRtpLiisg  201 (745)
T TIGR00963       125 -GLSVGLILSGMSPEERRE--AYACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSILIDEARTPLIISG  201 (745)
T ss_pred             -CCeEEEEeCCCCHHHHHH--hcCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHhHHhhhhHHhhcC
Confidence             599999999988655433  34589999999999 8887765      24678899999999997432 0000      


Q ss_pred             ---------HHHHHHHHhCC--------------------------------------------------------C---
Q 010709          288 ---------PQIREVMQNLP--------------------------------------------------------D---  299 (503)
Q Consensus       288 ---------~~~~~il~~~~--------------------------------------------------------~---  299 (503)
                               .....+.+.+.                                                        .   
T Consensus       202 ~~~~~~~ly~~a~~i~r~L~~~~dy~~de~~k~v~Lt~~G~~~~e~~~~~~~ly~~~~~~~~~~i~~Al~A~~l~~~d~d  281 (745)
T TIGR00963       202 PAEKSTELYLQANRFAKALEKEVHYEVDEKNRAVLLTEKGIKKAEDLLGVDNLYDLENSPLIHYINNALKAKELFEKDVD  281 (745)
T ss_pred             CCCCchHHHHHHHHHHHhhccCCCeEEecCCCceeECHHHHHHHHHHcCCccccChhhhHHHHHHHHHHHHHHHHhcCCc
Confidence                     00000000000                                                        0   


Q ss_pred             ----------------------------------------------------------CCcEEEEEeeCCHHHHHHHHHh
Q 010709          300 ----------------------------------------------------------KHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       300 ----------------------------------------------------------~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                                                                                -.++.+||+|...+...+.+-|
T Consensus       282 YiV~d~~V~ivD~~TGR~~~gr~ws~GLhQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E~~~iY  361 (745)
T TIGR00963       282 YIVRDGEVVIVDEFTGRIMEGRRWSDGLHQAIEAKEGVEIQNENQTLATITYQNFFRLYEKLSGMTGTAKTEEEEFEKIY  361 (745)
T ss_pred             EEEECCEEEEEECCCCcCCCCCccchHHHHHHHHhcCCCcCCCceeeeeeeHHHHHhhCchhhccCCCcHHHHHHHHHHh
Confidence                                                                      0146677888765555444444


Q ss_pred             cCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeE
Q 010709          322 LTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHA  401 (503)
Q Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v  401 (503)
                      -- .+.+.....+..... ..-........|...+...+.+...       .+.++||||++.+.++.+++.|.+.|+.+
T Consensus       362 ~l-~vv~IPtnkp~~R~d-~~d~i~~t~~~k~~ai~~~i~~~~~-------~grpvLV~t~si~~se~ls~~L~~~gi~~  432 (745)
T TIGR00963       362 NL-EVVVVPTNRPVIRKD-LSDLVYKTEEEKWKAVVDEIKERHA-------KGQPVLVGTTSVEKSELLSNLLKERGIPH  432 (745)
T ss_pred             CC-CEEEeCCCCCeeeee-CCCeEEcCHHHHHHHHHHHHHHHHh-------cCCCEEEEeCcHHHHHHHHHHHHHcCCCe
Confidence            33 332221111111111 1122334456677777776655432       34469999999999999999999999999


Q ss_pred             EEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCC-------CCEEEEccCCCChhHHHHhhCcceee
Q 010709          402 VALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMG-------VAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       402 ~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~-------v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ..+|++  +.+|+..+..|+.+...|+|||++++||+||+.       .-+||++++|.+...|.||+||+||.
T Consensus       433 ~~Lna~--q~~rEa~ii~~ag~~g~VtIATnmAgRGtDI~l~~V~~~GGl~VI~t~~p~s~ri~~q~~GRtGRq  504 (745)
T TIGR00963       433 NVLNAK--NHEREAEIIAQAGRKGAVTIATNMAGRGTDIKLEEVKELGGLYVIGTERHESRRIDNQLRGRSGRQ  504 (745)
T ss_pred             EEeeCC--hHHHHHHHHHhcCCCceEEEEeccccCCcCCCccchhhcCCcEEEecCCCCcHHHHHHHhccccCC
Confidence            999998  889999999999999999999999999999998       45999999999999999999999995

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.

>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]

Probab=100.00  E-value=7e-34  Score=259.24  Aligned_cols=313  Identities=17%  Similarity=0.269  Sum_probs=239.1

Q ss_pred             cccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          123 FTDMCLHPSIMKDIEF-HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       123 ~~~~~l~~~l~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      -++++++.+...-|+. +...+++|.|.++|.+.+.|+++++..|||.||++||++|++..           .+.+|+++
T Consensus        73 kd~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a-----------dg~alvi~  141 (695)
T KOG0353|consen   73 KDDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA-----------DGFALVIC  141 (695)
T ss_pred             cCCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc-----------CCceEeec
Confidence            3567788877777753 56788999999999999999999999999999999999999975           57799999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh------hCCCcEEEECcHHHHHH---HHc--CCCCCCCc
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL------RGGVSIVVATPGRFLDH---LQQ--GNTSLSRV  270 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~Ilv~Tp~~l~~~---l~~--~~~~l~~~  270 (503)
                      |...|+..+.-.++.++     +....+.......+..+..      .....+++.||+.+...   +.+  ..+....+
T Consensus       142 plislmedqil~lkqlg-----i~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~~~~~  216 (695)
T KOG0353|consen  142 PLISLMEDQILQLKQLG-----IDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALEAGFF  216 (695)
T ss_pred             hhHHHHHHHHHHHHHhC-----cchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhhccee
Confidence            99999998888888886     3334444444433322111      13478999999988321   111  24456778


Q ss_pred             cEEEecchhHHhhCC--CHHHHH--HHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEE
Q 010709          271 SFVILDEADRMLDMG--FEPQIR--EVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEK  346 (503)
Q Consensus       271 ~~vViDEaH~l~~~~--~~~~~~--~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  346 (503)
                      ++|.|||+|+..+||  |++.+.  .++++--+...+++++||.+..+...++..+.--..+.+. ......++...+..
T Consensus       217 ~~iaidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~-a~fnr~nl~yev~q  295 (695)
T KOG0353|consen  217 KLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFR-AGFNRPNLKYEVRQ  295 (695)
T ss_pred             EEEeecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheee-cccCCCCceeEeee
Confidence            999999999999886  777665  3455555667799999999998888887776533222221 22333444444333


Q ss_pred             cCh--hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q 010709          347 VSE--NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS  424 (503)
Q Consensus       347 ~~~--~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~  424 (503)
                      .+.  ++-+..+.+++....        .+...||||-+++.|+.++..|+..|+.+..+|..|.+.+|.-+-+.|-.|+
T Consensus       296 kp~n~dd~~edi~k~i~~~f--------~gqsgiiyc~sq~d~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~e  367 (695)
T KOG0353|consen  296 KPGNEDDCIEDIAKLIKGDF--------AGQSGIIYCFSQKDCEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGE  367 (695)
T ss_pred             CCCChHHHHHHHHHHhcccc--------CCCcceEEEeccccHHHHHHHHHhcCccccccccccCccccccccccccccc
Confidence            332  333344444443221        2234799999999999999999999999999999999999999999999999


Q ss_pred             CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHH
Q 010709          425 TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASE  460 (503)
Q Consensus       425 ~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Q  460 (503)
                      ++|+|||-++++|||-|+|++||+..+|+++++|.|
T Consensus       368 iqvivatvafgmgidkpdvrfvihhsl~ksienyyq  403 (695)
T KOG0353|consen  368 IQVIVATVAFGMGIDKPDVRFVIHHSLPKSIENYYQ  403 (695)
T ss_pred             eEEEEEEeeecccCCCCCeeEEEecccchhHHHHHH
Confidence            999999999999999999999999999999999999

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=100.00  E-value=3e-33  Score=286.89  Aligned_cols=303  Identities=17%  Similarity=0.157  Sum_probs=214.2

Q ss_pred             CcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCC
Q 010709          144 PTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS  223 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~  223 (503)
                      ++|+|.+++..+..++..|+.++||+|||++|.+|++...+.        ++.++|++|+++||.|+++.+..+...+ +
T Consensus        69 lrpydVQlig~l~l~~G~Iaem~TGeGKTLta~Lpa~l~aL~--------g~~V~VVTpn~yLA~Rdae~m~~l~~~L-G  139 (762)
T TIGR03714        69 MFPYDVQVLGAIVLHQGNIAEMKTGEGKTLTATMPLYLNALT--------GKGAMLVTTNDYLAKRDAEEMGPVYEWL-G  139 (762)
T ss_pred             CCccHHHHHHHHHhcCCceeEecCCcchHHHHHHHHHHHhhc--------CCceEEeCCCHHHHHHHHHHHHHHHhhc-C
Confidence            344444444444434447999999999999999998766543        4569999999999999999999998777 5


Q ss_pred             ceEEEEECCcc---HHHHHHHhhCCCcEEEECcHHH-HHHHHc------CCCCCCCccEEEecchhHHhhC-C-------
Q 010709          224 FKTAIVVGGTN---IAEQRSELRGGVSIVVATPGRF-LDHLQQ------GNTSLSRVSFVILDEADRMLDM-G-------  285 (503)
Q Consensus       224 ~~~~~~~~~~~---~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~------~~~~l~~~~~vViDEaH~l~~~-~-------  285 (503)
                      +.+.+++++..   .....+....+++|+++||++| .+.+..      ....+..+.++|+||||.++-. .       
T Consensus       140 Lsv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDsILiDeartpliis  219 (762)
T TIGR03714       140 LTVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDSVLLDSAQTPLVIS  219 (762)
T ss_pred             CcEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhhHhhccCcCCeeee
Confidence            88888777622   2222233446799999999999 454432      1345678999999999985310 0       


Q ss_pred             --------CHHHHHHHHHhCCC----------------------------------------------------------
Q 010709          286 --------FEPQIREVMQNLPD----------------------------------------------------------  299 (503)
Q Consensus       286 --------~~~~~~~il~~~~~----------------------------------------------------------  299 (503)
                              .......+...+.+                                                          
T Consensus       220 g~~~~~~~~y~~~~~~v~~l~~~~dy~~d~~~~~v~lt~~G~~~~e~~~~~~~l~~~~~~~~~~~i~~al~A~~~~~~d~  299 (762)
T TIGR03714       220 GAPRVQSNLYHIADTFVRTLKEDVDYIFKKDKKEVWLTDKGIEKAEQYFKIDNLYSEEYFELVRHINLALRAHYLFKRNK  299 (762)
T ss_pred             CCCccchHHHHHHHHHHHhcCCCCCeEEEcCCCeeeecHhHHHHHHHHcCCCccCChhhHHHHHHHHHHHHHHHHHhcCC
Confidence                    00011111111100                                                          


Q ss_pred             -----------------------------------------------------------CCcEEEEEeeCCHHHHHHHHH
Q 010709          300 -----------------------------------------------------------KHQTLLFSATMPVEIEALAQE  320 (503)
Q Consensus       300 -----------------------------------------------------------~~q~i~~SAT~~~~~~~~~~~  320 (503)
                                                                                 -.++.+||+|...+-.++.+-
T Consensus       300 dYiV~~~~v~ivD~~TGr~~~gr~~~~GLhQaieaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~~~~~Ef~~i  379 (762)
T TIGR03714       300 DYVVTNGEVVLLDRITGRLLEGTKLQSGIHQAIEAKEHVELSKETRAMASITYQNLFKMFNKLSGMTGTGKVAEKEFIET  379 (762)
T ss_pred             ceEEECCEEEEEECCCCcCCCCCCcchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCChhHHHHHHHH
Confidence                                                                       014667777775555555443


Q ss_pred             hcCCCeEEEeCCCCCCCC-ceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC
Q 010709          321 YLTDPVQVKVGKVSSPTA-NVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL  399 (503)
Q Consensus       321 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~  399 (503)
                      | +-.+.. +. ...+.. .-..-........|...+...+.+...       ...++||||++++.++.+++.|.+.|+
T Consensus       380 Y-~l~v~~-IP-t~kp~~r~d~~d~i~~~~~~K~~ai~~~i~~~~~-------~~~pvLIft~s~~~se~ls~~L~~~gi  449 (762)
T TIGR03714       380 Y-SLSVVK-IP-TNKPIIRIDYPDKIYATLPEKLMATLEDVKEYHE-------TGQPVLLITGSVEMSEIYSELLLREGI  449 (762)
T ss_pred             h-CCCEEE-cC-CCCCeeeeeCCCeEEECHHHHHHHHHHHHHHHhh-------CCCCEEEEECcHHHHHHHHHHHHHCCC
Confidence            3 333222 11 111111 112224555667888888887766432       234699999999999999999999999


Q ss_pred             eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCC---------CCCEEEEccCCCChhHHHHhhCcceee
Q 010709          400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM---------GVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       400 ~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip---------~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .+..+||.+.+.++..+.+.++.|  .|+|||++++||+||+         ++.+|+++++|..... .||+||+||.
T Consensus       450 ~~~~L~a~~~~~E~~ii~~ag~~g--~VlIATdmAgRGtDI~l~~~v~~~GGL~vIit~~~ps~rid-~qr~GRtGRq  524 (762)
T TIGR03714       450 PHNLLNAQNAAKEAQIIAEAGQKG--AVTVATSMAGRGTDIKLGKGVAELGGLAVIGTERMENSRVD-LQLRGRSGRQ  524 (762)
T ss_pred             CEEEecCCChHHHHHHHHHcCCCC--eEEEEccccccccCCCCCccccccCCeEEEEecCCCCcHHH-HHhhhcccCC
Confidence            999999999999988887777666  7999999999999999         9999999999998776 9999999993

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.

>TIGR00603 rad25 DNA repair helicase rad25

Probab=100.00  E-value=3e-33  Score=286.96  Aligned_cols=293  Identities=16%  Similarity=0.123  Sum_probs=200.2

Q ss_pred             CCCcHHHHHHHHHHhc-C--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          142 TRPTSIQAQAMPVALS-G--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~-~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..++++|.+++..+.. |  +..++++|||+|||++.+.. +..+          +.++|||||+.+|+.||.++|.++.
T Consensus       254 ~~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~a-a~~l----------~k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       254 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTA-ACTV----------KKSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             CCcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHH-HHHh----------CCCEEEEeCcHHHHHHHHHHHHHhc
Confidence            4689999999999874 3  36899999999999987543 3332          2459999999999999999999986


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC--------CCCCCCccEEEecchhHHhhCCCHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG--------NTSLSRVSFVILDEADRMLDMGFEPQI  290 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~--------~~~l~~~~~vViDEaH~l~~~~~~~~~  290 (503)
                      .. ....+..+.|+...     .......|+|+|++++.....+.        .+.-..+++||+||||++.    ...+
T Consensus       323 ~l-~~~~I~~~tg~~k~-----~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lp----A~~f  392 (732)
T TIGR00603       323 TI-DDSQICRFTSDAKE-----RFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVP----AAMF  392 (732)
T ss_pred             CC-CCceEEEEecCccc-----ccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEcccccc----HHHH
Confidence            32 23455555554321     11234789999999885332211        1233578999999999875    4556


Q ss_pred             HHHHHhCCCCCcEEEEEeeCCHHHHH--HHHHhcCCCeEEEeCCC----CCCCCceEEEEEEcC--h-------------
Q 010709          291 REVMQNLPDKHQTLLFSATMPVEIEA--LAQEYLTDPVQVKVGKV----SSPTANVIQILEKVS--E-------------  349 (503)
Q Consensus       291 ~~il~~~~~~~q~i~~SAT~~~~~~~--~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~--~-------------  349 (503)
                      .+++..+... ..+++||||..+-..  .+..+++ |......-.    ......+....+.++  .             
T Consensus       393 r~il~~l~a~-~RLGLTATP~ReD~~~~~L~~LiG-P~vye~~~~eLi~~G~LA~~~~~ev~v~~t~~~~~~yl~~~~~~  470 (732)
T TIGR00603       393 RRVLTIVQAH-CKLGLTATLVREDDKITDLNFLIG-PKLYEANWMELQKKGFIANVQCAEVWCPMTPEFYREYLRENSRK  470 (732)
T ss_pred             HHHHHhcCcC-cEEEEeecCcccCCchhhhhhhcC-CeeeecCHHHHHhCCccccceEEEEEecCCHHHHHHHHHhcchh
Confidence            6777776544 479999999543221  1222233 322222110    011111111111111  1             


Q ss_pred             --------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHh
Q 010709          350 --------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFR  421 (503)
Q Consensus       350 --------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~  421 (503)
                              ..|...+..++..+       .....++||||.+...+..+++.|.     +..+||++++.+|.++++.|+
T Consensus       471 k~~l~~~np~K~~~~~~Li~~h-------e~~g~kiLVF~~~~~~l~~~a~~L~-----~~~I~G~ts~~ER~~il~~Fr  538 (732)
T TIGR00603       471 RMLLYVMNPNKFRACQFLIRFH-------EQRGDKIIVFSDNVFALKEYAIKLG-----KPFIYGPTSQQERMQILQNFQ  538 (732)
T ss_pred             hhHHhhhChHHHHHHHHHHHHH-------hhcCCeEEEEeCCHHHHHHHHHHcC-----CceEECCCCHHHHHHHHHHHH
Confidence                    11222222222211       1245689999999999888888772     456899999999999999998


Q ss_pred             cC-CCcEEEEccccccCCCCCCCCEEEEccCC-CChhHHHHhhCcceeee
Q 010709          422 NG-STNILVATDVASRGLDVMGVAHVVNLDLP-KVLLAASESLCTTSFNI  469 (503)
Q Consensus       422 ~g-~~~vLvaT~~~~~Gldip~v~~VI~~~~p-~s~~~~~Qr~GR~gR~~  469 (503)
                      .| .+++||+|+++.+|||+|++++||+++.| .|..+|+||+||++|.-
T Consensus       539 ~~~~i~vLv~SkVgdeGIDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~  588 (732)
T TIGR00603       539 HNPKVNTIFLSKVGDTSIDLPEANVLIQISSHYGSRRQEAQRLGRILRAK  588 (732)
T ss_pred             hCCCccEEEEecccccccCCCCCCEEEEeCCCCCCHHHHHHHhcccccCC
Confidence            75 78999999999999999999999999987 59999999999999954

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).

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

Probab=100.00  E-value=9.5e-33  Score=286.65  Aligned_cols=297  Identities=19%  Similarity=0.215  Sum_probs=216.6

Q ss_pred             HHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCC--
Q 010709          146 SIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS--  223 (503)
Q Consensus       146 ~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~--  223 (503)
                      ....+.+.++.+++.+||+|+||+|||++  +|.+.....+     ..++++.++.|+|..|..+++++.+......+  
T Consensus        53 ~~~~~i~~ai~~~~vvii~getGsGKTTq--lP~~lle~g~-----~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~~  125 (845)
T COG1643          53 AVRDEILKAIEQNQVVIIVGETGSGKTTQ--LPQFLLEEGL-----GIAGKIGCTQPRRLAARSVAERVAEELGEKLGET  125 (845)
T ss_pred             HHHHHHHHHHHhCCEEEEeCCCCCChHHH--HHHHHHhhhc-----ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCce
Confidence            33555666677788899999999999994  6666554433     23567888889999999999888766533212  


Q ss_pred             ceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh-HHhhCCCHHH-HHHHHHhCCCCC
Q 010709          224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD-RMLDMGFEPQ-IREVMQNLPDKH  301 (503)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH-~l~~~~~~~~-~~~il~~~~~~~  301 (503)
                      +-+.+.+.+.        ....+.|.++|.|+|++++.. +..+..+++||||||| +.++.++.-. +..++...+++.
T Consensus       126 VGY~iRfe~~--------~s~~Trik~mTdGiLlrei~~-D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DL  196 (845)
T COG1643         126 VGYSIRFESK--------VSPRTRIKVMTDGILLREIQN-DPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDL  196 (845)
T ss_pred             eeEEEEeecc--------CCCCceeEEeccHHHHHHHhh-CcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCc
Confidence            3333444433        334589999999999999987 4559999999999999 4455554443 445577777789


Q ss_pred             cEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC-hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEE
Q 010709          302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS-ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVF  380 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF  380 (503)
                      ++|+||||+..  + ....|+.+...+.+.....   .+...+.... ...++...+.........     ...|.+|||
T Consensus       197 KiIimSATld~--~-rfs~~f~~apvi~i~GR~f---PVei~Y~~~~~~d~~l~~ai~~~v~~~~~-----~~~GdILvF  265 (845)
T COG1643         197 KLIIMSATLDA--E-RFSAYFGNAPVIEIEGRTY---PVEIRYLPEAEADYILLDAIVAAVDIHLR-----EGSGSILVF  265 (845)
T ss_pred             eEEEEecccCH--H-HHHHHcCCCCEEEecCCcc---ceEEEecCCCCcchhHHHHHHHHHHHhcc-----CCCCCEEEE
Confidence            99999999944  3 3455666544555544333   3334442222 222222222222222211     346789999


Q ss_pred             EcchhhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC---
Q 010709          381 VERKTRCDEVSEALVA----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK---  453 (503)
Q Consensus       381 ~~~~~~~~~l~~~L~~----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~---  453 (503)
                      .+++.+++.+++.|.+    ..+.++++||.++.++|.++++.-..|..+|++||++++++|+||+|++||+-+..+   
T Consensus       266 LpG~~EI~~~~~~L~~~~l~~~~~i~PLy~~L~~~eQ~rvF~p~~~~~RKVVlATNIAETSLTI~gIr~VIDsG~ak~~~  345 (845)
T COG1643         266 LPGQREIERTAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKR  345 (845)
T ss_pred             CCcHHHHHHHHHHHHhccccCCcEEeeccccCCHHHHHhhcCCCCCCcceEEEEccccccceeeCCeEEEecCCcccccc
Confidence            9999999999999998    357899999999999999999998888888999999999999999999999988754   


Q ss_pred             ---------------ChhHHHHhhCcceeee
Q 010709          454 ---------------VLLAASESLCTTSFNI  469 (503)
Q Consensus       454 ---------------s~~~~~Qr~GR~gR~~  469 (503)
                                     |-+++.||.|||||+.
T Consensus       346 y~~~~g~~~L~~~~ISqAsA~QRaGRAGR~~  376 (845)
T COG1643         346 YDPRTGLTRLETEPISKASADQRAGRAGRTG  376 (845)
T ss_pred             cccccCceeeeEEEechhhhhhhccccccCC
Confidence                           3489999999999963

>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]

Probab=100.00  E-value=2.7e-32  Score=267.49  Aligned_cols=297  Identities=19%  Similarity=0.222  Sum_probs=220.1

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc-C-C
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS-L-D  222 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~-~-~  222 (503)
                      +.+-.+.+..+..++.+||.|+||||||+  ++|.+.+...+.     ..+++.+..|+|..|..+++++.+-... + .
T Consensus        53 ~~~r~~il~~ve~nqvlIviGeTGsGKST--QipQyL~eaG~~-----~~g~I~~TQPRRVAavslA~RVAeE~~~~lG~  125 (674)
T KOG0922|consen   53 YKYRDQILYAVEDNQVLIVIGETGSGKST--QIPQYLAEAGFA-----SSGKIACTQPRRVAAVSLAKRVAEEMGCQLGE  125 (674)
T ss_pred             HHHHHHHHHHHHHCCEEEEEcCCCCCccc--cHhHHHHhcccc-----cCCcEEeecCchHHHHHHHHHHHHHhCCCcCc
Confidence            33455677777788889999999999998  577776654432     2344888899999998888887755422 1 2


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-HhhCCCHH-HHHHHHHhCCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-MLDMGFEP-QIREVMQNLPDK  300 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-l~~~~~~~-~~~~il~~~~~~  300 (503)
                      .+-+.+.+.+...        ..+.|.++|.|.|++.+.. +-.+.++++||+||||+ -+..+..- .++++++ .+++
T Consensus       126 ~VGY~IRFed~ts--------~~TrikymTDG~LLRE~l~-Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~~-~R~~  195 (674)
T KOG0922|consen  126 EVGYTIRFEDSTS--------KDTRIKYMTDGMLLREILK-DPLLSKYSVIILDEAHERSLHTDILLGLLKKILK-KRPD  195 (674)
T ss_pred             eeeeEEEecccCC--------CceeEEEecchHHHHHHhc-CCccccccEEEEechhhhhhHHHHHHHHHHHHHh-cCCC
Confidence            3455666665543        3489999999999999987 45689999999999994 22222222 2333333 3567


Q ss_pred             CcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEE
Q 010709          301 HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVF  380 (503)
Q Consensus       301 ~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF  380 (503)
                      .++|+||||+.  .+ ....|+.+...+.+....   ..+...+...+..+.++..+..+.+.+..     .+.+-+|||
T Consensus       196 LklIimSATld--a~-kfS~yF~~a~i~~i~GR~---fPVei~y~~~p~~dYv~a~~~tv~~Ih~~-----E~~GDILvF  264 (674)
T KOG0922|consen  196 LKLIIMSATLD--AE-KFSEYFNNAPILTIPGRT---FPVEILYLKEPTADYVDAALITVIQIHLT-----EPPGDILVF  264 (674)
T ss_pred             ceEEEEeeeec--HH-HHHHHhcCCceEeecCCC---CceeEEeccCCchhhHHHHHHHHHHHHcc-----CCCCCEEEE
Confidence            89999999994  33 445566654444444433   34555565566666666666665554433     466779999


Q ss_pred             EcchhhHHHHHHHHHHC--C------CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCC
Q 010709          381 VERKTRCDEVSEALVAE--G------LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP  452 (503)
Q Consensus       381 ~~~~~~~~~l~~~L~~~--~------~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p  452 (503)
                      .+++++++.+++.|.+.  .      .-+.++||.++.++|.++++.-..|.++|+++|+++++.++||++.+||+.|+-
T Consensus       265 LtGqeEIe~~~~~l~e~~~~~~~~~~~~~lply~aL~~e~Q~rvF~p~p~g~RKvIlsTNIAETSlTI~GI~YVVDsG~v  344 (674)
T KOG0922|consen  265 LTGQEEIEAACELLRERAKSLPEDCPELILPLYGALPSEEQSRVFDPAPPGKRKVILSTNIAETSLTIDGIRYVVDSGFV  344 (674)
T ss_pred             eCCHHHHHHHHHHHHHHhhhccccCcceeeeecccCCHHHhhccccCCCCCcceEEEEcceeeeeEEecceEEEEcCCce
Confidence            99999999999999765  1      135789999999999999999999999999999999999999999999998863


Q ss_pred             ------------------CChhHHHHhhCcceeee
Q 010709          453 ------------------KVLLAASESLCTTSFNI  469 (503)
Q Consensus       453 ------------------~s~~~~~Qr~GR~gR~~  469 (503)
                                        -|.++..||.|||||+-
T Consensus       345 K~~~y~p~~g~~~L~v~~ISkasA~QRaGRAGRt~  379 (674)
T KOG0922|consen  345 KQKKYNPRTGLDSLIVVPISKASANQRAGRAGRTG  379 (674)
T ss_pred             EEEeeccccCccceeEEechHHHHhhhcccCCCCC
Confidence                              36699999999999973

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

Probab=100.00  E-value=2.5e-32  Score=277.55  Aligned_cols=321  Identities=19%  Similarity=0.251  Sum_probs=229.0

Q ss_pred             HHHCCCCCCcHHHHHHHHHHhc-CCCeEEEccCCCchhHHhHHHHHHHHHhcCC--CCCCCCCeEEEEcccHHHHHHHHH
Q 010709          136 IEFHEYTRPTSIQAQAMPVALS-GRDLLGCAETGSGKTAAFTIPMIQHCVAQTP--VGRGDGPLALVLAPTRELAQQIEK  212 (503)
Q Consensus       136 l~~~~~~~~~~~Q~~~i~~i~~-~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~--~~~~~~~~~lil~Ptr~La~q~~~  212 (503)
                      ...++|..+..+|.+++|.+++ +.|+|||||||+|||-.|++.+|+.+.+...  .-..++-+++||+|+++||..+.+
T Consensus       103 k~~f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em~~  182 (1230)
T KOG0952|consen  103 KGFFSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEMVD  182 (1230)
T ss_pred             hhcccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEechHHHHHHHHH
Confidence            4557888999999999999985 5689999999999999999999887765221  112346789999999999999888


Q ss_pred             HHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC----CCCCCCccEEEecchhHHhhCCCHH
Q 010709          213 EVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG----NTSLSRVSFVILDEADRMLDMGFEP  288 (503)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~----~~~l~~~~~vViDEaH~l~~~~~~~  288 (503)
                      .+.+-+..+ ++.+..++|++......   -..++|+|+||+++- .+.+.    ...+..+++|||||+| ++....++
T Consensus       183 ~~~kkl~~~-gi~v~ELTGD~ql~~te---i~~tqiiVTTPEKwD-vvTRk~~~d~~l~~~V~LviIDEVH-lLhd~RGp  256 (1230)
T KOG0952|consen  183 KFSKKLAPL-GISVRELTGDTQLTKTE---IADTQIIVTTPEKWD-VVTRKSVGDSALFSLVRLVIIDEVH-LLHDDRGP  256 (1230)
T ss_pred             HHhhhcccc-cceEEEecCcchhhHHH---HHhcCEEEeccccee-eeeeeeccchhhhhheeeEEeeeeh-hhcCcccc
Confidence            887666554 58999999998765543   234999999999983 33322    1246678999999999 55555777


Q ss_pred             HHHHHHHhC-------CCCCcEEEEEeeCCHHHHHHHHHhcCCC-eEEEeCCCCCCCCceEEEEEEcChh---hHHHHHH
Q 010709          289 QIREVMQNL-------PDKHQTLLFSATMPVEIEALAQEYLTDP-VQVKVGKVSSPTANVIQILEKVSEN---EKVDRLL  357 (503)
Q Consensus       289 ~~~~il~~~-------~~~~q~i~~SAT~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~---~k~~~l~  357 (503)
                      .++.|+.+.       ....++|++|||+|+ ..+.+...-.+| ..+...........+.+.+...+..   .+.....
T Consensus       257 vlEtiVaRtlr~vessqs~IRivgLSATlPN-~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~iG~k~~~~~~~~~~~d  335 (1230)
T KOG0952|consen  257 VLETIVARTLRLVESSQSMIRIVGLSATLPN-YEDVARFLRVNPYAGLFSFDQRYRPVPLTQGFIGIKGKKNRQQKKNID  335 (1230)
T ss_pred             hHHHHHHHHHHHHHhhhhheEEEEeeccCCC-HHHHHHHhcCCCccceeeecccccccceeeeEEeeecccchhhhhhHH
Confidence            777776554       346789999999975 444555443442 2232222233334455555554433   2221111


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC-----------------------CeEEEEcCCCCHHHHH
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG-----------------------LHAVALHGGRNQSDRE  414 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~-----------------------~~v~~lh~~~~~~~r~  414 (503)
                      ..+........   ..+.+++|||.+++.....++.|.+..                       .....+|+||...+|.
T Consensus       336 ~~~~~kv~e~~---~~g~qVlvFvhsR~~Ti~tA~~l~~~a~~~g~~~~f~~~~~~k~l~elf~~g~~iHhAGm~r~DR~  412 (1230)
T KOG0952|consen  336 EVCYDKVVEFL---QEGHQVLVFVHSRNETIRTAKKLRERAETNGEKDLFLPSPRNKQLKELFQQGMGIHHAGMLRSDRQ  412 (1230)
T ss_pred             HHHHHHHHHHH---HcCCeEEEEEecChHHHHHHHHHHHHHHhcCcccccCCChhhHHHHHHHHhhhhhcccccchhhHH
Confidence            11111111111   234569999999999999999886521                       2466789999999999


Q ss_pred             HHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE-----ccCCC------ChhHHHHhhCccee
Q 010709          415 SALRDFRNGSTNILVATDVASRGLDVMGVAHVVN-----LDLPK------VLLAASESLCTTSF  467 (503)
Q Consensus       415 ~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~-----~~~p~------s~~~~~Qr~GR~gR  467 (503)
                      -+.+.|..|.++||+||..++.|+|+|+ .+||.     ||..+      .+-+-+|.+|||||
T Consensus       413 l~E~~F~~G~i~vL~cTaTLAwGVNLPA-~aViIKGT~~ydsskg~f~dlgilDVlQifGRAGR  475 (1230)
T KOG0952|consen  413 LVEKEFKEGHIKVLCCTATLAWGVNLPA-YAVIIKGTQVYDSSKGSFVDLGILDVLQIFGRAGR  475 (1230)
T ss_pred             HHHHHHhcCCceEEEecceeeeccCCcc-eEEEecCCcccccccCceeeehHHHHHHHHhccCC
Confidence            9999999999999999999999999994 56664     33333      35778899999999

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=8e-31  Score=237.97  Aligned_cols=202  Identities=51%  Similarity=0.851  Sum_probs=182.4

Q ss_pred             cccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       123 ~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      |+++++++.+.+.+..+|+..|+++|.++++.+.+|+++++++|||+|||++|++|++..+....   ...+++++|++|
T Consensus         1 ~~~~~~~~~i~~~l~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~---~~~~~~viii~p   77 (203)
T cd00268           1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP---KKDGPQALILAP   77 (203)
T ss_pred             CCcCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc---ccCCceEEEEcC
Confidence            67889999999999999999999999999999999999999999999999999999998877642   124688999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHh
Q 010709          203 TRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRML  282 (503)
Q Consensus       203 tr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~  282 (503)
                      +++|+.|+.+.++.+.... ++.+..+.|+....+.......+++|+|+||+.+.+.+.+....+.+++++|+||+|++.
T Consensus        78 ~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~l~~lIvDE~h~~~  156 (203)
T cd00268          78 TRELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRML  156 (203)
T ss_pred             CHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcCCCChhhCCEEEEeChHHhh
Confidence            9999999999999987654 588888999988777666666689999999999999998887888999999999999998


Q ss_pred             hCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEE
Q 010709          283 DMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQV  328 (503)
Q Consensus       283 ~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~  328 (503)
                      +.++...+..++..++.++|++++|||+++....++..++.+|..+
T Consensus       157 ~~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         157 DMGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             ccChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            8889999999999999899999999999999999999999988765

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.

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.98  E-value=5.2e-30  Score=268.85  Aligned_cols=298  Identities=20%  Similarity=0.203  Sum_probs=205.4

Q ss_pred             CCCcHHHHHHHHHHhcC---CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          142 TRPTSIQAQAMPVALSG---RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~---~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..+++.|.++++.+.++   +++++.|+||+|||.+|+.++...+..        ++++||++|+++|+.|+.+.+++.+
T Consensus       143 ~~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~--------g~~vLvLvPt~~L~~Q~~~~l~~~f  214 (679)
T PRK05580        143 PTLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ--------GKQALVLVPEIALTPQMLARFRARF  214 (679)
T ss_pred             CCCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc--------CCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            36899999999999874   679999999999999997766554432        5789999999999999999998865


Q ss_pred             ccCCCceEEEEECCccHHHHHHH----hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCC---HHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSE----LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGF---EPQIR  291 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~---~~~~~  291 (503)
                          +..+..++++....+....    ..+..+|+|+|++.+.       ..+.++++|||||+|.......   .-..+
T Consensus       215 ----g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~-------~p~~~l~liVvDEeh~~s~~~~~~p~y~~r  283 (679)
T PRK05580        215 ----GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF-------LPFKNLGLIIVDEEHDSSYKQQEGPRYHAR  283 (679)
T ss_pred             ----CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc-------ccccCCCEEEEECCCccccccCcCCCCcHH
Confidence                3578888888776543322    2356899999998764       3477899999999997543321   11112


Q ss_pred             H--HHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh-------HHHHHHHHHHH
Q 010709          292 E--VMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-------KVDRLLALLVE  362 (503)
Q Consensus       292 ~--il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------k~~~l~~~l~~  362 (503)
                      .  ++.....+.++|++|||++.+....+..  +....+...............+.......       -...++..+.+
T Consensus       284 ~va~~ra~~~~~~~il~SATps~~s~~~~~~--g~~~~~~l~~r~~~~~~p~v~~id~~~~~~~~~~~~ls~~l~~~i~~  361 (679)
T PRK05580        284 DLAVVRAKLENIPVVLGSATPSLESLANAQQ--GRYRLLRLTKRAGGARLPEVEIIDMRELLRGENGSFLSPPLLEAIKQ  361 (679)
T ss_pred             HHHHHHhhccCCCEEEEcCCCCHHHHHHHhc--cceeEEEeccccccCCCCeEEEEechhhhhhcccCCCCHHHHHHHHH
Confidence            2  2334456789999999997554443321  22223322222111111112222221110       11234444444


Q ss_pred             HHHhhhccCCCCCcEEEEEcchh---------------------------------------------------------
Q 010709          363 EAFLAEKSCHPFPLTIVFVERKT---------------------------------------------------------  385 (503)
Q Consensus       363 ~~~~~~~~~~~~~~~lIF~~~~~---------------------------------------------------------  385 (503)
                      ...       ...++|||+|++.                                                         
T Consensus       362 ~l~-------~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~  434 (679)
T PRK05580        362 RLE-------RGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVP  434 (679)
T ss_pred             HHH-------cCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeEE
Confidence            332       2235888877532                                                         


Q ss_pred             ---hHHHHHHHHHHC--CCeEEEEcCCCCH--HHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE--ccCCCC--
Q 010709          386 ---RCDEVSEALVAE--GLHAVALHGGRNQ--SDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN--LDLPKV--  454 (503)
Q Consensus       386 ---~~~~l~~~L~~~--~~~v~~lh~~~~~--~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~--~~~p~s--  454 (503)
                         .++.+++.|.+.  +.++..+|+++.+  .++.++++.|++|+.+|||+|+++++|+|+|+|++|+.  +|.+-+  
T Consensus       435 ~g~G~e~~~e~l~~~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~iakG~d~p~v~lV~il~aD~~l~~p  514 (679)
T PRK05580        435 VGPGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSP  514 (679)
T ss_pred             eeccHHHHHHHHHHhCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChhhccCCCCCCcCEEEEEcCchhccCC
Confidence               346778888775  7889999999874  67899999999999999999999999999999999954  454433  


Q ss_pred             --------hhHHHHhhCccee
Q 010709          455 --------LLAASESLCTTSF  467 (503)
Q Consensus       455 --------~~~~~Qr~GR~gR  467 (503)
                              ...|.|++||+||
T Consensus       515 dfra~Er~~~~l~q~~GRagR  535 (679)
T PRK05580        515 DFRASERTFQLLTQVAGRAGR  535 (679)
T ss_pred             ccchHHHHHHHHHHHHhhccC
Confidence                    3678999999999

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

Probab=99.98  E-value=8.5e-31  Score=262.24  Aligned_cols=301  Identities=21%  Similarity=0.199  Sum_probs=202.4

Q ss_pred             CCCcHHHHHHHHHHhc----CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALS----GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~----~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..|+++|.+++..+.+    ++..++++|||+|||..++. ++..+          +..+|||+|+++|+.||++.+.+.
T Consensus        35 ~~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~-~~~~~----------~~~~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAE-AIAEL----------KRSTLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHH-HHHHh----------cCCEEEEECcHHHHHHHHHHHHHh
Confidence            4799999999999998    78899999999999987643 33332          233999999999999999888776


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                      ....  ..++.+.|+. ...     .. ..|.|+|.+.+........+...++++||+||||++...    ....+...+
T Consensus       104 ~~~~--~~~g~~~~~~-~~~-----~~-~~i~vat~qtl~~~~~l~~~~~~~~~liI~DE~Hh~~a~----~~~~~~~~~  170 (442)
T COG1061         104 LLLN--DEIGIYGGGE-KEL-----EP-AKVTVATVQTLARRQLLDEFLGNEFGLIIFDEVHHLPAP----SYRRILELL  170 (442)
T ss_pred             cCCc--cccceecCce-ecc-----CC-CcEEEEEhHHHhhhhhhhhhcccccCEEEEEccccCCcH----HHHHHHHhh
Confidence            6321  1233333333 111     11 469999999997752112344557999999999998744    344555555


Q ss_pred             CCCCcEEEEEeeCCHHHHH---HHHHhcCCCeEEEeCCCC----CCCCceEEEEEEc--ChhhHHHH--HH---------
Q 010709          298 PDKHQTLLFSATMPVEIEA---LAQEYLTDPVQVKVGKVS----SPTANVIQILEKV--SENEKVDR--LL---------  357 (503)
Q Consensus       298 ~~~~q~i~~SAT~~~~~~~---~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~--~~~~k~~~--l~---------  357 (503)
                      .....++++|||++.....   .+..+++ |.........    ............+  ........  ..         
T Consensus       171 ~~~~~~LGLTATp~R~D~~~~~~l~~~~g-~~vy~~~~~~li~~g~Lap~~~~~i~~~~t~~~~~~~~~~~~~~~~~~~~  249 (442)
T COG1061         171 SAAYPRLGLTATPEREDGGRIGDLFDLIG-PIVYEVSLKELIDEGYLAPYKYVEIKVTLTEDEEREYAKESARFRELLRA  249 (442)
T ss_pred             hcccceeeeccCceeecCCchhHHHHhcC-CeEeecCHHHHHhCCCccceEEEEEEeccchHHHHHhhhhhhhhhhhhhh
Confidence            4433389999998643311   1122222 2232222110    0111111111111  11000000  00         


Q ss_pred             -------------HHHHH---HHHhhhccCC-CCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHH
Q 010709          358 -------------ALLVE---EAFLAEKSCH-PFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF  420 (503)
Q Consensus       358 -------------~~l~~---~~~~~~~~~~-~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f  420 (503)
                                   .....   .........+ ...+++|||.+..++..++..|...+. +..+.+..+..+|..+++.|
T Consensus       250 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~~~eR~~il~~f  328 (442)
T COG1061         250 RGTLRAENEARRIAIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAILERF  328 (442)
T ss_pred             hhhhhHHHHHHHHhhccHHHHHHHHHHHHHhcCCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCCHHHHHHHHHHH
Confidence                         00000   0000000001 345799999999999999999998888 88999999999999999999


Q ss_pred             hcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       421 ~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|..++||++.++.+|+|+|+++++|....+.|...|+||+||.=|.
T Consensus       329 r~g~~~~lv~~~vl~EGvDiP~~~~~i~~~~t~S~~~~~Q~lGR~LR~  376 (442)
T COG1061         329 RTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGRGLRP  376 (442)
T ss_pred             HcCCCCEEEEeeeccceecCCCCcEEEEeCCCCcHHHHHHHhhhhccC
Confidence            999999999999999999999999999999999999999999998884

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=99.97  E-value=1.1e-29  Score=269.82  Aligned_cols=305  Identities=19%  Similarity=0.221  Sum_probs=194.2

Q ss_pred             CCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          143 RPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      .|.|+|..+...++..  ..++++.++|.|||+.+.+ ++..+...     +...++|||||. .|..||..++.+.+  
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAgl-il~~l~~~-----g~~~rvLIVvP~-sL~~QW~~El~~kF--  222 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGM-IIHQQLLT-----GRAERVLILVPE-TLQHQWLVEMLRRF--  222 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHH-HHHHHHHc-----CCCCcEEEEcCH-HHHHHHHHHHHHHh--
Confidence            5999999998877644  4699999999999998754 44443332     224579999998 79999999997654  


Q ss_pred             CCCceEEEEECCccHHHHHH---HhhCCCcEEEECcHHHHHHHH-cCCCCCCCccEEEecchhHHhhCC-CHHHHHHHHH
Q 010709          221 LDSFKTAIVVGGTNIAEQRS---ELRGGVSIVVATPGRFLDHLQ-QGNTSLSRVSFVILDEADRMLDMG-FEPQIREVMQ  295 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~---~~~~~~~Ilv~Tp~~l~~~l~-~~~~~l~~~~~vViDEaH~l~~~~-~~~~~~~il~  295 (503)
                        ++...++.++.. .....   ......+++|++.+.+.+.-. ...+.-..+++||+||||++.... ......+.+.
T Consensus       223 --~l~~~i~~~~~~-~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y~~v~  299 (956)
T PRK04914        223 --NLRFSLFDEERY-AEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREYQVVE  299 (956)
T ss_pred             --CCCeEEEcCcch-hhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHHHHHH
Confidence              233333332221 11000   111246899999988764211 112233478999999999986321 1111122333


Q ss_pred             hC-CCCCcEEEEEeeCCH-HHHH------------------H-------------HH-----------------HhcCC-
Q 010709          296 NL-PDKHQTLLFSATMPV-EIEA------------------L-------------AQ-----------------EYLTD-  324 (503)
Q Consensus       296 ~~-~~~~q~i~~SAT~~~-~~~~------------------~-------------~~-----------------~~~~~-  324 (503)
                      .+ .....++++||||-. ...+                  +             +.                 .++.+ 
T Consensus       300 ~La~~~~~~LLLTATP~q~~~~e~falL~lLdP~~f~~~~~F~~e~~~~~~~a~~v~~l~~~~~~~~~~~~~l~~ll~~~  379 (956)
T PRK04914        300 QLAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRFHDYEAFVEEQQQYRPVADAVQALLAGEKLSDDALNALGELLGEQ  379 (956)
T ss_pred             HHhhccCCEEEEEcCcccCCcHHHHHhhhhhCCCcCCCHHHHHHHHHhhHHHHHHHHHHhcCCcCCHHHHHHHHHHhccc
Confidence            22 223458999999921 0000                  0             00                 01100 


Q ss_pred             ----------------------------------CeEEEeCCC---CCCCCceEEEEEEcCh------------------
Q 010709          325 ----------------------------------PVQVKVGKV---SSPTANVIQILEKVSE------------------  349 (503)
Q Consensus       325 ----------------------------------~~~~~~~~~---~~~~~~~~~~~~~~~~------------------  349 (503)
                                                        .+.++....   ..+...........+.                  
T Consensus       380 ~~~~l~~~~~~~~~~~~~~~~~~i~~L~d~hg~~rvm~RntR~~v~~fp~R~~~~~~l~~~~~y~~~~~~~~~~~~~~~l  459 (956)
T PRK04914        380 DIEPLLQAANSDSEEAQAARQELISELLDRHGTGRVLFRNTRAAVKGFPKRELHPIPLPLPEQYQTAIKVSLEARARDML  459 (956)
T ss_pred             chhHHHhhhcccccccHHHHHHHHHHHHhhcCcceEEEeccHHhhcCCCcCceeEeecCCCHHHHHHHHHhHHHHHHhhc
Confidence                                              000000000   0001111111111110                  


Q ss_pred             ------------------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHH-HCCCeEEEEcCCCCH
Q 010709          350 ------------------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV-AEGLHAVALHGGRNQ  410 (503)
Q Consensus       350 ------------------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~-~~~~~v~~lh~~~~~  410 (503)
                                        ..|+..+..++.         .....|+||||+++..+..+++.|+ ..|+.+..+||+|++
T Consensus       460 ~pe~~~~~~~~~~~~~~~d~Ki~~L~~~L~---------~~~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s~  530 (956)
T PRK04914        460 YPEQIYQEFEDNATWWNFDPRVEWLIDFLK---------SHRSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMSI  530 (956)
T ss_pred             CHHHHHHHHhhhhhccccCHHHHHHHHHHH---------hcCCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCCH
Confidence                              011111111111         1335689999999999999999994 569999999999999


Q ss_pred             HHHHHHHHHHhcC--CCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          411 SDRESALRDFRNG--STNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       411 ~~r~~~~~~f~~g--~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .+|.++++.|+++  ..+|||||+++++|+|++.+++||+||+|+++..|.||+||+||.
T Consensus       531 ~eR~~~~~~F~~~~~~~~VLIsTdvgseGlNlq~a~~VInfDlP~nP~~~eQRIGR~~Ri  590 (956)
T PRK04914        531 IERDRAAAYFADEEDGAQVLLCSEIGSEGRNFQFASHLVLFDLPFNPDLLEQRIGRLDRI  590 (956)
T ss_pred             HHHHHHHHHHhcCCCCccEEEechhhccCCCcccccEEEEecCCCCHHHHHHHhcccccC
Confidence            9999999999974  599999999999999999999999999999999999999999993

>PRK09694 helicase Cas3; Provisional

Probab=99.97  E-value=1.8e-29  Score=266.42  Aligned_cols=313  Identities=20%  Similarity=0.187  Sum_probs=201.8

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ...|+|+|..+......+.-+||.+|||+|||.+++..+. .+...     +...+++|..||+++++|++++++++...
T Consensus       284 ~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~-~l~~~-----~~~~gi~~aLPT~Atan~m~~Rl~~~~~~  357 (878)
T PRK09694        284 GYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAW-RLIDQ-----GLADSIIFALPTQATANAMLSRLEALASK  357 (878)
T ss_pred             CCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHH-HHHHh-----CCCCeEEEECcHHHHHHHHHHHHHHHHHH
Confidence            4589999998865444456699999999999999866544 33332     12467999999999999999999875532


Q ss_pred             C-CCceEEEEECCccHHHHH---------------------HHhh---C---CCcEEEECcHHHHHHHHcCC-CCCCC--
Q 010709          221 L-DSFKTAIVVGGTNIAEQR---------------------SELR---G---GVSIVVATPGRFLDHLQQGN-TSLSR--  269 (503)
Q Consensus       221 ~-~~~~~~~~~~~~~~~~~~---------------------~~~~---~---~~~Ilv~Tp~~l~~~l~~~~-~~l~~--  269 (503)
                      . .+..+.+.+|........                     ..+.   +   -..|+|||...++....... ..++.  
T Consensus       358 ~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR~~~  437 (878)
T PRK09694        358 LFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIRGFG  437 (878)
T ss_pred             hcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHHHHh
Confidence            2 234566776654321110                     0111   1   16899999999875554422 12222  


Q ss_pred             --ccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHHHHHhcCC--C--------eEEEeCCC---
Q 010709          270 --VSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTD--P--------VQVKVGKV---  333 (503)
Q Consensus       270 --~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~~--~--------~~~~~~~~---  333 (503)
                        -++|||||+|.+ +......+..+++.+ .....+|+||||+|......+..-+..  +        ........   
T Consensus       438 La~svvIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~~~~~~~~~~~~YPlvt~~~~~~~~  516 (878)
T PRK09694        438 LGRSVLIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTYGGHDPVELSSAYPLITWRGVNGAQ  516 (878)
T ss_pred             hccCeEEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhccccccccccccccccccccccce
Confidence              258999999954 322333445555443 235669999999998876544332221  0        00000000   


Q ss_pred             -----CCC---CCceEEEEEEc--ChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC---Ce
Q 010709          334 -----SSP---TANVIQILEKV--SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG---LH  400 (503)
Q Consensus       334 -----~~~---~~~~~~~~~~~--~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~---~~  400 (503)
                           ...   .......+...  ........++..+.+..       ...+++|||||+++.|+.+++.|++.+   .+
T Consensus       517 ~~~~~~~~~~~~~~~~v~v~~~~~~~~~~~~~~l~~i~~~~-------~~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~  589 (878)
T PRK09694        517 RFDLSAHPEQLPARFTIQLEPICLADMLPDLTLLQRMIAAA-------NAGAQVCLICNLVDDAQKLYQRLKELNNTQVD  589 (878)
T ss_pred             eeeccccccccCcceEEEEEeeccccccCHHHHHHHHHHHH-------hcCCEEEEEECCHHHHHHHHHHHHhhCCCCce
Confidence                 000   00011111111  11011123333333322       123469999999999999999999764   68


Q ss_pred             EEEEcCCCCHHHH----HHHHHHH-hcCC---CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeeee
Q 010709          401 AVALHGGRNQSDR----ESALRDF-RNGS---TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNIT  470 (503)
Q Consensus       401 v~~lh~~~~~~~r----~~~~~~f-~~g~---~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~  470 (503)
                      +..+||.+++.+|    .++++.| ++|+   ..|||||+++++||||+ ++++|....|  ++.++||+||+||...
T Consensus       590 v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQViE~GLDId-~DvlItdlaP--idsLiQRaGR~~R~~~  664 (878)
T PRK09694        590 IDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQVVEQSLDLD-FDWLITQLCP--VDLLFQRLGRLHRHHR  664 (878)
T ss_pred             EEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECcchhheeecC-CCeEEECCCC--HHHHHHHHhccCCCCC
Confidence            9999999999999    4567788 6666   47999999999999995 8999998888  7899999999999754

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

Probab=99.97  E-value=7.3e-31  Score=254.89  Aligned_cols=301  Identities=18%  Similarity=0.206  Sum_probs=226.9

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc-c
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR-S  220 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~-~  220 (503)
                      ...+++-.+.+.++.+++.+||.|+||||||+  ++|.+.+...+-    ..|+++-+..|+|..|..++.++.+-+. .
T Consensus       264 LPVy~ykdell~av~e~QVLiI~GeTGSGKTT--QiPQyL~EaGyt----k~gk~IgcTQPRRVAAmSVAaRVA~EMgvk  337 (902)
T KOG0923|consen  264 LPVYPYKDELLKAVKEHQVLIIVGETGSGKTT--QIPQYLYEAGYT----KGGKKIGCTQPRRVAAMSVAARVAEEMGVK  337 (902)
T ss_pred             CCchhhHHHHHHHHHhCcEEEEEcCCCCCccc--cccHHHHhcccc----cCCceEeecCcchHHHHHHHHHHHHHhCcc
Confidence            34566777888888899999999999999998  588887765542    2345588888999999998877765442 1


Q ss_pred             C-CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-HhhCCCHHHHHHHHHhCC
Q 010709          221 L-DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-MLDMGFEPQIREVMQNLP  298 (503)
Q Consensus       221 ~-~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-l~~~~~~~~~~~il~~~~  298 (503)
                      + ..+-+.+.+.+...        ..+-|.+||.|+|++.+.. ...|..+++|||||||. -+..+..-.+-+-+.+++
T Consensus       338 LG~eVGYsIRFEdcTS--------ekTvlKYMTDGmLlREfL~-epdLasYSViiiDEAHERTL~TDILfgLvKDIar~R  408 (902)
T KOG0923|consen  338 LGHEVGYSIRFEDCTS--------EKTVLKYMTDGMLLREFLS-EPDLASYSVIIVDEAHERTLHTDILFGLVKDIARFR  408 (902)
T ss_pred             cccccceEEEeccccC--------cceeeeeecchhHHHHHhc-cccccceeEEEeehhhhhhhhhhHHHHHHHHHHhhC
Confidence            1 12334455544432        3478999999999999876 66899999999999994 333333333444456678


Q ss_pred             CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEE
Q 010709          299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTI  378 (503)
Q Consensus       299 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~l  378 (503)
                      ++.+++++|||+..  + -...|+.+...+.+..   ....+..++...+....++..+..+.+.+..     .|.+-+|
T Consensus       409 pdLKllIsSAT~DA--e-kFS~fFDdapIF~iPG---RRyPVdi~Yt~~PEAdYldAai~tVlqIH~t-----qp~GDIL  477 (902)
T KOG0923|consen  409 PDLKLLISSATMDA--E-KFSAFFDDAPIFRIPG---RRYPVDIFYTKAPEADYLDAAIVTVLQIHLT-----QPLGDIL  477 (902)
T ss_pred             CcceEEeeccccCH--H-HHHHhccCCcEEeccC---cccceeeecccCCchhHHHHHHhhheeeEec-----cCCccEE
Confidence            99999999999943  3 3344555544443332   3345666777777778777777666554332     5667899


Q ss_pred             EEEcchhhHHHHHHHHHHC---------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEc
Q 010709          379 VFVERKTRCDEVSEALVAE---------GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNL  449 (503)
Q Consensus       379 IF~~~~~~~~~l~~~L~~~---------~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~  449 (503)
                      ||...+++++...+.|...         .+-++++|+.++.+.|..+++.-..|.++|++||++++++|+|++|.+||+-
T Consensus       478 VFltGQeEIEt~~e~l~~~~~~LGski~eliv~PiYaNLPselQakIFePtP~gaRKVVLATNIAETSlTIdgI~yViDp  557 (902)
T KOG0923|consen  478 VFLTGQEEIETVKENLKERCRRLGSKIRELIVLPIYANLPSELQAKIFEPTPPGARKVVLATNIAETSLTIDGIKYVIDP  557 (902)
T ss_pred             EEeccHHHHHHHHHHHHHHHHHhccccceEEEeeccccCChHHHHhhcCCCCCCceeEEEeecchhhceeecCeEEEecC
Confidence            9999999988877777542         3568899999999999999999999999999999999999999999999997


Q ss_pred             cCCC------------------ChhHHHHhhCcceee
Q 010709          450 DLPK------------------VLLAASESLCTTSFN  468 (503)
Q Consensus       450 ~~p~------------------s~~~~~Qr~GR~gR~  468 (503)
                      |+.+                  |.++..||.|||||+
T Consensus       558 Gf~K~nsynprtGmesL~v~piSKAsA~QRaGRAGRt  594 (902)
T KOG0923|consen  558 GFVKQNSYNPRTGMESLLVTPISKASANQRAGRAGRT  594 (902)
T ss_pred             ccccccCcCCCcCceeEEEeeechhhhhhhccccCCC
Confidence            7644                  458999999999996

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

Probab=99.97  E-value=1.3e-29  Score=254.96  Aligned_cols=297  Identities=21%  Similarity=0.216  Sum_probs=221.0

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|..+|++|+-++..|..|+|.|+|.+|||+++..++...-.        ++.+.+|..|-++|.+|-++.|++-+..  
T Consensus       297 elD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~--------h~TR~iYTSPIKALSNQKfRDFk~tF~D--  366 (1248)
T KOG0947|consen  297 ELDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQK--------HMTRTIYTSPIKALSNQKFRDFKETFGD--  366 (1248)
T ss_pred             CccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHh--------hccceEecchhhhhccchHHHHHHhccc--
Confidence            688999999999999999999999999999988766554322        2577999999999999999999876532  


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCc
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ  302 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q  302 (503)
                         +++++|+..       +.....++|||.+.|..++.++.-..+++.+||+||+|.+.+...+..|++++-.+|...+
T Consensus       367 ---vgLlTGDvq-------inPeAsCLIMTTEILRsMLYrgadliRDvE~VIFDEVHYiND~eRGvVWEEViIMlP~HV~  436 (1248)
T KOG0947|consen  367 ---VGLLTGDVQ-------INPEASCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYINDVERGVVWEEVIIMLPRHVN  436 (1248)
T ss_pred             ---cceeeccee-------eCCCcceEeehHHHHHHHHhcccchhhccceEEEeeeeecccccccccceeeeeeccccce
Confidence               237777763       4556899999999999999998878889999999999998888899999999999999999


Q ss_pred             EEEEEeeCCHHHHHHHHHh---cCCCeEEEeCCCCCCCCceEEEEEEcChhh----------------------------
Q 010709          303 TLLFSATMPVEIEALAQEY---LTDPVQVKVGKVSSPTANVIQILEKVSENE----------------------------  351 (503)
Q Consensus       303 ~i~~SAT~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------------------  351 (503)
                      +|++|||+|+..+ ++...   -.....+.  ........+.+++..-...-                            
T Consensus       437 ~IlLSATVPN~~E-FA~WIGRtK~K~IyVi--ST~kRPVPLEh~l~t~~~l~kiidq~g~fl~~~~~~a~~~~~~~ak~~  513 (1248)
T KOG0947|consen  437 FILLSATVPNTLE-FADWIGRTKQKTIYVI--STSKRPVPLEHYLYTKKSLFKIIDQNGIFLLKGIKDAKDSLKKEAKFV  513 (1248)
T ss_pred             EEEEeccCCChHH-HHHHhhhccCceEEEE--ecCCCccceEEEEEeccceehhhcccchhhhhcchhhhhhhccccccc
Confidence            9999999987654 44322   22222221  11111111111111100000                            


Q ss_pred             -----------------------------------HHH--HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHH
Q 010709          352 -----------------------------------KVD--RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL  394 (503)
Q Consensus       352 -----------------------------------k~~--~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L  394 (503)
                                                         +..  ....++. +...     ..--|+||||-+++.|++.++.|
T Consensus       514 ~~~~~~~~~~rgs~~~ggk~~~~~g~~r~~~~~~nrr~~~~~l~lin-~L~k-----~~lLP~VvFvFSkkrCde~a~~L  587 (1248)
T KOG0947|consen  514 DVEKSDARGGRGSQKRGGKTNYHNGGSRGSGIGKNRRKQPTWLDLIN-HLRK-----KNLLPVVVFVFSKKRCDEYADYL  587 (1248)
T ss_pred             ccccccccccccccccCCcCCCCCCCcccccccccccccchHHHHHH-HHhh-----cccCceEEEEEccccHHHHHHHH
Confidence                                               000  0111111 0000     11236999999999999999999


Q ss_pred             HHCC---------------------------------------CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccc
Q 010709          395 VAEG---------------------------------------LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS  435 (503)
Q Consensus       395 ~~~~---------------------------------------~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  435 (503)
                      ...+                                       -.+..+|||+-+--+.-+.-.|..|-++||+||..++
T Consensus       588 ~~~nL~~~~EKseV~lfl~k~~~rLk~~DR~LPQvl~m~~ll~RGiaVHH~GlLPivKE~VE~LFqrGlVKVLFATETFA  667 (1248)
T KOG0947|consen  588 TNLNLTDSKEKSEVHLFLSKAVARLKGEDRNLPQVLSMRSLLLRGIAVHHGGLLPIVKEVVELLFQRGLVKVLFATETFA  667 (1248)
T ss_pred             hccCcccchhHHHHHHHHHHHHHhcChhhccchHHHHHHHHHhhcchhhcccchHHHHHHHHHHHhcCceEEEeehhhhh
Confidence            6522                                       2477899999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCC---------ChhHHHHhhCcceeee
Q 010709          436 RGLDVMGVAHVVNLDLPK---------VLLAASESLCTTSFNI  469 (503)
Q Consensus       436 ~Gldip~v~~VI~~~~p~---------s~~~~~Qr~GR~gR~~  469 (503)
                      +|+|+| +++||+-.+.+         .+-+|.|+.|||||--
T Consensus       668 MGVNMP-ARtvVF~Sl~KhDG~efR~L~PGEytQMAGRAGRRG  709 (1248)
T KOG0947|consen  668 MGVNMP-ARTVVFSSLRKHDGNEFRELLPGEYTQMAGRAGRRG  709 (1248)
T ss_pred             hhcCCC-ceeEEeeehhhccCcceeecCChhHHhhhccccccc
Confidence            999999 57777665543         4689999999999953

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

Probab=99.97  E-value=5.4e-29  Score=246.99  Aligned_cols=309  Identities=21%  Similarity=0.258  Sum_probs=230.6

Q ss_pred             CHHHHHHHHHCCCCCCcHHHHHHHHHHhcC------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          129 HPSIMKDIEFHEYTRPTSIQAQAMPVALSG------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       129 ~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      ...+.+.+-..=.-++|..|.+++..|...      .+-++.|..|||||++++++++..+..        |.++.+++|
T Consensus       248 ~~~l~~~~~~~LPF~LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~--------G~Q~ALMAP  319 (677)
T COG1200         248 NGELLAKFLAALPFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA--------GYQAALMAP  319 (677)
T ss_pred             cHHHHHHHHHhCCCCccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc--------CCeeEEecc
Confidence            344455543333337999999999998843      257899999999999998888877554        788999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH---HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          203 TRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR---SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       203 tr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      |..||.|.++.+.+++..+ ++.+.+++|........   ..+. +..+|+|+|     +.+.+....+.++.+|||||=
T Consensus       320 TEILA~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGT-----HALiQd~V~F~~LgLVIiDEQ  393 (677)
T COG1200         320 TEILAEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGT-----HALIQDKVEFHNLGLVIIDEQ  393 (677)
T ss_pred             HHHHHHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEc-----chhhhcceeecceeEEEEecc
Confidence            9999999999999999887 49999999987654433   3333 459999999     444455778999999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCC-CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPD-KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~-~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      ||     |+..-+..+..-.. .+.++.|||||-+..  ++-..+++-..-.++..+.-...+.......   ++...++
T Consensus       394 HR-----FGV~QR~~L~~KG~~~Ph~LvMTATPIPRT--LAlt~fgDldvS~IdElP~GRkpI~T~~i~~---~~~~~v~  463 (677)
T COG1200         394 HR-----FGVHQRLALREKGEQNPHVLVMTATPIPRT--LALTAFGDLDVSIIDELPPGRKPITTVVIPH---ERRPEVY  463 (677)
T ss_pred             cc-----ccHHHHHHHHHhCCCCCcEEEEeCCCchHH--HHHHHhccccchhhccCCCCCCceEEEEecc---ccHHHHH
Confidence            99     56556666666555 577999999984433  3444455433333444444444444444433   4555666


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhH--------HHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRC--------DEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~--------~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                      ..+.+....       +.++.|.|+-.++.        ..+++.|...  ++++..+||.|+.++++++++.|++|+.+|
T Consensus       464 e~i~~ei~~-------GrQaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~I  536 (677)
T COG1200         464 ERIREEIAK-------GRQAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDI  536 (677)
T ss_pred             HHHHHHHHc-------CCEEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcE
Confidence            666655543       34589999987654        4566666643  567999999999999999999999999999


Q ss_pred             EEEccccccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee
Q 010709          428 LVATDVASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN  468 (503)
Q Consensus       428 LvaT~~~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~  468 (503)
                      ||||.+.+.|||+|++++.|..+.-+ -.++.=|--||+||.
T Consensus       537 LVaTTVIEVGVdVPnATvMVIe~AERFGLaQLHQLRGRVGRG  578 (677)
T COG1200         537 LVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGRG  578 (677)
T ss_pred             EEEeeEEEecccCCCCeEEEEechhhhhHHHHHHhccccCCC
Confidence            99999999999999999999887654 356667777888883

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

Probab=99.97  E-value=8e-29  Score=259.00  Aligned_cols=340  Identities=20%  Similarity=0.195  Sum_probs=258.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhc----CC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALS----GR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~----~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .+......+...-.-.-|+-|..||..+..    ++  |-+|||..|.|||-+++-+++..+..        |++|.|+|
T Consensus       579 ~d~~~q~~F~~~FPyeET~DQl~AI~eVk~DM~~~kpMDRLiCGDVGFGKTEVAmRAAFkAV~~--------GKQVAvLV  650 (1139)
T COG1197         579 PDTEWQEEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVMD--------GKQVAVLV  650 (1139)
T ss_pred             CChHHHHHHHhcCCCcCCHHHHHHHHHHHHHhccCCcchheeecCcCCcHHHHHHHHHHHHhcC--------CCeEEEEc
Confidence            344455555443333679999999999873    33  78999999999999998888877654        79999999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecc
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE  277 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDE  277 (503)
                      ||.-||+|.++.|++-+..+ ++++..+.-=...+++...+    .+..||+|+|     +.+.+..+.+.+++++||||
T Consensus       651 PTTlLA~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGT-----HrLL~kdv~FkdLGLlIIDE  724 (1139)
T COG1197         651 PTTLLAQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGT-----HRLLSKDVKFKDLGLLIIDE  724 (1139)
T ss_pred             ccHHhHHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEec-----hHhhCCCcEEecCCeEEEec
Confidence            99999999999999988877 48888777666655554443    2569999999     44455688899999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH
Q 010709          278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      -|+     |+..-.+-++.++.+.-++-|||||-+..-.+.-.-+++-..+...  +.....+..++......--...+.
T Consensus       725 EqR-----FGVk~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TP--P~~R~pV~T~V~~~d~~~ireAI~  797 (1139)
T COG1197         725 EQR-----FGVKHKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATP--PEDRLPVKTFVSEYDDLLIREAIL  797 (1139)
T ss_pred             hhh-----cCccHHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCC--CCCCcceEEEEecCChHHHHHHHH
Confidence            998     5666677788888899999999999666555555555554444322  223334444444433332222322


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccc
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS  435 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~  435 (503)
                      ..+           ..+|++--.+|..+.++.+++.|+..  ..++...||.|+..+-++++..|.+|+.+|||||.+.+
T Consensus       798 REl-----------~RgGQvfYv~NrV~~Ie~~~~~L~~LVPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TTIIE  866 (1139)
T COG1197         798 REL-----------LRGGQVFYVHNRVESIEKKAERLRELVPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIE  866 (1139)
T ss_pred             HHH-----------hcCCEEEEEecchhhHHHHHHHHHHhCCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEeeeee
Confidence            222           24566888889999999999999987  56789999999999999999999999999999999999


Q ss_pred             cCCCCCCCCEEEEccCCC-ChhHHHHhhCcceeee-------eec-------c-CchhhhhhHHHHHHHHHHHHHHHHhh
Q 010709          436 RGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFNI-------TTN-------L-DGDMKKLEFCLILAITVLLFVIFLSI  499 (503)
Q Consensus       436 ~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~~-------~~~-------~-~~~~~~~~~~~~~~~~~~~~~~~~~~  499 (503)
                      .|||||+++++|.-+.-+ -.++..|--||+||+-       +.+       . ..+++.+..+..+...+.++|-.|.|
T Consensus       867 tGIDIPnANTiIIe~AD~fGLsQLyQLRGRVGRS~~~AYAYfl~p~~k~lT~~A~kRL~aI~~~~~LGaGf~lA~~DLeI  946 (1139)
T COG1197         867 TGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSNKQAYAYFLYPPQKALTEDAEKRLEAIASFTELGAGFKLAMHDLEI  946 (1139)
T ss_pred             cCcCCCCCceEEEeccccccHHHHHHhccccCCccceEEEEEeecCccccCHHHHHHHHHHHhhhhcCchHHHHhcchhc
Confidence            999999999999766543 4688999999999952       222       2 26677777777888888888888765

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

Probab=99.97  E-value=8.4e-30  Score=248.02  Aligned_cols=298  Identities=17%  Similarity=0.168  Sum_probs=212.3

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC--C
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL--D  222 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~--~  222 (503)
                      ...+.+.+..+..++.+||+|+||||||+  ++|.+.+...+.     +++.+.+..|+|..|..+++++.+-+...  .
T Consensus       358 f~~R~~ll~~ir~n~vvvivgETGSGKTT--Ql~QyL~edGY~-----~~GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~  430 (1042)
T KOG0924|consen  358 FACRDQLLSVIRENQVVVIVGETGSGKTT--QLAQYLYEDGYA-----DNGMIGCTQPRRVAAISVAKRVAEEMGVTLGD  430 (1042)
T ss_pred             HHHHHHHHHHHhhCcEEEEEecCCCCchh--hhHHHHHhcccc-----cCCeeeecCchHHHHHHHHHHHHHHhCCcccc
Confidence            34455566666678889999999999998  466666655542     34567788899999999998887655221  1


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-HhhCCCHHHHHHHHHhCCCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-MLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-l~~~~~~~~~~~il~~~~~~~  301 (503)
                      .+-+.+.+.+...        ..+.|-++|.|.|++.... .-.|.++++||+||||. -++.+..-.+.+.+..-+.+.
T Consensus       431 ~VGYsIRFEdvT~--------~~T~IkymTDGiLLrEsL~-d~~L~kYSviImDEAHERslNtDilfGllk~~larRrdl  501 (1042)
T KOG0924|consen  431 TVGYSIRFEDVTS--------EDTKIKYMTDGILLRESLK-DRDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARRRDL  501 (1042)
T ss_pred             ccceEEEeeecCC--------CceeEEEeccchHHHHHhh-hhhhhheeEEEechhhhcccchHHHHHHHHHHHHhhccc
Confidence            2444555555432        3478999999999988776 45688999999999994 333332333344444445689


Q ss_pred             cEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEE
Q 010709          302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFV  381 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~  381 (503)
                      ++|.+|||+  +.+.+...|-+.|.. .+....   ..+...+...+.+..+...+......+     ...+.|-+|||.
T Consensus       502 KliVtSATm--~a~kf~nfFgn~p~f-~IpGRT---yPV~~~~~k~p~eDYVeaavkq~v~Ih-----l~~~~GdilIfm  570 (1042)
T KOG0924|consen  502 KLIVTSATM--DAQKFSNFFGNCPQF-TIPGRT---YPVEIMYTKTPVEDYVEAAVKQAVQIH-----LSGPPGDILIFM  570 (1042)
T ss_pred             eEEEeeccc--cHHHHHHHhCCCcee-eecCCc---cceEEEeccCchHHHHHHHHhhheEee-----ccCCCCCEEEec
Confidence            999999999  455554444334544 343333   334455555555555554444333222     224667899999


Q ss_pred             cchhhHHHHH----HHHHHC------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC
Q 010709          382 ERKTRCDEVS----EALVAE------GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL  451 (503)
Q Consensus       382 ~~~~~~~~l~----~~L~~~------~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~  451 (503)
                      ++++.++-.+    +.|.+.      ++.|+++|+.+++.-|.++++....|..+|+|||++++++|+||++.+||+.+.
T Consensus       571 tGqediE~t~~~i~~~l~ql~~~~~~~L~vlpiYSQLp~dlQ~kiFq~a~~~vRK~IvATNIAETSLTi~gI~yVID~Gy  650 (1042)
T KOG0924|consen  571 TGQEDIECTCDIIKEKLEQLDSAPTTDLAVLPIYSQLPADLQAKIFQKAEGGVRKCIVATNIAETSLTIPGIRYVIDTGY  650 (1042)
T ss_pred             CCCcchhHHHHHHHHHHHhhhcCCCCceEEEeehhhCchhhhhhhcccCCCCceeEEEeccchhhceeecceEEEEecCc
Confidence            9988765544    444432      678999999999999999999999999999999999999999999999999885


Q ss_pred             ------------------CCChhHHHHhhCcceeee
Q 010709          452 ------------------PKVLLAASESLCTTSFNI  469 (503)
Q Consensus       452 ------------------p~s~~~~~Qr~GR~gR~~  469 (503)
                                        |-|.++..||.|||||+.
T Consensus       651 ~K~kvyn~~~G~D~L~~~pIS~AnA~QRaGRAGRt~  686 (1042)
T KOG0924|consen  651 CKLKVYNPRIGMDALQIVPISQANADQRAGRAGRTG  686 (1042)
T ss_pred             eeeeecccccccceeEEEechhccchhhccccCCCC
Confidence                              445688999999999973

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

Probab=99.97  E-value=3.7e-29  Score=257.69  Aligned_cols=332  Identities=19%  Similarity=0.227  Sum_probs=237.2

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCC-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCC---CCCeEEEEcc
Q 010709          127 CLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRG---DGPLALVLAP  202 (503)
Q Consensus       127 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~---~~~~~lil~P  202 (503)
                      .++.+-..++  .|...+..+|.....+.+.+. ++++|||||+|||..+++-+++.+-........   ...+++|++|
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            3444544443  466779999999999998765 699999999999999999999887665432222   3458999999


Q ss_pred             cHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC---CCCCccEEEecchh
Q 010709          203 TRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT---SLSRVSFVILDEAD  279 (503)
Q Consensus       203 tr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~---~l~~~~~vViDEaH  279 (503)
                      .++|++.|...|.+....+ ++.+.-++|+......   .-.++.|+|+||+.. +.+.++..   ..+-++++||||.|
T Consensus       373 mKaLvqE~VgsfSkRla~~-GI~V~ElTgD~~l~~~---qieeTqVIV~TPEK~-DiITRk~gdraY~qlvrLlIIDEIH  447 (1674)
T KOG0951|consen  373 MKALVQEMVGSFSKRLAPL-GITVLELTGDSQLGKE---QIEETQVIVTTPEKW-DIITRKSGDRAYEQLVRLLIIDEIH  447 (1674)
T ss_pred             HHHHHHHHHHHHHhhcccc-CcEEEEecccccchhh---hhhcceeEEeccchh-hhhhcccCchhHHHHHHHHhhhhhh
Confidence            9999999999998887776 5999999998764332   124589999999998 34444322   24457899999999


Q ss_pred             HHhhCCCHHHHHHHHHhC-------CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhH
Q 010709          280 RMLDMGFEPQIREVMQNL-------PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEK  352 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~-------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k  352 (503)
                       |+....++.++.+..+.       ...++++++|||+|+- .+.......++.-+...........+.|.++.+.....
T Consensus       448 -LLhDdRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy-~DV~~Fl~v~~~glf~fd~syRpvPL~qq~Igi~ek~~  525 (1674)
T KOG0951|consen  448 -LLHDDRGPVLESIVARTFRRSESTEEGSRLVGLSATLPNY-EDVASFLRVDPEGLFYFDSSYRPVPLKQQYIGITEKKP  525 (1674)
T ss_pred             -hcccccchHHHHHHHHHHHHhhhcccCceeeeecccCCch-hhhHHHhccCcccccccCcccCcCCccceEeccccCCc
Confidence             55555777777665543       2368899999999754 33343333444444444444444556666666544332


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHH------------------------------------
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA------------------------------------  396 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~------------------------------------  396 (503)
                      ... .+.+.+..+...-.....+++|||+.++++..+.|+.++.                                    
T Consensus       526 ~~~-~qamNe~~yeKVm~~agk~qVLVFVHsRkET~ktA~aIRd~~le~dtls~fmre~s~s~eilrtea~~~kn~dLkd  604 (1674)
T KOG0951|consen  526 LKR-FQAMNEACYEKVLEHAGKNQVLVFVHSRKETAKTARAIRDKALEEDTLSRFMREDSASREILRTEAGQAKNPDLKD  604 (1674)
T ss_pred             hHH-HHHHHHHHHHHHHHhCCCCcEEEEEEechHHHHHHHHHHHHHhhhhHHHHHHhcccchhhhhhhhhhcccChhHHH
Confidence            222 2222222222221112336799999999998888887763                                    


Q ss_pred             -CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE-----ccC------CCChhHHHHhhCc
Q 010709          397 -EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN-----LDL------PKVLLAASESLCT  464 (503)
Q Consensus       397 -~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~-----~~~------p~s~~~~~Qr~GR  464 (503)
                       ..+.+..+|+||+..+|..+.+.|++|.++|+|+|..+++|+|+|+ +.||.     |++      +.++.+..||+||
T Consensus       605 LLpygfaIHhAGl~R~dR~~~EdLf~~g~iqvlvstatlawgvnlpa-htViikgtqvy~pekg~w~elsp~dv~qmlgr  683 (1674)
T KOG0951|consen  605 LLPYGFAIHHAGLNRKDRELVEDLFADGHIQVLVSTATLAWGVNLPA-HTVIIKGTQVYDPEKGRWTELSPLDVMQMLGR  683 (1674)
T ss_pred             HhhccceeeccCCCcchHHHHHHHHhcCceeEEEeehhhhhhcCCCc-ceEEecCccccCcccCccccCCHHHHHHHHhh
Confidence             1256889999999999999999999999999999999999999995 55554     444      3467899999999


Q ss_pred             ceeee
Q 010709          465 TSFNI  469 (503)
Q Consensus       465 ~gR~~  469 (503)
                      |||.-
T Consensus       684 agrp~  688 (1674)
T KOG0951|consen  684 AGRPQ  688 (1674)
T ss_pred             cCCCc
Confidence            99964

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

Probab=99.97  E-value=5.4e-30  Score=251.82  Aligned_cols=303  Identities=19%  Similarity=0.188  Sum_probs=228.7

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .+.|+|..++.++-.+..|+|+|.|.+|||.++..++...+..        +.++||..|-++|.+|-++++..-++   
T Consensus       129 ~LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~--------kQRVIYTSPIKALSNQKYREl~~EF~---  197 (1041)
T KOG0948|consen  129 TLDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE--------KQRVIYTSPIKALSNQKYRELLEEFK---  197 (1041)
T ss_pred             ccCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh--------cCeEEeeChhhhhcchhHHHHHHHhc---
Confidence            6889999999999999999999999999999987776666544        57899999999999999999886653   


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCc
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ  302 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q  302 (503)
                        .+++.+|+..       +...+..+|||.+.|..++.++.--++.+.+||+||+|.|-+...+..|++.+-.+|++.+
T Consensus       198 --DVGLMTGDVT-------InP~ASCLVMTTEILRsMLYRGSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~~vr  268 (1041)
T KOG0948|consen  198 --DVGLMTGDVT-------INPDASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPDNVR  268 (1041)
T ss_pred             --ccceeeccee-------eCCCCceeeeHHHHHHHHHhccchHhheeeeEEeeeehhccccccceeeeeeEEeccccce
Confidence              2566777764       3455789999999999999998888999999999999999999889999999999999999


Q ss_pred             EEEEEeeCCHHHH--HHHHHhcCCCeEEEeCCCCCCCCceEEEE------------EEcCh---hhHHHHHHHHHHHHHH
Q 010709          303 TLLFSATMPVEIE--ALAQEYLTDPVQVKVGKVSSPTANVIQIL------------EKVSE---NEKVDRLLALLVEEAF  365 (503)
Q Consensus       303 ~i~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~~---~~k~~~l~~~l~~~~~  365 (503)
                      .+++|||+|+..+  +.+...-..|+.+......   +...|++            +..+.   ++........+.....
T Consensus       269 ~VFLSATiPNA~qFAeWI~~ihkQPcHVVYTdyR---PTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~  345 (1041)
T KOG0948|consen  269 FVFLSATIPNARQFAEWICHIHKQPCHVVYTDYR---PTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGE  345 (1041)
T ss_pred             EEEEeccCCCHHHHHHHHHHHhcCCceEEeecCC---CCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCC
Confidence            9999999987654  2334445667766433211   1111221            11111   1222222222222111


Q ss_pred             hhh--------cc---------------------CCCCCcEEEEEcchhhHHHHHHHHHHCC------------------
Q 010709          366 LAE--------KS---------------------CHPFPLTIVFVERKTRCDEVSEALVAEG------------------  398 (503)
Q Consensus       366 ~~~--------~~---------------------~~~~~~~lIF~~~~~~~~~l~~~L~~~~------------------  398 (503)
                      ...        +.                     .....++|||+-++++|+.++-.+.+..                  
T Consensus       346 ~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~~~PVIvFSFSkkeCE~~Alqm~kldfN~deEk~~V~~iF~nAi  425 (1041)
T KOG0948|consen  346 SDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERNYLPVIVFSFSKKECEAYALQMSKLDFNTDEEKELVETIFNNAI  425 (1041)
T ss_pred             CccccccccccccCCcCCCCCCcccHHHHHHHHHhhcCCceEEEEecHhHHHHHHHhhccCcCCChhHHHHHHHHHHHHH
Confidence            110        00                     0123569999999999999998885522                  


Q ss_pred             ---------------------CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC----
Q 010709          399 ---------------------LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK----  453 (503)
Q Consensus       399 ---------------------~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~----  453 (503)
                                           -.+..+|||+-+--++-+.-.|++|-++||+||..++.|+|+| +++|++...-+    
T Consensus       426 ~~LseeDr~LPqie~iLPLL~RGIGIHHsGLLPIlKE~IEILFqEGLvKvLFATETFsiGLNMP-AkTVvFT~~rKfDG~  504 (1041)
T KOG0948|consen  426 DQLSEEDRELPQIENILPLLRRGIGIHHSGLLPILKEVIEILFQEGLVKVLFATETFSIGLNMP-AKTVVFTAVRKFDGK  504 (1041)
T ss_pred             HhcChhhccchHHHHHHHHHHhccccccccchHHHHHHHHHHHhccHHHHHHhhhhhhhccCCc-ceeEEEeeccccCCc
Confidence                                 2467899999999999999999999999999999999999999 56676654432    


Q ss_pred             -----ChhHHHHhhCcceeee
Q 010709          454 -----VLLAASESLCTTSFNI  469 (503)
Q Consensus       454 -----s~~~~~Qr~GR~gR~~  469 (503)
                           +.-+|+|+.|||||--
T Consensus       505 ~fRwissGEYIQMSGRAGRRG  525 (1041)
T KOG0948|consen  505 KFRWISSGEYIQMSGRAGRRG  525 (1041)
T ss_pred             ceeeecccceEEecccccccC
Confidence                 4578999999999953

>TIGR00595 priA primosomal protein N'

Probab=99.97  E-value=2.7e-28  Score=247.04  Aligned_cols=277  Identities=20%  Similarity=0.231  Sum_probs=185.6

Q ss_pred             EEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH--
Q 010709          162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR--  239 (503)
Q Consensus       162 ii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  239 (503)
                      ++.|+||+|||.+|+.. +...+..       ++++||++|+++|+.|+++.+++.+    +..+..++++....+..  
T Consensus         1 LL~g~TGsGKT~v~l~~-i~~~l~~-------g~~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er~~~   68 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQA-IEKVLAL-------GKSVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEKLQA   68 (505)
T ss_pred             CccCCCCCCHHHHHHHH-HHHHHHc-------CCeEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHHHHH
Confidence            47899999999998554 4444443       5789999999999999999998865    34577788877654432  


Q ss_pred             -HH-hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-----C-HHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          240 -SE-LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-----F-EPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       240 -~~-~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-----~-~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                       .. ..+..+|+|+|+..+.       ..+.++++|||||+|....++     | ...+.. +.....+.++|++|||+.
T Consensus        69 ~~~~~~g~~~IVVGTrsalf-------~p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~-~ra~~~~~~vil~SATPs  140 (505)
T TIGR00595        69 WRKVKNGEILVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAV-YRAKKFNCPVVLGSATPS  140 (505)
T ss_pred             HHHHHcCCCCEEECChHHHc-------CcccCCCEEEEECCCccccccccCCCCcHHHHHH-HHHHhcCCCEEEEeCCCC
Confidence             22 2346899999998764       347789999999999765332     1 112222 233335678999999986


Q ss_pred             HHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh----HHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhh-
Q 010709          312 VEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE----KVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR-  386 (503)
Q Consensus       312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~-  386 (503)
                      .+....+.  .+....+...............+.......    -...++..+.+...       .++++|||+|++.. 
T Consensus       141 les~~~~~--~g~~~~~~l~~r~~~~~~p~v~vid~~~~~~~~~ls~~l~~~i~~~l~-------~g~qvLvflnrrGya  211 (505)
T TIGR00595       141 LESYHNAK--QKAYRLLVLTRRVSGRKPPEVKLIDMRKEPRQSFLSPELITAIEQTLA-------AGEQSILFLNRRGYS  211 (505)
T ss_pred             HHHHHHHh--cCCeEEeechhhhcCCCCCeEEEEecccccccCCccHHHHHHHHHHHH-------cCCcEEEEEeCCcCC
Confidence            55443332  122222222211111111122222222211    11234444444332       23459999887653 


Q ss_pred             -----------------------------------------------------------HHHHHHHHHHC--CCeEEEEc
Q 010709          387 -----------------------------------------------------------CDEVSEALVAE--GLHAVALH  405 (503)
Q Consensus       387 -----------------------------------------------------------~~~l~~~L~~~--~~~v~~lh  405 (503)
                                                                                 .+.+++.|.+.  +.++..+|
T Consensus       212 ~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d  291 (505)
T TIGR00595       212 KNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARID  291 (505)
T ss_pred             CeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEe
Confidence                                                                       37778888776  77899999


Q ss_pred             CCCCHHHH--HHHHHHHhcCCCcEEEEccccccCCCCCCCCEEE--EccC----CC------ChhHHHHhhCccee
Q 010709          406 GGRNQSDR--ESALRDFRNGSTNILVATDVASRGLDVMGVAHVV--NLDL----PK------VLLAASESLCTTSF  467 (503)
Q Consensus       406 ~~~~~~~r--~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI--~~~~----p~------s~~~~~Qr~GR~gR  467 (503)
                      +++++.++  .++++.|++|+.+|||+|+++++|+|+|+|++|+  ++|.    |.      ....|.|++||+||
T Consensus       292 ~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~i~kG~d~~~v~lV~vl~aD~~l~~pd~ra~E~~~~ll~q~~GRagR  367 (505)
T TIGR00595       292 SDTTSRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGR  367 (505)
T ss_pred             cccccCccHHHHHHHHHhcCCCCEEEeCcccccCCCCCcccEEEEEcCcccccCcccchHHHHHHHHHHHHhccCC
Confidence            99987765  8999999999999999999999999999999985  5554    31      24678999999998

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).

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

Probab=99.96  E-value=1.7e-28  Score=256.48  Aligned_cols=313  Identities=20%  Similarity=0.240  Sum_probs=226.5

Q ss_pred             HHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       137 ~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      ..++| .|.++|++++-.+..|..|++|||||+|||.+...++...+..        +.+++|++|.++|.+|.++.+..
T Consensus       114 ~~~~F-~LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~--------~qrviYTsPIKALsNQKyrdl~~  184 (1041)
T COG4581         114 REYPF-ELDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD--------GQRVIYTSPIKALSNQKYRDLLA  184 (1041)
T ss_pred             HhCCC-CcCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc--------CCceEeccchhhhhhhHHHHHHH
Confidence            34455 6899999999999999999999999999999886665554433        56799999999999999999986


Q ss_pred             HhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN  296 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~  296 (503)
                      ..... .-.+++++|+..       +..++.++|||.+.|.+++.++...+..+.+||+||+|.+.+...+..|+.++..
T Consensus       185 ~fgdv-~~~vGL~TGDv~-------IN~~A~clvMTTEILRnMlyrg~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~Ii~  256 (1041)
T COG4581         185 KFGDV-ADMVGLMTGDVS-------INPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERGVVWEEVIIL  256 (1041)
T ss_pred             Hhhhh-hhhccceeccee-------eCCCCceEEeeHHHHHHHhccCcccccccceEEEEeeeeccccccchhHHHHHHh
Confidence            65322 123567777764       4567899999999999999998888999999999999999999999999999999


Q ss_pred             CCCCCcEEEEEeeCCHHHH--HHHHHhcCCCeEEEeCCCCCCCCceEEEEEE------cChhhH-----HHHHHHHHH--
Q 010709          297 LPDKHQTLLFSATMPVEIE--ALAQEYLTDPVQVKVGKVSSPTANVIQILEK------VSENEK-----VDRLLALLV--  361 (503)
Q Consensus       297 ~~~~~q~i~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~k-----~~~l~~~l~--  361 (503)
                      ++...++|++|||+|+..+  ..+...-..|..+.... ..+.+.....+..      +....+     .......+.  
T Consensus       257 lP~~v~~v~LSATv~N~~EF~~Wi~~~~~~~~~vv~t~-~RpvPL~~~~~~~~~l~~lvde~~~~~~~~~~~a~~~l~~~  335 (1041)
T COG4581         257 LPDHVRFVFLSATVPNAEEFAEWIQRVHSQPIHVVSTE-HRPVPLEHFVYVGKGLFDLVDEKKKFNAENFPSANRSLSCF  335 (1041)
T ss_pred             cCCCCcEEEEeCCCCCHHHHHHHHHhccCCCeEEEeec-CCCCCeEEEEecCCceeeeecccccchhhcchhhhhhhhcc
Confidence            9999999999999976543  33333334444443221 1111111111111      111110     000000000  


Q ss_pred             -HHHHhhh------------------------------ccCCCCCcEEEEEcchhhHHHHHHHHHH--------------
Q 010709          362 -EEAFLAE------------------------------KSCHPFPLTIVFVERKTRCDEVSEALVA--------------  396 (503)
Q Consensus       362 -~~~~~~~------------------------------~~~~~~~~~lIF~~~~~~~~~l~~~L~~--------------  396 (503)
                       .......                              .......++|+|+-++..|+..+..+..              
T Consensus       336 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~iv~~l~~~~~lP~I~F~FSr~~Ce~~a~~~~~ldl~~~~~~e~~i~  415 (1041)
T COG4581         336 SEKVRETDDGDVGRYARRTKALRGSAKGPAGRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIR  415 (1041)
T ss_pred             chhccccCccccccccccccccCCcccccccchHHHhhhhhhcCCceEEEEEchhhHHHHHHHhcccccccCCcHHHHHH
Confidence             0000000                              0001224699999999999888877742              


Q ss_pred             --------------CCC-------------eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEc
Q 010709          397 --------------EGL-------------HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNL  449 (503)
Q Consensus       397 --------------~~~-------------~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~  449 (503)
                                    .++             .+..+|+||-+..+..+...|..|-++|++||..++.|+|+| +++|++.
T Consensus       416 ~ii~~~i~~L~~ed~~lp~~~~~~~~~L~RGiavHH~GlLP~~K~~vE~Lfq~GLvkvvFaTeT~s~GiNmP-artvv~~  494 (1041)
T COG4581         416 EIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVKVVFATETFAIGINMP-ARTVVFT  494 (1041)
T ss_pred             HHHHHHHhhcChhhhcCcccHHHHHHHHhhhhhhhccccchHHHHHHHHHHhccceeEEeehhhhhhhcCCc-ccceeee
Confidence                          011             245799999999999999999999999999999999999999 6777776


Q ss_pred             cCC---------CChhHHHHhhCcceee
Q 010709          450 DLP---------KVLLAASESLCTTSFN  468 (503)
Q Consensus       450 ~~p---------~s~~~~~Qr~GR~gR~  468 (503)
                      .+.         -+..+|.|..|||||-
T Consensus       495 ~l~K~dG~~~r~L~~gEy~QmsGRAGRR  522 (1041)
T COG4581         495 SLSKFDGNGHRWLSPGEYTQMSGRAGRR  522 (1041)
T ss_pred             eeEEecCCceeecChhHHHHhhhhhccc
Confidence            654         3678999999999995

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

Probab=99.96  E-value=1.2e-27  Score=259.93  Aligned_cols=307  Identities=18%  Similarity=0.223  Sum_probs=199.5

Q ss_pred             CCCcHHHHHHHHHHh----cC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVAL----SG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~----~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      ..++++|.+|+..+.    +| +.++++++||+|||.++ +.++..++...     ..+++|||+|+++|+.|+.+.|+.
T Consensus       412 ~~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~ta-i~li~~L~~~~-----~~~rVLfLvDR~~L~~Qa~~~F~~  485 (1123)
T PRK11448        412 LGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTA-IALMYRLLKAK-----RFRRILFLVDRSALGEQAEDAFKD  485 (1123)
T ss_pred             CCCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHH-HHHHHHHHhcC-----ccCeEEEEecHHHHHHHHHHHHHh
Confidence            358999999998775    33 56999999999999875 44555544431     246899999999999999999988


Q ss_pred             HhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-----CCCCCCccEEEecchhHHhhC-------
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-----NTSLSRVSFVILDEADRMLDM-------  284 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-----~~~l~~~~~vViDEaH~l~~~-------  284 (503)
                      +.... ......+++.....+.  .......|+|+|.+.+.+.+...     .+.+..+++|||||||+....       
T Consensus       486 ~~~~~-~~~~~~i~~i~~L~~~--~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~  562 (1123)
T PRK11448        486 TKIEG-DQTFASIYDIKGLEDK--FPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEG  562 (1123)
T ss_pred             ccccc-ccchhhhhchhhhhhh--cccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccc
Confidence            74221 1111111111111111  11245799999999997765432     245678999999999985310       


Q ss_pred             --------CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeE---------------------EEeC--CC
Q 010709          285 --------GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQ---------------------VKVG--KV  333 (503)
Q Consensus       285 --------~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~---------------------~~~~--~~  333 (503)
                              .+...+++++.++.  ...|+|||||.....    .+++.|+.                     +...  ..
T Consensus       563 ~~~~~~~~~~~~~yr~iL~yFd--A~~IGLTATP~r~t~----~~FG~pv~~Ysl~eAI~DG~Lv~~~~p~~i~t~~~~~  636 (1123)
T PRK11448        563 ELQFRDQLDYVSKYRRVLDYFD--AVKIGLTATPALHTT----EIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQE  636 (1123)
T ss_pred             hhccchhhhHHHHHHHHHhhcC--ccEEEEecCCccchh----HHhCCeeEEeeHHHHHhcCCcccCcCCEEEEEEeccc
Confidence                    12467888888774  357999999964432    22333321                     1110  00


Q ss_pred             CC--CCCc-e---EE---EE--EEcChh---------------hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhH
Q 010709          334 SS--PTAN-V---IQ---IL--EKVSEN---------------EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRC  387 (503)
Q Consensus       334 ~~--~~~~-~---~~---~~--~~~~~~---------------~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~  387 (503)
                      +.  .... +   ..   .+  ...+..               .....++..+.+..    .. ..++|+||||.++.+|
T Consensus       637 gi~~~~~e~~~~~~~~~~~i~~~~l~d~~~~~~~~~~~~vi~~~~~~~i~~~l~~~l----~~-~~~~KtiIF~~s~~HA  711 (1123)
T PRK11448        637 GIHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELAKYL----DP-TGEGKTLIFAATDAHA  711 (1123)
T ss_pred             cccccccchhhhcchhhhhhhhccCcHHHhhhHHHHHHHHhhHHHHHHHHHHHHHHH----hc-cCCCcEEEEEcCHHHH
Confidence            00  0000 0   00   00  000000               00011111121111    11 1237899999999999


Q ss_pred             HHHHHHHHHC------CC---eEEEEcCCCCHHHHHHHHHHHhcCCC-cEEEEccccccCCCCCCCCEEEEccCCCChhH
Q 010709          388 DEVSEALVAE------GL---HAVALHGGRNQSDRESALRDFRNGST-NILVATDVASRGLDVMGVAHVVNLDLPKVLLA  457 (503)
Q Consensus       388 ~~l~~~L~~~------~~---~v~~lh~~~~~~~r~~~~~~f~~g~~-~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~  457 (503)
                      +.+++.|.+.      ++   .+..++|+.+  ++..+++.|+++.. .|+|+++++.+|+|+|.|.+||++++++|...
T Consensus       712 ~~i~~~L~~~f~~~~~~~~~~~v~~itg~~~--~~~~li~~Fk~~~~p~IlVsvdmL~TG~DvP~v~~vVf~rpvkS~~l  789 (1123)
T PRK11448        712 DMVVRLLKEAFKKKYGQVEDDAVIKITGSID--KPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRIL  789 (1123)
T ss_pred             HHHHHHHHHHHHhhcCCcCccceEEEeCCcc--chHHHHHHHhCCCCCeEEEEecccccCCCcccccEEEEecCCCCHHH
Confidence            9999887653      22   4567888876  46789999999886 69999999999999999999999999999999


Q ss_pred             HHHhhCcceeeee
Q 010709          458 ASESLCTTSFNIT  470 (503)
Q Consensus       458 ~~Qr~GR~gR~~~  470 (503)
                      |.||+||+.|...
T Consensus       790 f~QmIGRgtR~~~  802 (1123)
T PRK11448        790 YEQMLGRATRLCP  802 (1123)
T ss_pred             HHHHHhhhccCCc
Confidence            9999999999653

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=3.9e-27  Score=243.69  Aligned_cols=301  Identities=19%  Similarity=0.199  Sum_probs=218.7

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+++|.-.--.+.+|  -|..++||+|||++|.+|++...+.        +..++|++||++||.|.++.+..+...+ 
T Consensus        82 ~~ydvQliGg~~Lh~G--~Iaem~TGeGKTL~a~Lpa~~~al~--------G~~V~VvTpn~yLA~qd~e~m~~l~~~l-  150 (896)
T PRK13104         82 RHFDVQLIGGMVLHEG--NIAEMRTGEGKTLVATLPAYLNAIS--------GRGVHIVTVNDYLAKRDSQWMKPIYEFL-  150 (896)
T ss_pred             CcchHHHhhhhhhccC--ccccccCCCCchHHHHHHHHHHHhc--------CCCEEEEcCCHHHHHHHHHHHHHHhccc-
Confidence            6788887766666555  4789999999999999999977654        4569999999999999999999999877 


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC-CCCC-----CCccEEEecchhHHh-hCC---------
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG-NTSL-----SRVSFVILDEADRML-DMG---------  285 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~-~~~l-----~~~~~vViDEaH~l~-~~~---------  285 (503)
                      ++.+.+++|+.........  ..++|+|+||++| .+++..+ .+.+     ..+.++||||||.++ +..         
T Consensus       151 GLtv~~i~gg~~~~~r~~~--y~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiLIDeArtPLIISg~  228 (896)
T PRK13104        151 GLTVGVIYPDMSHKEKQEA--YKADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSILIDEARTPLIISGA  228 (896)
T ss_pred             CceEEEEeCCCCHHHHHHH--hCCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhhhhccCCceeeeCC
Confidence            5999999999877665433  3689999999999 8888765 2333     589999999999733 100         


Q ss_pred             ------CHHHHHHHHHhCCC--------------C---------------------------------------------
Q 010709          286 ------FEPQIREVMQNLPD--------------K---------------------------------------------  300 (503)
Q Consensus       286 ------~~~~~~~il~~~~~--------------~---------------------------------------------  300 (503)
                            .......++..+..              +                                             
T Consensus       229 ~~~~~~~y~~~~~~v~~l~~~~~~~~~~dy~idek~~~v~Lte~G~~~~e~~~~~~~il~~~~~l~~~~~~~~~~~i~~a  308 (896)
T PRK13104        229 AEDSSELYIKINSLIPQLKKQEEEGDEGDYTIDEKQKQAHLTDAGHLHIEELLTKAKLLDPGESLYHASNIMLMHHVNAA  308 (896)
T ss_pred             CccchHHHHHHHHHHHHHHhccccCCCCCEEEEcCCCceEEchHHHHHHHHHHHhCCccCCcccccCchhhhHHHHHHHH
Confidence                  00000011110000              0                                             


Q ss_pred             -----------------------------------------------------------------------CcEEEEEee
Q 010709          301 -----------------------------------------------------------------------HQTLLFSAT  309 (503)
Q Consensus       301 -----------------------------------------------------------------------~q~i~~SAT  309 (503)
                                                                                             .++-+||+|
T Consensus       309 L~A~~lf~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQaiEaKE~v~i~~e~~t~AsIT~Qn~Fr~Y~kLsGMTGT  388 (896)
T PRK13104        309 LKAHAMFHRDIDYIVKDNQVVIVDEHTGRTMPGRRWSEGLHQAVEAKEGVPIQNENQTLASITFQNFFRMYNKLSGMTGT  388 (896)
T ss_pred             HHHHHHhcCCCceEEECCEEEEEECCCCCcCCCCCcChHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhccCCCC
Confidence                                                                                   134456666


Q ss_pred             CCHHHHHHHHHhcCCCeEEEeCCCCCCCC-ceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHH
Q 010709          310 MPVEIEALAQEYLTDPVQVKVGKVSSPTA-NVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCD  388 (503)
Q Consensus       310 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~  388 (503)
                      ...+-.++.+-|-- .+.+..  ...+.. ....-.+......|...+...+...+.       .+.|+||||++++.++
T Consensus       389 a~te~~Ef~~iY~l-~Vv~IP--tnkp~~R~d~~d~v~~t~~~k~~av~~~i~~~~~-------~g~PVLVgt~Sie~sE  458 (896)
T PRK13104        389 ADTEAYEFQQIYNL-EVVVIP--TNRSMIRKDEADLVYLTQADKFQAIIEDVRECGV-------RKQPVLVGTVSIEASE  458 (896)
T ss_pred             ChhHHHHHHHHhCC-CEEECC--CCCCcceecCCCeEEcCHHHHHHHHHHHHHHHHh-------CCCCEEEEeCcHHHHH
Confidence            54444444333322 222211  111111 112223455667788888877765543       3457999999999999


Q ss_pred             HHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCC--------------------------
Q 010709          389 EVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMG--------------------------  442 (503)
Q Consensus       389 ~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~--------------------------  442 (503)
                      .+++.|.+.|+.+..+|+.+.+.++..+.+.|+.|  .|+|||++++||+||.=                          
T Consensus       459 ~ls~~L~~~gi~h~vLnak~~q~Ea~iia~Ag~~G--~VtIATNmAGRGtDI~Lggn~~~~~~~~~~~~~~~~~~~~~~~  536 (896)
T PRK13104        459 FLSQLLKKENIKHQVLNAKFHEKEAQIIAEAGRPG--AVTIATNMAGRGTDIVLGGSLAADLANLPADASEQEKEAVKKE  536 (896)
T ss_pred             HHHHHHHHcCCCeEeecCCCChHHHHHHHhCCCCC--cEEEeccCccCCcceecCCchhhhhhccccchhhHHHHHHHHH
Confidence            99999999999999999999999999999999999  49999999999999871                          


Q ss_pred             ------------CCEEEEccCCCChhHHHHhhCcceee
Q 010709          443 ------------VAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       443 ------------v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                                  ==+||-...+.|..-=.|-.||+||.
T Consensus       537 ~~~~~~~V~~~GGL~VIgTerhesrRID~QLrGRaGRQ  574 (896)
T PRK13104        537 WQKRHDEVIAAGGLRIIGSERHESRRIDNQLRGRAGRQ  574 (896)
T ss_pred             hhhhhhHHHHcCCCEEEeeccCchHHHHHHhccccccC
Confidence                        12788888999988888999999985

>KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]

Probab=99.96  E-value=1.1e-27  Score=247.77  Aligned_cols=307  Identities=17%  Similarity=0.178  Sum_probs=216.9

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      ..+..+.+.+.++.+++.++|+|+||+|||++....++......+     ...++++..|+|--|..+++++..--....
T Consensus       173 Pa~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~-----~~~~IicTQPRRIsAIsvAeRVa~ER~~~~  247 (924)
T KOG0920|consen  173 PAYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESG-----AACNIICTQPRRISAISVAERVAKERGESL  247 (924)
T ss_pred             ccHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC-----CCCeEEecCCchHHHHHHHHHHHHHhcccc
Confidence            346667778888888899999999999999976555666655543     456688889999999989988875442222


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh-HHhhCCCHHHHHHHHHhCCCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD-RMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH-~l~~~~~~~~~~~il~~~~~~~  301 (503)
                      +-.++.-.....      .....+.+++||.|.|++.+.. ...+..++.||+||+| +-++.+|.-.+.+.+-..+++.
T Consensus       248 g~~VGYqvrl~~------~~s~~t~L~fcTtGvLLr~L~~-~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~p~L  320 (924)
T KOG0920|consen  248 GEEVGYQVRLES------KRSRETRLLFCTTGVLLRRLQS-DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRNPDL  320 (924)
T ss_pred             CCeeeEEEeeec------ccCCceeEEEecHHHHHHHhcc-CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhCCCc
Confidence            222222111111      1223489999999999999987 5678899999999999 4455667777777777777999


Q ss_pred             cEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCc----------------eEEE------------EEEcChhhHH
Q 010709          302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTAN----------------VIQI------------LEKVSENEKV  353 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~------------~~~~~~~~k~  353 (503)
                      ++|+||||+..+   ....|++....+++.....+...                ..+.            ......+-. 
T Consensus       321 kvILMSAT~dae---~fs~YF~~~pvi~i~grtfpV~~~fLEDil~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~id-  396 (924)
T KOG0920|consen  321 KVILMSATLDAE---LFSDYFGGCPVITIPGRTFPVKEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKLWEPEID-  396 (924)
T ss_pred             eEEEeeeecchH---HHHHHhCCCceEeecCCCcchHHHHHHHHHHHhcccccccccccccccCccccccchhcccccc-
Confidence            999999999632   45556655444444332221100                0000            000001111 


Q ss_pred             HHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-------CCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q 010709          354 DRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-------GLHAVALHGGRNQSDRESALRDFRNGSTN  426 (503)
Q Consensus       354 ~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-------~~~v~~lh~~~~~~~r~~~~~~f~~g~~~  426 (503)
                      ..++..+..+....    ...+.+|||.++..++..+.+.|...       .+-+.++|+.++..++..+++....|..+
T Consensus       397 ~~Li~~li~~I~~~----~~~GaILVFLPG~~eI~~~~~~L~~~~~f~~~~~~~ilplHs~~~s~eQ~~VF~~pp~g~RK  472 (924)
T KOG0920|consen  397 YDLIEDLIEYIDER----EFEGAILVFLPGWEEILQLKELLEVNLPFADSLKFAILPLHSSIPSEEQQAVFKRPPKGTRK  472 (924)
T ss_pred             HHHHHHHHHhcccC----CCCceEEEEcCCHHHHHHHHHHhhhccccccccceEEEeccccCChHHHHHhcCCCCCCcch
Confidence            12222222222221    45678999999999999999999652       36788999999999999999999999999


Q ss_pred             EEEEccccccCCCCCCCCEEEEccCCC------------------ChhHHHHhhCcceeee
Q 010709          427 ILVATDVASRGLDVMGVAHVVNLDLPK------------------VLLAASESLCTTSFNI  469 (503)
Q Consensus       427 vLvaT~~~~~Gldip~v~~VI~~~~p~------------------s~~~~~Qr~GR~gR~~  469 (503)
                      ||+||++++++|+|++|-+||+.+.-+                  +.++..||.|||||..
T Consensus       473 IIlaTNIAETSITIdDVvyVIDsG~~Ke~~yD~~~~~s~l~~~wvSkAna~QR~GRAGRv~  533 (924)
T KOG0920|consen  473 IILATNIAETSITIDDVVYVIDSGLVKEKSYDPERKVSCLLLSWVSKANAKQRRGRAGRVR  533 (924)
T ss_pred             hhhhhhhHhhcccccCeEEEEecCeeeeeeecccCCcchhheeeccccchHHhcccccCcc
Confidence            999999999999999999999977643                  3388899999999953

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.96  E-value=1.2e-26  Score=240.09  Aligned_cols=302  Identities=20%  Similarity=0.236  Sum_probs=222.9

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|++.|.-..-.+.+|+  |..++||+|||+++.+|++...+.        |..+-|++|+..||.|.++.+..+...+
T Consensus        80 ~~~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~--------G~~V~IvTpn~yLA~rd~e~~~~l~~~L  149 (830)
T PRK12904         80 MRHFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT--------GKGVHVVTVNDYLAKRDAEWMGPLYEFL  149 (830)
T ss_pred             CCCCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc--------CCCEEEEecCHHHHHHHHHHHHHHHhhc
Confidence            378899988887776664  889999999999999999754443        3457899999999999999999999877


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcCC------CCCCCccEEEecchhHHh-hCC--------
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQGN------TSLSRVSFVILDEADRML-DMG--------  285 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~l~~~~~vViDEaH~l~-~~~--------  285 (503)
                       +++++++.|+....+.....  .++|+++|++.| .+++..+.      ..+..+.++||||||.++ +..        
T Consensus       150 -Glsv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiLIDeArtpLiiSg  226 (830)
T PRK12904        150 -GLSVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSILIDEARTPLIISG  226 (830)
T ss_pred             -CCeEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhheeccCCCceeeEC
Confidence             69999999998877655543  489999999999 88887643      236789999999999733 100        


Q ss_pred             -------CHHHHHHHHHhCCC-----------------------------------------------------------
Q 010709          286 -------FEPQIREVMQNLPD-----------------------------------------------------------  299 (503)
Q Consensus       286 -------~~~~~~~il~~~~~-----------------------------------------------------------  299 (503)
                             ....+..+...+..                                                           
T Consensus       227 ~~~~~~~~y~~~~~~v~~l~~~~dy~vde~~~~v~lte~G~~~~e~~~~~~~ly~~~~~~~~~~i~~AL~A~~l~~~d~d  306 (830)
T PRK12904        227 PAEDSSELYKRANKIVPTLEKEGDYTVDEKSRTVGLTEEGIEKAEKLLGIENLYDPENIALVHHLNQALRAHELFKRDVD  306 (830)
T ss_pred             CCCcccHHHHHHHHHHHhcCCCCCeEEEcCCCeeeECHHHHHHHHHHhCCccccChhhhHHHHHHHHHHHHHHHHhcCCc
Confidence                   00111111111100                                                           


Q ss_pred             ----------------------------------------------------------CCcEEEEEeeCCHHHHHHHHHh
Q 010709          300 ----------------------------------------------------------KHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       300 ----------------------------------------------------------~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                                                                                -.++.+||+|...+-..+.+-|
T Consensus       307 YiV~dg~V~ivDe~TGR~~~gr~ws~GLHQaiEaKE~v~i~~e~~t~a~It~qn~Fr~Y~kl~GmTGTa~te~~E~~~iY  386 (830)
T PRK12904        307 YIVKDGEVVIVDEFTGRLMPGRRYSDGLHQAIEAKEGVKIQNENQTLASITFQNYFRMYEKLAGMTGTADTEAEEFREIY  386 (830)
T ss_pred             EEEECCEEEEEECCCCccCCCCccchHHHHHHHHhcCCCCCCCceeeeeeeHHHHHHhcchhcccCCCcHHHHHHHHHHh
Confidence                                                                      0146678888765555544444


Q ss_pred             cCCCeEEEeCCCCCCCCce-EEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCe
Q 010709          322 LTDPVQVKVGKVSSPTANV-IQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLH  400 (503)
Q Consensus       322 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~  400 (503)
                      --+ +.....  ..+.... ..-........|...+...+.+...       ...++||||++++.++.+++.|.+.|+.
T Consensus       387 ~l~-vv~IPt--nkp~~r~d~~d~i~~t~~~K~~aI~~~I~~~~~-------~grpVLIft~Si~~se~Ls~~L~~~gi~  456 (830)
T PRK12904        387 NLD-VVVIPT--NRPMIRIDHPDLIYKTEKEKFDAVVEDIKERHK-------KGQPVLVGTVSIEKSELLSKLLKKAGIP  456 (830)
T ss_pred             CCC-EEEcCC--CCCeeeeeCCCeEEECHHHHHHHHHHHHHHHHh-------cCCCEEEEeCcHHHHHHHHHHHHHCCCc
Confidence            332 222111  1111111 1223444666788888877765432       2346999999999999999999999999


Q ss_pred             EEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCC-------------------------------------
Q 010709          401 AVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGV-------------------------------------  443 (503)
Q Consensus       401 v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v-------------------------------------  443 (503)
                      +..+|+.  +.+|...+..|+.+...|+|||++++||+||+-=                                     
T Consensus       457 ~~vLnak--q~eREa~Iia~Ag~~g~VtIATNmAGRGtDI~LgGn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~G  534 (830)
T PRK12904        457 HNVLNAK--NHEREAEIIAQAGRPGAVTIATNMAGRGTDIKLGGNPEMLAAALLEEETEEQIAKIKAEWQEEHEEVLEAG  534 (830)
T ss_pred             eEeccCc--hHHHHHHHHHhcCCCceEEEecccccCCcCccCCCchhhhhhhhhhhhhhHHHHHHHHHHhhhhhhHHHcC
Confidence            9999995  7899999999999999999999999999999832                                     


Q ss_pred             -CEEEEccCCCChhHHHHhhCcceee
Q 010709          444 -AHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       444 -~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                       =|||-...|.|..--.|-.||+||.
T Consensus       535 GLhVigTerhesrRid~QlrGRagRQ  560 (830)
T PRK12904        535 GLHVIGTERHESRRIDNQLRGRSGRQ  560 (830)
T ss_pred             CCEEEecccCchHHHHHHhhcccccC
Confidence             2789999999998889999999995

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

Probab=99.95  E-value=9.7e-26  Score=203.99  Aligned_cols=295  Identities=17%  Similarity=0.162  Sum_probs=207.3

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ++++.|+.+-..+.    +.++.+|.|-||+|||... .+.+...+++       |.++.+..|+...+..++.++++-+
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMi-f~~i~~al~~-------G~~vciASPRvDVclEl~~Rlk~aF  168 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMI-FQGIEQALNQ-------GGRVCIASPRVDVCLELYPRLKQAF  168 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhh-HHHHHHHHhc-------CCeEEEecCcccchHHHHHHHHHhh
Confidence            67888988776654    5678999999999999854 6667777765       7889999999999999999998766


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP  298 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~  298 (503)
                      .   +..+.+++|+.....       ...++|+|...|++...       .++++||||+|.+--..-......+-+..+
T Consensus       169 ~---~~~I~~Lyg~S~~~f-------r~plvVaTtHQLlrFk~-------aFD~liIDEVDAFP~~~d~~L~~Av~~ark  231 (441)
T COG4098         169 S---NCDIDLLYGDSDSYF-------RAPLVVATTHQLLRFKQ-------AFDLLIIDEVDAFPFSDDQSLQYAVKKARK  231 (441)
T ss_pred             c---cCCeeeEecCCchhc-------cccEEEEehHHHHHHHh-------hccEEEEeccccccccCCHHHHHHHHHhhc
Confidence            4   356888998875432       27899999998887664       478999999996432221222233334445


Q ss_pred             CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHH-------HHHHHHHHHHHhhhccC
Q 010709          299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVD-------RLLALLVEEAFLAEKSC  371 (503)
Q Consensus       299 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~-------~l~~~l~~~~~~~~~~~  371 (503)
                      +..-+|.+|||+++.++.-+..-  +-..+.+.......+.+.-.+..+....|.-       .+...+..+.       
T Consensus       232 ~~g~~IylTATp~k~l~r~~~~g--~~~~~klp~RfH~~pLpvPkf~w~~~~~k~l~r~kl~~kl~~~lekq~-------  302 (441)
T COG4098         232 KEGATIYLTATPTKKLERKILKG--NLRILKLPARFHGKPLPVPKFVWIGNWNKKLQRNKLPLKLKRWLEKQR-------  302 (441)
T ss_pred             ccCceEEEecCChHHHHHHhhhC--CeeEeecchhhcCCCCCCCceEEeccHHHHhhhccCCHHHHHHHHHHH-------
Confidence            55668999999998877654432  2222222222222222222223333222221       3334443332       


Q ss_pred             CCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEc
Q 010709          372 HPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNL  449 (503)
Q Consensus       372 ~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~  449 (503)
                      ....+++||+++.+..++++..|++.  ...+...|+..  ..|.+..+.|++|+..+||+|.+++||+++|+|++.|.-
T Consensus       303 ~~~~P~liF~p~I~~~eq~a~~lk~~~~~~~i~~Vhs~d--~~R~EkV~~fR~G~~~lLiTTTILERGVTfp~vdV~Vlg  380 (441)
T COG4098         303 KTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHSED--QHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLG  380 (441)
T ss_pred             hcCCcEEEEecchHHHHHHHHHHHhhCCccceeeeeccC--ccHHHHHHHHHcCceEEEEEeehhhcccccccceEEEec
Confidence            23457999999999999999999554  34567888865  478899999999999999999999999999999986653


Q ss_pred             cCC--CChhHHHHhhCcceeeeeecc
Q 010709          450 DLP--KVLLAASESLCTTSFNITTNL  473 (503)
Q Consensus       450 ~~p--~s~~~~~Qr~GR~gR~~~~~~  473 (503)
                      .--  -+-+..+|..||+||++.-++
T Consensus       381 aeh~vfTesaLVQIaGRvGRs~~~Pt  406 (441)
T COG4098         381 AEHRVFTESALVQIAGRVGRSLERPT  406 (441)
T ss_pred             CCcccccHHHHHHHhhhccCCCcCCC
Confidence            332  456889999999999875554

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.95  E-value=5e-26  Score=234.42  Aligned_cols=302  Identities=19%  Similarity=0.221  Sum_probs=217.3

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|++.|.-+.-.+.+|+  |..+.||+|||+++.+|++...+.        |..+-+++|+..||.|-++.+..+...+
T Consensus        79 ~~~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~--------G~~v~vvT~neyLA~Rd~e~~~~~~~~L  148 (796)
T PRK12906         79 LRPFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT--------GKGVHVVTVNEYLSSRDATEMGELYRWL  148 (796)
T ss_pred             CCCchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc--------CCCeEEEeccHHHHHhhHHHHHHHHHhc
Confidence            478999998887777765  899999999999999888877665        6779999999999999999999999887


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHH-HHHHcC------CCCCCCccEEEecchhHHh-h----------
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFL-DHLQQG------NTSLSRVSFVILDEADRML-D----------  283 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~-~~l~~~------~~~l~~~~~vViDEaH~l~-~----------  283 (503)
                       ++.++++.++....+..  ....++|+++|...|. +.+..+      ....+.+.+.||||+|.++ +          
T Consensus       149 -Gl~vg~i~~~~~~~~r~--~~y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiLiDeartPLiisg  225 (796)
T PRK12906        149 -GLTVGLNLNSMSPDEKR--AAYNCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSILIDEARTPLIISG  225 (796)
T ss_pred             -CCeEEEeCCCCCHHHHH--HHhcCCCeecCCccccccchhhccccchhhhhccCcceeeeccchheeeccCCCceecCC
Confidence             59999998877665543  3346899999998773 333221      1224568899999999622 1          


Q ss_pred             CC-----CHHHHHHHHHhCC------------------------------------------------------------
Q 010709          284 MG-----FEPQIREVMQNLP------------------------------------------------------------  298 (503)
Q Consensus       284 ~~-----~~~~~~~il~~~~------------------------------------------------------------  298 (503)
                      ..     ....+.++...+.                                                            
T Consensus       226 ~~~~~~~~y~~~~~~v~~l~~~~~~~~~~~~~~~dy~id~~~k~v~lte~G~~~~e~~~~i~~l~~~~~~~~~~~i~~Al  305 (796)
T PRK12906        226 QAEKATDLYIRADRFVKTLIKDEAEDGDDDEDTGDYKIDEKTKTISLTEQGIRKAEKLFGLDNLYDSENTALAHHIDQAL  305 (796)
T ss_pred             CCCcchHHHHHHHHHHHHHHhhhhccccccCCCCceEEEcccCceeecHHHHHHHHHHcCCccccCchhhhHHHHHHHHH
Confidence            00     0000011110000                                                            


Q ss_pred             -------CC-------------------------------------------------------------CcEEEEEeeC
Q 010709          299 -------DK-------------------------------------------------------------HQTLLFSATM  310 (503)
Q Consensus       299 -------~~-------------------------------------------------------------~q~i~~SAT~  310 (503)
                             .+                                                             .++.+||+|.
T Consensus       306 ~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~ws~GLHQaieaKe~v~i~~e~~t~a~It~qnfFr~Y~kl~GmTGTa  385 (796)
T PRK12906        306 RANYIMLKDIDYVVQDGEVLIVDEFTGRVMEGRRYSDGLHQAIEAKEGVKIQEENQTLATITYQNFFRMYKKLSGMTGTA  385 (796)
T ss_pred             HHHHHHhcCCcEEEECCEEEEEeCCCCCcCCCCccChHHHHHHHHhcCCCcCCCceeeeeehHHHHHHhcchhhccCCCC
Confidence                   00                                                             1456777777


Q ss_pred             CHHHHHHHHHhcCCCeEEEeCCCCCCCC-ceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHH
Q 010709          311 PVEIEALAQEYLTDPVQVKVGKVSSPTA-NVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDE  389 (503)
Q Consensus       311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~  389 (503)
                      ..+-..+.+-| +-++.. +.. ..+.. ....-........|...+...+.....       ...++||||++++.++.
T Consensus       386 ~~e~~Ef~~iY-~l~vv~-IPt-nkp~~r~d~~d~i~~t~~~K~~al~~~i~~~~~-------~g~pvLI~t~si~~se~  455 (796)
T PRK12906        386 KTEEEEFREIY-NMEVIT-IPT-NRPVIRKDSPDLLYPTLDSKFNAVVKEIKERHA-------KGQPVLVGTVAIESSER  455 (796)
T ss_pred             HHHHHHHHHHh-CCCEEE-cCC-CCCeeeeeCCCeEEcCHHHHHHHHHHHHHHHHh-------CCCCEEEEeCcHHHHHH
Confidence            55544444433 322222 111 11111 111223344556788888877765432       34579999999999999


Q ss_pred             HHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCC---CCC-----EEEEccCCCChhHHHHh
Q 010709          390 VSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM---GVA-----HVVNLDLPKVLLAASES  461 (503)
Q Consensus       390 l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip---~v~-----~VI~~~~p~s~~~~~Qr  461 (503)
                      +++.|.+.|+.+..+|+++.+.++..+.+.++.|.  |+|||++++||.||+   +|.     +||++++|.+...+.||
T Consensus       456 ls~~L~~~gi~~~~Lna~~~~~Ea~ii~~ag~~g~--VtIATnmAGRGtDI~l~~~V~~~GGLhVI~te~pes~ri~~Ql  533 (796)
T PRK12906        456 LSHLLDEAGIPHAVLNAKNHAKEAEIIMNAGQRGA--VTIATNMAGRGTDIKLGPGVKELGGLAVIGTERHESRRIDNQL  533 (796)
T ss_pred             HHHHHHHCCCCeeEecCCcHHHHHHHHHhcCCCce--EEEEeccccCCCCCCCCcchhhhCCcEEEeeecCCcHHHHHHH
Confidence            99999999999999999999888888888777775  999999999999995   899     99999999999999999


Q ss_pred             hCcceee
Q 010709          462 LCTTSFN  468 (503)
Q Consensus       462 ~GR~gR~  468 (503)
                      +||+||.
T Consensus       534 ~GRtGRq  540 (796)
T PRK12906        534 RGRSGRQ  540 (796)
T ss_pred             hhhhccC
Confidence            9999994

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

Probab=99.95  E-value=3.9e-26  Score=200.95  Aligned_cols=165  Identities=31%  Similarity=0.569  Sum_probs=140.7

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCc
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSF  224 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~  224 (503)
                      ||+|.++++.+..|+++++.||||+|||++|+++++..+...      ...++++++|+++|+.|+.+.+.+++.. .++
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~------~~~~~lii~P~~~l~~q~~~~~~~~~~~-~~~   73 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG------KDARVLIIVPTRALAEQQFERLRKFFSN-TNV   73 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT------SSSEEEEEESSHHHHHHHHHHHHHHTTT-TTS
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC------CCceEEEEeecccccccccccccccccc-ccc
Confidence            689999999999999999999999999999999999877663      1348999999999999999999999866 357


Q ss_pred             eEEEEECCccHH-HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC--CCC
Q 010709          225 KTAIVVGGTNIA-EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP--DKH  301 (503)
Q Consensus       225 ~~~~~~~~~~~~-~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~--~~~  301 (503)
                      .+..++++.... +....+..+++|+|+||++|.+.+......+.++++||+||+|.+....+...+..++..+.  .+.
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~~~  153 (169)
T PF00270_consen   74 RVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFKNI  153 (169)
T ss_dssp             SEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTTTS
T ss_pred             ccccccccccccccccccccccccccccCcchhhccccccccccccceeeccCcccccccccHHHHHHHHHHHhcCCCCC
Confidence            888888888755 44455566799999999999999988655677799999999999998888888988888873  368


Q ss_pred             cEEEEEeeCCHHHHH
Q 010709          302 QTLLFSATMPVEIEA  316 (503)
Q Consensus       302 q~i~~SAT~~~~~~~  316 (503)
                      |++++|||++.++++
T Consensus       154 ~~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  154 QIILLSATLPSNVEK  168 (169)
T ss_dssp             EEEEEESSSTHHHHH
T ss_pred             cEEEEeeCCChhHhh
Confidence            999999999976654

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 ....

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.95  E-value=1.3e-25  Score=239.53  Aligned_cols=304  Identities=16%  Similarity=0.195  Sum_probs=206.0

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++++|.+++.+++    +|.++|++.++|.|||++. +.++.++....    +..+.+|||||. .+..||.+++.+++
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQa-IalL~~L~~~~----~~~gp~LIVvP~-SlL~nW~~Ei~kw~  242 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQT-ISLLGYLHEYR----GITGPHMVVAPK-STLGNWMNEIRRFC  242 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHH-HHHHHHHHHhc----CCCCCEEEEeCh-HHHHHHHHHHHHHC
Confidence            68999999999986    5678999999999999986 44555544321    123458999998 45677999999987


Q ss_pred             ccCCCceEEEEECCccHHHHHHH---hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSE---LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      .   .+.+..++|..........   .....+|+|+|++.+.....  .+.-..+++|||||||++-+.  ...+.+.+.
T Consensus       243 p---~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~--~L~k~~W~~VIvDEAHrIKN~--~Sklskalr  315 (1033)
T PLN03142        243 P---VLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT--ALKRFSWRYIIIDEAHRIKNE--NSLLSKTMR  315 (1033)
T ss_pred             C---CCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH--HhccCCCCEEEEcCccccCCH--HHHHHHHHH
Confidence            4   3566666665543322111   12468999999999876443  233346889999999998654  444566666


Q ss_pred             hCCCCCcEEEEEeeCCH-HHHHHH---H--------------HhcC------------------CCeEEEeCC----CCC
Q 010709          296 NLPDKHQTLLFSATMPV-EIEALA---Q--------------EYLT------------------DPVQVKVGK----VSS  335 (503)
Q Consensus       296 ~~~~~~q~i~~SAT~~~-~~~~~~---~--------------~~~~------------------~~~~~~~~~----~~~  335 (503)
                      .+.... .+++||||-. ++.++.   .              .++.                  .|..++...    ...
T Consensus       316 ~L~a~~-RLLLTGTPlqNnl~ELwsLL~FL~P~~f~s~~~F~~~f~~~~~~~~~e~i~~L~~~L~pf~LRR~KsdV~~~L  394 (1033)
T PLN03142        316 LFSTNY-RLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISGENDQQEVVQQLHKVLRPFLLRRLKSDVEKGL  394 (1033)
T ss_pred             HhhcCc-EEEEecCCCCCCHHHHHHHHhcCCCCcCCCHHHHHHHHccccccchHHHHHHHHHHhhHHHhhhhHHHHhhhC
Confidence            766554 5889999821 111110   0              0000                  000000000    000


Q ss_pred             CCCceEEEE-------------------------------------------------------------EEcChhhHHH
Q 010709          336 PTANVIQIL-------------------------------------------------------------EKVSENEKVD  354 (503)
Q Consensus       336 ~~~~~~~~~-------------------------------------------------------------~~~~~~~k~~  354 (503)
                      +........                                                             ..+....|+.
T Consensus       395 PpK~e~iv~v~LS~~Qk~lY~~ll~k~~~~l~~g~~~~~LlnilmqLRk~cnHP~L~~~~ep~~~~~~~e~lie~SgKl~  474 (1033)
T PLN03142        395 PPKKETILKVGMSQMQKQYYKALLQKDLDVVNAGGERKRLLNIAMQLRKCCNHPYLFQGAEPGPPYTTGEHLVENSGKMV  474 (1033)
T ss_pred             CCceeEEEeeCCCHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhCCHHhhhcccccCcccchhHHhhhhhHHH
Confidence            000000000                                                             0001123333


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC---CCcEEEEc
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNG---STNILVAT  431 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g---~~~vLvaT  431 (503)
                      .+..++....       ..+.++|||+......+.|.++|...|+.++.+||+++..+|..+++.|++.   ...+|++|
T Consensus       475 lLdkLL~~Lk-------~~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts~~eRq~~Id~Fn~~~s~~~VfLLST  547 (1033)
T PLN03142        475 LLDKLLPKLK-------ERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLST  547 (1033)
T ss_pred             HHHHHHHHHH-------hcCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCCHHHHHHHHHHhccccCCceEEEEec
Confidence            3333333322       2345799999999999999999999999999999999999999999999753   24578999


Q ss_pred             cccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          432 DVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       432 ~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      .+++.|||+..+++||+||+++++....|++||+.|
T Consensus       548 rAGGlGINLt~Ad~VIiyD~dWNP~~d~QAidRaHR  583 (1033)
T PLN03142        548 RAGGLGINLATADIVILYDSDWNPQVDLQAQDRAHR  583 (1033)
T ss_pred             cccccCCchhhCCEEEEeCCCCChHHHHHHHHHhhh
Confidence            999999999999999999999999999999999888

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.95  E-value=3.1e-25  Score=229.20  Aligned_cols=148  Identities=20%  Similarity=0.329  Sum_probs=127.9

Q ss_pred             ccCCCCHHHHHHHH-----HCCCCCC---cHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCC
Q 010709          124 TDMCLHPSIMKDIE-----FHEYTRP---TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGP  195 (503)
Q Consensus       124 ~~~~l~~~l~~~l~-----~~~~~~~---~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~  195 (503)
                      +.+.+.+++.+.+.     ..|+..|   +|+|.++++.+..++++|+.++||+|||++|++|++..++.        +.
T Consensus        65 eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~--------g~  136 (970)
T PRK12899         65 EAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALT--------GK  136 (970)
T ss_pred             HHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhh--------cC
Confidence            55678888888776     6789998   99999999999999999999999999999999999987754        23


Q ss_pred             eEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcCCCCCC------
Q 010709          196 LALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQGNTSLS------  268 (503)
Q Consensus       196 ~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~~~l~------  268 (503)
                      .++||+||++||.|.++.+..+...+ ++++.+++||....++....  +++|+|+||++| ++++..+.+.+.      
T Consensus       137 ~v~IVTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~~~~~~~~~~vq  213 (970)
T PRK12899        137 PVHLVTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDNSIATRKEEQVG  213 (970)
T ss_pred             CeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCCCCCcCHHHhhc
Confidence            48999999999999999999998876 59999999999988776554  599999999999 999987655544      


Q ss_pred             -CccEEEecchhHHh
Q 010709          269 -RVSFVILDEADRML  282 (503)
Q Consensus       269 -~~~~vViDEaH~l~  282 (503)
                       .+.++||||||.|+
T Consensus       214 r~~~~~IIDEADsmL  228 (970)
T PRK12899        214 RGFYFAIIDEVDSIL  228 (970)
T ss_pred             ccccEEEEechhhhh
Confidence             56899999999855

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

Probab=99.95  E-value=4.1e-26  Score=214.85  Aligned_cols=319  Identities=18%  Similarity=0.197  Sum_probs=222.7

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      .+..|...+.++...+-|++..-...+..+.+.+..+.+++-++++|+||||||++  +|.+........     ...+.
T Consensus        23 ~~Npf~~~p~s~rY~~ilk~R~~LPvw~~k~~F~~~l~~nQ~~v~vGetgsGKttQ--iPq~~~~~~~~~-----~~~v~   95 (699)
T KOG0925|consen   23 AINPFNGKPYSQRYYDILKKRRELPVWEQKEEFLKLLLNNQIIVLVGETGSGKTTQ--IPQFVLEYELSH-----LTGVA   95 (699)
T ss_pred             hcCCCCCCcCcHHHHHHHHHHhcCchHHhHHHHHHHHhcCceEEEEecCCCCcccc--CcHHHHHHHHhh-----cccee
Confidence            36678889999999999888765445555555555666777899999999999985  565543332211     24578


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      ...|+|..|.+++.++..-+    ++..+.-.|..-..+..  ...++-+-+||.++|++..... -.+..+++||+|||
T Consensus        96 CTQprrvaamsva~RVadEM----Dv~lG~EVGysIrfEdC--~~~~T~Lky~tDgmLlrEams~-p~l~~y~viiLDea  168 (699)
T KOG0925|consen   96 CTQPRRVAAMSVAQRVADEM----DVTLGEEVGYSIRFEDC--TSPNTLLKYCTDGMLLREAMSD-PLLGRYGVIILDEA  168 (699)
T ss_pred             ecCchHHHHHHHHHHHHHHh----ccccchhcccccccccc--CChhHHHHHhcchHHHHHHhhC-cccccccEEEechh
Confidence            88899999999998887766    34444333333221110  1112345689999999988874 45889999999999


Q ss_pred             hH-HhhCCCHH-HHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHH
Q 010709          279 DR-MLDMGFEP-QIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRL  356 (503)
Q Consensus       279 H~-l~~~~~~~-~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l  356 (503)
                      |. -+..+..- .+..++.. +++.++|.||||+...   ..+.|+.++..+.+..    ...++.++......+.+...
T Consensus       169 hERtlATDiLmGllk~v~~~-rpdLk~vvmSatl~a~---Kfq~yf~n~Pll~vpg----~~PvEi~Yt~e~erDylEaa  240 (699)
T KOG0925|consen  169 HERTLATDILMGLLKEVVRN-RPDLKLVVMSATLDAE---KFQRYFGNAPLLAVPG----THPVEIFYTPEPERDYLEAA  240 (699)
T ss_pred             hhhhHHHHHHHHHHHHHHhh-CCCceEEEeecccchH---HHHHHhCCCCeeecCC----CCceEEEecCCCChhHHHHH
Confidence            94 23222222 23333333 4799999999999432   4667788877776654    22344455555555666666


Q ss_pred             HHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC---------CCeEEEEcCCCCHHHHHHHHHHHhc---C-
Q 010709          357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE---------GLHAVALHGGRNQSDRESALRDFRN---G-  423 (503)
Q Consensus       357 ~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~---------~~~v~~lh~~~~~~~r~~~~~~f~~---g-  423 (503)
                      +..+.+.+..     ..+|-+|||.++.++++..++.+...         .+.|+++|    +.++..+++....   | 
T Consensus       241 irtV~qih~~-----ee~GDilvFLtgeeeIe~aC~~i~re~~~L~~~~g~l~v~PLy----P~~qq~iFep~p~~~~~~  311 (699)
T KOG0925|consen  241 IRTVLQIHMC-----EEPGDILVFLTGEEEIEDACRKISREVDNLGPQVGPLKVVPLY----PAQQQRIFEPAPEKRNGA  311 (699)
T ss_pred             HHHHHHHHhc-----cCCCCEEEEecCHHHHHHHHHHHHHHHHhhccccCCceEEecC----chhhccccCCCCcccCCC
Confidence            6655554433     34667999999999999999988753         35789999    5556666665542   1 


Q ss_pred             -CCcEEEEccccccCCCCCCCCEEEEccCC------------------CChhHHHHhhCcceee
Q 010709          424 -STNILVATDVASRGLDVMGVAHVVNLDLP------------------KVLLAASESLCTTSFN  468 (503)
Q Consensus       424 -~~~vLvaT~~~~~Gldip~v~~VI~~~~p------------------~s~~~~~Qr~GR~gR~  468 (503)
                       .++|+|+|++++..+.|+++.+||+-|+.                  -|.++..||.|||||+
T Consensus       312 ~~RkvVvstniaetsltidgiv~VIDpGf~kqkVYNPRIRvesllv~PISkasA~qR~gragrt  375 (699)
T KOG0925|consen  312 YGRKVVVSTNIAETSLTIDGIVFVIDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT  375 (699)
T ss_pred             ccceEEEEecchheeeeeccEEEEecCchhhhcccCcceeeeeeeeccchHhHHHHHhhhccCC
Confidence             47899999999999999999999998863                  4568999999999997

>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]

Probab=99.94  E-value=2.5e-26  Score=233.20  Aligned_cols=316  Identities=18%  Similarity=0.197  Sum_probs=222.3

Q ss_pred             HHHHCCCCCCcHHHHHHH--HHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q 010709          135 DIEFHEYTRPTSIQAQAM--PVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEK  212 (503)
Q Consensus       135 ~l~~~~~~~~~~~Q~~~i--~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~  212 (503)
                      ..+..|...++.||.+++  +.++.+++.|..+||+.|||+++.+-++...+..       +..++.+.|....+..-..
T Consensus       215 ~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~-------rr~~llilp~vsiv~Ek~~  287 (1008)
T KOG0950|consen  215 YAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCR-------RRNVLLILPYVSIVQEKIS  287 (1008)
T ss_pred             HHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHH-------hhceeEecceeehhHHHHh
Confidence            345678899999999998  5678999999999999999999999999888876       4668999999988887777


Q ss_pred             HHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc--CCCCCCCccEEEecchhHHhhCCCHHHH
Q 010709          213 EVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ--GNTSLSRVSFVILDEADRMLDMGFEPQI  290 (503)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~--~~~~l~~~~~vViDEaH~l~~~~~~~~~  290 (503)
                      .+..+.... ++.+..++|......    ..+..++.|||.++-..++..  ..-.+..+++||+||.|.+.+.+.+..+
T Consensus       288 ~l~~~~~~~-G~~ve~y~g~~~p~~----~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~l  362 (1008)
T KOG0950|consen  288 ALSPFSIDL-GFPVEEYAGRFPPEK----RRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAIL  362 (1008)
T ss_pred             hhhhhcccc-CCcchhhcccCCCCC----cccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHH
Confidence            787777665 577777776654433    234478999999987655544  1335778999999999998888888888


Q ss_pred             HHHHHhC-----CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCce--EEEEEEcChhhHHHHHHHHHHHH
Q 010709          291 REVMQNL-----PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANV--IQILEKVSENEKVDRLLALLVEE  363 (503)
Q Consensus       291 ~~il~~~-----~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~k~~~l~~~l~~~  363 (503)
                      +.++.++     ....|+|+||||+++. . +++.++.......-..+-.....+  ...+....   +...+ ..+...
T Consensus       363 E~~l~k~~y~~~~~~~~iIGMSATi~N~-~-lL~~~L~A~~y~t~fRPv~L~E~ik~G~~i~~~~---r~~~l-r~ia~l  436 (1008)
T KOG0950|consen  363 ELLLAKILYENLETSVQIIGMSATIPNN-S-LLQDWLDAFVYTTRFRPVPLKEYIKPGSLIYESS---RNKVL-REIANL  436 (1008)
T ss_pred             HHHHHHHHHhccccceeEeeeecccCCh-H-HHHHHhhhhheecccCcccchhccCCCcccccch---hhHHH-HHhhhh
Confidence            7776553     3357899999999753 2 344444432222111111000000  00111111   11111 111110


Q ss_pred             HHhhhc------------cCCC-CCcEEEEEcchhhHHHHHHHHHH----------------------------------
Q 010709          364 AFLAEK------------SCHP-FPLTIVFVERKTRCDEVSEALVA----------------------------------  396 (503)
Q Consensus       364 ~~~~~~------------~~~~-~~~~lIF~~~~~~~~~l~~~L~~----------------------------------  396 (503)
                      ......            ...+ ...+||||+++..|+.++..+..                                  
T Consensus       437 ~~~~~g~~dpD~~v~L~tet~~e~~~~lvfc~sk~~ce~~a~~~~~~vpk~~~~e~~~~~~~~~s~s~~lr~~~~~ld~V  516 (1008)
T KOG0950|consen  437 YSSNLGDEDPDHLVGLCTETAPEGSSVLVFCPSKKNCENVASLIAKKVPKHIKSEKRLGLWELLSISNLLRRIPGILDPV  516 (1008)
T ss_pred             hhhhcccCCCcceeeehhhhhhcCCeEEEEcCcccchHHHHHHHHHHhhHhhhhhhhhhHHHHHHHHhHhhcCCcccchH
Confidence            000000            0012 23499999999999988765532                                  


Q ss_pred             ----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEcc----CCCChhHHHHhhCcceee
Q 010709          397 ----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLD----LPKVLLAASESLCTTSFN  468 (503)
Q Consensus       397 ----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~----~p~s~~~~~Qr~GR~gR~  468 (503)
                          ..+.+.++|+|++.++|..+...|++|...|++||+.++.|+++|..+++|-.-    ...+..+|.|++|||||+
T Consensus       517 l~~ti~~GvAyHhaGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIiraP~~g~~~l~~~~YkQM~GRAGR~  596 (1008)
T KOG0950|consen  517 LAKTIPYGVAYHHAGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRAPYVGREFLTRLEYKQMVGRAGRT  596 (1008)
T ss_pred             HheeccccceecccccccchHHHHHHHHHhcCeEEEEecchhhccCcCCcceeEEeCCccccchhhhhhHHhhhhhhhhc
Confidence                124588899999999999999999999999999999999999999888777533    235678999999999998

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.93  E-value=5.3e-24  Score=219.87  Aligned_cols=302  Identities=18%  Similarity=0.173  Sum_probs=217.4

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+++|.-.--.+.+|  -|..++||.|||+++.+|++...+.        |..+.||+|++.||.|.++.+..+...+ 
T Consensus        82 ~~ydVQliGgl~L~~G--~IaEm~TGEGKTL~a~lp~~l~al~--------g~~VhIvT~ndyLA~RD~e~m~~l~~~l-  150 (908)
T PRK13107         82 RHFDVQLLGGMVLDSN--RIAEMRTGEGKTLTATLPAYLNALT--------GKGVHVITVNDYLARRDAENNRPLFEFL-  150 (908)
T ss_pred             CcCchHHhcchHhcCC--ccccccCCCCchHHHHHHHHHHHhc--------CCCEEEEeCCHHHHHHHHHHHHHHHHhc-
Confidence            6788887666666555  5889999999999999999877654        4559999999999999999999999887 


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC-CCC-----CCCccEEEecchhHHhhCC----------
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG-NTS-----LSRVSFVILDEADRMLDMG----------  285 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~-~~~-----l~~~~~vViDEaH~l~~~~----------  285 (503)
                      ++.+.++.++....+  +.....++|+++|++.| .+++..+ ...     ...+.++||||||.++-..          
T Consensus       151 Glsv~~i~~~~~~~~--r~~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLiDEArtPLIISg~  228 (908)
T PRK13107        151 GLTVGINVAGLGQQE--KKAAYNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILIDEARTPLIISGA  228 (908)
T ss_pred             CCeEEEecCCCCHHH--HHhcCCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhccccCCCceeecCC
Confidence            699999999887643  23334799999999999 7777664 222     3678999999999743100          


Q ss_pred             ------CHH-------H------------------------------------HHHHH---Hh-----------------
Q 010709          286 ------FEP-------Q------------------------------------IREVM---QN-----------------  296 (503)
Q Consensus       286 ------~~~-------~------------------------------------~~~il---~~-----------------  296 (503)
                            ...       .                                    +...+   ..                 
T Consensus       229 ~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~l~~~~~~~~~~~l~~~~~~~~~~  308 (908)
T PRK13107        229 AEDSSELYIKINTLIPNLIRQDKEDTEEYVGEGDYSIDEKAKQVHFTERGQEKVENLLIERGMLAEGDSLYSAANISLLH  308 (908)
T ss_pred             CccchHHHHHHHHHHHHHHhhhhccccccCCCCCEEEecCCCeeeechHHHHHHHHHHHhCCcccCcccccCchhhHHHH
Confidence                  000       0                                    00111   00                 


Q ss_pred             -----------CCCC-------------------------------------------------------------CcEE
Q 010709          297 -----------LPDK-------------------------------------------------------------HQTL  304 (503)
Q Consensus       297 -----------~~~~-------------------------------------------------------------~q~i  304 (503)
                                 +..+                                                             .++-
T Consensus       309 ~i~~aL~A~~lf~~d~dYiV~dg~V~IVDe~TGRim~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kL~  388 (908)
T PRK13107        309 HVNAALRAHTLFEKDVDYIVQDNEVIIVDEHTGRTMPGRRWSEGLHQAVEAKEGVHIQNENQTLASITFQNYFRQYEKLA  388 (908)
T ss_pred             HHHHHHHHHHHHhcCCceEEECCEEEEEECCCCCCCCCCccchHHHHHHHHhcCCCCCCCceeeeeehHHHHHHhhhHhh
Confidence                       0000                                                             1345


Q ss_pred             EEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcch
Q 010709          305 LFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERK  384 (503)
Q Consensus       305 ~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~  384 (503)
                      +||+|...+-.++.+-|--+-+.+ ....+.... -..-..+.....|...+...+......       +.++||||.+.
T Consensus       389 GMTGTa~te~~Ef~~iY~l~Vv~I-PTnkp~~R~-d~~d~iy~t~~~K~~Aii~ei~~~~~~-------GrpVLV~t~sv  459 (908)
T PRK13107        389 GMTGTADTEAFEFQHIYGLDTVVV-PTNRPMVRK-DMADLVYLTADEKYQAIIKDIKDCRER-------GQPVLVGTVSI  459 (908)
T ss_pred             cccCCChHHHHHHHHHhCCCEEEC-CCCCCccce-eCCCcEEeCHHHHHHHHHHHHHHHHHc-------CCCEEEEeCcH
Confidence            666666554444444443322222 111111111 111223445677888888877665433       34699999999


Q ss_pred             hhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCC----------------------
Q 010709          385 TRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMG----------------------  442 (503)
Q Consensus       385 ~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~----------------------  442 (503)
                      +.++.+++.|...|+.+..+|+.+.+.++..+.+.|+.|.  |+|||++++||.||.=                      
T Consensus       460 ~~se~ls~~L~~~gi~~~vLnak~~~~Ea~ii~~Ag~~G~--VtIATnmAGRGTDIkLggn~~~~~~~~~~~~~~~~~~~  537 (908)
T PRK13107        460 EQSELLARLMVKEKIPHEVLNAKFHEREAEIVAQAGRTGA--VTIATNMAGRGTDIVLGGNWNMEIEALENPTAEQKAKI  537 (908)
T ss_pred             HHHHHHHHHHHHCCCCeEeccCcccHHHHHHHHhCCCCCc--EEEecCCcCCCcceecCCchHHhhhhhcchhhHHHHHH
Confidence            9999999999999999999999999999999999999997  9999999999999871                      


Q ss_pred             ---------------CCEEEEccCCCChhHHHHhhCcceee
Q 010709          443 ---------------VAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       443 ---------------v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                                     ==+||-...+.|..-=.|-.||+||.
T Consensus       538 ~~~~~~~~~~V~~~GGL~VIgTerheSrRID~QLrGRaGRQ  578 (908)
T PRK13107        538 KADWQIRHDEVVAAGGLHILGTERHESRRIDNQLRGRAGRQ  578 (908)
T ss_pred             HHHHHhhHHHHHHcCCCEEEecccCchHHHHhhhhcccccC
Confidence                           13789899999988888999999985

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

Probab=99.93  E-value=3.1e-24  Score=215.90  Aligned_cols=306  Identities=18%  Similarity=0.178  Sum_probs=207.4

Q ss_pred             CCCCcHHHHHHHHHHh----cCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q 010709          141 YTRPTSIQAQAMPVAL----SGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK  215 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~----~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~  215 (503)
                      -..|+.+|..||..+.    +|++ ++++++||+|||..+ +.++..++..     +..+++|+|+-+++|+.|.+..+.
T Consensus       163 ~i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~-----~~~KRVLFLaDR~~Lv~QA~~af~  236 (875)
T COG4096         163 AIGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKS-----GWVKRVLFLADRNALVDQAYGAFE  236 (875)
T ss_pred             cccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhc-----chhheeeEEechHHHHHHHHHHHH
Confidence            3468999999997765    4554 999999999999887 5566666664     346889999999999999999998


Q ss_pred             HHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-----CCCCCCccEEEecchhHHhhCCCHHHH
Q 010709          216 ALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-----NTSLSRVSFVILDEADRMLDMGFEPQI  290 (503)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-----~~~l~~~~~vViDEaH~l~~~~~~~~~  290 (503)
                      .+.....  .+..+.+...        ...++|.|+|.+++...+...     .+....+++|||||||+-+    ...+
T Consensus       237 ~~~P~~~--~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHRgi----~~~~  302 (875)
T COG4096         237 DFLPFGT--KMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHRGI----YSEW  302 (875)
T ss_pred             HhCCCcc--ceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhhhH----Hhhh
Confidence            8875432  2222322211        124799999999998877664     3456679999999999855    5567


Q ss_pred             HHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhc-CCCeEEE------------------e----CCCCCCCCce-------
Q 010709          291 REVMQNLPDKHQTLLFSATMPVEIEALAQEYL-TDPVQVK------------------V----GKVSSPTANV-------  340 (503)
Q Consensus       291 ~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~-~~~~~~~------------------~----~~~~~~~~~~-------  340 (503)
                      ..++.++..-.  ++++|||...+...--.|+ ++|....                  +    ...+......       
T Consensus       303 ~~I~dYFdA~~--~gLTATP~~~~d~~T~~~F~g~Pt~~YsleeAV~DGfLvpy~vi~i~~~~~~~G~~~~~~serek~~  380 (875)
T COG4096         303 SSILDYFDAAT--QGLTATPKETIDRSTYGFFNGEPTYAYSLEEAVEDGFLVPYKVIRIDTDFDLDGWKPDAGSEREKLQ  380 (875)
T ss_pred             HHHHHHHHHHH--HhhccCcccccccccccccCCCcceeecHHHHhhccccCCCCceEEeeeccccCcCcCccchhhhhh
Confidence            78888876543  4459999765554444444 4443321                  0    0000000000       


Q ss_pred             -------EEEEEEcC------hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-----CCeEE
Q 010709          341 -------IQILEKVS------ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-----GLHAV  402 (503)
Q Consensus       341 -------~~~~~~~~------~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-----~~~v~  402 (503)
                             .+.+...+      -......+...+.+..... ......+|+||||.+..+|+.+...|...     +--+.
T Consensus       381 g~~i~~dd~~~~~~d~dr~~v~~~~~~~V~r~~~~~l~~~-~~g~~~~KTIvFa~n~dHAe~i~~~~~~~ype~~~~~a~  459 (875)
T COG4096         381 GEAIDEDDQNFEARDFDRTLVIPFRTETVARELTEYLKRG-ATGDEIGKTIVFAKNHDHAERIREALVNEYPEYNGRYAM  459 (875)
T ss_pred             ccccCcccccccccccchhccccchHHHHHHHHHHHhccc-cCCCccCceEEEeeCcHHHHHHHHHHHHhCccccCceEE
Confidence                   01111111      1122333444444443332 22233689999999999999999999865     33466


Q ss_pred             EEcCCCCHHHHHHHHHHHhc--CCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeeeee
Q 010709          403 ALHGGRNQSDRESALRDFRN--GSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITT  471 (503)
Q Consensus       403 ~lh~~~~~~~r~~~~~~f~~--g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~~  471 (503)
                      .+.++-.+.+  ..++.|..  .-.+|.|+.+++.+|+|+|.|.++|++..-+|..-|.|++||+-|..-.
T Consensus       460 ~IT~d~~~~q--~~Id~f~~ke~~P~IaitvdlL~TGiDvpev~nlVF~r~VrSktkF~QMvGRGTRl~~~  528 (875)
T COG4096         460 KITGDAEQAQ--ALIDNFIDKEKYPRIAITVDLLTTGVDVPEVVNLVFDRKVRSKTKFKQMVGRGTRLCPD  528 (875)
T ss_pred             EEeccchhhH--HHHHHHHhcCCCCceEEehhhhhcCCCchheeeeeehhhhhhHHHHHHHhcCccccCcc
Confidence            6777655433  34555544  4467999999999999999999999999999999999999999886433

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=99.91  E-value=1.6e-22  Score=200.30  Aligned_cols=324  Identities=17%  Similarity=0.199  Sum_probs=221.8

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++++|.+.+.++.    +|-++|+..++|.|||++. +.+|.++.....   . .+..||++|...|.+ |.+++++|+
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQt-Is~l~yl~~~~~---~-~GPfLVi~P~StL~N-W~~Ef~rf~  240 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQT-ISLLGYLKGRKG---I-PGPFLVIAPKSTLDN-WMNEFKRFT  240 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHH-HHHHHHHHHhcC---C-CCCeEEEeeHhhHHH-HHHHHHHhC
Confidence            68999999999976    4668999999999999986 677777776432   1 233699999999877 888899987


Q ss_pred             ccCCCceEEEEECCccHHHHHH-H--hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRS-E--LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      .   ++++.+++|+...+.... .  .....+|+|+|+++.++.-  ..+.--.++++||||||++-+.  ...+.++++
T Consensus       241 P---~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk--~~lk~~~W~ylvIDEaHRiKN~--~s~L~~~lr  313 (971)
T KOG0385|consen  241 P---SLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK--SFLKKFNWRYLVIDEAHRIKNE--KSKLSKILR  313 (971)
T ss_pred             C---CcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH--HHHhcCCceEEEechhhhhcch--hhHHHHHHH
Confidence            4   678888998875433221 1  1246899999999987642  2334456899999999999776  556778888


Q ss_pred             hCCCCCcEEEEEeeCC-HHHHHHH----------------------------------------HHh-------------
Q 010709          296 NLPDKHQTLLFSATMP-VEIEALA----------------------------------------QEY-------------  321 (503)
Q Consensus       296 ~~~~~~q~i~~SAT~~-~~~~~~~----------------------------------------~~~-------------  321 (503)
                      .+....+ +++|+||- +++.++.                                        +-|             
T Consensus       314 ~f~~~nr-LLlTGTPLQNNL~ELWaLLnFllPdiF~~~e~F~swF~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sL  392 (971)
T KOG0385|consen  314 EFKTDNR-LLLTGTPLQNNLHELWALLNFLLPDIFNSAEDFDSWFDFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSL  392 (971)
T ss_pred             Hhcccce-eEeeCCcccccHHHHHHHHHhhchhhccCHHHHHHHHcccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcC
Confidence            8876664 67788871 1111110                                        000             


Q ss_pred             ----------------------------------------------------cCCCeEEEeCCCCCCCCceEEEEEEcCh
Q 010709          322 ----------------------------------------------------LTDPVQVKVGKVSSPTANVIQILEKVSE  349 (503)
Q Consensus       322 ----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~  349 (503)
                                                                          ...|..+. +..+.+...  ..-..+..
T Consensus       393 ppKkE~~iyvgms~mQkk~Y~~iL~kdl~~~n~~~~~~k~kL~NI~mQLRKccnHPYLF~-g~ePg~pyt--tdehLv~n  469 (971)
T KOG0385|consen  393 PPKKELIIYVGMSSMQKKWYKAILMKDLDALNGEGKGEKTKLQNIMMQLRKCCNHPYLFD-GAEPGPPYT--TDEHLVTN  469 (971)
T ss_pred             CCcceeeEeccchHHHHHHHHHHHHhcchhhcccccchhhHHHHHHHHHHHhcCCccccC-CCCCCCCCC--cchHHHhc
Confidence                                                                00011110 000101111  11111233


Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC---Cc
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS---TN  426 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~---~~  426 (503)
                      ..|+..|-+++.....       .+.++|||.+.....+-|.+++.-+++..+.+.|.++-++|...++.|....   .-
T Consensus       470 SGKm~vLDkLL~~Lk~-------~GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~~eeR~~aI~~fn~~~s~~Fi  542 (971)
T KOG0385|consen  470 SGKMLVLDKLLPKLKE-------QGHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTSHEEREDAIEAFNAPPSEKFI  542 (971)
T ss_pred             CcceehHHHHHHHHHh-------CCCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCCcHHHHHHHHhcCCCCcceEE
Confidence            4566566666655543       3456999999999999999999999999999999999999999999997643   44


Q ss_pred             EEEEccccccCCCCCCCCEEEEccCCCChh------HHHHhhCc-----ceeeeeecc--CchhhhhhHHHHHHHHH
Q 010709          427 ILVATDVASRGLDVMGVAHVVNLDLPKVLL------AASESLCT-----TSFNITTNL--DGDMKKLEFCLILAITV  490 (503)
Q Consensus       427 vLvaT~~~~~Gldip~v~~VI~~~~p~s~~------~~~Qr~GR-----~gR~~~~~~--~~~~~~~~~~~~~~~~~  490 (503)
                      .|++|.+++.|||+..+++||.||--+++.      +..||||.     +-|..+...  ..-+++....+.++..+
T Consensus       543 FlLSTRAGGLGINL~aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~IveRA~~KL~Ld~~V  619 (971)
T KOG0385|consen  543 FLLSTRAGGLGINLTAADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVERAAAKLRLDKLV  619 (971)
T ss_pred             EEEeccccccccccccccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHHHHHHHHHHhchhhhh
Confidence            689999999999999999999999988873      44566665     223222222  14455555555444433

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=99.90  E-value=4.3e-22  Score=203.62  Aligned_cols=281  Identities=25%  Similarity=0.360  Sum_probs=199.2

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      |+ .|+..|+--...+..|+++-+.||||.|||+- .+.+-.++...       |++++||+||+.|+.|+++.+++++.
T Consensus        80 G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTf-g~~~sl~~a~k-------gkr~yii~PT~~Lv~Q~~~kl~~~~e  150 (1187)
T COG1110          80 GF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTF-GLLMSLYLAKK-------GKRVYIIVPTTTLVRQVYERLKKFAE  150 (1187)
T ss_pred             CC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHH-HHHHHHHHHhc-------CCeEEEEecCHHHHHHHHHHHHHHHh
Confidence            44 99999999999999999999999999999973 34344444432       68899999999999999999999986


Q ss_pred             cCCCceEEE-EECCccHH---HHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC---------
Q 010709          220 SLDSFKTAI-VVGGTNIA---EQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG---------  285 (503)
Q Consensus       220 ~~~~~~~~~-~~~~~~~~---~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~---------  285 (503)
                      ......+.. +++.....   +....+. ++.+|+|+|.+-|.+....  +.--++++|++|++|.++..+         
T Consensus       151 ~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~--L~~~kFdfifVDDVDA~LkaskNvDriL~L  228 (1187)
T COG1110         151 DAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE--LSKLKFDFIFVDDVDAILKASKNVDRLLRL  228 (1187)
T ss_pred             hcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH--hcccCCCEEEEccHHHHHhccccHHHHHHH
Confidence            654344433 34433322   2223333 5799999998888665543  222478999999999655322         


Q ss_pred             --CHHH-----------------------HHHHHHh--------CCCCCcEEEEEeeCCHHH--HHHHHHhcCCCeEEEe
Q 010709          286 --FEPQ-----------------------IREVMQN--------LPDKHQTLLFSATMPVEI--EALAQEYLTDPVQVKV  330 (503)
Q Consensus       286 --~~~~-----------------------~~~il~~--------~~~~~q~i~~SAT~~~~~--~~~~~~~~~~~~~~~~  330 (503)
                        |...                       +++++..        -.+..++|..|||..+.-  ..+.+..++    +.+
T Consensus       229 lGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSATg~~rg~R~~LfReLlg----Fev  304 (1187)
T COG1110         229 LGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSATGKPRGSRLKLFRELLG----FEV  304 (1187)
T ss_pred             cCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeeccCCCCCchHHHHHHHhC----Ccc
Confidence              1111                       1111111        123467999999984432  223444443    234


Q ss_pred             CCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcc---hhhHHHHHHHHHHCCCeEEEEcCC
Q 010709          331 GKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVER---KTRCDEVSEALVAEGLHAVALHGG  407 (503)
Q Consensus       331 ~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~---~~~~~~l~~~L~~~~~~v~~lh~~  407 (503)
                      +.......++...+......++...+++.+..             ..|||++.   ++.+++++++|+..|+++..+|++
T Consensus       305 G~~~~~LRNIvD~y~~~~~~e~~~elvk~lG~-------------GgLIfV~~d~G~e~aeel~e~Lr~~Gi~a~~~~a~  371 (1187)
T COG1110         305 GSGGEGLRNIVDIYVESESLEKVVELVKKLGD-------------GGLIFVPIDYGREKAEELAEYLRSHGINAELIHAE  371 (1187)
T ss_pred             CccchhhhheeeeeccCccHHHHHHHHHHhCC-------------CeEEEEEcHHhHHHHHHHHHHHHhcCceEEEeecc
Confidence            44444555666655555555555555554432             38999999   999999999999999999999994


Q ss_pred             CCHHHHHHHHHHHhcCCCcEEEEc----cccccCCCCCC-CCEEEEccCCC
Q 010709          408 RNQSDRESALRDFRNGSTNILVAT----DVASRGLDVMG-VAHVVNLDLPK  453 (503)
Q Consensus       408 ~~~~~r~~~~~~f~~g~~~vLvaT----~~~~~Gldip~-v~~VI~~~~p~  453 (503)
                      -     .+.++.|..|++++||++    .++-||||+|. ++++|++|.|+
T Consensus       372 ~-----~~~le~F~~GeidvLVGvAsyYG~lVRGlDLP~rirYaIF~GvPk  417 (1187)
T COG1110         372 K-----EEALEDFEEGEVDVLVGVASYYGVLVRGLDLPHRIRYAVFYGVPK  417 (1187)
T ss_pred             c-----hhhhhhhccCceeEEEEecccccceeecCCchhheeEEEEecCCc
Confidence            3     678999999999999976    68899999996 89999999995

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.90  E-value=4.5e-22  Score=211.16  Aligned_cols=312  Identities=19%  Similarity=0.167  Sum_probs=199.1

Q ss_pred             CCcHHHHHHHHHHhcC---C-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVALSG---R-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~---~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .+++.|..++..+...   . .+++.||||+|||++.+++++......    .....+++++.|++.++++++++++.+.
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~----~~~~~r~i~vlP~~t~ie~~~~r~~~~~  270 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK----IKLKSRVIYVLPFRTIIEDMYRRAKEIF  270 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc----ccccceEEEEccHHHHHHHHHHHHHhhh
Confidence            3588999999988743   4 689999999999999888777665542    1146889999999999999999999877


Q ss_pred             ccCCCceEEEEECCccHHHHHHH-----h---------hCCCcEEEECcHHHHHHHHc-CCCC-C--CCccEEEecchhH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSE-----L---------RGGVSIVVATPGRFLDHLQQ-GNTS-L--SRVSFVILDEADR  280 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~-----~---------~~~~~Ilv~Tp~~l~~~l~~-~~~~-l--~~~~~vViDEaH~  280 (503)
                      .... +.....++.....-....     .         .....+.++||-........ ..+. +  -..+.+|+||+|.
T Consensus       271 ~~~~-~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~  349 (733)
T COG1203         271 GLFS-VIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHL  349 (733)
T ss_pred             cccc-cccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHh
Confidence            4432 111112222221110000     0         01133444444444332111 1111 1  1246899999997


Q ss_pred             HhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCC-CceEEEEEE-cChhhHH-HHH
Q 010709          281 MLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPT-ANVIQILEK-VSENEKV-DRL  356 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~k~-~~l  356 (503)
                      +.+......+..++..+ ..+..+|+||||+|+.+...+...+.+...+......... ......... ....... ...
T Consensus       350 ~~~~~~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~  429 (733)
T COG1203         350 YADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEEL  429 (733)
T ss_pred             hcccchHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceeccccccccccccccccccchhhhhhhhHhh
Confidence            65542333334443333 2356799999999999999888887765554433210000 000000000 0000000 011


Q ss_pred             HHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHh----cCCCcEEEEcc
Q 010709          357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFR----NGSTNILVATD  432 (503)
Q Consensus       357 ~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~----~g~~~vLvaT~  432 (503)
                      .....       ......++++|-|||+..|.++++.|+..+..+..+||.+...+|.+.++.+.    .+...|+|||+
T Consensus       430 ~~~~~-------~~~~~~~kvlvI~NTV~~Aie~Y~~Lk~~~~~v~LlHSRf~~~dR~~ke~~l~~~~~~~~~~IvVaTQ  502 (733)
T COG1203         430 IELIS-------EEVKEGKKVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ  502 (733)
T ss_pred             hhcch-------hhhccCCcEEEEEecHHHHHHHHHHHHhcCCCEEEEecccchhhHHHHHHHHHHHHhccCCeEEEEee
Confidence            11111       11135578999999999999999999999888999999999999999888654    46889999999


Q ss_pred             ccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          433 VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      +.+-|+|+. .+++|-=  +..+.+.+||+||++|..
T Consensus       503 VIEagvDid-fd~mITe--~aPidSLIQR~GRv~R~g  536 (733)
T COG1203         503 VIEAGVDID-FDVLITE--LAPIDSLIQRAGRVNRHG  536 (733)
T ss_pred             EEEEEeccc-cCeeeec--CCCHHHHHHHHHHHhhcc
Confidence            999999997 6666543  334788999999999965

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

Probab=99.89  E-value=7.3e-22  Score=204.72  Aligned_cols=340  Identities=17%  Similarity=0.196  Sum_probs=232.6

Q ss_pred             CCCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..++.+|.+.+.+++    .++++|+..++|.|||++- +.+|.++......   .|| .|||+|...+.. |.++|..+
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqt-i~fl~~l~~~~~~---~gp-flvvvplst~~~-W~~ef~~w  442 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQT-ITFLSYLFHSLQI---HGP-FLVVVPLSTITA-WEREFETW  442 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHH-HHHHHHHHHhhhc---cCC-eEEEeehhhhHH-HHHHHHHH
Confidence            689999999999987    6788999999999999875 5566666554321   233 699999988776 88999998


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhh----C-----CCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHH
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELR----G-----GVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEP  288 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~-----~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~  288 (503)
                      .    ++++.+++|....++.++...    .     ..+++++|.+.++.-..  .+.--.+.+++|||||++-+.  ..
T Consensus       443 ~----~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~--~L~~i~w~~~~vDeahrLkN~--~~  514 (1373)
T KOG0384|consen  443 T----DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA--ELSKIPWRYLLVDEAHRLKND--ES  514 (1373)
T ss_pred             h----hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh--hhccCCcceeeecHHhhcCch--HH
Confidence            8    578999999888777665542    2     47899999998864322  122335789999999998765  45


Q ss_pred             HHHHHHHhCCCCCcEEEEEeeC-CHHHHHHHHHh-cCCCeEEE---------------------------------eCCC
Q 010709          289 QIREVMQNLPDKHQTLLFSATM-PVEIEALAQEY-LTDPVQVK---------------------------------VGKV  333 (503)
Q Consensus       289 ~~~~il~~~~~~~q~i~~SAT~-~~~~~~~~~~~-~~~~~~~~---------------------------------~~~~  333 (503)
                      .+...+..+.-+.+ +++|+|| .+++.++..-. +..|..+.                                 -+-.
T Consensus       515 ~l~~~l~~f~~~~r-llitgTPlQNsikEL~sLl~Fl~P~kf~~~~~f~~~~~~~~e~~~~~L~~~L~P~~lRr~kkdve  593 (1373)
T KOG0384|consen  515 KLYESLNQFKMNHR-LLITGTPLQNSLKELWSLLHFLMPGKFDSWDEFLEEFDEETEEQVRKLQQILKPFLLRRLKKDVE  593 (1373)
T ss_pred             HHHHHHHHhcccce-eeecCCCccccHHHHHHHhcccCCCCCCcHHHHHHhhcchhHHHHHHHHHHhhHHHHHHHHhhhc
Confidence            56666777776665 5666676 44555543211 11221110                                 0111


Q ss_pred             CCCCCceEEEEEE-cChhhHHHH---------------------HHHHHHHH----------------------------
Q 010709          334 SSPTANVIQILEK-VSENEKVDR---------------------LLALLVEE----------------------------  363 (503)
Q Consensus       334 ~~~~~~~~~~~~~-~~~~~k~~~---------------------l~~~l~~~----------------------------  363 (503)
                      ........+.+.. +...+|-.+                     ++..+.+.                            
T Consensus       594 kslp~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmELkKccNHpyLi~gaee~~~~~~~~~~~d~  673 (1373)
T KOG0384|consen  594 KSLPPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMMELKKCCNHPYLIKGAEEKILGDFRDKMRDE  673 (1373)
T ss_pred             cCCCCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHHHHHhcCCccccCcHHHHHHHhhhhcchHH
Confidence            1122222222211 110000000                     00000000                            


Q ss_pred             ----HHhh-----------hccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc---CCC
Q 010709          364 ----AFLA-----------EKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRN---GST  425 (503)
Q Consensus       364 ----~~~~-----------~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~---g~~  425 (503)
                          ..+.           .+....+++||||.+.....+.|+++|..++++.-.+.|....+-|+..++.|..   ...
T Consensus       674 ~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvrgelRq~AIDhFnap~SddF  753 (1373)
T KOG0384|consen  674 ALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVRGELRQQAIDHFNAPDSDDF  753 (1373)
T ss_pred             HHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcchHHHHHHHHhccCCCCCce
Confidence                0000           0001234789999999999999999999999999999999999999999999975   356


Q ss_pred             cEEEEccccccCCCCCCCCEEEEccCCCChhHHH------HhhCc-----ceeeeeecc--CchhhhhhHHHHHHHHHHH
Q 010709          426 NILVATDVASRGLDVMGVAHVVNLDLPKVLLAAS------ESLCT-----TSFNITTNL--DGDMKKLEFCLILAITVLL  492 (503)
Q Consensus       426 ~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~------Qr~GR-----~gR~~~~~~--~~~~~~~~~~~~~~~~~~~  492 (503)
                      ..|+||.+++-|||+..+++||.||--+++.+=+      ||||.     +-|.++...  ...+.+......|+-+|+|
T Consensus       754 vFLLSTRAGGLGINLatADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilERAk~KmvLD~aVIQ  833 (1373)
T KOG0384|consen  754 VFLLSTRAGGLGINLATADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILERAKLKMVLDHAVIQ  833 (1373)
T ss_pred             EEEEecccCcccccccccceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHHHHHHhhhHHHHHH
Confidence            7899999999999999999999999999885444      56665     344444333  4889999999999999999


Q ss_pred             HHHH
Q 010709          493 FVIF  496 (503)
Q Consensus       493 ~~~~  496 (503)
                      -|.+
T Consensus       834 ~m~t  837 (1373)
T KOG0384|consen  834 RMDT  837 (1373)
T ss_pred             hhcc
Confidence            9875

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=99.89  E-value=6.7e-21  Score=200.21  Aligned_cols=304  Identities=18%  Similarity=0.163  Sum_probs=181.7

Q ss_pred             CcHHHHHHHHHHh----c------CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          144 PTSIQAQAMPVAL----S------GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       144 ~~~~Q~~~i~~i~----~------~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      ++.+|..|+..+.    .      .+..+++.+||||||++.+.. ...+...     ...+++|||+|+++|..|+.+.
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~l-a~~l~~~-----~~~~~vl~lvdR~~L~~Q~~~~  312 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFA-ARKALEL-----LKNPKVFFVVDRRELDYQLMKE  312 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHH-HHHHHhh-----cCCCeEEEEECcHHHHHHHHHH
Confidence            7889999998764    2      245999999999999876433 3333321     2367899999999999999999


Q ss_pred             HHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcC--CCCCCCc-cEEEecchhHHhhCCCHHH
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQG--NTSLSRV-SFVILDEADRMLDMGFEPQ  289 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~--~~~l~~~-~~vViDEaH~l~~~~~~~~  289 (503)
                      |..++...  .     .+..+.......+. ....|+|+|.+.|...+...  .+..... -+||+||||+...    ..
T Consensus       313 f~~~~~~~--~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~~----~~  381 (667)
T TIGR00348       313 FQSLQKDC--A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQY----GE  381 (667)
T ss_pred             HHhhCCCC--C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCccccc----hH
Confidence            99886321  0     11112222223232 34689999999997644321  1221112 2899999998642    23


Q ss_pred             HHHHHH-hCCCCCcEEEEEeeCCHHHHHHHHHhc----CCCeEEEeCCCCCCCCc--eEEEEEE------cCh-------
Q 010709          290 IREVMQ-NLPDKHQTLLFSATMPVEIEALAQEYL----TDPVQVKVGKVSSPTAN--VIQILEK------VSE-------  349 (503)
Q Consensus       290 ~~~il~-~~~~~~q~i~~SAT~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~--~~~~~~~------~~~-------  349 (503)
                      +...+. .++ +...++|||||-..........+    +++... ..-.......  +...+..      +..       
T Consensus       382 ~~~~l~~~~p-~a~~lGfTaTP~~~~d~~t~~~f~~~fg~~i~~-Y~~~~AI~dG~~~~i~Y~~~~~~~~~~~~~l~~~~  459 (667)
T TIGR00348       382 LAKNLKKALK-NASFFGFTGTPIFKKDRDTSLTFAYVFGRYLHR-YFITDAIRDGLTVKIDYEDRLPEDHLDRKKLDAFF  459 (667)
T ss_pred             HHHHHHhhCC-CCcEEEEeCCCcccccccccccccCCCCCeEEE-eeHHHHhhcCCeeeEEEEecchhhccChHHHHHHH
Confidence            445553 444 46699999999432111000111    122111 0000000000  0000000      000       


Q ss_pred             --------------------------------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC
Q 010709          350 --------------------------------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE  397 (503)
Q Consensus       350 --------------------------------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~  397 (503)
                                                      ...+..+...+.++......  ...+|++|||.++..|..+++.|.+.
T Consensus       460 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ia~~i~~h~~~~~~--~~~~kamvv~~sr~~a~~~~~~l~~~  537 (667)
T TIGR00348       460 DEIFELLPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKE--LFKFKAMVVAISRYACVEEKNALDEE  537 (667)
T ss_pred             HHHHHhhhccccHHHHHHHHHHHHHHHhhhcChHHHHHHHHHHHHHHHHhhh--cccCceeEEEecHHHHHHHHHHHHhh
Confidence                                            00011111112222111111  12478999999999999999988664


Q ss_pred             -----CCeEEEEcCCCCHH---------------------HHHHHHHHHhc-CCCcEEEEccccccCCCCCCCCEEEEcc
Q 010709          398 -----GLHAVALHGGRNQS---------------------DRESALRDFRN-GSTNILVATDVASRGLDVMGVAHVVNLD  450 (503)
Q Consensus       398 -----~~~v~~lh~~~~~~---------------------~r~~~~~~f~~-g~~~vLvaT~~~~~Gldip~v~~VI~~~  450 (503)
                           +...+.+++.....                     ....++++|++ +..+|||.++++.+|+|.|.+.+++...
T Consensus       538 ~~~~~~~~~vv~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Fk~~~~~~ilIVvdmllTGFDaP~l~tLyldK  617 (667)
T TIGR00348       538 LNEKFEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKKEENPKLLIVVDMLLTGFDAPILNTLYLDK  617 (667)
T ss_pred             cccccCCeeEEecCCccchhHHHHHHHHhccccccchhhhHHHHHHHHhcCCCCceEEEEEcccccccCCCccceEEEec
Confidence                 23455565543322                     22468888976 6789999999999999999999988888


Q ss_pred             CCCChhHHHHhhCcceeee
Q 010709          451 LPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       451 ~p~s~~~~~Qr~GR~gR~~  469 (503)
                      +-++. .++|.+||+.|..
T Consensus       618 plk~h-~LlQai~R~nR~~  635 (667)
T TIGR00348       618 PLKYH-GLLQAIARTNRID  635 (667)
T ss_pred             ccccc-HHHHHHHHhcccc
Confidence            77765 5899999999964

Members of this family are assumed to differ from each other in DNA site specificity.

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=99.88  E-value=1.5e-20  Score=195.13  Aligned_cols=113  Identities=22%  Similarity=0.311  Sum_probs=101.7

Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      ...++..++..+....       ..+.++||||++++.++.+++.|...|+.+..+||++++.+|.++++.|+.|++.||
T Consensus       424 ~~~qi~~Ll~eI~~~~-------~~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VL  496 (655)
T TIGR00631       424 TDGQVDDLLSEIRQRV-------ARNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVL  496 (655)
T ss_pred             ccchHHHHHHHHHHHH-------cCCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCCHHHHHHHHHHHhcCCceEE
Confidence            3456666666666543       234469999999999999999999999999999999999999999999999999999


Q ss_pred             EEccccccCCCCCCCCEEEEcc-----CCCChhHHHHhhCcceee
Q 010709          429 VATDVASRGLDVMGVAHVVNLD-----LPKVLLAASESLCTTSFN  468 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~-----~p~s~~~~~Qr~GR~gR~  468 (503)
                      |||+++++|+|+|++++||++|     .|.+..+|+||+||+||.
T Consensus       497 V~t~~L~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~  541 (655)
T TIGR00631       497 VGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARN  541 (655)
T ss_pred             EEcChhcCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCC
Confidence            9999999999999999999988     899999999999999996

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

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

Probab=99.88  E-value=6.2e-21  Score=182.65  Aligned_cols=156  Identities=21%  Similarity=0.207  Sum_probs=121.8

Q ss_pred             CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEE
Q 010709          300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIV  379 (503)
Q Consensus       300 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lI  379 (503)
                      ..|+|.+||||.+--....   -++.+.-.+...+...+    .+..-+....++.|+..+.......       .++||
T Consensus       386 ~~q~i~VSATPg~~E~e~s---~~~vveQiIRPTGLlDP----~ievRp~~~QvdDL~~EI~~r~~~~-------eRvLV  451 (663)
T COG0556         386 IPQTIYVSATPGDYELEQS---GGNVVEQIIRPTGLLDP----EIEVRPTKGQVDDLLSEIRKRVAKN-------ERVLV  451 (663)
T ss_pred             cCCEEEEECCCChHHHHhc---cCceeEEeecCCCCCCC----ceeeecCCCcHHHHHHHHHHHHhcC-------CeEEE
Confidence            4699999999965322111   11222222222222222    2233355667888888887766544       35999


Q ss_pred             EEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC-----CCC
Q 010709          380 FVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL-----PKV  454 (503)
Q Consensus       380 F~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~-----p~s  454 (503)
                      -+-+++.++.|.++|.+.|+++..+|++..+-+|.++++.++.|..+|||..+++-+|+|+|.|.+|..+|.     .+|
T Consensus       452 TtLTKkmAEdLT~Yl~e~gikv~YlHSdidTlER~eIirdLR~G~~DvLVGINLLREGLDiPEVsLVAIlDADKeGFLRs  531 (663)
T COG0556         452 TTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRS  531 (663)
T ss_pred             EeehHHHHHHHHHHHHhcCceEEeeeccchHHHHHHHHHHHhcCCccEEEeehhhhccCCCcceeEEEEeecCccccccc
Confidence            999999999999999999999999999999999999999999999999999999999999999999998885     467


Q ss_pred             hhHHHHhhCcceeee
Q 010709          455 LLAASESLCTTSFNI  469 (503)
Q Consensus       455 ~~~~~Qr~GR~gR~~  469 (503)
                      -.+.+|-+|||.|+.
T Consensus       532 e~SLIQtIGRAARN~  546 (663)
T COG0556         532 ERSLIQTIGRAARNV  546 (663)
T ss_pred             cchHHHHHHHHhhcc
Confidence            899999999999975

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=99.88  E-value=1.6e-21  Score=197.60  Aligned_cols=160  Identities=18%  Similarity=0.207  Sum_probs=116.6

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|..||.+.+..+-.++.++|+|||.+|||.+- ..++...+..     .+...+|+++|+++|++|+...+........
T Consensus       511 ~Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfis-fY~iEKVLRe-----sD~~VVIyvaPtKaLVnQvsa~VyaRF~~~t  584 (1330)
T KOG0949|consen  511 CPDEWQRELLDSVDRNESAVIVAPTSAGKTFIS-FYAIEKVLRE-----SDSDVVIYVAPTKALVNQVSANVYARFDTKT  584 (1330)
T ss_pred             CCcHHHHHHhhhhhcccceEEEeeccCCceecc-HHHHHHHHhh-----cCCCEEEEecchHHHhhhhhHHHHHhhccCc
Confidence            588999999999999999999999999999754 3345555543     3467799999999999999988876653221


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc---CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ---GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD  299 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~---~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~  299 (503)
                      -.+-..+.|....+-...  .-.|.|+|+-|+.+..++..   ......++++||+||+|.+.+..-...+++++...+ 
T Consensus       585 ~~rg~sl~g~ltqEYsin--p~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~li~-  661 (1330)
T KOG0949|consen  585 FLRGVSLLGDLTQEYSIN--PWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLLLIP-  661 (1330)
T ss_pred             cccchhhHhhhhHHhcCC--chhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHHhcC-
Confidence            122222333322221111  22599999999999888876   344578899999999998877765666777777665 


Q ss_pred             CCcEEEEEeeCCH
Q 010709          300 KHQTLLFSATMPV  312 (503)
Q Consensus       300 ~~q~i~~SAT~~~  312 (503)
                       +.++++|||+.+
T Consensus       662 -CP~L~LSATigN  673 (1330)
T KOG0949|consen  662 -CPFLVLSATIGN  673 (1330)
T ss_pred             -CCeeEEecccCC
Confidence             668999999843

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.87  E-value=1e-19  Score=197.36  Aligned_cols=308  Identities=19%  Similarity=0.236  Sum_probs=188.3

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHH----HHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMP----VALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~----~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      +.+...+.+...||. +++.|.+.+.    .+.+++++++.||||+|||++|++|++.+.. .       +.+++|.+||
T Consensus       231 ~~~~~~~~~~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~-~-------~~~vvi~t~t  301 (850)
T TIGR01407       231 LSSLFSKNIDRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAI-T-------EKPVVISTNT  301 (850)
T ss_pred             ccHHHHHhhhhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhc-C-------CCeEEEEeCc
Confidence            334666777777876 8899998776    4447788999999999999999999987654 1       4579999999


Q ss_pred             HHHHHHHHH-HHHHHhccCC-CceEEEEECCccH--------------------------------------H-------
Q 010709          204 RELAQQIEK-EVKALSRSLD-SFKTAIVVGGTNI--------------------------------------A-------  236 (503)
Q Consensus       204 r~La~q~~~-~~~~~~~~~~-~~~~~~~~~~~~~--------------------------------------~-------  236 (503)
                      ++|..|+.. .+..+.+.++ ++++.++.|+...                                      .       
T Consensus       302 ~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~~~ylcl~k~~~~l~~~~~~~~~~~~~~~~~~wl~~T~tGD~~el~~~~~  381 (850)
T TIGR01407       302 KVLQSQLLEKDIPLLNEILNFKINAALIKGKSNYLSLGKFSQILKDNTDNYEFNIFKMQVLVWLTETETGDLDELNLKGG  381 (850)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCceEEEEEcchhhccHHHHHHHHhcCCCcHHHHHHHHHHHHHhccCCccCHhhccCCCc
Confidence            999999865 4555543321 3566666653321                                      0       


Q ss_pred             --------------------------HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-----
Q 010709          237 --------------------------EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-----  285 (503)
Q Consensus       237 --------------------------~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-----  285 (503)
                                                ...+.....++|+|+...-|+..+......+...+++||||||++.+..     
T Consensus       382 ~~~~~~~i~~~~~l~~~c~~~~~Cf~~~ar~~a~~AdivItNHa~L~~~~~~~~~ilp~~~~lIiDEAH~L~d~a~~~~~  461 (850)
T TIGR01407       382 NKMFFAQVRHDGNLSKKDLFYEVDFYNRAQKNAEQAQILITNHAYLITRLVDNPELFPSFRDLIIDEAHHLPDIAENQLQ  461 (850)
T ss_pred             chhhHHHhhcCCCCCCCCCCccccHHHHHHHHHhcCCEEEecHHHHHHHhhcccccCCCCCEEEEECcchHHHHHHHHhc
Confidence                                      0001111346899999888877765443345667899999999854310     


Q ss_pred             --C-----HH----------------------------------------------------------------HHHHHH
Q 010709          286 --F-----EP----------------------------------------------------------------QIREVM  294 (503)
Q Consensus       286 --~-----~~----------------------------------------------------------------~~~~il  294 (503)
                        +     ..                                                                .+...+
T Consensus       462 ~~ls~~~~~~~l~~l~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~~~  541 (850)
T TIGR01407       462 EELDYADIKYQIDLIGKGENEQLLKRIQQLEKQEILEKLFDFETKDILKDLQAILDKLNKLLQIFSELSHKTVDQLRKFD  541 (850)
T ss_pred             ceeCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence              0     00                                                                000000


Q ss_pred             Hh-----------C-------------------------------------CCCCcEEEEEeeCCHH-HHHHHHHhcCCC
Q 010709          295 QN-----------L-------------------------------------PDKHQTLLFSATMPVE-IEALAQEYLTDP  325 (503)
Q Consensus       295 ~~-----------~-------------------------------------~~~~q~i~~SAT~~~~-~~~~~~~~~~~~  325 (503)
                      ..           +                                     +....+|++|||+... -.......++-+
T Consensus       542 ~~~~~~~~~l~~~~~~~~~~wi~~~~~~~~~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~~~~lGl~  621 (850)
T TIGR01407       542 LALKDDFKNIEQSLKEGHTSWISIENLQQKSTIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLT  621 (850)
T ss_pred             HHHHHHHHHHHHHhccCCeEEEEecCCCCCceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHHHHhcCCC
Confidence            00           0                                     0123578999999632 122333334422


Q ss_pred             --eEEEeCCCCCC-CCceEEEE-EEcC------hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHH
Q 010709          326 --VQVKVGKVSSP-TANVIQIL-EKVS------ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV  395 (503)
Q Consensus       326 --~~~~~~~~~~~-~~~~~~~~-~~~~------~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~  395 (503)
                        ........... ..+...++ ...+      .......+...+.+...      ..++++|||+++.+..+.++..|.
T Consensus       622 ~~~~~~~~~spf~~~~~~~l~v~~d~~~~~~~~~~~~~~~ia~~i~~l~~------~~~g~~LVlftS~~~l~~v~~~L~  695 (850)
T TIGR01407       622 DVHFNTIEPTPLNYAENQRVLIPTDAPAIQNKSLEEYAQEIASYIIEITA------ITSPKILVLFTSYEMLHMVYDMLN  695 (850)
T ss_pred             ccccceecCCCCCHHHcCEEEecCCCCCCCCCChHHHHHHHHHHHHHHHH------hcCCCEEEEeCCHHHHHHHHHHHh
Confidence              11112111111 11111111 1111      11222233333333221      134679999999999999999997


Q ss_pred             H----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCC--EEEEccCCC
Q 010709          396 A----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVA--HVVNLDLPK  453 (503)
Q Consensus       396 ~----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~--~VI~~~~p~  453 (503)
                      .    .++.+.  ..+.. ..|.++++.|++|+..||++|+.+++|||+|+..  +||..++|-
T Consensus       696 ~~~~~~~~~~l--~q~~~-~~r~~ll~~F~~~~~~iLlgt~sf~EGVD~~g~~l~~viI~~LPf  756 (850)
T TIGR01407       696 ELPEFEGYEVL--AQGIN-GSRAKIKKRFNNGEKAILLGTSSFWEGVDFPGNGLVCLVIPRLPF  756 (850)
T ss_pred             hhccccCceEE--ecCCC-ccHHHHHHHHHhCCCeEEEEcceeecccccCCCceEEEEEeCCCC
Confidence            5    234433  33333 4788999999999999999999999999999865  677888763

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.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=99.87  E-value=1.8e-20  Score=192.76  Aligned_cols=299  Identities=21%  Similarity=0.251  Sum_probs=202.2

Q ss_pred             CCCcHHHHHHHHHHhcC----CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALSG----RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~----~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..+.+-|..++..+...    +..++.|.||||||.+| +.++...+.+       |+.+|+++|-..|..|+.++|+..
T Consensus       197 ~~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvY-l~~i~~~L~~-------GkqvLvLVPEI~Ltpq~~~rf~~r  268 (730)
T COG1198         197 LALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVY-LEAIAKVLAQ-------GKQVLVLVPEIALTPQLLARFKAR  268 (730)
T ss_pred             cccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHH-HHHHHHHHHc-------CCEEEEEeccccchHHHHHHHHHH
Confidence            36788899999998755    45999999999999998 5566666664       788999999999999999999988


Q ss_pred             hccCCCceEEEEECCccHH----HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC---C--CHH
Q 010709          218 SRSLDSFKTAIVVGGTNIA----EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM---G--FEP  288 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~---~--~~~  288 (503)
                      +.    .++.+++++-+..    .+.+...+...|+|+|-..+.       ..+.++++|||||-|.-...   +  +..
T Consensus       269 Fg----~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF-------~Pf~~LGLIIvDEEHD~sYKq~~~prYhA  337 (730)
T COG1198         269 FG----AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF-------LPFKNLGLIIVDEEHDSSYKQEDGPRYHA  337 (730)
T ss_pred             hC----CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc-------CchhhccEEEEeccccccccCCcCCCcCH
Confidence            73    5566666665543    334444577999999955553       46889999999999953321   1  111


Q ss_pred             HHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChh-hH-----HHHHHHHHHH
Q 010709          289 QIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSEN-EK-----VDRLLALLVE  362 (503)
Q Consensus       289 ~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~k-----~~~l~~~l~~  362 (503)
                      .--.+++.-..++++|+-|||+.-+  .+..-.-+....+...............+..+... .+     ...++..+.+
T Consensus       338 RdvA~~Ra~~~~~pvvLgSATPSLE--S~~~~~~g~y~~~~L~~R~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~  415 (730)
T COG1198         338 RDVAVLRAKKENAPVVLGSATPSLE--SYANAESGKYKLLRLTNRAGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRK  415 (730)
T ss_pred             HHHHHHHHHHhCCCEEEecCCCCHH--HHHhhhcCceEEEEccccccccCCCcceEEeccccccccCccCCHHHHHHHHH
Confidence            1222333334567899999999543  33333223233343333322221222233333222 11     1456666655


Q ss_pred             HHHhhhccCCCCCcEEEEEcchhhH-------------------------------------------------------
Q 010709          363 EAFLAEKSCHPFPLTIVFVERKTRC-------------------------------------------------------  387 (503)
Q Consensus       363 ~~~~~~~~~~~~~~~lIF~~~~~~~-------------------------------------------------------  387 (503)
                      ....+       .++|+|+|.+..+                                                       
T Consensus       416 ~l~~g-------eQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~L~~  488 (730)
T COG1198         416 TLERG-------EQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRA  488 (730)
T ss_pred             HHhcC-------CeEEEEEccCCccceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCeeEE
Confidence            54433       3488888886533                                                       


Q ss_pred             -----HHHHHHHHHC--CCeEEEEcCCCCHH--HHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC-----
Q 010709          388 -----DEVSEALVAE--GLHAVALHGGRNQS--DRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK-----  453 (503)
Q Consensus       388 -----~~l~~~L~~~--~~~v~~lh~~~~~~--~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~-----  453 (503)
                           +++++.|.+.  +.++..+.++.+..  .-...++.|.+|+.+|||.|++++.|.|+|++..|...|.-.     
T Consensus       489 ~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~  568 (730)
T COG1198         489 VGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSP  568 (730)
T ss_pred             ecccHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCC
Confidence                 5666666554  56788888877643  356789999999999999999999999999999977655432     


Q ss_pred             -------ChhHHHHhhCcceee
Q 010709          454 -------VLLAASESLCTTSFN  468 (503)
Q Consensus       454 -------s~~~~~Qr~GR~gR~  468 (503)
                             ....+.|-.|||||.
T Consensus       569 DfRA~Er~fqll~QvaGRAgR~  590 (730)
T COG1198         569 DFRASERTFQLLMQVAGRAGRA  590 (730)
T ss_pred             CcchHHHHHHHHHHHHhhhccC
Confidence                   225577888999995

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.87  E-value=2.5e-20  Score=168.40  Aligned_cols=188  Identities=44%  Similarity=0.608  Sum_probs=152.2

Q ss_pred             HCCCCCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      .+++..++++|.+++..+.++ ++++++++||+|||.++..+++..+...+      ..+++|++|++.++.|+.+.+..
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~------~~~~l~~~p~~~~~~~~~~~~~~   76 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK------GKRVLVLVPTRELAEQWAEELKK   76 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC------CCcEEEEeCCHHHHHHHHHHHHH
Confidence            346788999999999999988 99999999999999988787777655421      46799999999999999999998


Q ss_pred             HhccCCCceEEEEECCccHHHHHHHhhCCC-cEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      ++.... .......++............+. +++++|++.+.+.+.........++++|+||+|++....+...+..++.
T Consensus        77 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~~~~~~iIiDE~h~~~~~~~~~~~~~~~~  155 (201)
T smart00487       77 LGPSLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELSNVDLVILDEAHRLLDGGFGDQLEKLLK  155 (201)
T ss_pred             HhccCC-eEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCCcCHhHCCEEEEECHHHHhcCCcHHHHHHHHH
Confidence            875432 23444555555344444455555 9999999999999988666778899999999999886567888899998


Q ss_pred             hCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCC
Q 010709          296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK  332 (503)
Q Consensus       296 ~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  332 (503)
                      .+++..+++++|||+++........++.+...+....
T Consensus       156 ~~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      156 LLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             hCCccceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            8878889999999999999999998888776665543

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=99.85  E-value=1.4e-19  Score=188.16  Aligned_cols=115  Identities=17%  Similarity=0.150  Sum_probs=100.6

Q ss_pred             EEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q 010709          345 EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS  424 (503)
Q Consensus       345 ~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~  424 (503)
                      ++.....|...+...+.....       .+.++||||++++.++.+++.|...|+.+..+|+  .+.+|+..+..|..+.
T Consensus       576 vy~t~~eK~~Ali~~I~~~~~-------~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLna--kq~~REa~Iia~AG~~  646 (1025)
T PRK12900        576 VYKTRREKYNAIVLKVEELQK-------KGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNA--KQHDREAEIVAEAGQK  646 (1025)
T ss_pred             EecCHHHHHHHHHHHHHHHhh-------CCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecC--CHHHhHHHHHHhcCCC
Confidence            445566788888888866542       3447999999999999999999999999999997  6889999999999999


Q ss_pred             CcEEEEccccccCCCCC---CCC-----EEEEccCCCChhHHHHhhCcceee
Q 010709          425 TNILVATDVASRGLDVM---GVA-----HVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       425 ~~vLvaT~~~~~Gldip---~v~-----~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ..|+|||++++||+||+   +|.     +||++..|.+...|.||+||+||.
T Consensus       647 g~VtIATNMAGRGtDIkl~~~V~~vGGL~VIgterhes~Rid~Ql~GRtGRq  698 (1025)
T PRK12900        647 GAVTIATNMAGRGTDIKLGEGVRELGGLFILGSERHESRRIDRQLRGRAGRQ  698 (1025)
T ss_pred             CeEEEeccCcCCCCCcCCccchhhhCCceeeCCCCCchHHHHHHHhhhhhcC
Confidence            99999999999999999   554     459999999999999999999994

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

Probab=99.84  E-value=2.2e-19  Score=179.21  Aligned_cols=304  Identities=17%  Similarity=0.185  Sum_probs=204.1

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .+.++|++++.++.    ++.-.|+...+|.|||++. +.+|..+......    -+.+|||||. .+..||..+|+.|.
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQi-isFLaaL~~S~k~----~~paLIVCP~-Tii~qW~~E~~~w~  278 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQI-ISFLAALHHSGKL----TKPALIVCPA-TIIHQWMKEFQTWW  278 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhH-HHHHHHHhhcccc----cCceEEEccH-HHHHHHHHHHHHhC
Confidence            46788999999986    3456899999999999875 4455555544211    2568999998 57788999999987


Q ss_pred             ccCCCceEEEEECCccH--------HHHH-----HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          219 RSLDSFKTAIVVGGTNI--------AEQR-----SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~--------~~~~-----~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      .   .+++.++++....        ...+     +......+|+++|++.+.-  ....+.-..+.++|+||.|++-+. 
T Consensus       279 p---~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~--~~d~l~~~~W~y~ILDEGH~IrNp-  352 (923)
T KOG0387|consen  279 P---PFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRI--QGDDLLGILWDYVILDEGHRIRNP-  352 (923)
T ss_pred             c---ceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcc--cCcccccccccEEEecCcccccCC-
Confidence            4   4778888876552        0111     1112346799999877742  122344456899999999998776 


Q ss_pred             CHHHHHHHHHhCCCCCcEEEEEeeC-CHHHHHHHH---------------------------------------------
Q 010709          286 FEPQIREVMQNLPDKHQTLLFSATM-PVEIEALAQ---------------------------------------------  319 (503)
Q Consensus       286 ~~~~~~~il~~~~~~~q~i~~SAT~-~~~~~~~~~---------------------------------------------  319 (503)
                       ...+...+..++... .|++|+|| .+++.++..                                             
T Consensus       353 -ns~islackki~T~~-RiILSGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~~~f~~pI~~GgyaNAs~~qv~~aykca~  430 (923)
T KOG0387|consen  353 -NSKISLACKKIRTVH-RIILSGTPIQNNLTELWSLFDFVFPGKLGTLPVFQQNFEHPINRGGYANASPRQVQTAYKCAV  430 (923)
T ss_pred             -ccHHHHHHHhccccc-eEEeeCccccchHHHHHHHhhhccCCcccchHHHHhhhhhheeccccCCCCHHHHHHHHHHHH
Confidence             344555666665544 46677776 112221110                                             


Q ss_pred             -------Hh-------------------------------------c----------CCCeEE-----------E---eC
Q 010709          320 -------EY-------------------------------------L----------TDPVQV-----------K---VG  331 (503)
Q Consensus       320 -------~~-------------------------------------~----------~~~~~~-----------~---~~  331 (503)
                             -|                                     +          +++...           +   ..
T Consensus       431 ~Lr~lI~PylLRR~K~dv~~~~Lp~K~E~VlfC~LT~~QR~~Y~~fl~s~~v~~i~ng~~~~l~Gi~iLrkICnHPdll~  510 (923)
T KOG0387|consen  431 ALRDLISPYLLRRMKSDVKGLKLPKKEEIVLFCRLTKLQRRLYQRFLNSSEVNKILNGKRNCLSGIDILRKICNHPDLLD  510 (923)
T ss_pred             HHHHHhHHHHHHHHHHHhhhccCCCccceEEEEeccHHHHHHHHHHhhhHHHHHHHcCCccceechHHHHhhcCCccccc
Confidence                   00                                     0          000000           0   00


Q ss_pred             CCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHH-HCCCeEEEEcCCCCH
Q 010709          332 KVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV-AEGLHAVALHGGRNQ  410 (503)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~-~~~~~v~~lh~~~~~  410 (503)
                      ........-..+.-..+...|+..+.+++.....+       +.++|+|..++...+.|..+|. ..|+.++.+.|..+.
T Consensus       511 ~~~~~~~~~~D~~g~~k~sGKm~vl~~ll~~W~kq-------g~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~~  583 (923)
T KOG0387|consen  511 RRDEDEKQGPDYEGDPKRSGKMKVLAKLLKDWKKQ-------GDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTPA  583 (923)
T ss_pred             CcccccccCCCcCCChhhcchHHHHHHHHHHHhhC-------CCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCcc
Confidence            00000000000112234456777777777766543       4469999999999999999998 689999999999999


Q ss_pred             HHHHHHHHHHhcCCC-c-EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          411 SDRESALRDFRNGST-N-ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       411 ~~r~~~~~~f~~g~~-~-vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      ..|..+++.|.+++. . .|++|.+.+-|+|+.+++-||.||+-+++..=.|-.-||-|
T Consensus       584 ~~R~~lVd~Fne~~s~~VFLLTTrvGGLGlNLTgAnRVIIfDPdWNPStD~QAreRawR  642 (923)
T KOG0387|consen  584 ALRQKLVDRFNEDESIFVFLLTTRVGGLGLNLTGANRVIIFDPDWNPSTDNQARERAWR  642 (923)
T ss_pred             chhhHHHHhhcCCCceEEEEEEecccccccccccCceEEEECCCCCCccchHHHHHHHh
Confidence            999999999998763 3 57889999999999999999999999998666664444444

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=99.84  E-value=8.1e-19  Score=183.80  Aligned_cols=112  Identities=22%  Similarity=0.295  Sum_probs=99.7

Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEE
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILV  429 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLv  429 (503)
                      ..++..++..+.....       ...++||||++++.++.+++.|...|+.+..+||++++.+|..+++.|+.|++.|+|
T Consensus       429 ~~q~~~L~~~L~~~~~-------~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV  501 (652)
T PRK05298        429 KGQVDDLLSEIRKRVA-------KGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLV  501 (652)
T ss_pred             cccHHHHHHHHHHHHh-------CCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCCHHHHHHHHHHHHcCCceEEE
Confidence            3455666666655432       344699999999999999999999999999999999999999999999999999999


Q ss_pred             EccccccCCCCCCCCEEEEccC-----CCChhHHHHhhCcceee
Q 010709          430 ATDVASRGLDVMGVAHVVNLDL-----PKVLLAASESLCTTSFN  468 (503)
Q Consensus       430 aT~~~~~Gldip~v~~VI~~~~-----p~s~~~~~Qr~GR~gR~  468 (503)
                      ||+++++|+|+|++++||++|.     |.+..+|+||+||+||.
T Consensus       502 ~t~~L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~  545 (652)
T PRK05298        502 GINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN  545 (652)
T ss_pred             EeCHHhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCC
Confidence            9999999999999999999875     78999999999999995

>KOG4150 consensus Predicted ATP-dependent RNA helicase [RNA processing and modification]

Probab=99.83  E-value=6.8e-20  Score=176.04  Aligned_cols=315  Identities=12%  Similarity=0.032  Sum_probs=220.3

Q ss_pred             HHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       137 ~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      +.+.-...+.+|.+++..+.+|+++++.-.|.+||.++|.+........-+      ....+++.|+.++++...+-+.-
T Consensus       280 ~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~~------~s~~~~~~~~~~~~~~~~~~~~V  353 (1034)
T KOG4150|consen  280 NKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLCH------ATNSLLPSEMVEHLRNGSKGQVV  353 (1034)
T ss_pred             hcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcCc------ccceecchhHHHHhhccCCceEE
Confidence            445556778999999999999999999999999999999988877655532      34578999999998765543332


Q ss_pred             HhccCCC--ceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC----CCCCccEEEecchhHHhhC---CCH
Q 010709          217 LSRSLDS--FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT----SLSRVSFVILDEADRMLDM---GFE  287 (503)
Q Consensus       217 ~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~----~l~~~~~vViDEaH~l~~~---~~~  287 (503)
                      .....+.  -.++-.+.+....+.....+.+.+++++.|......+..+..    .+-...++++||+|-....   ...
T Consensus       354 ~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~  433 (1034)
T KOG4150|consen  354 HVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPTKALAQ  433 (1034)
T ss_pred             EEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecchhhHHH
Confidence            2211111  224445566666666666778899999999988665554332    3445678999999954332   122


Q ss_pred             HHHHHHHHhC-----CCCCcEEEEEeeCCHHHHHHHHHhcCCCeE-EEeCCCCCCCCceEEEEEEc---------ChhhH
Q 010709          288 PQIREVMQNL-----PDKHQTLLFSATMPVEIEALAQEYLTDPVQ-VKVGKVSSPTANVIQILEKV---------SENEK  352 (503)
Q Consensus       288 ~~~~~il~~~-----~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~---------~~~~k  352 (503)
                      .+++++++.+     ..+.|++-.+||+...++..-..+-.+.+. ++.+..+.   .-...+..-         +...+
T Consensus       434 ~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGSPs---~~K~~V~WNP~~~P~~~~~~~~~  510 (1034)
T KOG4150|consen  434 DQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGSPS---SEKLFVLWNPSAPPTSKSEKSSK  510 (1034)
T ss_pred             HHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCCCC---ccceEEEeCCCCCCcchhhhhhH
Confidence            3344444333     347889999999977776544444333332 22222211   111122111         22345


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC----C----CeEEEEcCCCCHHHHHHHHHHHhcCC
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE----G----LHAVALHGGRNQSDRESALRDFRNGS  424 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~----~----~~v~~lh~~~~~~~r~~~~~~f~~g~  424 (503)
                      +.+..+++.+......       ++|.||..++.|+.+....+..    +    -.+..+.||...++|.++....--|+
T Consensus       511 i~E~s~~~~~~i~~~~-------R~IAFC~~R~~CEL~~~~~R~I~~ET~~~LV~~i~SYRGGY~A~DRRKIE~~~F~G~  583 (1034)
T KOG4150|consen  511 VVEVSHLFAEMVQHGL-------RCIAFCPSRKLCELVLCLTREILAETAPHLVEAITSYRGGYIAEDRRKIESDLFGGK  583 (1034)
T ss_pred             HHHHHHHHHHHHHcCC-------cEEEeccHHHHHHHHHHHHHHHHHHhhHHHHHHHHhhcCccchhhHHHHHHHhhCCe
Confidence            5555555555443333       4999999999999887665542    2    14667899999999999999999999


Q ss_pred             CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          425 TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       425 ~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      ..-+|||++++.||||.+++.|+++++|.|++++.|+.|||||
T Consensus       584 L~giIaTNALELGIDIG~LDAVl~~GFP~S~aNl~QQ~GRAGR  626 (1034)
T KOG4150|consen  584 LCGIIATNALELGIDIGHLDAVLHLGFPGSIANLWQQAGRAGR  626 (1034)
T ss_pred             eeEEEecchhhhccccccceeEEEccCchhHHHHHHHhccccc
Confidence            9999999999999999999999999999999999999999999

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

Probab=99.82  E-value=3.6e-19  Score=168.62  Aligned_cols=304  Identities=16%  Similarity=0.177  Sum_probs=196.9

Q ss_pred             CCCcHHHHHHHHHHh-cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          142 TRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ..+.|+|.+.+...+ .|..+++...+|.|||++++..+-.+...+         -.||+||.. +--.|++.+..|...
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAlaIA~yyraEw---------plliVcPAs-vrftWa~al~r~lps  266 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALAIARYYRAEW---------PLLIVCPAS-VRFTWAKALNRFLPS  266 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHHHHHHHhhcC---------cEEEEecHH-HhHHHHHHHHHhccc
Confidence            456888999998766 567899999999999999854433333332         279999985 445699999999866


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCC
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK  300 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~  300 (503)
                      ...  +.++.++.+...   .+.....|.|++++.+..+-.  .+.-.++++||+||.|++-+.. ....+.++..+...
T Consensus       267 ~~p--i~vv~~~~D~~~---~~~t~~~v~ivSye~ls~l~~--~l~~~~~~vvI~DEsH~Lk~sk-tkr~Ka~~dllk~a  338 (689)
T KOG1000|consen  267 IHP--IFVVDKSSDPLP---DVCTSNTVAIVSYEQLSLLHD--ILKKEKYRVVIFDESHMLKDSK-TKRTKAATDLLKVA  338 (689)
T ss_pred             ccc--eEEEecccCCcc---ccccCCeEEEEEHHHHHHHHH--HHhcccceEEEEechhhhhccc-hhhhhhhhhHHHHh
Confidence            543  444555443221   123346788999988865433  3344569999999999776542 33355555555556


Q ss_pred             CcEEEEEeeC----CHHHH---------------HHHHHhcC-CCeEEEeCCC---------------------------
Q 010709          301 HQTLLFSATM----PVEIE---------------ALAQEYLT-DPVQVKVGKV---------------------------  333 (503)
Q Consensus       301 ~q~i~~SAT~----~~~~~---------------~~~~~~~~-~~~~~~~~~~---------------------------  333 (503)
                      .++|++|+|+    |.++.               ++...|-. .-+.+..+..                           
T Consensus       339 khvILLSGTPavSRP~elytqi~avd~tlfp~f~efa~rYCd~k~vr~~~Dykg~tnl~EL~~lL~k~lMIRRlK~dvL~  418 (689)
T KOG1000|consen  339 KHVILLSGTPAVSRPSELYTQIRAVDHTLFPNFHEFAIRYCDGKQVRFCFDYKGCTNLEELAALLFKRLMIRRLKADVLK  418 (689)
T ss_pred             hheEEecCCcccCCchhhhhhhhhhcccccccHHHHHHHhcCccccceeeecCCCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6799999998    22111               11111110 0000000000                           


Q ss_pred             CCCCCceEEEEEEcC---------------------hh----------------hHHHHHHHHHHHHHHhhhccCCCCCc
Q 010709          334 SSPTANVIQILEKVS---------------------EN----------------EKVDRLLALLVEEAFLAEKSCHPFPL  376 (503)
Q Consensus       334 ~~~~~~~~~~~~~~~---------------------~~----------------~k~~~l~~~l~~~~~~~~~~~~~~~~  376 (503)
                      ..+.. -.+.+....                     ..                .|.......+..+...   ...+..|
T Consensus       419 qLPpK-rr~Vv~~~~gr~da~~~~lv~~a~~~t~~~~~e~~~~~l~l~y~~tgiaK~~av~eyi~~~~~l---~d~~~~K  494 (689)
T KOG1000|consen  419 QLPPK-RREVVYVSGGRIDARMDDLVKAAADYTKVNSMERKHESLLLFYSLTGIAKAAAVCEYILENYFL---PDAPPRK  494 (689)
T ss_pred             hCCcc-ceEEEEEcCCccchHHHHHHHHhhhcchhhhhhhhhHHHHHHHHHhcccccHHHHHHHHhCccc---ccCCCce
Confidence            00111 111111110                     00                0111111111111000   2245678


Q ss_pred             EEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC-Cc-EEEEccccccCCCCCCCCEEEEccCCCC
Q 010709          377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS-TN-ILVATDVASRGLDVMGVAHVVNLDLPKV  454 (503)
Q Consensus       377 ~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~-~~-vLvaT~~~~~Gldip~v~~VI~~~~p~s  454 (503)
                      ++|||......+.+...+.++++..+.+.|..+..+|....+.|+..+ +. .+++..+++.|+|+...+.||+..++++
T Consensus       495 flVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~s~~R~ll~qsFQ~seev~VAvlsItA~gvGLt~tAa~~VVFaEL~wn  574 (689)
T KOG1000|consen  495 FLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTPSHRRTLLCQSFQTSEEVRVAVLSITAAGVGLTLTAASVVVFAELHWN  574 (689)
T ss_pred             EEEEehhHHHHHHHHHHHHHcCCCeEEecCCCCchhHHHHHHHhccccceEEEEEEEeecccceeeeccceEEEEEecCC
Confidence            999999999999999999999999999999999999999999998754 44 4667789999999999999999999998


Q ss_pred             h------hHHHHhhCccee
Q 010709          455 L------LAASESLCTTSF  467 (503)
Q Consensus       455 ~------~~~~Qr~GR~gR  467 (503)
                      +      ++.+||+|...-
T Consensus       575 PgvLlQAEDRaHRiGQkss  593 (689)
T KOG1000|consen  575 PGVLLQAEDRAHRIGQKSS  593 (689)
T ss_pred             CceEEechhhhhhccccce
Confidence            6      778888888654

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.81  E-value=7.8e-18  Score=170.52  Aligned_cols=302  Identities=21%  Similarity=0.186  Sum_probs=208.9

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|++.|.-+...+++|+  |..+.||.|||+++.+|++...+.        |..+-|++|+..||.|-++.+..+...+
T Consensus        77 ~r~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~--------G~~VhvvT~NdyLA~RDae~m~~ly~~L  146 (764)
T PRK12326         77 LRPFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ--------GRRVHVITVNDYLARRDAEWMGPLYEAL  146 (764)
T ss_pred             CCcchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc--------CCCeEEEcCCHHHHHHHHHHHHHHHHhc
Confidence            379999999998888774  679999999999999998877655        6779999999999999999999998877


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHc------CCCCCCCccEEEecchhHHh-hC---------
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQ------GNTSLSRVSFVILDEADRML-DM---------  284 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~------~~~~l~~~~~vViDEaH~l~-~~---------  284 (503)
                       ++.++++.++....+...  ...++|+++|..-| .+.+..      .......+.++||||+|.++ +.         
T Consensus       147 -GLsvg~i~~~~~~~err~--aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiLIDeArtPLiISg  223 (764)
T PRK12326        147 -GLTVGWITEESTPEERRA--AYACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVLVDEALVPLVLAG  223 (764)
T ss_pred             -CCEEEEECCCCCHHHHHH--HHcCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhheeccccCceeeeC
Confidence             599999988877554333  34589999998776 222221      12234668899999999622 00         


Q ss_pred             -----CCHHHHHHHHHhCC---------------------------------------------------------CC--
Q 010709          285 -----GFEPQIREVMQNLP---------------------------------------------------------DK--  300 (503)
Q Consensus       285 -----~~~~~~~~il~~~~---------------------------------------------------------~~--  300 (503)
                           .....+.++...+.                                                         .+  
T Consensus       224 ~~~~~~~y~~~~~~v~~L~~~~dy~ide~~k~v~LTe~G~~~~e~~l~~~~ly~~~~~~~~~~~i~~AL~A~~l~~~d~d  303 (764)
T PRK12326        224 STPGEAPRGEIAELVRRLREGKDYEIDDDGRNVHLTDKGARKVEKALGGIDLYSEEHVGTTLTQVNVALHAHALLQRDVH  303 (764)
T ss_pred             CCcchhHHHHHHHHHHhcCcCCcEEEEcCCCeeEecHHHHHHHHHHcCCccccCcchhHHHHHHHHHHHHHHHHHhcCCc
Confidence                 00000001111000                                                         00  


Q ss_pred             -----------------------------------------------------------CcEEEEEeeCCHHHHHHHHHh
Q 010709          301 -----------------------------------------------------------HQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       301 -----------------------------------------------------------~q~i~~SAT~~~~~~~~~~~~  321 (503)
                                                                                 .++-+||+|.......+.+-|
T Consensus       304 YiV~dgeV~iVDe~TGRvm~grrwsdGLHQaIEaKE~v~i~~e~~t~AsIT~QnfFr~Y~kLsGMTGTa~t~~~Ef~~iY  383 (764)
T PRK12326        304 YIVRDGKVHLINASRGRIAQLQRWPDGLQAAVEAKEGLETTETGEVLDTITVQALIGRYPTVCGMTGTAVAAGEQLRQFY  383 (764)
T ss_pred             EEEECCEEEEEECCCCCcCCCCccChHHHHHHHHHcCCCCCCCceeeehhhHHHHHHhcchheeecCCChhHHHHHHHHh
Confidence                                                                       146778888766555544444


Q ss_pred             cCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeE
Q 010709          322 LTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHA  401 (503)
Q Consensus       322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v  401 (503)
                      -- .+.+.....+.. ..............|...+...+.....       .+.|+||.+.+.+..+.+++.|.+.|++.
T Consensus       384 ~l-~Vv~IPtnkp~~-R~d~~d~iy~t~~~k~~Aii~ei~~~~~-------~GrPVLVgt~sI~~SE~ls~~L~~~gI~h  454 (764)
T PRK12326        384 DL-GVSVIPPNKPNI-REDEADRVYATAAEKNDAIVEHIAEVHE-------TGQPVLVGTHDVAESEELAERLRAAGVPA  454 (764)
T ss_pred             CC-cEEECCCCCCce-eecCCCceEeCHHHHHHHHHHHHHHHHH-------cCCCEEEEeCCHHHHHHHHHHHHhCCCcc
Confidence            33 322211111111 1111223444567788888777766543       34479999999999999999999999999


Q ss_pred             EEEcCCCCHHHHHHHHHHHhcCC-CcEEEEccccccCCCCCC---------------CCEEEEccCCCChhHHHHhhCcc
Q 010709          402 VALHGGRNQSDRESALRDFRNGS-TNILVATDVASRGLDVMG---------------VAHVVNLDLPKVLLAASESLCTT  465 (503)
Q Consensus       402 ~~lh~~~~~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip~---------------v~~VI~~~~p~s~~~~~Qr~GR~  465 (503)
                      ..+++.....|- +++.  +.|+ -.|-|||++++||-||.-               ==|||-...+.|...-.|-.||+
T Consensus       455 ~vLNAk~~~~EA-~IIa--~AG~~gaVTIATNMAGRGTDIkLg~~~~~~~~~V~~~GGLhVIgTerheSrRID~QLrGRa  531 (764)
T PRK12326        455 VVLNAKNDAEEA-RIIA--EAGKYGAVTVSTQMAGRGTDIRLGGSDEADRDRVAELGGLHVIGTGRHRSERLDNQLRGRA  531 (764)
T ss_pred             eeeccCchHhHH-HHHH--hcCCCCcEEEEecCCCCccCeecCCCcccchHHHHHcCCcEEEeccCCchHHHHHHHhccc
Confidence            999887554442 3332  3454 569999999999999872               23799999999998889999999


Q ss_pred             eee
Q 010709          466 SFN  468 (503)
Q Consensus       466 gR~  468 (503)
                      ||.
T Consensus       532 GRQ  534 (764)
T PRK12326        532 GRQ  534 (764)
T ss_pred             ccC
Confidence            995

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=99.81  E-value=4.5e-18  Score=169.68  Aligned_cols=329  Identities=18%  Similarity=0.185  Sum_probs=209.9

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ++-++|.-.+.++.    ++-+.|+..++|.|||.+. ++.|.++...+    .+|| -|||||...|-+ |.++|.+|+
T Consensus       399 ~LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQv-IaFlayLkq~g----~~gp-HLVVvPsSTleN-WlrEf~kwC  471 (941)
T KOG0389|consen  399 QLKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQV-IAFLAYLKQIG----NPGP-HLVVVPSSTLEN-WLREFAKWC  471 (941)
T ss_pred             cccchhhhhHHHHHHHHHccccceehhhccCcchhHH-HHHHHHHHHcC----CCCC-cEEEecchhHHH-HHHHHHHhC
Confidence            37889999999865    4446899999999999875 66777776653    2344 499999998877 888899988


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhh----CCCcEEEECcHHHHHHHH-cCCCCCCCccEEEecchhHHhhCCCHHHHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELR----GGVSIVVATPGRFLDHLQ-QGNTSLSRVSFVILDEADRMLDMGFEPQIREV  293 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~Ilv~Tp~~l~~~l~-~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~i  293 (503)
                      .   .+++..++|....+...+..-    .+.+|+++|+.....--. +.-+.-.++.++|+||+|.+-+.. ...+..+
T Consensus       472 P---sl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeRy~~L  547 (941)
T KOG0389|consen  472 P---SLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SERYKHL  547 (941)
T ss_pred             C---ceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHHHHHh
Confidence            4   578899999886555443332    368999999876631111 112335678999999999776653 2334444


Q ss_pred             HHhCCCCCcEEEEEeeCC-HHHHHHHH---------------------------------------------H-------
Q 010709          294 MQNLPDKHQTLLFSATMP-VEIEALAQ---------------------------------------------E-------  320 (503)
Q Consensus       294 l~~~~~~~q~i~~SAT~~-~~~~~~~~---------------------------------------------~-------  320 (503)
                      +.- +.+ +.+++|+||- +++.+++.                                             .       
T Consensus       548 M~I-~An-~RlLLTGTPLQNNL~ELiSLL~FvlP~vF~~~~~dl~~if~~k~~~d~d~e~~~l~qerIsrAK~im~PFIL  625 (941)
T KOG0389|consen  548 MSI-NAN-FRLLLTGTPLQNNLKELISLLAFVLPKVFDSSMEDLDVIFKAKKTSDGDIENALLSQERISRAKTIMKPFIL  625 (941)
T ss_pred             ccc-ccc-ceEEeeCCcccccHHHHHHHHHHHhhHhhhccchHHHHHHhccCCccchhhHHHHHHHHHHHHHHhhhHHHH
Confidence            433 233 3577788871 11111100                                             0       


Q ss_pred             ------hc----CCCeEEEe----------------------CCCCCC--CCc--e--------------EEEE------
Q 010709          321 ------YL----TDPVQVKV----------------------GKVSSP--TAN--V--------------IQIL------  344 (503)
Q Consensus       321 ------~~----~~~~~~~~----------------------~~~~~~--~~~--~--------------~~~~------  344 (503)
                            .+    .....+..                      ......  ...  +              +.++      
T Consensus       626 RR~K~qVL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~ns~~~~~~vlmqlRK~AnHPLL~R~~Y~de~L~  705 (941)
T KOG0389|consen  626 RRLKSQVLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKNSELKSGNVLMQLRKAANHPLLFRSIYTDEKLR  705 (941)
T ss_pred             HHHHHHHHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHhcChhHHHHhccHHHHH
Confidence                  00    00000000                      000000  000  0              0000      


Q ss_pred             -------------------------------------------------EEcChhhHHHHHHHHHHHHHHhhhccCCCCC
Q 010709          345 -------------------------------------------------EKVSENEKVDRLLALLVEEAFLAEKSCHPFP  375 (503)
Q Consensus       345 -------------------------------------------------~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~  375 (503)
                                                                       ...-...|...|..++.+...       .+.
T Consensus       706 ~mak~il~e~ay~~~n~qyIfEDm~~msDfelHqLc~~f~~~~~f~L~d~~~mdSgK~r~L~~LLp~~k~-------~G~  778 (941)
T KOG0389|consen  706 KMAKRILNEPAYKKANEQYIFEDMEVMSDFELHQLCCQFRHLSKFQLKDDLWMDSGKCRKLKELLPKIKK-------KGD  778 (941)
T ss_pred             HHHHHHhCchhhhhcCHHHHHHHHHhhhHHHHHHHHHhcCCCcccccCCchhhhhhhHhHHHHHHHHHhh-------cCC
Confidence                                                             000112233344444433322       235


Q ss_pred             cEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC--CcEEEEccccccCCCCCCCCEEEEccCCC
Q 010709          376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS--TNILVATDVASRGLDVMGVAHVVNLDLPK  453 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~--~~vLvaT~~~~~Gldip~v~~VI~~~~p~  453 (503)
                      ++|||.+--...+-|...|.-.++....+.|...-..|+.+++.|...+  .-.|++|.+++-|||+..+++||.+|..-
T Consensus       779 RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTqV~~RQ~lId~Fn~d~difVFLLSTKAGG~GINLt~An~VIihD~dF  858 (941)
T KOG0389|consen  779 RVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQVNDRQDLIDEFNTDKDIFVFLLSTKAGGFGINLTCANTVIIHDIDF  858 (941)
T ss_pred             EEEEeeHHHHHHHHHHHHHHhcCceEEeecCCccchHHHHHHHhhccCCceEEEEEeeccCcceecccccceEEEeecCC
Confidence            7999999999999999999999999999999999999999999998754  44689999999999999999999999865


Q ss_pred             Ch------hHHHHhhCcc-----eeeeeecc--CchhhhhhHHHHHHHHHH
Q 010709          454 VL------LAASESLCTT-----SFNITTNL--DGDMKKLEFCLILAITVL  491 (503)
Q Consensus       454 s~------~~~~Qr~GR~-----gR~~~~~~--~~~~~~~~~~~~~~~~~~  491 (503)
                      ++      ++..||+|..     -|.+....  ++..+-....+.++.+++
T Consensus       859 NP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIEE~I~~lA~~KL~Le~~lt  909 (941)
T KOG0389|consen  859 NPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIEEGILRLAKTKLALEADLT  909 (941)
T ss_pred             CCcccchhHHHHHhhCCcceeEEEEEEecCcHHHHHHHHHHHhhhhhhhhc
Confidence            54      6777888873     33333333  244444444555555543

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

Probab=99.81  E-value=2.9e-17  Score=175.69  Aligned_cols=329  Identities=17%  Similarity=0.168  Sum_probs=194.4

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH-HHHHHHH
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI-EKEVKAL  217 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~-~~~~~~~  217 (503)
                      .+++-|.+....+.    +++.+++.|+||+|||++|++|++...         .+.++||++||++|+.|+ .+.+..+
T Consensus       245 e~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~---------~~~~vvI~t~T~~Lq~Ql~~~~i~~l  315 (820)
T PRK07246        245 EERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS---------DQRQIIVSVPTKILQDQIMAEEVKAI  315 (820)
T ss_pred             ccCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc---------CCCcEEEEeCcHHHHHHHHHHHHHHH
Confidence            68999999665544    567799999999999999999988753         246799999999999999 4667766


Q ss_pred             hccCCCceEEEEECCccHH---H--------------------------------------------HH-----------
Q 010709          218 SRSLDSFKTAIVVGGTNIA---E--------------------------------------------QR-----------  239 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~---~--------------------------------------------~~-----------  239 (503)
                      .+.. ++++.++.|+...-   .                                            .+           
T Consensus       316 ~~~~-~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~~~~~  394 (820)
T PRK07246        316 QEVF-HIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDGNLSQ  394 (820)
T ss_pred             HHhc-CCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccCCCCC
Confidence            6554 35666666533210   0                                            00           


Q ss_pred             -------------HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-----CH-------HH-----
Q 010709          240 -------------SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-----FE-------PQ-----  289 (503)
Q Consensus       240 -------------~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-----~~-------~~-----  289 (503)
                                   +.....++|+|+.-..|...+.... .+..++++||||||++.+..     ..       ..     
T Consensus       395 ~cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~-~~p~~~~lIiDEAH~l~~~~~~~~~~~~~~~~~~~~l~~~~  473 (820)
T PRK07246        395 SSLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDK-DFARNKVLVFDEAQKLMLQLEQLSRHQLNITSFLQTIQKAL  473 (820)
T ss_pred             CCCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc-CCCCCCEEEEECcchhHHHHHHHhcceecHHHHHHHHHHHH
Confidence                         0011246899999888777664432 36789999999999854310     00       00     


Q ss_pred             --------------------------------------H------------------HHHHHhC----------------
Q 010709          290 --------------------------------------I------------------REVMQNL----------------  297 (503)
Q Consensus       290 --------------------------------------~------------------~~il~~~----------------  297 (503)
                                                            +                  ..++..-                
T Consensus       474 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~W~e~~~~~~~~~  553 (820)
T PRK07246        474 SGPLPLLQKRLLESISFELLQLSEQFYQGKERQLIHDSLSRLHQYFSELEVAGFQELQAFFATAEGDYWLESEKQSEKRV  553 (820)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEecCCCCcce
Confidence                                                  0                  0000000                


Q ss_pred             -----------------CCCCcEEEEEeeCC--HHHHHHHHHhcCC--CeEEEeCCCCCCCCceEEEEE--EcCh-----
Q 010709          298 -----------------PDKHQTLLFSATMP--VEIEALAQEYLTD--PVQVKVGKVSSPTANVIQILE--KVSE-----  349 (503)
Q Consensus       298 -----------------~~~~q~i~~SAT~~--~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~--~~~~-----  349 (503)
                                       +....+|++|||++  +... + ...++-  .......   .........+.  .++.     
T Consensus       554 ~~l~~~pl~v~~~~~~~~~~~~~i~tSATL~v~~~f~-~-~~~lGl~~~~~~~~~---~~~~~~~~~~i~~~~p~~~~~~  628 (820)
T PRK07246        554 TYLNSASKAFTHFSQLLPETCKTYFVSATLQISPRVS-L-ADLLGFEEYLFHKIE---KDKKQDQLVVVDQDMPLVTETS  628 (820)
T ss_pred             eEEEeeeCcHHHHHHHHhcCCeEEEEecccccCCCCc-H-HHHcCCCccceecCC---CChHHccEEEeCCCCCCCCCCC
Confidence                             00135788888885  2222 3 222231  1111111   11111111111  1121     


Q ss_pred             -hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          350 -NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       350 -~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                       ......+...+....       ...++++|+++|.+..+.+++.|....+.+ ...|...  .+.+++++|++++..||
T Consensus       629 ~~~~~~~~~~~i~~~~-------~~~g~~LVLFtS~~~l~~v~~~l~~~~~~~-l~Qg~~~--~~~~l~~~F~~~~~~vL  698 (820)
T PRK07246        629 DEVYAEEIAKRLEELK-------QLQQPILVLFNSKKHLLAVSDLLDQWQVSH-LAQEKNG--TAYNIKKRFDRGEQQIL  698 (820)
T ss_pred             hHHHHHHHHHHHHHHH-------hcCCCEEEEECcHHHHHHHHHHHhhcCCcE-EEeCCCc--cHHHHHHHHHcCCCeEE
Confidence             222233444443221       134679999999999999999997665544 4444222  24668999999989999


Q ss_pred             EEccccccCCCCCC--CCEEEEccCCC----Ch-----hHHHHhhCc------------------ceeeeeeccC-chhh
Q 010709          429 VATDVASRGLDVMG--VAHVVNLDLPK----VL-----LAASESLCT------------------TSFNITTNLD-GDMK  478 (503)
Q Consensus       429 vaT~~~~~Gldip~--v~~VI~~~~p~----s~-----~~~~Qr~GR------------------~gR~~~~~~~-~~~~  478 (503)
                      ++|..+.+|||+|+  ...||...+|-    ++     .+|..+-|+                  +||.+.+..| |.+.
T Consensus       699 lG~~sFwEGVD~p~~~~~~viI~kLPF~~P~dP~~~a~~~~~~~~g~~~F~~~~lP~A~iklkQg~GRLIRs~~D~Gvv~  778 (820)
T PRK07246        699 LGLGSFWEGVDFVQADRMIEVITRLPFDNPEDPFVKKMNQYLLQEGKNPFYDYFLPMTILRLKQAIGRTMRREDQKSAVL  778 (820)
T ss_pred             EecchhhCCCCCCCCCeEEEEEecCCCCCCCCHHHHHHHHHHHHhCCCchhheeHHHHHHHHHHHhcccccCCCCcEEEE
Confidence            99999999999974  56677777662    21     233333343                  4566666666 5555


Q ss_pred             hhhHHHHHHHHHHHHHHHH
Q 010709          479 KLEFCLILAITVLLFVIFL  497 (503)
Q Consensus       479 ~~~~~~~~~~~~~~~~~~~  497 (503)
                      -++.-+.--.+..+|...|
T Consensus       779 ilD~R~~~k~Yg~~~l~sL  797 (820)
T PRK07246        779 ILDRRILTKSYGKQILASL  797 (820)
T ss_pred             EECCcccccHHHHHHHHhC
Confidence            5555544334444444433

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=99.80  E-value=2.9e-17  Score=168.95  Aligned_cols=154  Identities=18%  Similarity=0.269  Sum_probs=113.5

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++.||...+.++.    ++-|.|+..++|.|||++. +.+|.++.+...   +.||. ||||||..+.+ |.-+|++|+
T Consensus       615 qLReYQkiGLdWLatLYeknlNGILADEmGLGKTIQt-ISllAhLACeeg---nWGPH-LIVVpTsviLn-WEMElKRwc  688 (1958)
T KOG0391|consen  615 QLREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQT-ISLLAHLACEEG---NWGPH-LIVVPTSVILN-WEMELKRWC  688 (1958)
T ss_pred             HHHHHHHhhHHHHHHHHHhcccceehhhhcccchhHH-HHHHHHHHhccc---CCCCc-eEEeechhhhh-hhHHHhhhC
Confidence            46777999999875    4457999999999999985 778888888643   33444 99999988877 899999998


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhC---CCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRG---GVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      .   ++++..++|........+.-+.   ..||.|+++..+.+-+.  .|...+|.|+|+||||++-++ -...|..++ 
T Consensus       689 P---glKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~--AFkrkrWqyLvLDEaqnIKnf-ksqrWQAll-  761 (1958)
T KOG0391|consen  689 P---GLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLT--AFKRKRWQYLVLDEAQNIKNF-KSQRWQALL-  761 (1958)
T ss_pred             C---cceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHH--HHHhhccceeehhhhhhhcch-hHHHHHHHh-
Confidence            5   5788899998876666655553   36899999888876655  466778999999999987654 122333333 


Q ss_pred             hCCCCCcEEEEEeeC
Q 010709          296 NLPDKHQTLLFSATM  310 (503)
Q Consensus       296 ~~~~~~q~i~~SAT~  310 (503)
                      .++.. |.+++++|+
T Consensus       762 nfnsq-rRLLLtgTP  775 (1958)
T KOG0391|consen  762 NFNSQ-RRLLLTGTP  775 (1958)
T ss_pred             ccchh-heeeecCCc
Confidence            33332 345666665

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=99.80  E-value=1e-19  Score=172.54  Aligned_cols=292  Identities=16%  Similarity=0.141  Sum_probs=187.1

Q ss_pred             CCCcHHHHHHHHHHhcC---CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          142 TRPTSIQAQAMPVALSG---RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~---~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..++|+|..++..+.-+   +..||+.|+|+|||++-+-+ .+.+          ++.+|+++.+-.-+.||..+|+.|.
T Consensus       301 t~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTA-a~ti----------kK~clvLcts~VSVeQWkqQfk~ws  369 (776)
T KOG1123|consen  301 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTA-ACTI----------KKSCLVLCTSAVSVEQWKQQFKQWS  369 (776)
T ss_pred             cccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeee-eeee----------cccEEEEecCccCHHHHHHHHHhhc
Confidence            46899999999998843   46899999999999865332 2222          4569999999999999999999997


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC--------CCCCCCccEEEecchhHHhhCCCHHHH
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG--------NTSLSRVSFVILDEADRMLDMGFEPQI  290 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~--------~~~l~~~~~vViDEaH~l~~~~~~~~~  290 (503)
                      .- .+-.++..+.+. +    .....++.|+|+|+.++..--.+.        -+.-+.++++++||+|.+-..-|+..+
T Consensus       370 ti-~d~~i~rFTsd~-K----e~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRVl  443 (776)
T KOG1123|consen  370 TI-QDDQICRFTSDA-K----ERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRVL  443 (776)
T ss_pred             cc-CccceEEeeccc-c----ccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHHH
Confidence            43 233333333332 1    224567899999998874322211        123467999999999976544455444


Q ss_pred             HHHHHhCCCCCcEEEEEeeCCHHHHHHHH-HhcCCCeEEEeCCCC----CCCCce-----------------------EE
Q 010709          291 REVMQNLPDKHQTLLFSATMPVEIEALAQ-EYLTDPVQVKVGKVS----SPTANV-----------------------IQ  342 (503)
Q Consensus       291 ~~il~~~~~~~q~i~~SAT~~~~~~~~~~-~~~~~~~~~~~~~~~----~~~~~~-----------------------~~  342 (503)
                      ..+-.+    + -+++|||+-++-..+.. .|+.-|.....+-..    .....+                       ..
T Consensus       444 siv~aH----c-KLGLTATLvREDdKI~DLNFLIGPKlYEAnWmdL~~kGhIA~VqCaEVWCpMt~eFy~eYL~~~t~kr  518 (776)
T KOG1123|consen  444 SIVQAH----C-KLGLTATLVREDDKITDLNFLIGPKLYEANWMDLQKKGHIAKVQCAEVWCPMTPEFYREYLRENTRKR  518 (776)
T ss_pred             HHHHHH----h-hccceeEEeeccccccccceeecchhhhccHHHHHhCCceeEEeeeeeecCCCHHHHHHHHhhhhhhh
Confidence            444333    3 38999998443222211 111111111100000    000111                       11


Q ss_pred             EEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc
Q 010709          343 ILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRN  422 (503)
Q Consensus       343 ~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~  422 (503)
                      ....+-...|.. .++++.+.+.+      .+.|+|||..+.-...+.+-.|.+     -.++|..+|.+|+++++.|+-
T Consensus       519 ~lLyvMNP~KFr-aCqfLI~~HE~------RgDKiIVFsDnvfALk~YAikl~K-----pfIYG~Tsq~ERm~ILqnFq~  586 (776)
T KOG1123|consen  519 MLLYVMNPNKFR-ACQFLIKFHER------RGDKIIVFSDNVFALKEYAIKLGK-----PFIYGPTSQNERMKILQNFQT  586 (776)
T ss_pred             heeeecCcchhH-HHHHHHHHHHh------cCCeEEEEeccHHHHHHHHHHcCC-----ceEECCCchhHHHHHHHhccc
Confidence            122222333433 23333333322      345799999887665555555433     268999999999999999985


Q ss_pred             -CCCcEEEEccccccCCCCCCCCEEEEccCC-CChhHHHHhhCccee
Q 010709          423 -GSTNILVATDVASRGLDVMGVAHVVNLDLP-KVLLAASESLCTTSF  467 (503)
Q Consensus       423 -g~~~vLvaT~~~~~Gldip~v~~VI~~~~p-~s~~~~~Qr~GR~gR  467 (503)
                       ..++.++-..++.+++|+|.++++|+..-- .|..+=.||.||.=|
T Consensus       587 n~~vNTIFlSKVgDtSiDLPEAnvLIQISSH~GSRRQEAQRLGRILR  633 (776)
T KOG1123|consen  587 NPKVNTIFLSKVGDTSIDLPEANVLIQISSHGGSRRQEAQRLGRILR  633 (776)
T ss_pred             CCccceEEEeeccCccccCCcccEEEEEcccccchHHHHHHHHHHHH
Confidence             468899999999999999999999987653 467778899998655

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=3.1e-17  Score=170.28  Aligned_cols=302  Identities=20%  Similarity=0.218  Sum_probs=204.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      -.|+++|.-.--.+.+|  -|..+.||.|||+++.+|++...+.        |..+-|++|+..||.|-++.+..+...+
T Consensus        81 m~~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al~--------G~~VhvvT~ndyLA~RD~e~m~~l~~~l  150 (913)
T PRK13103         81 MRHFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNALS--------GKGVHVVTVNDYLARRDANWMRPLYEFL  150 (913)
T ss_pred             CCcchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHc--------CCCEEEEeCCHHHHHHHHHHHHHHhccc
Confidence            47888888776666554  6779999999999999998876555        6779999999999999999999999877


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hCC--------
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DMG--------  285 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~~--------  285 (503)
                       ++.+.++.++....+.....  .++|+++|..-| .+.|..+      ......+.++||||+|.++ +..        
T Consensus       151 -Gl~v~~i~~~~~~~err~~Y--~~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiLIDEArtPLIISg  227 (913)
T PRK13103        151 -GLSVGIVTPFQPPEEKRAAY--AADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSILIDEARTPLIISG  227 (913)
T ss_pred             -CCEEEEECCCCCHHHHHHHh--cCCEEEEcccccccchhhccceechhhhcccccceeEechhhheeccccCCceeecC
Confidence             59999998877665543333  499999998886 3333321      1123788999999999722 100        


Q ss_pred             --------------CHH------------------------------------HHHHHH---------------------
Q 010709          286 --------------FEP------------------------------------QIREVM---------------------  294 (503)
Q Consensus       286 --------------~~~------------------------------------~~~~il---------------------  294 (503)
                                    +..                                    .+..++                     
T Consensus       228 ~~~~~~~~y~~~~~~v~~L~~~~~~~~~~~~~~~~y~idek~~~v~LTe~G~~~~e~~~~~~~i~~~~~~ly~~~~~~~~  307 (913)
T PRK13103        228 QAEDSSKLYIEINRLIPRLKQHIEEVEGQVTQEGHFTIDEKTRQVELNEAGHQFIEEMLTQAGLLAEGESLYSAHNLGLL  307 (913)
T ss_pred             CCccchHHHHHHHHHHHHHHhhhhccccccCCCCCeEEEcCCCeeeechHHHHHHHHHhhhCCCcccchhccChhhhHHH
Confidence                          000                                    000000                     


Q ss_pred             -------Hh---CCCC-------------------------------------------------------------CcE
Q 010709          295 -------QN---LPDK-------------------------------------------------------------HQT  303 (503)
Q Consensus       295 -------~~---~~~~-------------------------------------------------------------~q~  303 (503)
                             +.   +..+                                                             .++
T Consensus       308 ~~i~~AL~A~~lf~~d~dYiV~dg~V~IVDe~TGR~m~grrwsdGLHQaIEaKE~v~I~~e~~t~AsIT~QnfFr~Y~kL  387 (913)
T PRK13103        308 THVYAGLRAHKLFHRNVEYIVQDGQVLLIDEHTGRTMPGRRLSEGLHQAIEAKENLNIQAESQTLASTTFQNYFRLYNKL  387 (913)
T ss_pred             HHHHHHHHHHHHHhcCCcEEEECCEEEEEECCCCCcCCCCccchHHHHHHHHHcCCCcCCCceeEEeehHHHHHHhcchh
Confidence                   00   0000                                                             145


Q ss_pred             EEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcc
Q 010709          304 LLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVER  383 (503)
Q Consensus       304 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~  383 (503)
                      -+||+|...+-..+.+-|-- .+.+.....+..... ..-.++.....|...+...+.....       .+.|+||-+.+
T Consensus       388 sGMTGTa~te~~Ef~~iY~l-~Vv~IPTnkP~~R~D-~~d~vy~t~~eK~~Ai~~ei~~~~~-------~GrPVLVGT~S  458 (913)
T PRK13103        388 SGMTGTADTEAFEFRQIYGL-DVVVIPPNKPLARKD-FNDLVYLTAEEKYAAIITDIKECMA-------LGRPVLVGTAT  458 (913)
T ss_pred             ccCCCCCHHHHHHHHHHhCC-CEEECCCCCCccccc-CCCeEEcCHHHHHHHHHHHHHHHHh-------CCCCEEEEeCC
Confidence            56677765554444444432 222212111111111 1223455667788888888776553       34479999999


Q ss_pred             hhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC-CcEEEEccccccCCCCC---------------------
Q 010709          384 KTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS-TNILVATDVASRGLDVM---------------------  441 (503)
Q Consensus       384 ~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip---------------------  441 (503)
                      .+..+.+++.|.+.|+..-.++......|-..+-   +.|. -.|-|||++++||-||.                     
T Consensus       459 Ve~SE~ls~~L~~~gi~h~VLNAk~~~~EA~IIa---~AG~~GaVTIATNMAGRGTDIkLg~n~~~~~~~~~~~~~~~~~  535 (913)
T PRK13103        459 IETSEHMSNLLKKEGIEHKVLNAKYHEKEAEIIA---QAGRPGALTIATNMAGRGTDILLGGNWEVEVAALENPTPEQIA  535 (913)
T ss_pred             HHHHHHHHHHHHHcCCcHHHhccccchhHHHHHH---cCCCCCcEEEeccCCCCCCCEecCCchHHHHHhhhhhhHHHHH
Confidence            9999999999999999887777765544433332   3553 57999999999999995                     


Q ss_pred             ----------------CCCEEEEccCCCChhHHHHhhCcceee
Q 010709          442 ----------------GVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       442 ----------------~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                                      +==+||-...+.|..-=.|-.||+||.
T Consensus       536 ~~~~~~~~~~e~V~e~GGLhVIgTerheSrRID~QLrGRaGRQ  578 (913)
T PRK13103        536 QIKADWQKRHQQVIEAGGLHVIASERHESRRIDNQLRGRAGRQ  578 (913)
T ss_pred             HHHHHHHhHHHHHHHcCCCEEEeeccCchHHHHHHhccccccC
Confidence                            123789999999998888999999994

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=99.77  E-value=2e-16  Score=162.09  Aligned_cols=317  Identities=15%  Similarity=0.165  Sum_probs=195.7

Q ss_pred             CCcHHHHHHHHHHhcC----------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVALSG----------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEK  212 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~----------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~  212 (503)
                      .++|+|++++..+..+          .-+|++-.+|+|||+.. ++++..++.+.+.....-.+.|||+|. .|+.-|++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~-IsflwtlLrq~P~~~~~~~k~lVV~P~-sLv~nWkk  315 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQC-ISFIWTLLRQFPQAKPLINKPLVVAPS-SLVNNWKK  315 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHH-HHHHHHHHHhCcCccccccccEEEccH-HHHHHHHH
Confidence            5789999999887632          23889999999999986 566666666543322233678999998 57788999


Q ss_pred             HHHHHhccCCCceEEEEECCccH--HHHHHHh-----hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          213 EVKALSRSLDSFKTAIVVGGTNI--AEQRSEL-----RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~-----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      +|.+|.... .+....+++....  ......+     .-..-|++-+.+.+.+...  .+....++++|+||.|++-+. 
T Consensus       316 EF~KWl~~~-~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~--~il~~~~glLVcDEGHrlkN~-  391 (776)
T KOG0390|consen  316 EFGKWLGNH-RINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCR--KILLIRPGLLVCDEGHRLKNS-  391 (776)
T ss_pred             HHHHhcccc-ccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHH--HHhcCCCCeEEECCCCCccch-
Confidence            999998542 3555666666553  0000111     1124577788888876655  355778999999999987665 


Q ss_pred             CHHHHHHHHHhCCCCCcEEEEEeeCC-HHHHHHHHH-----------------hcCCC----------------------
Q 010709          286 FEPQIREVMQNLPDKHQTLLFSATMP-VEIEALAQE-----------------YLTDP----------------------  325 (503)
Q Consensus       286 ~~~~~~~il~~~~~~~q~i~~SAT~~-~~~~~~~~~-----------------~~~~~----------------------  325 (503)
                       ...+.+.+..+.-++ -|++|+||= +++.++..-                 .+..|                      
T Consensus       392 -~s~~~kaL~~l~t~r-RVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~sf~k~~~~~i~~~~~~~~s~e~~~~~~rl~e  469 (776)
T KOG0390|consen  392 -DSLTLKALSSLKTPR-RVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISSFKKKFEIPILRGRDADASEEDREREERLQE  469 (776)
T ss_pred             -hhHHHHHHHhcCCCc-eEEeeCCcccccHHHHHHHHhhcChhhccchHHHHHHhhcccccccCCCcchhhhhhHHHHHH
Confidence             555677777776655 578899981 122211100                 00000                      


Q ss_pred             --------eEEEeC-CCCCCCCceEEEEEEcChhhHHHHHHHHHHHHH---------H-----hhhccCCC---------
Q 010709          326 --------VQVKVG-KVSSPTANVIQILEKVSENEKVDRLLALLVEEA---------F-----LAEKSCHP---------  373 (503)
Q Consensus       326 --------~~~~~~-~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~---------~-----~~~~~~~~---------  373 (503)
                              +..+.+ ......+....++..+.....-..++..+....         .     ......+|         
T Consensus       470 L~~~t~~fi~rrt~~il~k~LP~k~e~vv~~n~t~~Q~~~~~~l~~~~~~~~~~~~~l~~~~~L~k~cnhP~L~~~~~~~  549 (776)
T KOG0390|consen  470 LRELTNKFILRRTGDILLKYLPGKYEYVVFCNPTPIQKELYKKLLDSMKMRTLKGYALELITKLKKLCNHPSLLLLCEKT  549 (776)
T ss_pred             HHHHHHhheeecccchhhhhCCCceeEEEEeCCcHHHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHhcCHHhhcccccc
Confidence                    000001 011112222233333332222222221111110         0     00000000         


Q ss_pred             -----------------------------------------CCcEEEEE----cchhhHHHHHHHHHHCCCeEEEEcCCC
Q 010709          374 -----------------------------------------FPLTIVFV----ERKTRCDEVSEALVAEGLHAVALHGGR  408 (503)
Q Consensus       374 -----------------------------------------~~~~lIF~----~~~~~~~~l~~~L~~~~~~v~~lh~~~  408 (503)
                                                               ..++++|+    |.+...+.+...++-.|+.++.+||.+
T Consensus       550 ~~e~~~~~~~~~~~~~~~~~~~~~~~ks~kl~~L~~ll~~~~ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~  629 (776)
T KOG0390|consen  550 EKEKAFKNPALLLDPGKLKLDAGDGSKSGKLLVLVFLLEVIREKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKT  629 (776)
T ss_pred             cccccccChHhhhcccccccccccchhhhHHHHHHHHHHHHhhhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCC
Confidence                                                     01233333    334444555555555699999999999


Q ss_pred             CHHHHHHHHHHHhcCC---CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          409 NQSDRESALRDFRNGS---TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       409 ~~~~r~~~~~~f~~g~---~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      +..+|+.+++.|.+..   .-.|.+|.+.+.||++-+++.||.||+.++++.=.|.+.||-|
T Consensus       630 ~~~qRq~~vd~FN~p~~~~~vfLlSsKAgg~GinLiGAsRlil~D~dWNPa~d~QAmaR~~R  691 (776)
T KOG0390|consen  630 SIKQRQKLVDTFNDPESPSFVFLLSSKAGGEGLNLIGASRLILFDPDWNPAVDQQAMARAWR  691 (776)
T ss_pred             chHHHHHHHHhccCCCCCceEEEEecccccCceeecccceEEEeCCCCCchhHHHHHHHhcc
Confidence            9999999999998743   3356677899999999999999999999999999999999888

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

Probab=99.77  E-value=1.8e-17  Score=171.99  Aligned_cols=312  Identities=18%  Similarity=0.226  Sum_probs=196.7

Q ss_pred             CCcHHHHHHHHHHh--c--CCCeEEEccCCCchhHHhHHHHHHHHHhcC--CCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVAL--S--GRDLLGCAETGSGKTAAFTIPMIQHCVAQT--PVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~--~--~~~vii~~~TGsGKTl~~~lp~l~~~~~~~--~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      .++.+|++.+.++.  +  +=+.|+|..+|.|||++.+ -+++.-...+  ..........|||||. .|+-.|..++++
T Consensus       975 ~LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQti-cilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~k 1052 (1549)
T KOG0392|consen  975 KLRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTI-CILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKK 1052 (1549)
T ss_pred             HHHHHHHhccHHHHHHHHhcccceeeccccccHHHHHH-HHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHH
Confidence            35888999998865  3  2368999999999999863 3443322222  1111223347999998 699999999999


Q ss_pred             HhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN  296 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~  296 (503)
                      |+..   +++..+.|+...+...+..-++.+|+|+.++.+.+-+..  +.-..+.|+|+||-|-+-+.  ...+.+.++.
T Consensus      1053 f~pf---L~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~--l~~~~wNYcVLDEGHVikN~--ktkl~kavkq 1125 (1549)
T KOG0392|consen 1053 FFPF---LKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY--LIKIDWNYCVLDEGHVIKNS--KTKLTKAVKQ 1125 (1549)
T ss_pred             hcch---hhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH--HHhcccceEEecCcceecch--HHHHHHHHHH
Confidence            9865   566667777666655555556789999999998644332  22346789999999976544  5567777777


Q ss_pred             CCCCCcEEEEEeeCC-HHHHHHH---------------------------------------------------------
Q 010709          297 LPDKHQTLLFSATMP-VEIEALA---------------------------------------------------------  318 (503)
Q Consensus       297 ~~~~~q~i~~SAT~~-~~~~~~~---------------------------------------------------------  318 (503)
                      ++...+ +++|+||- +++.++.                                                         
T Consensus      1126 L~a~hR-LILSGTPIQNnvleLWSLFdFLMPGfLGtEKqFqsrf~kpI~asRd~K~Sske~EaG~lAleaLHKqVLPF~L 1204 (1549)
T KOG0392|consen 1126 LRANHR-LILSGTPIQNNVLELWSLFDFLMPGFLGTEKQFQSRFGKPILASRDPKSSSKEQEAGVLALEALHKQVLPFLL 1204 (1549)
T ss_pred             Hhhcce-EEeeCCCcccCHHHHHHHHHHhcccccCcHHHHHHHhcchhhhhcCcccchhHHHhhHHHHHHHHHHHHHHHH
Confidence            776664 66788871 1111110                                                         


Q ss_pred             ----------------HHhc---------------CC---CeEEEeCCCCCCCC----ceEE------------EEEE--
Q 010709          319 ----------------QEYL---------------TD---PVQVKVGKVSSPTA----NVIQ------------ILEK--  346 (503)
Q Consensus       319 ----------------~~~~---------------~~---~~~~~~~~~~~~~~----~~~~------------~~~~--  346 (503)
                                      +.|+               ..   -+.-..+.......    .+.|            ..+.  
T Consensus      1205 RRlKedVL~DLPpKIIQDyyCeLs~lQ~kLY~df~~~~k~~~~~~~d~~~~S~gt~~~HvFqaLqYlrKLcnHpaLvlt~ 1284 (1549)
T KOG0392|consen 1205 RRLKEDVLKDLPPKIIQDYYCELSPLQKKLYRDFVKKAKQCVSSQIDGGEESLGTDKTHVFQALQYLRKLCNHPALVLTP 1284 (1549)
T ss_pred             HHHHHHHHhhCChhhhhheeeccCHHHHHHHHHHHHHhccccccccccchhccCcchHHHHHHHHHHHHhcCCcceeeCC
Confidence                            0000               00   00000000000000    0000            0000  


Q ss_pred             ---------------------cChhhHHHHHHHHHHHHHHhhhc-------cCCCCCcEEEEEcchhhHHHHHHHHHHC-
Q 010709          347 ---------------------VSENEKVDRLLALLVEEAFLAEK-------SCHPFPLTIVFVERKTRCDEVSEALVAE-  397 (503)
Q Consensus       347 ---------------------~~~~~k~~~l~~~l~~~~~~~~~-------~~~~~~~~lIF~~~~~~~~~l~~~L~~~-  397 (503)
                                           +...-|+..|.+++.+=......       .....+++||||+-+...+.+.+-|.+. 
T Consensus      1285 ~hp~la~i~~~l~~~~~~LHdi~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~ 1364 (1549)
T KOG0392|consen 1285 VHPDLAAIVSHLAHFNSSLHDIQHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKY 1364 (1549)
T ss_pred             CcchHHHHHHHHHHhhhhHHHhhhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhh
Confidence                                 01122333333333221111000       0013468999999999999999888765 


Q ss_pred             --CCeEEEEcCCCCHHHHHHHHHHHhcC-CCcEE-EEccccccCCCCCCCCEEEEccCCCChhHHHHhhCc
Q 010709          398 --GLHAVALHGGRNQSDRESALRDFRNG-STNIL-VATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCT  464 (503)
Q Consensus       398 --~~~v~~lh~~~~~~~r~~~~~~f~~g-~~~vL-vaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR  464 (503)
                        .+....+.|..++.+|+++.++|.++ .++|| ++|.+++-|+|+.++++||+++--+++..=.|-+-|
T Consensus      1365 mpsVtymRLDGSVpp~~R~kiV~~FN~DptIDvLlLTThVGGLGLNLTGADTVVFvEHDWNPMrDLQAMDR 1435 (1549)
T KOG0392|consen 1365 MPSVTYMRLDGSVPPGDRQKIVERFNEDPTIDVLLLTTHVGGLGLNLTGADTVVFVEHDWNPMRDLQAMDR 1435 (1549)
T ss_pred             cCceeEEEecCCCCcHHHHHHHHHhcCCCceeEEEEeeeccccccccCCCceEEEEecCCCchhhHHHHHH
Confidence              34456899999999999999999998 78876 566899999999999999999999887444443333

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

Probab=99.75  E-value=4.2e-16  Score=169.95  Aligned_cols=81  Identities=21%  Similarity=0.221  Sum_probs=63.7

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHCCC--eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCC--CCEEEE
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAEGL--HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMG--VAHVVN  448 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~~~--~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~--v~~VI~  448 (503)
                      ..+++|||+++.+..+.+++.|.....  ....+.-++....|.++++.|++++..||++|..+.+|||+|+  +++||.
T Consensus       751 ~~g~~LVLFtSy~~l~~v~~~l~~~~~~~~~~ll~Qg~~~~~r~~l~~~F~~~~~~iLlG~~sFwEGVD~pg~~l~~viI  830 (928)
T PRK08074        751 TKGRMLVLFTSYEMLKKTYYNLKNEEELEGYVLLAQGVSSGSRARLTKQFQQFDKAILLGTSSFWEGIDIPGDELSCLVI  830 (928)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHhhcccccCceEEecCCCCCCHHHHHHHHHhcCCeEEEecCcccCccccCCCceEEEEE
Confidence            345799999999999999999975422  1222333444446788999999999999999999999999997  588999


Q ss_pred             ccCCC
Q 010709          449 LDLPK  453 (503)
Q Consensus       449 ~~~p~  453 (503)
                      ..+|-
T Consensus       831 ~kLPF  835 (928)
T PRK08074        831 VRLPF  835 (928)
T ss_pred             ecCCC
Confidence            88774

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.75  E-value=7.4e-17  Score=137.01  Aligned_cols=144  Identities=44%  Similarity=0.630  Sum_probs=110.2

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ  238 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (503)
                      +++++.++||+|||+.++..+......      ...++++|++|++.++.|+.+.+..+...  ...+..+.+.......
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~------~~~~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~   72 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS------LKGGQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQ   72 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc------ccCCCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhHH
Confidence            468999999999999886666655433      12578999999999999999999888754  4667777777666655


Q ss_pred             HHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       239 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ........+|+++|++.+.+.+.........+++|||||+|.+....................+++++||||
T Consensus        73 ~~~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046          73 EKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             HHHhcCCCCEEEECcHHHHHHHHcCCcchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            555567899999999999888877655667899999999998876654443223344445677899999996

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

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

Probab=99.75  E-value=5e-18  Score=128.19  Aligned_cols=77  Identities=25%  Similarity=0.431  Sum_probs=74.6

Q ss_pred             HHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          392 EALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       392 ~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++|+..++.+..+||++++.+|..+++.|++|+..|||||+++++|+|+|++++||++++|++...|.|++||+||.
T Consensus         1 ~~L~~~~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gid~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~   77 (78)
T PF00271_consen    1 KFLEKKGIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATDILGEGIDLPDASHVIFYDPPWSPEEYIQRIGRAGRI   77 (78)
T ss_dssp             HHHHHTTSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESCGGTTSSTSTTESEEEESSSESSHHHHHHHHTTSSTT
T ss_pred             CChHHCCCcEEEEECCCCHHHHHHHHHHhhccCceEEEeeccccccccccccccccccccCCCHHHHHHHhhcCCCC
Confidence            46888999999999999999999999999999999999999999999999999999999999999999999999994

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=99.74  E-value=5.5e-16  Score=159.39  Aligned_cols=300  Identities=17%  Similarity=0.179  Sum_probs=201.3

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|++.|.-.--.+..|  -|..+.||-|||+++.+|+....+.        |..|-|++...-||..=++.+..+...+ 
T Consensus        78 r~ydVQliGglvLh~G--~IAEMkTGEGKTLvAtLpayLnAL~--------GkgVhVVTvNdYLA~RDae~mg~vy~fL-  146 (925)
T PRK12903         78 RPYDVQIIGGIILDLG--SVAEMKTGEGKTITSIAPVYLNALT--------GKGVIVSTVNEYLAERDAEEMGKVFNFL-  146 (925)
T ss_pred             CcCchHHHHHHHHhcC--CeeeecCCCCccHHHHHHHHHHHhc--------CCceEEEecchhhhhhhHHHHHHHHHHh-
Confidence            7899998888777666  4789999999999999988765554        5668888999999998888888777666 


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hCC---------
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DMG---------  285 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~~---------  285 (503)
                      ++.++++..+....+..  ....++|+++|..-| .+.+..+      ....+.+.+.||||+|.++ +..         
T Consensus       147 GLsvG~i~~~~~~~~rr--~aY~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSILIDEArTPLIISg~  224 (925)
T PRK12903        147 GLSVGINKANMDPNLKR--EAYACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSILIDEAKTPLIISGG  224 (925)
T ss_pred             CCceeeeCCCCChHHHH--HhccCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchheeecccCCcccccCC
Confidence            69999888776655433  334699999998876 3333321      1234678899999999622 100         


Q ss_pred             ------CHHHHHHHHHhCCC-------------------------------------------------------C----
Q 010709          286 ------FEPQIREVMQNLPD-------------------------------------------------------K----  300 (503)
Q Consensus       286 ------~~~~~~~il~~~~~-------------------------------------------------------~----  300 (503)
                            +......++..+..                                                       +    
T Consensus       225 ~~~~~~~Y~~~~~~v~~L~~~dy~iDek~k~v~LTe~G~~~~E~~l~i~nLy~~~n~~l~h~i~~AL~A~~lf~rd~dYi  304 (925)
T PRK12903        225 QSNDSNLYLAADQFVRTLKEDDYKIDEETKAISLTEKGIKKANKFFKLKNLYDIENSELVHRIQNALRAHKVMKEDVEYI  304 (925)
T ss_pred             CccchHHHHHHHHHHHhccccceEEecccceEEECHhHHHHHHHHcCCCcccChhhHHHHHHHHHHHHHHHHHhcCCceE
Confidence                  00111111111100                                                       0    


Q ss_pred             ---------------------------------------------------------CcEEEEEeeCCHHHHHHHHHhcC
Q 010709          301 ---------------------------------------------------------HQTLLFSATMPVEIEALAQEYLT  323 (503)
Q Consensus       301 ---------------------------------------------------------~q~i~~SAT~~~~~~~~~~~~~~  323 (503)
                                                                               .++-+||+|...+-.++.+-|--
T Consensus       305 V~dg~V~IVDefTGR~m~gRrwsdGLHQaIEAKEgv~I~~e~~TlAsIT~QnfFr~Y~kLsGMTGTA~te~~Ef~~iY~l  384 (925)
T PRK12903        305 VRDGKIELVDQFTGRIMEGRSYSEGLQQAIQAKEMVEIEPETKTLATITYQNFFRLFKKLSGMTGTAKTEEQEFIDIYNM  384 (925)
T ss_pred             EECCEEEEEECCCCCCCCCCccchHHHHHHHHHcCCCCCCCceeeeeehHHHHHHhcchhhccCCCCHHHHHHHHHHhCC
Confidence                                                                     14556777765554444443322


Q ss_pred             CCeEEEeCCCCCCCCc-eEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEE
Q 010709          324 DPVQVKVGKVSSPTAN-VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV  402 (503)
Q Consensus       324 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~  402 (503)
                      + +.. +. ...+... -..-........|...++..+.....       .+.|+||.|.+.+..+.+++.|.+.|+...
T Consensus       385 ~-Vv~-IP-TnkP~~R~D~~d~iy~t~~~K~~Aii~ei~~~~~-------~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~  454 (925)
T PRK12903        385 R-VNV-VP-TNKPVIRKDEPDSIFGTKHAKWKAVVKEVKRVHK-------KGQPILIGTAQVEDSETLHELLLEANIPHT  454 (925)
T ss_pred             C-EEE-CC-CCCCeeeeeCCCcEEEcHHHHHHHHHHHHHHHHh-------cCCCEEEEeCcHHHHHHHHHHHHHCCCCce
Confidence            2 222 11 1111111 11113344566777777777765542       344799999999999999999999999988


Q ss_pred             EEcCCCCHHHHHHHHHHHhcCC-CcEEEEccccccCCCCCCCC--------EEEEccCCCChhHHHHhhCcceee
Q 010709          403 ALHGGRNQSDRESALRDFRNGS-TNILVATDVASRGLDVMGVA--------HVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       403 ~lh~~~~~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip~v~--------~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .++......+-..+ .  +.|. ..|.|||++++||-||.--.        |||....|.|..-=.|-.||+||.
T Consensus       455 vLNAk~~e~EA~II-a--~AG~~GaVTIATNMAGRGTDI~Lg~~V~~~GGLhVIgTerheSrRIDnQLrGRaGRQ  526 (925)
T PRK12903        455 VLNAKQNAREAEII-A--KAGQKGAITIATNMAGRGTDIKLSKEVLELGGLYVLGTDKAESRRIDNQLRGRSGRQ  526 (925)
T ss_pred             eecccchhhHHHHH-H--hCCCCCeEEEecccccCCcCccCchhHHHcCCcEEEecccCchHHHHHHHhcccccC
Confidence            88886544333322 2  4564 67999999999999998322        899999999998888999999995

>COG4889 Predicted helicase [General function prediction only]

Probab=99.73  E-value=9.1e-18  Score=168.70  Aligned_cols=333  Identities=19%  Similarity=0.225  Sum_probs=196.5

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC----CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG----RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLA  197 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~----~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~  197 (503)
                      .|+.+.. .++..++.-..-.+|+|+|+.|+.+..++    ...=+.+++|+|||+.. +-+...+..         .++
T Consensus       141 DW~~f~p-~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTs-LkisEala~---------~~i  209 (1518)
T COG4889         141 DWDIFDP-TELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTS-LKISEALAA---------ARI  209 (1518)
T ss_pred             ChhhcCc-cccccccccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchH-HHHHHHHhh---------hhe
Confidence            4555432 45556676777889999999999998854    23556678999999876 444444333         569


Q ss_pred             EEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH--------------------HHH-----HHhhCCCcEEEEC
Q 010709          198 LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA--------------------EQR-----SELRGGVSIVVAT  252 (503)
Q Consensus       198 lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~-----~~~~~~~~Ilv~T  252 (503)
                      |+++|+..|..|..+.+..-.. + +++...+..+....                    ...     +....+--|+++|
T Consensus       210 L~LvPSIsLLsQTlrew~~~~~-l-~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsT  287 (1518)
T COG4889         210 LFLVPSISLLSQTLREWTAQKE-L-DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFST  287 (1518)
T ss_pred             EeecchHHHHHHHHHHHhhccC-c-cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEc
Confidence            9999999999998777765432 1 34444444332211                    100     1112345699999


Q ss_pred             cHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC-----CCCcEEEEEeeCC---HHHHHHH------
Q 010709          253 PGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP-----DKHQTLLFSATMP---VEIEALA------  318 (503)
Q Consensus       253 p~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~-----~~~q~i~~SAT~~---~~~~~~~------  318 (503)
                      ++.+...-.....-+..+++||+||||+-.+-.....-..-+.++.     +..+.+.|+|||.   +..+..+      
T Consensus       288 YQSl~~i~eAQe~G~~~fDliicDEAHRTtGa~~a~dd~saFt~vHs~~niKa~kRlYmTATPkiy~eS~K~kAkd~s~~  367 (1518)
T COG4889         288 YQSLPRIKEAQEAGLDEFDLIICDEAHRTTGATLAGDDKSAFTRVHSDQNIKAAKRLYMTATPKIYSESSKAKAKDHSAE  367 (1518)
T ss_pred             ccchHHHHHHHHcCCCCccEEEecchhccccceecccCcccceeecCcchhHHHHhhhcccCchhhchhhhhhhhhccce
Confidence            9999766665566788999999999998543211110000000000     1234578899982   1111111      


Q ss_pred             ------------------------HHhcCCCeEEEeCCCCCCCCceEEE-EEEcChh------hHHHHHHHHHHHHHHhh
Q 010709          319 ------------------------QEYLTDPVQVKVGKVSSPTANVIQI-LEKVSEN------EKVDRLLALLVEEAFLA  367 (503)
Q Consensus       319 ------------------------~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~------~k~~~l~~~l~~~~~~~  367 (503)
                                              +..+.+...+...-.........+. .......      .|+--.+.-+..+....
T Consensus       368 l~SMDDe~~fGeef~rl~FgeAv~rdlLTDYKVmvlaVd~~~i~~~~~~~~~~~~~~L~~dd~~kIvG~wnGlakr~g~~  447 (1518)
T COG4889         368 LSSMDDELTFGEEFHRLGFGEAVERDLLTDYKVMVLAVDKEVIAGVLQSVLSGPSKGLALDDVSKIVGCWNGLAKRNGED  447 (1518)
T ss_pred             eeccchhhhhchhhhcccHHHHHHhhhhccceEEEEEechhhhhhhhhhhccCcccccchhhhhhhhhhhhhhhhhcccc
Confidence                                    1222222222111111111111111 1111111      12222222222221100


Q ss_pred             h------ccCCCCCcEEEEEcchhhHHHHHHHHHH-------------CCC--eEEEEcCCCCHHHHHHHHH---HHhcC
Q 010709          368 E------KSCHPFPLTIVFVERKTRCDEVSEALVA-------------EGL--HAVALHGGRNQSDRESALR---DFRNG  423 (503)
Q Consensus       368 ~------~~~~~~~~~lIF~~~~~~~~~l~~~L~~-------------~~~--~v~~lh~~~~~~~r~~~~~---~f~~g  423 (503)
                      .      ....|-.+.|-||.+.++...+++.|..             .++  .+-...|.|...+|...+.   .|...
T Consensus       448 n~~~~~~~d~ap~~RAIaF~k~I~tSK~i~~sFe~Vve~Y~~Elk~d~~nL~iSi~HvDGtmNal~R~~l~~l~~~~~~n  527 (1518)
T COG4889         448 NDLKNIKADTAPMQRAIAFAKDIKTSKQIAESFETVVEAYDEELKKDFKNLKISIDHVDGTMNALERLDLLELKNTFEPN  527 (1518)
T ss_pred             ccccCCcCCchHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcCCCceEEeecccccccHHHHHHHHhccCCCCcc
Confidence            0      0111223478899999888887776642             233  4455778999888855544   34567


Q ss_pred             CCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          424 STNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       424 ~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      +++||--...+++|+|+|.++-||++++-.++.+.+|-+||+=|
T Consensus       528 eckIlSNaRcLSEGVDVPaLDsViFf~pr~smVDIVQaVGRVMR  571 (1518)
T COG4889         528 ECKILSNARCLSEGVDVPALDSVIFFDPRSSMVDIVQAVGRVMR  571 (1518)
T ss_pred             hheeeccchhhhcCCCccccceEEEecCchhHHHHHHHHHHHHH
Confidence            88999888999999999999999999999999999999999766

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

Probab=99.72  E-value=8.8e-15  Score=149.94  Aligned_cols=78  Identities=17%  Similarity=0.207  Sum_probs=60.8

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc----CCCcEEEEccccccCCCC--------
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRN----GSTNILVATDVASRGLDV--------  440 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~----g~~~vLvaT~~~~~Gldi--------  440 (503)
                      ..|.++|.+.+...++.+++.|...--..+.+.|..+  .+..++++|++    |...||++|+.+.+|||+        
T Consensus       469 ~~G~~lvLfTS~~~~~~~~~~l~~~l~~~~l~qg~~~--~~~~l~~~f~~~~~~~~~~vL~gt~sfweGvDv~~~~~~p~  546 (636)
T TIGR03117       469 AQGGTLVLTTAFSHISAIGQLVELGIPAEIVIQSEKN--RLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTHKPVSPD  546 (636)
T ss_pred             cCCCEEEEechHHHHHHHHHHHHhhcCCCEEEeCCCc--cHHHHHHHHHHhhcCCCCcEEEeCCccccccccCCccCCCC
Confidence            3457999999999999999999764223345566543  34568888887    478999999999999999        


Q ss_pred             CC--CCEEEEccCC
Q 010709          441 MG--VAHVVNLDLP  452 (503)
Q Consensus       441 p~--v~~VI~~~~p  452 (503)
                      |+  +++||...+|
T Consensus       547 ~G~~Ls~ViI~kLP  560 (636)
T TIGR03117       547 KDNLLTDLIITCAP  560 (636)
T ss_pred             CCCcccEEEEEeCC
Confidence            33  8899988777

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.

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

Probab=99.71  E-value=2.4e-16  Score=132.16  Aligned_cols=112  Identities=37%  Similarity=0.512  Sum_probs=101.7

Q ss_pred             hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEE
Q 010709          351 EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVA  430 (503)
Q Consensus       351 ~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLva  430 (503)
                      .|...+...+.+..       ...+++||||++...++.+++.|.+.+..+..+||+++..+|..+++.|.+|...+|++
T Consensus        12 ~k~~~i~~~i~~~~-------~~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~   84 (131)
T cd00079          12 EKLEALLELLKEHL-------KKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVA   84 (131)
T ss_pred             HHHHHHHHHHHhcc-------cCCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEE
Confidence            66767766665532       13567999999999999999999998999999999999999999999999999999999


Q ss_pred             ccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          431 TDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       431 T~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      |.++++|+|+|++++||++++|++...+.|++||++|.-
T Consensus        85 t~~~~~G~d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~  123 (131)
T cd00079          85 TDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAG  123 (131)
T ss_pred             cChhhcCcChhhCCEEEEeCCCCCHHHheecccccccCC
Confidence            999999999999999999999999999999999999975

>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=99.70  E-value=1.4e-16  Score=142.12  Aligned_cols=153  Identities=20%  Similarity=0.234  Sum_probs=101.4

Q ss_pred             CCcHHHHHHHHHHhc-------CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVALS-------GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK  215 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~-------~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~  215 (503)
                      .|+++|.+++..+..       .+++++.+|||+|||.+++..+... ..          ++++++|+..|+.|+.+.+.
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l-~~----------~~l~~~p~~~l~~Q~~~~~~   71 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILEL-AR----------KVLIVAPNISLLEQWYDEFD   71 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHH-HC----------EEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcc-cc----------ceeEecCHHHHHHHHHHHHH
Confidence            578999999999883       5789999999999999875433333 22          59999999999999999997


Q ss_pred             HHhccCCCceE----------EEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC-----------CCCCCccEEE
Q 010709          216 ALSRSLDSFKT----------AIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN-----------TSLSRVSFVI  274 (503)
Q Consensus       216 ~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~-----------~~l~~~~~vV  274 (503)
                      .+.........          ....................+++++|.+.+........           .....+++||
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~vI  151 (184)
T PF04851_consen   72 DFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLVI  151 (184)
T ss_dssp             HHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEEE
T ss_pred             HhhhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEEE
Confidence            76643210100          00111111112223334568899999999987765321           2345678999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          275 LDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      +||||++....   .+..++.  .+...+|+|||||.
T Consensus       152 ~DEaH~~~~~~---~~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  152 IDEAHHYPSDS---SYREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             EETGGCTHHHH---HHHHHHH--SSCCEEEEEESS-S
T ss_pred             EehhhhcCCHH---HHHHHHc--CCCCeEEEEEeCcc
Confidence            99999876431   1566666  44566999999985

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 ....

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.69  E-value=9.3e-15  Score=151.36  Aligned_cols=274  Identities=18%  Similarity=0.149  Sum_probs=178.3

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|++.|.-+.-.+.  +.-|..+.||.|||+++.+|+....+.        |..|-|++++..||.+-++.+..+...+ 
T Consensus        76 r~ydvQlig~l~L~--~G~IaEm~TGEGKTL~a~l~ayl~aL~--------G~~VhVvT~NdyLA~RD~e~m~pvy~~L-  144 (870)
T CHL00122         76 RHFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNALT--------GKGVHIVTVNDYLAKRDQEWMGQIYRFL-  144 (870)
T ss_pred             CCCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHhc--------CCceEEEeCCHHHHHHHHHHHHHHHHHc-
Confidence            58888877765554  457889999999999999998755443        5779999999999999999999988777 


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHH-HHHHcC------CCCCCCccEEEecchhHHh-hCC---------
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFL-DHLQQG------NTSLSRVSFVILDEADRML-DMG---------  285 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~-~~l~~~------~~~l~~~~~vViDEaH~l~-~~~---------  285 (503)
                      ++.++++.++....+..  ....++|+++|..-|- +.+..+      ......+.++||||+|.++ +..         
T Consensus       145 GLsvg~i~~~~~~~err--~aY~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiLIDeArTPLiISg~  222 (870)
T CHL00122        145 GLTVGLIQEGMSSEERK--KNYLKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSILIDEARTPLIISGQ  222 (870)
T ss_pred             CCceeeeCCCCChHHHH--HhcCCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhheeccCCCceeccCC
Confidence            59999988877765533  3445899999987652 222221      1234668899999999622 100         


Q ss_pred             ------CHHHHHHHHHhCC-------------------------------------------------------C-----
Q 010709          286 ------FEPQIREVMQNLP-------------------------------------------------------D-----  299 (503)
Q Consensus       286 ------~~~~~~~il~~~~-------------------------------------------------------~-----  299 (503)
                            ......++.+.+.                                                       .     
T Consensus       223 ~~~~~~~y~~~~~~v~~L~~~~dy~vdek~k~v~LTe~G~~~~e~~l~i~~ly~~~~~~~~~i~~AL~A~~lf~~d~dYi  302 (870)
T CHL00122        223 SKTNIDKYIVADELAKYLEKNVHYEVDEKNKNVILTEQGILFIEKILKIEDLYSANDPWIPYILNALKAKELFFKNVHYI  302 (870)
T ss_pred             CccchHHHHHHHHHHHhcCcCCCeEEEcCCCceEecHHHHHHHHHHcCCccccccccHHHHHHHHHHHHHHHHhcCCcEE
Confidence                  0000000000000                                                       0     


Q ss_pred             --------------------------------------------------------CCcEEEEEeeCCHHHHHHHHHhcC
Q 010709          300 --------------------------------------------------------KHQTLLFSATMPVEIEALAQEYLT  323 (503)
Q Consensus       300 --------------------------------------------------------~~q~i~~SAT~~~~~~~~~~~~~~  323 (503)
                                                                              -.++.+||+|....-..+.+-| +
T Consensus       303 V~dgeV~iVDe~TGR~m~grrws~GLHQaiEaKEgv~It~e~~tlAsIT~QnfFr~Y~kL~GMTGTa~te~~Ef~~iY-~  381 (870)
T CHL00122        303 VRNNEIIIVDEFTGRIMPGRRWSDGLHQAIEAKENLPIRQETETLASITYQNFFLLYPKLSGMTGTAKTEELEFEKIY-N  381 (870)
T ss_pred             EECCEEEEEECCCCcCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHHhCchhcccCCCCHHHHHHHHHHh-C
Confidence                                                                    0156778888765544444443 3


Q ss_pred             CCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEE
Q 010709          324 DPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVA  403 (503)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~  403 (503)
                      -.+.+.....+.... -....+......|...+...+.....       .+.|+||-+.+.+..+.+++.|.+.|+....
T Consensus       382 l~vv~IPtnkp~~R~-d~~d~v~~t~~~K~~AI~~ei~~~~~-------~grPVLIgT~SIe~SE~ls~~L~~~gi~h~v  453 (870)
T CHL00122        382 LEVVCIPTHRPMLRK-DLPDLIYKDELSKWRAIADECLQMHQ-------TGRPILIGTTTIEKSELLSQLLKEYRLPHQL  453 (870)
T ss_pred             CCEEECCCCCCccce-eCCCeEEeCHHHHHHHHHHHHHHHHh-------cCCCEEEeeCCHHHHHHHHHHHHHcCCccce
Confidence            333221111111111 11223344556677777776655432       3447999999999999999999999999988


Q ss_pred             EcCCCC--HHHHHHHHHHHhcCC-CcEEEEccccccCCCCC
Q 010709          404 LHGGRN--QSDRESALRDFRNGS-TNILVATDVASRGLDVM  441 (503)
Q Consensus       404 lh~~~~--~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip  441 (503)
                      +++.-.  ..|- +++.+  .|. ..|-|||++++||.||.
T Consensus       454 LNAk~~~~~~EA-~IIA~--AG~~G~VTIATNMAGRGTDI~  491 (870)
T CHL00122        454 LNAKPENVRRES-EIVAQ--AGRKGSITIATNMAGRGTDII  491 (870)
T ss_pred             eeCCCccchhHH-HHHHh--cCCCCcEEEeccccCCCcCee
Confidence            888632  3333 33332  454 56999999999999976

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

Probab=99.68  E-value=4.8e-16  Score=149.83  Aligned_cols=255  Identities=17%  Similarity=0.142  Sum_probs=170.5

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ  238 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (503)
                      +-++-+|||.||||.-    +|+++..        .+..++.-|.|-||..+++++++.+     +.+.+++|.......
T Consensus       192 kIi~H~GPTNSGKTy~----ALqrl~~--------aksGvycGPLrLLA~EV~~r~na~g-----ipCdL~TGeE~~~~~  254 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYR----ALQRLKS--------AKSGVYCGPLRLLAHEVYDRLNALG-----IPCDLLTGEERRFVL  254 (700)
T ss_pred             eEEEEeCCCCCchhHH----HHHHHhh--------hccceecchHHHHHHHHHHHhhhcC-----CCccccccceeeecC
Confidence            4478899999999954    4455443        3457999999999999999998875     677777776543221


Q ss_pred             HHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHH
Q 010709          239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEAL  317 (503)
Q Consensus       239 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~  317 (503)
                      ..  ...+..+-||-++..        .-..+++.||||.+.|.+...+-.|.+.+--+ .....+-+     .+.+-.+
T Consensus       255 ~~--~~~a~hvScTVEM~s--------v~~~yeVAViDEIQmm~Dp~RGwAWTrALLGl~AdEiHLCG-----epsvldl  319 (700)
T KOG0953|consen  255 DN--GNPAQHVSCTVEMVS--------VNTPYEVAVIDEIQMMRDPSRGWAWTRALLGLAADEIHLCG-----EPSVLDL  319 (700)
T ss_pred             CC--CCcccceEEEEEEee--------cCCceEEEEehhHHhhcCcccchHHHHHHHhhhhhhhhccC-----CchHHHH
Confidence            11  123566777766652        12458899999999988877666666554332 22222211     1122233


Q ss_pred             HHH---hcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHH
Q 010709          318 AQE---YLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL  394 (503)
Q Consensus       318 ~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L  394 (503)
                      ++.   ..++.+.+.....-.+             ..-...+..-+.+         ..+|-+| .|-+++.+..+...+
T Consensus       320 V~~i~k~TGd~vev~~YeRl~p-------------L~v~~~~~~sl~n---------lk~GDCv-V~FSkk~I~~~k~kI  376 (700)
T KOG0953|consen  320 VRKILKMTGDDVEVREYERLSP-------------LVVEETALGSLSN---------LKPGDCV-VAFSKKDIFTVKKKI  376 (700)
T ss_pred             HHHHHhhcCCeeEEEeecccCc-------------ceehhhhhhhhcc---------CCCCCeE-EEeehhhHHHHHHHH
Confidence            333   3344444433221111             0000111111111         2334465 455788899999999


Q ss_pred             HHCCCe-EEEEcCCCCHHHHHHHHHHHhc--CCCcEEEEccccccCCCCCCCCEEEEccCCC---------ChhHHHHhh
Q 010709          395 VAEGLH-AVALHGGRNQSDRESALRDFRN--GSTNILVATDVASRGLDVMGVAHVVNLDLPK---------VLLAASESL  462 (503)
Q Consensus       395 ~~~~~~-v~~lh~~~~~~~r~~~~~~f~~--g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~---------s~~~~~Qr~  462 (503)
                      .+.|.. +..+||++|++.|.+--..|.+  ++.+||||||+.++|+|+. ++.||++++-+         ...+..|-.
T Consensus       377 E~~g~~k~aVIYGsLPPeTr~aQA~~FNd~~~e~dvlVAsDAIGMGLNL~-IrRiiF~sl~Kysg~e~~~it~sqikQIA  455 (700)
T KOG0953|consen  377 EKAGNHKCAVIYGSLPPETRLAQAALFNDPSNECDVLVASDAIGMGLNLN-IRRIIFYSLIKYSGRETEDITVSQIKQIA  455 (700)
T ss_pred             HHhcCcceEEEecCCCCchhHHHHHHhCCCCCccceEEeecccccccccc-eeEEEEeecccCCcccceeccHHHHHHHh
Confidence            988765 9999999999999999999987  8999999999999999996 99999998752         457889999


Q ss_pred             Ccceeee
Q 010709          463 CTTSFNI  469 (503)
Q Consensus       463 GR~gR~~  469 (503)
                      |||||.-
T Consensus       456 GRAGRf~  462 (700)
T KOG0953|consen  456 GRAGRFG  462 (700)
T ss_pred             hcccccc
Confidence            9999963

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

Probab=99.65  E-value=4.6e-15  Score=154.72  Aligned_cols=298  Identities=18%  Similarity=0.196  Sum_probs=197.3

Q ss_pred             CcHHHHHHHHHHhcCC-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          144 PTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      ..++|.+.++.+.+.+ ++++++|+|+|||.|+.++++.         .....++++++|..+.+..+++.+.+-+....
T Consensus      1144 ~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~---------~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~~~ 1214 (1674)
T KOG0951|consen 1144 FNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR---------PDTIGRAVYIAPLEEIADEQYRDWEKKFSKLL 1214 (1674)
T ss_pred             cCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC---------CccceEEEEecchHHHHHHHHHHHHHhhcccc
Confidence            3889999999998665 5999999999999999887765         13457899999999999988888776555555


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCH------HHHHHHHHh
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFE------PQIREVMQN  296 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~------~~~~~il~~  296 (503)
                      +..+..+.|.......   +....+|+|+||+++-.. +    ..+.+++.|.||+|.+.+. .+      -.++.+-..
T Consensus      1215 G~~~~~l~ge~s~~lk---l~~~~~vii~tpe~~d~l-q----~iQ~v~l~i~d~lh~igg~-~g~v~evi~S~r~ia~q 1285 (1674)
T KOG0951|consen 1215 GLRIVKLTGETSLDLK---LLQKGQVIISTPEQWDLL-Q----SIQQVDLFIVDELHLIGGV-YGAVYEVICSMRYIASQ 1285 (1674)
T ss_pred             CceEEecCCccccchH---HhhhcceEEechhHHHHH-h----hhhhcceEeeehhhhhccc-CCceEEEEeeHHHHHHH
Confidence            6777777776655432   334579999999998544 2    5678899999999976633 12      125566666


Q ss_pred             CCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCc--eEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCC
Q 010709          297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTAN--VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPF  374 (503)
Q Consensus       297 ~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~  374 (503)
                      +-++.+++++|..+.+. .+++  .......+.+.....+.+.  -.+.+........+....+.......+.   ....
T Consensus      1286 ~~k~ir~v~ls~~lana-~d~i--g~s~~~v~Nf~p~~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~---a~~~ 1359 (1674)
T KOG0951|consen 1286 LEKKIRVVALSSSLANA-RDLI--GASSSGVFNFSPSVRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRH---AGNR 1359 (1674)
T ss_pred             HHhheeEEEeehhhccc-hhhc--cccccceeecCcccCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHH---hcCC
Confidence            77788999999888532 2221  1111112222221222211  1222222333333333322221111111   1244


Q ss_pred             CcEEEEEcchhhHHHHHHHHHH----------------------CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          375 PLTIVFVERKTRCDEVSEALVA----------------------EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~----------------------~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      ++.+||+++++.|..++..|..                      ..+....-|.+++..+++.+-..|..|.+.|+|...
T Consensus      1360 k~~~vf~p~rk~~~~~a~~~~~~s~~~~~~~l~~~~e~~~~~l~e~l~~gvg~e~~s~~d~~iv~~l~e~g~i~v~v~s~ 1439 (1674)
T KOG0951|consen 1360 KPAIVFLPTRKHARLVAVDLVTFSHADEPDYLLSELEECDETLRESLKHGVGHEGLSSNDQEIVQQLFEAGAIQVCVMSR 1439 (1674)
T ss_pred             CCeEEEeccchhhhhhhhccchhhccCcHHHHHHHHhcchHhhhhcccccccccccCcchHHHHHHHHhcCcEEEEEEEc
Confidence            5799999999999877665522                      112233339999999999999999999999998876


Q ss_pred             ccccCCCCCCCCEEEEcc-----------CCCChhHHHHhhCccee
Q 010709          433 VASRGLDVMGVAHVVNLD-----------LPKVLLAASESLCTTSF  467 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~-----------~p~s~~~~~Qr~GR~gR  467 (503)
                      - ..|+-.. .+.||-+|           .+-.++...|+.|+|.|
T Consensus      1440 ~-~~~~~~~-~~lVvvmgt~~ydg~e~~~~~y~i~~ll~m~G~a~~ 1483 (1674)
T KOG0951|consen 1440 D-CYGTKLK-AHLVVVMGTQYYDGKEHSYEDYPIAELLQMVGLASG 1483 (1674)
T ss_pred             c-ccccccc-ceEEEEecceeecccccccccCchhHHHHHhhhhcC
Confidence            6 7787765 34555433           24567899999999988

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

Probab=99.64  E-value=1.4e-15  Score=155.78  Aligned_cols=307  Identities=17%  Similarity=0.172  Sum_probs=190.7

Q ss_pred             CCCcHHHHHHHHHHh---cC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVAL---SG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~---~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..+.++|...+.++.   +| -+.|+..+||.|||.+- +.++.+++....   ..|| .||+||+..|.+ |..+|..|
T Consensus       393 G~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQt-IsLitYLmE~K~---~~GP-~LvivPlstL~N-W~~Ef~kW  466 (1157)
T KOG0386|consen  393 GELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQT-ISLITYLMEHKQ---MQGP-FLIIVPLSTLVN-WSSEFPKW  466 (1157)
T ss_pred             CCCchhhhhhhHHHhhccCCCcccccchhcccchHHHH-HHHHHHHHHHcc---cCCC-eEEeccccccCC-chhhcccc
Confidence            378889999999876   33 36999999999999875 667777777532   3345 599999999988 88888888


Q ss_pred             hccCCCceEEEEECCccHHH--HHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          218 SRSLDSFKTAIVVGGTNIAE--QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      ...   +....+.|....+.  .......+.+|+++|++.+.+  .+..+.--++.++||||.|+|.+.  ...+...+.
T Consensus       467 aPS---v~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk~lLsKI~W~yMIIDEGHRmKNa--~~KLt~~L~  539 (1157)
T KOG0386|consen  467 APS---VQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DKALLSKISWKYMIIDEGHRMKNA--ICKLTDTLN  539 (1157)
T ss_pred             ccc---eeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CHHHHhccCCcceeecccccccch--hhHHHHHhh
Confidence            743   44444444332221  112223679999999887754  111122235779999999997653  333333333


Q ss_pred             hCCCCCcEEEEEeeCCHH----HHHH-----------------------------------------------H------
Q 010709          296 NLPDKHQTLLFSATMPVE----IEAL-----------------------------------------------A------  318 (503)
Q Consensus       296 ~~~~~~q~i~~SAT~~~~----~~~~-----------------------------------------------~------  318 (503)
                      -.-.....+++|+|+-.+    +-.+                                               +      
T Consensus       540 t~y~~q~RLLLTGTPLQN~LpELWaLLNFlLP~IFnS~~~FeqWFN~PFantGek~eLteEEtlLIIrRLHkVLRPFlLR  619 (1157)
T KOG0386|consen  540 THYRAQRRLLLTGTPLQNNLPELWALLNFLLPNIFNSCKAFEQWFNQPFANTGEKVELTEEETLLIIRRLHKVLRPFLLR  619 (1157)
T ss_pred             ccccchhhhhhcCChhhhccHHHHHHHHHhccchhhhHhHHHHHhhhhhhhcCCcccccchHHHHHHHHHHHhhhHHHHH
Confidence            211222234555554100    0000                                               0      


Q ss_pred             ------HHhcCCCeEE-----------------------EeCC----------------------CCCCCCceEEEE---
Q 010709          319 ------QEYLTDPVQV-----------------------KVGK----------------------VSSPTANVIQIL---  344 (503)
Q Consensus       319 ------~~~~~~~~~~-----------------------~~~~----------------------~~~~~~~~~~~~---  344 (503)
                            ...+.+.+..                       .++.                      -+....++...+   
T Consensus       620 RlKkeVE~~LPdKve~viKC~mSalQq~lY~~m~~~g~l~~d~~~g~~g~k~L~N~imqLRKiCNHP~lf~~ve~~~~~~  699 (1157)
T KOG0386|consen  620 RLKKEVEQELPDKVEDVIKCDMSALQQSLYKQMQNKGQLLKDTAKGKKGYKPLFNTIMQLRKLCNHPYLFANVENSYTLH  699 (1157)
T ss_pred             hhhHHHhhhCchhhhHhhheehhhhhHhhhHHHHhCCCCCcCchhccccchhhhhHhHHHHHhcCCchhhhhhccccccc
Confidence                  0000000000                       0000                      000000000000   


Q ss_pred             -EE---cChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHH
Q 010709          345 -EK---VSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF  420 (503)
Q Consensus       345 -~~---~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f  420 (503)
                       ..   +....|...+-..+.+..       ..++.+|.||........+.++|.-.++....+.|....++|...++.|
T Consensus       700 ~~~~dL~R~sGKfELLDRiLPKLk-------atgHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK~~eRg~ll~~F  772 (1157)
T KOG0386|consen  700 YDIKDLVRVSGKFELLDRILPKLK-------ATGHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTKVEERGDLLEIF  772 (1157)
T ss_pred             cChhHHHHhccHHHHHHhhhHHHH-------hcCcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcchhhHHHHHHHh
Confidence             00   011112222222222211       2456799999999999999999999999999999999999999999999


Q ss_pred             hcCC---CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          421 RNGS---TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       421 ~~g~---~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ....   ...|++|.+.+.|+|+..+++||.||.-+++....|+--||.|.
T Consensus       773 N~Pds~yf~FllstragglglNlQtadtviifdsdwnp~~d~qaqdrahri  823 (1157)
T KOG0386|consen  773 NAPDSPYFIFLLSTRAGGLGLNLQTADTVIIFDSDWNPHQDLQAQDRAHRI  823 (1157)
T ss_pred             cCCCCceeeeeeeecccccccchhhcceEEEecCCCCchhHHHHHHHHHHh
Confidence            8754   44688999999999999999999999999997777766665553

>smart00490 HELICc helicase superfamily c-terminal domain

Probab=99.61  E-value=2.7e-15  Score=114.48  Aligned_cols=80  Identities=40%  Similarity=0.576  Sum_probs=76.7

Q ss_pred             HHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          389 EVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       389 ~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .+++.|...++.+..+||+++..+|..+++.|++|...|||+|+++++|+|+|.+++||.+++|.+...|.|++||++|.
T Consensus         2 ~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vli~t~~~~~Gi~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~   81 (82)
T smart00490        2 ELAELLKELGIKVARLHGGLSQEEREEILEKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA   81 (82)
T ss_pred             HHHHHHHHCCCeEEEEECCCCHHHHHHHHHHHHcCCCeEEEECChhhCCcChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence            56788888899999999999999999999999999999999999999999999999999999999999999999999994

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

Probab=99.61  E-value=3.7e-13  Score=143.57  Aligned_cols=77  Identities=26%  Similarity=0.276  Sum_probs=62.1

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHCCCe-EEEEcCCCCHHHHHHHHHHHhcCCC-cEEEEccccccCCCCCC--CCEEEEc
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAEGLH-AVALHGGRNQSDRESALRDFRNGST-NILVATDVASRGLDVMG--VAHVVNL  449 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~~~~-v~~lh~~~~~~~r~~~~~~f~~g~~-~vLvaT~~~~~Gldip~--v~~VI~~  449 (503)
                      ++++|||+++.+..+.+++.+...... .+..+|..+.   ...++.|.++.- .++|+|..+++|||+|+  .+.||..
T Consensus       479 ~~~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~~~~~---~~~l~~f~~~~~~~~lv~~gsf~EGVD~~g~~l~~vvI~  555 (654)
T COG1199         479 PGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGEDER---EELLEKFKASGEGLILVGGGSFWEGVDFPGDALRLVVIV  555 (654)
T ss_pred             CCCEEEEeccHHHHHHHHHHHhhcCccceeeecCCCcH---HHHHHHHHHhcCCeEEEeeccccCcccCCCCCeeEEEEE
Confidence            347999999999999999999877653 4455665543   377888876655 89999999999999997  5889998


Q ss_pred             cCCC
Q 010709          450 DLPK  453 (503)
Q Consensus       450 ~~p~  453 (503)
                      ++|-
T Consensus       556 ~lPf  559 (654)
T COG1199         556 GLPF  559 (654)
T ss_pred             ecCC
Confidence            8874

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.60  E-value=6.7e-13  Score=140.57  Aligned_cols=119  Identities=18%  Similarity=0.248  Sum_probs=80.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHh----cCCCcEEEEccccccCCCCCC--CCEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFR----NGSTNILVATDVASRGLDVMG--VAHVV  447 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~----~g~~~vLvaT~~~~~Gldip~--v~~VI  447 (503)
                      +.+|||+++.+..+.+++.|... +.. +..+|..   .+..+++.|+    .|+..||++|..+.+|||+|+  +++||
T Consensus       535 gg~LVlFtSy~~l~~v~~~l~~~~~~~-ll~Q~~~---~~~~ll~~f~~~~~~~~~~VL~g~~sf~EGVD~pGd~l~~vI  610 (697)
T PRK11747        535 KGSLVLFASRRQMQKVADLLPRDLRLM-LLVQGDQ---PRQRLLEKHKKRVDEGEGSVLFGLQSFAEGLDLPGDYLTQVI  610 (697)
T ss_pred             CCEEEEeCcHHHHHHHHHHHHHhcCCc-EEEeCCc---hHHHHHHHHHHHhccCCCeEEEEeccccccccCCCCceEEEE
Confidence            34899999999999999998743 333 3445542   4667887776    467889999999999999997  78999


Q ss_pred             EccCCCC----h-----hHHHHhhCc------------------ceeeeeeccC-chhhhhhHHHHHHHHHHHHHHHH
Q 010709          448 NLDLPKV----L-----LAASESLCT------------------TSFNITTNLD-GDMKKLEFCLILAITVLLFVIFL  497 (503)
Q Consensus       448 ~~~~p~s----~-----~~~~Qr~GR------------------~gR~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  497 (503)
                      ..++|-.    +     .+|..+.|+                  +||.+.+..| |.+.-++.-+.--.+..+|...|
T Consensus       611 I~kLPF~~p~dp~~~ar~~~~~~~g~~~F~~~~lP~A~~kl~Qg~GRlIRs~~D~G~i~ilD~R~~~~~Yg~~~l~sL  688 (697)
T PRK11747        611 ITKIPFAVPDSPVEATLAEWLKSRGGNPFMEISVPDASFKLIQAVGRLIRSEQDRGRVTILDRRLLTKRYGKRLLDAL  688 (697)
T ss_pred             EEcCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHhccccccCCceEEEEEEcccccchhHHHHHHHhC
Confidence            9887732    2     122222232                  4555555666 66666666555455555555444

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

Probab=99.58  E-value=5.8e-14  Score=138.75  Aligned_cols=94  Identities=18%  Similarity=0.257  Sum_probs=82.5

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc-EEEEccccccCCCCCCCCEEEEccCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTN-ILVATDVASRGLDVMGVAHVVNLDLP  452 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~-vLvaT~~~~~Gldip~v~~VI~~~~p  452 (503)
                      ++++|+|++..+.++.+.++|...++..+.+.|.....+|..++..|+..++- .|++|.+.+.|||+..+++||+||--
T Consensus      1044 gHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk~~dRrd~vrDwQ~sdiFvFLLSTRAGGLGINLTAADTViFYdSD 1123 (1185)
T KOG0388|consen 1044 GHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSKASDRRDVVRDWQASDIFVFLLSTRAGGLGINLTAADTVIFYDSD 1123 (1185)
T ss_pred             CceEEehhHHHHHHHHHHHHHHhhccceEEecCcchhhHHHHHHhhccCCceEEEEEecccCcccccccccceEEEecCC
Confidence            45699999999999999999999999999999999999999999999986654 57899999999999999999999999


Q ss_pred             CChhHHHHhhCccee
Q 010709          453 KVLLAASESLCTTSF  467 (503)
Q Consensus       453 ~s~~~~~Qr~GR~gR  467 (503)
                      +++..-.|..-||.|
T Consensus      1124 WNPT~D~QAMDRAHR 1138 (1185)
T KOG0388|consen 1124 WNPTADQQAMDRAHR 1138 (1185)
T ss_pred             CCcchhhHHHHHHHh
Confidence            887555554444444

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.58  E-value=6e-13  Score=137.88  Aligned_cols=275  Identities=19%  Similarity=0.176  Sum_probs=179.9

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+++|.-+--.+.+|  -|..+.||-|||+++.+|++...+.        |..|-||+++..||..=++.+..+...+ 
T Consensus        85 r~ydVQliGgl~Lh~G--~IAEM~TGEGKTL~atlpaylnAL~--------GkgVhVVTvNdYLA~RDae~m~~vy~~L-  153 (939)
T PRK12902         85 RHFDVQLIGGMVLHEG--QIAEMKTGEGKTLVATLPSYLNALT--------GKGVHVVTVNDYLARRDAEWMGQVHRFL-  153 (939)
T ss_pred             CcchhHHHhhhhhcCC--ceeeecCCCChhHHHHHHHHHHhhc--------CCCeEEEeCCHHHHHhHHHHHHHHHHHh-
Confidence            6788887776666544  6789999999999999998876555        6779999999999999999998888777 


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-----HHHHHc--CCCCCCCccEEEecchhHHh-hCC---------
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-----LDHLQQ--GNTSLSRVSFVILDEADRML-DMG---------  285 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-----~~~l~~--~~~~l~~~~~vViDEaH~l~-~~~---------  285 (503)
                      ++.++++.++....+  +.....++|+++|...|     .+.+..  .......+.++||||+|.++ +..         
T Consensus       154 GLtvg~i~~~~~~~e--rr~aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSILIDEArTPLIISg~  231 (939)
T PRK12902        154 GLSVGLIQQDMSPEE--RKKNYACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSILIDEARTPLIISGQ  231 (939)
T ss_pred             CCeEEEECCCCChHH--HHHhcCCCeEEecCCcccccchhhhhcccccccccCccceEEEecccceeeccCCCcccccCC
Confidence            699999887765544  33456799999999887     333332  12345678899999999622 100         


Q ss_pred             ------CHHHHHHHHHhCCC------------------------------------------------------------
Q 010709          286 ------FEPQIREVMQNLPD------------------------------------------------------------  299 (503)
Q Consensus       286 ------~~~~~~~il~~~~~------------------------------------------------------------  299 (503)
                            ......++...+.+                                                            
T Consensus       232 ~~~~~~~y~~~~~~~~~L~~~~~~~~~~dy~idek~~~v~LTe~G~~~~e~~~~i~nLy~~~~~~~~~i~~AL~A~~lf~  311 (939)
T PRK12902        232 VERPQEKYQKAAEVAAALQRKDGIDPEGDYEVDEKQRNVLLTDEGFAKAEQLLGVSDLFDPQDPWAHYIFNALKAKELFI  311 (939)
T ss_pred             CccchHHHHHHHHHHHHhhhhcccCCCCCeEEecCCCeeeEcHHHHHHHHHHhCchhhcCcccHHHHHHHHHHHHHHHHh
Confidence                  00000000000000                                                            


Q ss_pred             -C-------------------------------------------------------------CcEEEEEeeCCHHHHHH
Q 010709          300 -K-------------------------------------------------------------HQTLLFSATMPVEIEAL  317 (503)
Q Consensus       300 -~-------------------------------------------------------------~q~i~~SAT~~~~~~~~  317 (503)
                       +                                                             .++.+||+|...+-.++
T Consensus       312 ~d~dYiV~dg~V~IVDe~TGR~m~grrws~GLHQaIEaKE~v~it~e~~tlAsIT~QnfFr~Y~kLsGMTGTa~te~~Ef  391 (939)
T PRK12902        312 KDVNYIVRNGEVVIVDEFTGRVMPGRRWSDGLHQAIEAKEGVEIQPETQTLASITYQNFFLLYPKLAGMTGTAKTEEVEF  391 (939)
T ss_pred             cCCeEEEECCEEEEEECCCCCCCCCCccchHHHHHHHhhcCCCCCCCceeeeeeeHHHHHhhCchhcccCCCCHHHHHHH
Confidence             0                                                             14566777765444444


Q ss_pred             HHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC
Q 010709          318 AQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE  397 (503)
Q Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~  397 (503)
                      .+-|-- .+.......+... ....-........|...+...+.+...       .+.|+||-+.+.+..+.+++.|.+.
T Consensus       392 ~~iY~l-~Vv~IPTnkP~~R-~d~~d~vy~t~~~K~~Ai~~ei~~~~~-------~GrPVLIgT~SVe~SE~ls~~L~~~  462 (939)
T PRK12902        392 EKTYKL-EVTVIPTNRPRRR-QDWPDQVYKTEIAKWRAVANETAEMHK-------QGRPVLVGTTSVEKSELLSALLQEQ  462 (939)
T ss_pred             HHHhCC-cEEEcCCCCCeee-ecCCCeEEcCHHHHHHHHHHHHHHHHh-------CCCCEEEeeCCHHHHHHHHHHHHHc
Confidence            444322 2222111111111 111223344556788888777766543       3457999999999999999999999


Q ss_pred             CCeEEEEcCCC-CHHHHHHHHHHHhcCC-CcEEEEccccccCCCCC
Q 010709          398 GLHAVALHGGR-NQSDRESALRDFRNGS-TNILVATDVASRGLDVM  441 (503)
Q Consensus       398 ~~~v~~lh~~~-~~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip  441 (503)
                      |+....++..- ..+.-.+++.  ..|+ ..|-|||++++||-||.
T Consensus       463 gi~h~vLNAk~~~~~~EA~IIa--~AG~~GaVTIATNMAGRGTDIk  506 (939)
T PRK12902        463 GIPHNLLNAKPENVEREAEIVA--QAGRKGAVTIATNMAGRGTDII  506 (939)
T ss_pred             CCchheeeCCCcchHhHHHHHH--hcCCCCcEEEeccCCCCCcCEe
Confidence            99988888862 2222223333  2454 56999999999999986

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=99.57  E-value=8.3e-13  Score=138.90  Aligned_cols=318  Identities=20%  Similarity=0.147  Sum_probs=181.1

Q ss_pred             CCCcHHHHHHHHHHhc--------CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALS--------GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~--------~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      ..-..||..|+..+..        |--+|-.|.||+|||++= .-++..+..     ...|.++.|..-.|.|..|.-+.
T Consensus       407 ~~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aN-ARImyaLsd-----~~~g~RfsiALGLRTLTLQTGda  480 (1110)
T TIGR02562       407 HPRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLAN-ARAMYALRD-----DKQGARFAIALGLRSLTLQTGHA  480 (1110)
T ss_pred             CCCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHH-HHHHHHhCC-----CCCCceEEEEccccceeccchHH
Confidence            3457899999988763        223778899999999864 333333322     23466888888888888888777


Q ss_pred             HHHHhccCCCceEEEEECCccHHHHH-------------------------------------------HHhh-------
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQR-------------------------------------------SELR-------  243 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~~-------  243 (503)
                      +++-.. +.+-...++.|+....+-.                                           ..+.       
T Consensus       481 ~r~rL~-L~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~r  559 (1110)
T TIGR02562       481 LKTRLN-LSDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKT  559 (1110)
T ss_pred             HHHhcC-CCccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhh
Confidence            776542 2233344444433221111                                           0000       


Q ss_pred             -CCCcEEEECcHHHHHHHHcCC--C-CCC----CccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHH
Q 010709          244 -GGVSIVVATPGRFLDHLQQGN--T-SLS----RVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEI  314 (503)
Q Consensus       244 -~~~~Ilv~Tp~~l~~~l~~~~--~-~l~----~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~  314 (503)
                       -...++|||++.++.......  . .+.    .-+.|||||+|..-.. ....+.+++.-. .-..++++||||+|+.+
T Consensus       560 ll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~~-~~~~L~rlL~w~~~lG~~VlLmSATLP~~l  638 (1110)
T TIGR02562       560 LLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEPE-DLPALLRLVQLAGLLGSRVLLSSATLPPAL  638 (1110)
T ss_pred             hhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCHH-HHHHHHHHHHHHHHcCCCEEEEeCCCCHHH
Confidence             125699999999987763211  1 111    1368999999953211 122233333311 12466999999999886


Q ss_pred             HHHHHH-h----------cCC---CeEE---EeCCCCC----------------------------CCCceEEEEEEcCh
Q 010709          315 EALAQE-Y----------LTD---PVQV---KVGKVSS----------------------------PTANVIQILEKVSE  349 (503)
Q Consensus       315 ~~~~~~-~----------~~~---~~~~---~~~~~~~----------------------------~~~~~~~~~~~~~~  349 (503)
                      ...+.. |          .+.   +..+   .++....                            ....-...+..++.
T Consensus       639 ~~~L~~Ay~~G~~~~q~~~g~~~~~~~i~CaW~DE~~~~~~~~~~~~~F~~~H~~Fv~~R~~~L~~~p~~R~a~i~~~~~  718 (1110)
T TIGR02562       639 VKTLFRAYEAGRQMYQALYGQPKKPLNICCAWVDEPQVWQADCNQKSEFIQRHQDFLRDRAVQLAKKPVRRLAELLSLSS  718 (1110)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCcceeEEeecccCchhhhhcCHHHHHHHHHHHHHHHHHHHhcCcccceEEEeecCC
Confidence            654322 1          221   1111   1111000                            00011111222222


Q ss_pred             h-----hHHHHHHHHHHHHHHhhh---ccCCC-CCc----EEEEEcchhhHHHHHHHHHHC------CCeEEEEcCCCCH
Q 010709          350 N-----EKVDRLLALLVEEAFLAE---KSCHP-FPL----TIVFVERKTRCDEVSEALVAE------GLHAVALHGGRNQ  410 (503)
Q Consensus       350 ~-----~k~~~l~~~l~~~~~~~~---~~~~~-~~~----~lIF~~~~~~~~~l~~~L~~~------~~~v~~lh~~~~~  410 (503)
                      .     .....+.+.+.+....-.   ....+ .+|    .+|-+.+.+.+-.+++.|...      .+.++.||+..+.
T Consensus       719 ~~~~~~~~~~~~a~~i~~~~~~LH~~h~~~~~~sgk~VSfGliR~anI~p~V~~A~~L~~~~~~~~~~i~~~~yHSr~~l  798 (1110)
T TIGR02562       719 LPRENESTYLALAQSLLEGALRLHQAHAQTDPKSEKKVSVGLIRVANIDPLIRLAQFLYALLAEEKYQIHLCCYHAQDPL  798 (1110)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHhCccCCCCCeEEEEEEEEEcCchHHHHHHHHHHhhccccCCceeEEEecccChH
Confidence            1     122222222222211111   11111 122    478888888888888888754      2458889999988


Q ss_pred             HHHHHHHHHH----------------------hc----CCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCc
Q 010709          411 SDRESALRDF----------------------RN----GSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCT  464 (503)
Q Consensus       411 ~~r~~~~~~f----------------------~~----g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR  464 (503)
                      ..|..+.+..                      .+    +...|+|+|.+.|.|+|+. .+++|-  -|.++.+.+||.||
T Consensus       799 ~~Rs~~E~~Ld~~L~R~~~~~~~~~~~i~~~l~~~~~~~~~~i~v~Tqv~E~g~D~d-fd~~~~--~~~~~~sliQ~aGR  875 (1110)
T TIGR02562       799 LLRSYIERRLDQLLTRHKPEQLFQDDEIIDLMQNSPALNHLFIVLATPVEEVGRDHD-YDWAIA--DPSSMRSIIQLAGR  875 (1110)
T ss_pred             HHHHHHHHHHHHHhcccChhhhhchHHHHHHHhcccccCCCeEEEEeeeEEEEeccc-CCeeee--ccCcHHHHHHHhhc
Confidence            7777766553                      11    4678999999999999985 555543  35678999999999


Q ss_pred             ceeeee
Q 010709          465 TSFNIT  470 (503)
Q Consensus       465 ~gR~~~  470 (503)
                      +.|...
T Consensus       876 ~~R~~~  881 (1110)
T TIGR02562       876 VNRHRL  881 (1110)
T ss_pred             cccccc
Confidence            988654

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.

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=99.54  E-value=4.8e-12  Score=135.16  Aligned_cols=74  Identities=16%  Similarity=0.158  Sum_probs=61.0

Q ss_pred             CCCCCCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          139 HEYTRPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      +.|..++|.|.+.+..+.    .++++++.+|||+|||++.+.|++.+....+     ..++++|.+.|..=..|+.+++
T Consensus         6 FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~-----~~~kIiy~sRThsQl~q~i~El   80 (705)
T TIGR00604         6 FPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP-----EVRKIIYASRTHSQLEQATEEL   80 (705)
T ss_pred             cCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc-----ccccEEEEcccchHHHHHHHHH
Confidence            456677999999887765    6788999999999999999999998765432     2368999999998888898888


Q ss_pred             HHH
Q 010709          215 KAL  217 (503)
Q Consensus       215 ~~~  217 (503)
                      ++.
T Consensus        81 k~~   83 (705)
T TIGR00604        81 RKL   83 (705)
T ss_pred             Hhh
Confidence            885

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).

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

Probab=99.54  E-value=1.5e-12  Score=124.19  Aligned_cols=90  Identities=19%  Similarity=0.248  Sum_probs=78.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC-CCcE-EEEccccccCCCCCCCCEEEEccCC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNG-STNI-LVATDVASRGLDVMGVAHVVNLDLP  452 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g-~~~v-LvaT~~~~~Gldip~v~~VI~~~~p  452 (503)
                      -|.|||.+--...+.+.-.|.+.|+.++-+.|+|++..|...++.|.+. .++| |++-.+.+..+|+..+.+|+++|+-
T Consensus       639 ~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs~~ardatik~F~nd~~c~vfLvSLkAGGVALNLteASqVFmmDPW  718 (791)
T KOG1002|consen  639 AKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMSPAARDATIKYFKNDIDCRVFLVSLKAGGVALNLTEASQVFMMDPW  718 (791)
T ss_pred             hhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCChHHHHHHHHHhccCCCeEEEEEEeccCceEeeechhceeEeeccc
Confidence            4689999999999999999999999999999999999999999999875 4554 5566888889999999999999999


Q ss_pred             CCh------hHHHHhhCc
Q 010709          453 KVL------LAASESLCT  464 (503)
Q Consensus       453 ~s~------~~~~Qr~GR  464 (503)
                      +++      .+.+||||+
T Consensus       719 WNpaVe~Qa~DRiHRIGQ  736 (791)
T KOG1002|consen  719 WNPAVEWQAQDRIHRIGQ  736 (791)
T ss_pred             ccHHHHhhhhhhHHhhcC
Confidence            886      456677775

>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=99.51  E-value=3.7e-11  Score=117.45  Aligned_cols=271  Identities=21%  Similarity=0.228  Sum_probs=183.4

Q ss_pred             CCCCeEEEEcccHHHHHHHHHHHHHHhccCCC----------ce--------EEEEEC-CccHHHHHHHhh---------
Q 010709          192 GDGPLALVLAPTRELAQQIEKEVKALSRSLDS----------FK--------TAIVVG-GTNIAEQRSELR---------  243 (503)
Q Consensus       192 ~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~----------~~--------~~~~~~-~~~~~~~~~~~~---------  243 (503)
                      -..|+||||+|+|..|.++.+.+.++......          +.        ...-.. .....+......         
T Consensus        35 ftRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~Frl  114 (442)
T PF06862_consen   35 FTRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRL  114 (442)
T ss_pred             CCCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEE
Confidence            35799999999999999998888877643100          00        000000 011111111111         


Q ss_pred             ---------------CCCcEEEECcHHHHHHHHc------CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC---CC
Q 010709          244 ---------------GGVSIVVATPGRFLDHLQQ------GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL---PD  299 (503)
Q Consensus       244 ---------------~~~~Ilv~Tp~~l~~~l~~------~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~---~~  299 (503)
                                     ..+||+||+|=-|...+..      ..-.|+.+.++|||.||.+. +..-..+..++..+   |.
T Consensus       115 Gik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~-MQNW~Hv~~v~~~lN~~P~  193 (442)
T PF06862_consen  115 GIKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLL-MQNWEHVLHVFEHLNLQPK  193 (442)
T ss_pred             eEEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHH-HhhHHHHHHHHHHhccCCC
Confidence                           2589999999988877764      12247889999999999654 33344455555444   32


Q ss_pred             ---------------------CCcEEEEEeeCCHHHHHHHHHhcCCCeEE-Ee--CC-----CCCCCCceEEEEEEcCh-
Q 010709          300 ---------------------KHQTLLFSATMPVEIEALAQEYLTDPVQV-KV--GK-----VSSPTANVIQILEKVSE-  349 (503)
Q Consensus       300 ---------------------~~q~i~~SAT~~~~~~~~~~~~~~~~~~~-~~--~~-----~~~~~~~~~~~~~~~~~-  349 (503)
                                           -+|+|++|+...+++..+...+..|..-. .+  ..     .......+.|.+..++. 
T Consensus       194 ~~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~~g~i~~v~~~v~Q~F~r~~~~  273 (442)
T PF06862_consen  194 KSHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEASGVISQVVVQVRQVFQRFDCS  273 (442)
T ss_pred             CCCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeeccccceeeeccccCCceEEEEecCC
Confidence                                 25999999999999999988866553321 11  11     12334455666665432 


Q ss_pred             --hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          350 --NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       350 --~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                        ....+...+...+............+.+|||+++--+--.|..+|++.++..+.+|.-.++.+-.+.-..|..|+..+
T Consensus       274 s~~~~~d~Rf~yF~~~iLP~l~~~~~~~~~LIfIPSYfDfVRlRN~lk~~~~sF~~i~EYts~~~isRAR~~F~~G~~~i  353 (442)
T PF06862_consen  274 SPADDPDARFKYFTKKILPQLKRDSKMSGTLIFIPSYFDFVRLRNYLKKENISFVQISEYTSNSDISRARSQFFHGRKPI  353 (442)
T ss_pred             CcchhhhHHHHHHHHHHHHHhhhccCCCcEEEEecchhhhHHHHHHHHhcCCeEEEecccCCHHHHHHHHHHHHcCCceE
Confidence              222233333333333322221345567999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccccc--cCCCCCCCCEEEEccCCCChhHHHHhhC
Q 010709          428 LVATDVAS--RGLDVMGVAHVVNLDLPKVLLAASESLC  463 (503)
Q Consensus       428 LvaT~~~~--~Gldip~v~~VI~~~~p~s~~~~~Qr~G  463 (503)
                      |+.|.-+-  +=..|.++++||+|++|..+.-|...++
T Consensus       354 LL~TER~HFfrRy~irGi~~viFY~~P~~p~fY~El~n  391 (442)
T PF06862_consen  354 LLYTERFHFFRRYRIRGIRHVIFYGPPENPQFYSELLN  391 (442)
T ss_pred             EEEEhHHhhhhhceecCCcEEEEECCCCChhHHHHHHh
Confidence            99997544  6678999999999999999866665554

; GO: 0005634 nucleus

>PRK14873 primosome assembly protein PriA; Provisional

Probab=99.49  E-value=6.4e-12  Score=130.83  Aligned_cols=138  Identities=20%  Similarity=0.239  Sum_probs=93.3

Q ss_pred             EEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH--
Q 010709          162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR--  239 (503)
Q Consensus       162 ii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  239 (503)
                      +..+-+|||||.+|+ -++...+..       |+.+||++|...|+.|+.+.|++.+.   +..+..++++....+..  
T Consensus       164 i~~~~~GSGKTevyl-~~i~~~l~~-------Gk~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~  232 (665)
T PRK14873        164 VWQALPGEDWARRLA-AAAAATLRA-------GRGALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRR  232 (665)
T ss_pred             HhhcCCCCcHHHHHH-HHHHHHHHc-------CCeEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHH
Confidence            344446999999994 455555553       67899999999999999999998773   24577777777655432  


Q ss_pred             --HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC---CHHHHHH--HHHhCCCCCcEEEEEeeCCH
Q 010709          240 --SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG---FEPQIRE--VMQNLPDKHQTLLFSATMPV  312 (503)
Q Consensus       240 --~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~---~~~~~~~--il~~~~~~~q~i~~SAT~~~  312 (503)
                        ....+..+|+|+|-..++       ..+.++++|||||-|.-.-..   ..-..+.  +++....+..+|+.|||+.-
T Consensus       233 w~~~~~G~~~IViGtRSAvF-------aP~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTPSl  305 (665)
T PRK14873        233 WLAVLRGQARVVVGTRSAVF-------APVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQHGCALLIGGHARTA  305 (665)
T ss_pred             HHHHhCCCCcEEEEcceeEE-------eccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHcCCcEEEECCCCCH
Confidence              233456899999955443       367899999999999533221   1111222  22333456779999999965


Q ss_pred             HHHHH
Q 010709          313 EIEAL  317 (503)
Q Consensus       313 ~~~~~  317 (503)
                      +....
T Consensus       306 es~~~  310 (665)
T PRK14873        306 EAQAL  310 (665)
T ss_pred             HHHHH
Confidence            54433

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=99.45  E-value=4.4e-13  Score=135.84  Aligned_cols=307  Identities=17%  Similarity=0.175  Sum_probs=187.4

Q ss_pred             HHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEE
Q 010709          148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA  227 (503)
Q Consensus       148 Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~  227 (503)
                      -...+..+..+..++|-+.||+|||+.+.-.+|..++......   -..+.+..|+|..+..+++++.+--..    .++
T Consensus       383 ~~~i~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g~---~~na~v~qprrisaisiaerva~er~e----~~g  455 (1282)
T KOG0921|consen  383 RSEILQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNGA---SFNAVVSQPRRISAISLAERVANERGE----EVG  455 (1282)
T ss_pred             HHHHHHHHhcCceeeEeecccccchhHHHHHHHHHHhhccccc---cccceeccccccchHHHHHHHHHhhHH----hhc
Confidence            3445556667777999999999999999888888877753211   233667779998888888777543211    111


Q ss_pred             EEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHh-hCCCHHHHHHHHHhCCCCCcEEEE
Q 010709          228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRML-DMGFEPQIREVMQNLPDKHQTLLF  306 (503)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~-~~~~~~~~~~il~~~~~~~q~i~~  306 (503)
                      -..|.....+. ..-...-.|++||-+.+++++...   +..+.++|+||.|... +..|...+.+-+.-.-++..+++|
T Consensus       456 ~tvgy~vRf~S-a~prpyg~i~fctvgvllr~~e~g---lrg~sh~i~deiherdv~~dfll~~lr~m~~ty~dl~v~lm  531 (1282)
T KOG0921|consen  456 ETCGYNVRFDS-ATPRPYGSIMFCTVGVLLRMMENG---LRGISHVIIDEIHERDVDTDFVLIVLREMISTYRDLRVVLM  531 (1282)
T ss_pred             ccccccccccc-cccccccceeeeccchhhhhhhhc---ccccccccchhhhhhccchHHHHHHHHhhhccchhhhhhhh
Confidence            11111111110 001123468999999999998764   5678899999999532 223544444444444556777888


Q ss_pred             EeeCCHHHHHHHHHhcCCCeEEEe----------------------CCCCCCCC----------ceE----EEEEEcC--
Q 010709          307 SATMPVEIEALAQEYLTDPVQVKV----------------------GKVSSPTA----------NVI----QILEKVS--  348 (503)
Q Consensus       307 SAT~~~~~~~~~~~~~~~~~~~~~----------------------~~~~~~~~----------~~~----~~~~~~~--  348 (503)
                      |||+..+.   ...|+.+-..+.+                      ........          ...    ..-..+.  
T Consensus       532 satIdTd~---f~~~f~~~p~~~~~grt~pvq~F~led~~~~~~~vp~~~~~~k~k~~~~~~~~~~ddK~~n~n~~~dd~  608 (1282)
T KOG0921|consen  532 SATIDTDL---FTNFFSSIPDVTVHGRTFPVQSFFLEDIIQMTQFVPSEPSQKKRKKDDDEEDEEVDDKGRNMNILCDPS  608 (1282)
T ss_pred             hcccchhh---hhhhhccccceeeccccccHHHHHHHHhhhhhhccCCCcCccchhhcccccCchhhhcccccccccChh
Confidence            88874331   1122211111100                      00000000          000    0000000  


Q ss_pred             ----------hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-------CCeEEEEcCCCCHH
Q 010709          349 ----------ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-------GLHAVALHGGRNQS  411 (503)
Q Consensus       349 ----------~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-------~~~v~~lh~~~~~~  411 (503)
                                ...+.+....++. .........+-.+-++||.+....+-.|...|...       .+.+.++|+.....
T Consensus       609 ~~~~~~~am~~~se~d~~f~l~E-al~~~i~s~~i~gailvflpgwa~i~~L~~~ll~~~~fg~~~~y~ilp~Hsq~~~~  687 (1282)
T KOG0921|consen  609 YNESTRTAMSRLSEKDIPFGLIE-ALLNDIASRNIDGAVLVFLPGWAEIMTLCNRLLEHQEFGQANKYEILPLHSQLTSQ  687 (1282)
T ss_pred             hcchhhhhhhcchhhcchhHHHH-HHHhhhcccCCccceeeecCchHHhhhhhhhhhhhhhhccchhcccccchhhcccH
Confidence                      0001111111111 11111122234566999999999999888888654       35788999999999


Q ss_pred             HHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC------------------ChhHHHHhhCcceeee
Q 010709          412 DRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK------------------VLLAASESLCTTSFNI  469 (503)
Q Consensus       412 ~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~------------------s~~~~~Qr~GR~gR~~  469 (503)
                      ++.++++..+.|..++++.|++++..++|.++.+||+.+..+                  +..+..||.||+||..
T Consensus       688 eqrkvf~~~p~gv~kii~stniaetsiTidd~v~vid~cka~~~~~~s~nn~~~~Atvw~sktn~eqr~gr~grvR  763 (1282)
T KOG0921|consen  688 EQRKVFEPVPEGVTKIILSTNIAETSITIDDVVYVIDSCKAKEKLFTSHNNMTHYATVWASKTNLEQRKGRAGRVR  763 (1282)
T ss_pred             hhhhccCcccccccccccccceeeEeeeecceeEEEeeeeeeeeeeccccceeeeeeecccccchHhhcccCceec
Confidence            999999999999999999999999999999999998766432                  3467789999988853

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

Probab=99.41  E-value=7.1e-12  Score=124.42  Aligned_cols=110  Identities=15%  Similarity=0.213  Sum_probs=80.8

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc--CCCcE-EEEccccccCCCCCCCCEEEEccC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRN--GSTNI-LVATDVASRGLDVMGVAHVVNLDL  451 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~--g~~~v-LvaT~~~~~Gldip~v~~VI~~~~  451 (503)
                      .|++|...-.....-+..+|.+.|+....+||....++|+.+++.|..  |..+| |++-.+.+.|+|+-+.+|+|.+|+
T Consensus       747 eK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~vK~Rq~iv~~FN~~k~~~rVmLlSLtAGGVGLNL~GaNHlilvDl  826 (901)
T KOG4439|consen  747 EKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVLVKDRQEIVDEFNQEKGGARVMLLSLTAGGVGLNLIGANHLILVDL  826 (901)
T ss_pred             ceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccchhHHHHHHHHHHhccCCceEEEEEEccCcceeeecccceEEEEec
Confidence            356666665666677888899999999999999999999999999964  44555 556688899999999999999999


Q ss_pred             CCChhHHHH------hhCc-----ceeeeeeccC-chhhhhhHHH
Q 010709          452 PKVLLAASE------SLCT-----TSFNITTNLD-GDMKKLEFCL  484 (503)
Q Consensus       452 p~s~~~~~Q------r~GR-----~gR~~~~~~~-~~~~~~~~~~  484 (503)
                      -++++-=.|      |+|.     ..|.++...- .++..+..+-
T Consensus       827 HWNPaLEqQAcDRIYR~GQkK~V~IhR~~~~gTvEqrV~~LQdkK  871 (901)
T KOG4439|consen  827 HWNPALEQQACDRIYRMGQKKDVFIHRLMCKGTVEQRVKSLQDKK  871 (901)
T ss_pred             ccCHHHHHHHHHHHHHhcccCceEEEEEEecCcHHHHHHHHHHHH
Confidence            999854333      3333     2344444443 5555555443

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

Probab=99.40  E-value=7.1e-13  Score=107.92  Aligned_cols=135  Identities=21%  Similarity=0.250  Sum_probs=81.3

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      |+-.++-..+|+|||.-.+.-++...+..       +.++|||.|||.++..+.+.++...     +++.  ..... . 
T Consensus         4 g~~~~~d~hpGaGKTr~vlp~~~~~~i~~-------~~rvLvL~PTRvva~em~~aL~~~~-----~~~~--t~~~~-~-   67 (148)
T PF07652_consen    4 GELTVLDLHPGAGKTRRVLPEIVREAIKR-------RLRVLVLAPTRVVAEEMYEALKGLP-----VRFH--TNARM-R-   67 (148)
T ss_dssp             TEEEEEE--TTSSTTTTHHHHHHHHHHHT-------T--EEEEESSHHHHHHHHHHTTTSS-----EEEE--STTSS---
T ss_pred             CceeEEecCCCCCCcccccHHHHHHHHHc-------cCeEEEecccHHHHHHHHHHHhcCC-----cccC--ceeee-c-
Confidence            44578899999999987655455555553       6889999999999988877775431     2222  11111 0 


Q ss_pred             HHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeCCHHH
Q 010709          238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATMPVEI  314 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~~  314 (503)
                         ....+.-|-++|.+.+.+.+.+ ...+.++++||+||||..-...  +...+... .. .....+|+||||+|-..
T Consensus        68 ---~~~g~~~i~vMc~at~~~~~~~-p~~~~~yd~II~DEcH~~Dp~sIA~rg~l~~~-~~-~g~~~~i~mTATPPG~~  140 (148)
T PF07652_consen   68 ---THFGSSIIDVMCHATYGHFLLN-PCRLKNYDVIIMDECHFTDPTSIAARGYLREL-AE-SGEAKVIFMTATPPGSE  140 (148)
T ss_dssp             ------SSSSEEEEEHHHHHHHHHT-SSCTTS-SEEEECTTT--SHHHHHHHHHHHHH-HH-TTS-EEEEEESS-TT--
T ss_pred             ---cccCCCcccccccHHHHHHhcC-cccccCccEEEEeccccCCHHHHhhheeHHHh-hh-ccCeeEEEEeCCCCCCC
Confidence               1235577899999999888877 5567899999999999532111  12222222 22 23467999999998654

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 ....

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=99.39  E-value=3.5e-11  Score=126.31  Aligned_cols=114  Identities=15%  Similarity=0.126  Sum_probs=90.3

Q ss_pred             EEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC
Q 010709          345 EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS  424 (503)
Q Consensus       345 ~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~  424 (503)
                      .+.....|...++..+.....       .+.|+||-+.+.+..+.|++.|...|+..-.++......|-..+-+   .|.
T Consensus       606 vy~t~~eK~~Aii~ei~~~~~-------~GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK~h~~EAeIVA~---AG~  675 (1112)
T PRK12901        606 VYKTKREKYNAVIEEITELSE-------AGRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAKLHQKEAEIVAE---AGQ  675 (1112)
T ss_pred             EecCHHHHHHHHHHHHHHHHH-------CCCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhccchhhHHHHHHh---cCC
Confidence            344566788888887776653       3347999999999999999999999998777777655555443333   343


Q ss_pred             -CcEEEEccccccCCCCC--------CCCEEEEccCCCChhHHHHhhCcceee
Q 010709          425 -TNILVATDVASRGLDVM--------GVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       425 -~~vLvaT~~~~~Gldip--------~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                       -.|-|||++++||-||.        +==+||-...+.|..--.|-.||+||.
T Consensus       676 ~GaVTIATNMAGRGTDIkLg~~V~e~GGL~VIgTerheSrRID~QLrGRaGRQ  728 (1112)
T PRK12901        676 PGTVTIATNMAGRGTDIKLSPEVKAAGGLAIIGTERHESRRVDRQLRGRAGRQ  728 (1112)
T ss_pred             CCcEEEeccCcCCCcCcccchhhHHcCCCEEEEccCCCcHHHHHHHhcccccC
Confidence             56899999999999998        334799999999999999999999995

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=99.34  E-value=2e-10  Score=118.17  Aligned_cols=277  Identities=15%  Similarity=0.158  Sum_probs=169.0

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      +.-.+|-+|+|+|||.+. +..+...+..      ...++|+|..++.|+.+.+..++..+-.  ++.  .+......  
T Consensus        49 ~~V~vVRSpMGTGKTtaL-i~wLk~~l~~------~~~~VLvVShRrSL~~sL~~rf~~~~l~--gFv--~Y~d~~~~--  115 (824)
T PF02399_consen   49 RGVLVVRSPMGTGKTTAL-IRWLKDALKN------PDKSVLVVSHRRSLTKSLAERFKKAGLS--GFV--NYLDSDDY--  115 (824)
T ss_pred             CCeEEEECCCCCCcHHHH-HHHHHHhccC------CCCeEEEEEhHHHHHHHHHHHHhhcCCC--cce--eeeccccc--
Confidence            344899999999999864 4455544322      2577999999999999999999765421  122  11111110  


Q ss_pred             HHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHH-------HHHHHhCCCCCcEEEEEee
Q 010709          238 QRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQI-------REVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       238 ~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~-------~~il~~~~~~~q~i~~SAT  309 (503)
                         .+. ...+-+++..+.|.+..   ...+.++++|||||+-..+..-|.+.+       ..+...+.....+|+|-|+
T Consensus       116 ---~i~~~~~~rLivqIdSL~R~~---~~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~  189 (824)
T PF02399_consen  116 ---IIDGRPYDRLIVQIDSLHRLD---GSLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDAD  189 (824)
T ss_pred             ---cccccccCeEEEEehhhhhcc---cccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCC
Confidence               011 12466777777776543   234677999999999866554232222       2223334556779999999


Q ss_pred             CCHHHHHHHHHhcCC-CeEEEeCCCCCCCCceEEEEEEcC----------------------------------hhhHHH
Q 010709          310 MPVEIEALAQEYLTD-PVQVKVGKVSSPTANVIQILEKVS----------------------------------ENEKVD  354 (503)
Q Consensus       310 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~----------------------------------~~~k~~  354 (503)
                      +....-++++.+.++ ++.+.++....+...-+..+..-.                                  ......
T Consensus       190 ln~~tvdFl~~~Rp~~~i~vI~n~y~~~~fs~R~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (824)
T PF02399_consen  190 LNDQTVDFLASCRPDENIHVIVNTYASPGFSNRRCTFLRSLGTDTLAAALNPEDENADTSPTPKHSPDPTATAAISNDET  269 (824)
T ss_pred             CCHHHHHHHHHhCCCCcEEEEEeeeecCCcccceEEEecccCcHHHHHHhCCcccccccCCCcCCCCccccccccccchh
Confidence            999999998887653 223322221111110000000000                                  000011


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccc
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA  434 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~  434 (503)
                      .....+.....       .++++-||+.+...++.+++........+..++|..+..+   + +.  -++.+|++=|.+.
T Consensus       270 tF~~~L~~~L~-------~gknIcvfsSt~~~~~~v~~~~~~~~~~Vl~l~s~~~~~d---v-~~--W~~~~VviYT~~i  336 (824)
T PF02399_consen  270 TFFSELLARLN-------AGKNICVFSSTVSFAEIVARFCARFTKKVLVLNSTDKLED---V-ES--WKKYDVVIYTPVI  336 (824)
T ss_pred             hHHHHHHHHHh-------CCCcEEEEeChHHHHHHHHHHHHhcCCeEEEEcCCCCccc---c-cc--ccceeEEEEeceE
Confidence            12222222221       2345778999999999999999988889999988776652   2 22  3578999999999


Q ss_pred             ccCCCCCCCC--EEEEccCC----CChhHHHHhhCcce
Q 010709          435 SRGLDVMGVA--HVVNLDLP----KVLLAASESLCTTS  466 (503)
Q Consensus       435 ~~Gldip~v~--~VI~~~~p----~s~~~~~Qr~GR~g  466 (503)
                      .-|+++....  -|.-|=-|    .++.+..|++||+-
T Consensus       337 tvG~Sf~~~HF~~~f~yvk~~~~gpd~~s~~Q~lgRvR  374 (824)
T PF02399_consen  337 TVGLSFEEKHFDSMFAYVKPMSYGPDMVSVYQMLGRVR  374 (824)
T ss_pred             EEEeccchhhceEEEEEecCCCCCCcHHHHHHHHHHHH
Confidence            9999987543  34433222    34567899999953

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

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

Probab=99.31  E-value=8.1e-11  Score=130.62  Aligned_cols=92  Identities=17%  Similarity=0.225  Sum_probs=82.8

Q ss_pred             cEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC--CCcEEEEccccccCCCCCCCCEEEEccCCC
Q 010709          376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNG--STNILVATDVASRGLDVMGVAHVVNLDLPK  453 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g--~~~vLvaT~~~~~Gldip~v~~VI~~~~p~  453 (503)
                      ++|||.+.....+.+...+...++..+.++|.++.+.|...++.|.++  ..-.++++.+++.|+|+...++||.+|+.+
T Consensus       713 kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~~~~r~~~i~~f~~~~~~~v~lls~kagg~glnLt~a~~vi~~d~~w  792 (866)
T COG0553         713 KVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWW  792 (866)
T ss_pred             cEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCChhhHHHHHHHhhcCCCCceEEEEecccccceeecccceEEEecccc
Confidence            799999999999999999999998999999999999999999999986  455677778999999999999999999999


Q ss_pred             ChhHHHHhhCccee
Q 010709          454 VLLAASESLCTTSF  467 (503)
Q Consensus       454 s~~~~~Qr~GR~gR  467 (503)
                      +++...|...|+.|
T Consensus       793 np~~~~Qa~dRa~R  806 (866)
T COG0553         793 NPAVELQAIDRAHR  806 (866)
T ss_pred             ChHHHHHHHHHHHH
Confidence            99777776666555

>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=99.30  E-value=2e-11  Score=117.79  Aligned_cols=154  Identities=21%  Similarity=0.218  Sum_probs=92.3

Q ss_pred             HHHHHHHHHh-------------cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          147 IQAQAMPVAL-------------SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       147 ~Q~~~i~~i~-------------~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      +|.+++.+++             ..+.++++.++|+|||+..+ .++..+......  .....+|||+|. .+..||.++
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i-~~~~~l~~~~~~--~~~~~~LIv~P~-~l~~~W~~E   76 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAI-ALISYLKNEFPQ--RGEKKTLIVVPS-SLLSQWKEE   76 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHH-HHHHHHHHCCTT--SS-S-EEEEE-T-TTHHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhh-hhhhhhhhcccc--ccccceeEeecc-chhhhhhhh
Confidence            4777777664             22459999999999998764 444444443211  111349999999 777899999


Q ss_pred             HHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHH-----HHHHcCCCCCCCccEEEecchhHHhhCCCHH
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFL-----DHLQQGNTSLSRVSFVILDEADRMLDMGFEP  288 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~-----~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~  288 (503)
                      +.++.... .+++..+.+...............+++++|++.+.     ....  .+..-++++||+||+|.+-+.  ..
T Consensus        77 ~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~--~l~~~~~~~vIvDEaH~~k~~--~s  151 (299)
T PF00176_consen   77 IEKWFDPD-SLRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKE--DLKQIKWDRVIVDEAHRLKNK--DS  151 (299)
T ss_dssp             HHHHSGT--TS-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTH--HHHTSEEEEEEETTGGGGTTT--TS
T ss_pred             hccccccc-cccccccccccccccccccccccceeeecccccccccccccccc--ccccccceeEEEecccccccc--cc
Confidence            99998542 35555555554223222233456899999999998     1111  111235899999999988544  33


Q ss_pred             HHHHHHHhCCCCCcEEEEEeeC
Q 010709          289 QIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       289 ~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      .....+..+. ....+++||||
T Consensus       152 ~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  152 KRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             HHHHHHHCCC-ECEEEEE-SS-
T ss_pred             cccccccccc-cceEEeecccc
Confidence            3444555565 45578899998

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.

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

Probab=99.28  E-value=1.1e-09  Score=112.31  Aligned_cols=93  Identities=17%  Similarity=0.228  Sum_probs=77.3

Q ss_pred             CcEEEEEcchhhHHHHHHHHHH----------------------CCCeEEEEcCCCCHHHHHHHHHHHhcCC----CcEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVA----------------------EGLHAVALHGGRNQSDRESALRDFRNGS----TNIL  428 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~----------------------~~~~v~~lh~~~~~~~r~~~~~~f~~g~----~~vL  428 (503)
                      .|.|||.++....+.+..+|..                      .|.....+.|.....+|..+.+.|.+..    ...|
T Consensus      1143 DKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~s~~R~k~~~~FNdp~NlRaRl~L 1222 (1567)
T KOG1015|consen 1143 DKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTTSQSRKKWAEEFNDPTNLRARLFL 1222 (1567)
T ss_pred             ceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCcccHHHHHHHHHHhcCcccceeEEEE
Confidence            5789999999998888888854                      2456788999999999999999998642    4479


Q ss_pred             EEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          429 VATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |+|.+.+.|||+-+++.||.||..+++.--+|-|=|+-|
T Consensus      1223 ISTRAGsLGiNLvAANRVIIfDasWNPSyDtQSIFRvyR 1261 (1567)
T KOG1015|consen 1223 ISTRAGSLGINLVAANRVIIFDASWNPSYDTQSIFRVYR 1261 (1567)
T ss_pred             EeeccCccccceeecceEEEEecccCCccchHHHHHHHh
Confidence            999999999999999999999999998665665555444

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.16  E-value=4.7e-10  Score=106.37  Aligned_cols=73  Identities=19%  Similarity=0.100  Sum_probs=57.1

Q ss_pred             CCcHHHHHHHHH----HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPV----ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       143 ~~~~~Q~~~i~~----i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .|++.|.+.+..    +.+|+++++.+|||+|||++|+.|++.+....+..  ..+.+++|.++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00488        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            469999995554    44788999999999999999999999886654311  02347999999999988887777665

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.16  E-value=4.7e-10  Score=106.37  Aligned_cols=73  Identities=19%  Similarity=0.100  Sum_probs=57.1

Q ss_pred             CCcHHHHHHHHH----HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPV----ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       143 ~~~~~Q~~~i~~----i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .|++.|.+.+..    +.+|+++++.+|||+|||++|+.|++.+....+..  ..+.+++|.++|..+..|....++++
T Consensus         8 ~~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~--~~~~kvi~~t~T~~~~~q~i~~l~~~   84 (289)
T smart00489        8 EPYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER--IQKIKLIYLSRTVSEIEKRLEELRKL   84 (289)
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc--ccccceeEEeccHHHHHHHHHHHHhc
Confidence            469999995554    44788999999999999999999999886654311  02347999999999988887777665

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

Probab=99.15  E-value=7.2e-09  Score=113.10  Aligned_cols=293  Identities=16%  Similarity=0.165  Sum_probs=160.6

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ  238 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (503)
                      +..+|.=-+|||||+... -+...+...     ...+.+++|+-+++|-.|+.+.+..+.....  ..  . ...+..+.
T Consensus       274 ~~G~IWHtqGSGKTlTm~-~~A~~l~~~-----~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~--~~--~-~~~s~~~L  342 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMF-KLARLLLEL-----PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAF--ND--P-KAESTSEL  342 (962)
T ss_pred             CceEEEeecCCchHHHHH-HHHHHHHhc-----cCCCeEEEEechHHHHHHHHHHHHHHHHhhh--hc--c-cccCHHHH
Confidence            358889999999998642 222233332     4578999999999999999999999885432  11  1 34444454


Q ss_pred             HHHhhCC-CcEEEECcHHHHHHHHcCC--CCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHH
Q 010709          239 RSELRGG-VSIVVATPGRFLDHLQQGN--TSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       239 ~~~~~~~-~~Ilv~Tp~~l~~~l~~~~--~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~  315 (503)
                      ...+..+ ..|+|+|.+.|-.......  ..-.+=-+||+|||||--   ++..-..+-..+ ++...++||+||-..-.
T Consensus       343 k~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRSQ---~G~~~~~~~~~~-~~a~~~gFTGTPi~~~d  418 (962)
T COG0610         343 KELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQ---YGELAKLLKKAL-KKAIFIGFTGTPIFKED  418 (962)
T ss_pred             HHHHhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhcc---ccHHHHHHHHHh-ccceEEEeeCCcccccc
Confidence            5555533 4899999999987776541  112223378999999842   222222222333 33669999999832211


Q ss_pred             HH-HHHhcCCCeEEEeCCCCCCCCce-EEEEEEc----------C---------------------------------hh
Q 010709          316 AL-AQEYLTDPVQVKVGKVSSPTANV-IQILEKV----------S---------------------------------EN  350 (503)
Q Consensus       316 ~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~----------~---------------------------------~~  350 (503)
                      .. ....+++...............+ ...+...          .                                 ..
T Consensus       419 ~~tt~~~fg~ylh~Y~i~daI~Dg~vl~i~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~  498 (962)
T COG0610         419 KDTTKDVFGDYLHTYTITDAIRDGAVLPVYYENRVELELIEESIKEEAEELDERIEEITEDILEKIKKKTKNLEFLAMLA  498 (962)
T ss_pred             ccchhhhhcceeEEEecchhhccCceeeEEEeecccccccccchhhhhhhhHHHHhhhHHHHHHHHHHHHhhhhHHhcch
Confidence            11 12222222222111111000000 0000000          0                                 00


Q ss_pred             hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC-------------------e----EEEEcCC
Q 010709          351 EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL-------------------H----AVALHGG  407 (503)
Q Consensus       351 ~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~-------------------~----v~~lh~~  407 (503)
                      .+.......+..+...   ......++++.+.++..|..+.+.......                   .    ....|..
T Consensus       499 ~r~~~~a~~i~~~f~~---~~~~~~kam~V~~sr~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  575 (962)
T COG0610         499 VRLIRAAKDIYDHFKK---EEVFDLKAMVVASSRKVAVELYEAEIAARLDWHSKESLEGAIKDYNTEFETDFDKKQSHAK  575 (962)
T ss_pred             HHHHHHHHHHHHHHHh---hcccCceEEEEEechHHHHHhHHHHhhhhhhhhhhhhhhhHHHHHHhhcccchhhhhhhHH
Confidence            0011111111111111   234456777777777755555544432110                   0    0000111


Q ss_pred             CCHHHHHHHHHHH--hcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeeeee
Q 010709          408 RNQSDRESALRDF--RNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITT  471 (503)
Q Consensus       408 ~~~~~r~~~~~~f--~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~~  471 (503)
                      . ...+......|  +....++||.++++-+|+|-|- -+.+-+|-|----..+|-+-|+.|.+..
T Consensus       576 ~-~~~~~~~~~r~~~~~d~~kilIV~dmlLTGFDaP~-L~TmYvDK~Lk~H~L~QAisRtNR~~~~  639 (962)
T COG0610         576 L-KDEKKDLIKRFKLKDDPLDLLIVVDMLLTGFDAPC-LNTLYVDKPLKYHNLIQAISRTNRVFPG  639 (962)
T ss_pred             H-HHHHhhhhhhhcCcCCCCCEEEEEccccccCCccc-cceEEeccccccchHHHHHHHhccCCCC
Confidence            1 22233334443  4567899999999999999994 5566777777778899999999998776

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.13  E-value=1.9e-09  Score=104.20  Aligned_cols=317  Identities=22%  Similarity=0.224  Sum_probs=197.2

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEE-ccCCCch--hHHhHHHHHHHHHhcCC-----------------------CCCCCCC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGC-AETGSGK--TAAFTIPMIQHCVAQTP-----------------------VGRGDGP  195 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~-~~TGsGK--Tl~~~lp~l~~~~~~~~-----------------------~~~~~~~  195 (503)
                      ..+|+.|.+.+-.+.+-+|++.. +-.+.|+  +-.|.+.++.++++.+.                       -.+...|
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            46899999999998888886543 2224455  45677888888664220                       0122368


Q ss_pred             eEEEEcccHHHHHHHHHHHHHHhccCCCce--------EEEEECCc--------cHHHHHHH------------------
Q 010709          196 LALVLAPTRELAQQIEKEVKALSRSLDSFK--------TAIVVGGT--------NIAEQRSE------------------  241 (503)
Q Consensus       196 ~~lil~Ptr~La~q~~~~~~~~~~~~~~~~--------~~~~~~~~--------~~~~~~~~------------------  241 (503)
                      +||||||+|+.|-.+...+..+..+...-+        ...-++|.        ...+....                  
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            999999999999999988888754332100        01111110        00000000                  


Q ss_pred             ----h---hCCCcEEEECcHHHHHHHHcC-----C-CCCCCccEEEecchhHHhhCCCHHHHHHHHHhC---CC------
Q 010709          242 ----L---RGGVSIVVATPGRFLDHLQQG-----N-TSLSRVSFVILDEADRMLDMGFEPQIREVMQNL---PD------  299 (503)
Q Consensus       242 ----~---~~~~~Ilv~Tp~~l~~~l~~~-----~-~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~---~~------  299 (503)
                          +   ....+|+||+|=-|...+.+.     . -.+..+.++|||-||-++... -..+..++..+   |.      
T Consensus       375 KtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEhl~~ifdHLn~~P~k~h~~D  453 (698)
T KOG2340|consen  375 KTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEHLLHIFDHLNLQPSKQHDVD  453 (698)
T ss_pred             HHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHHHHHHHHHhhcCcccccCCC
Confidence                0   135899999998887777632     1 136778999999999776443 23344444443   22      


Q ss_pred             ---------------CCcEEEEEeeCCHHHHHHHHHhcCCCeEE-Ee---------CCCCCCCCceEEEEEEcCh----h
Q 010709          300 ---------------KHQTLLFSATMPVEIEALAQEYLTDPVQV-KV---------GKVSSPTANVIQILEKVSE----N  350 (503)
Q Consensus       300 ---------------~~q~i~~SAT~~~~~~~~~~~~~~~~~~~-~~---------~~~~~~~~~~~~~~~~~~~----~  350 (503)
                                     -+|+++||+--.+....+...+..|..-. ..         .....+...+.+.+..-..    .
T Consensus       454 fSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~Gkv~~~~~~~~gsi~~v~~~l~Qvf~ri~~~si~~~~D  533 (698)
T KOG2340|consen  454 FSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMAGKVKARNLQSGGSISNVGIPLCQVFQRIEVKSIIETPD  533 (698)
T ss_pred             hhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhcceeeeccccCCCchhhccchhhhhhhheeccCcccCch
Confidence                           14788888887777666666555442211 11         1111111222222222222    2


Q ss_pred             hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEE
Q 010709          351 EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVA  430 (503)
Q Consensus       351 ~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLva  430 (503)
                      .+.......+......     .....+|||.++.-.--++..++.+..+..+.+|.-.++.+-.+.-+.|..|...||+-
T Consensus       534 ~RFkyFv~~ImPq~~k-----~t~s~~LiyIPSYfDFVRvRNy~K~e~i~F~~i~EYssk~~vsRAR~lF~qgr~~vlLy  608 (698)
T KOG2340|consen  534 ARFKYFVDKIMPQLIK-----RTESGILIYIPSYFDFVRVRNYMKKEEISFVMINEYSSKSKVSRARELFFQGRKSVLLY  608 (698)
T ss_pred             HHHHHHHHhhchhhcc-----cccCceEEEecchhhHHHHHHHhhhhhcchHHHhhhhhHhhhhHHHHHHHhcCceEEEE
Confidence            2333333222222111     11234899999999999999999999888888887777777777778899999999999


Q ss_pred             ccccc--cCCCCCCCCEEEEccCCCChhHHH---HhhCc
Q 010709          431 TDVAS--RGLDVMGVAHVVNLDLPKVLLAAS---ESLCT  464 (503)
Q Consensus       431 T~~~~--~Gldip~v~~VI~~~~p~s~~~~~---Qr~GR  464 (503)
                      |.-+.  +-.+|.+|+.||+|.+|..+.-|.   -+++|
T Consensus       609 TER~hffrR~~ikGVk~vVfYqpP~~P~FYsEiinm~~k  647 (698)
T KOG2340|consen  609 TERAHFFRRYHIKGVKNVVFYQPPNNPHFYSEIINMSDK  647 (698)
T ss_pred             ehhhhhhhhheecceeeEEEecCCCCcHHHHHHHhhhhh
Confidence            97554  678999999999999999985444   44444

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

Probab=99.10  E-value=6.7e-09  Score=107.90  Aligned_cols=319  Identities=20%  Similarity=0.194  Sum_probs=194.0

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+.+|.-.-  +.-...-|.-+.||-|||+++.+|+....+.        |..+.+++-.--||.--++++..+...+ 
T Consensus        80 ~~~dVQliG~--i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~--------gkgVhvVTvNdYLA~RDae~m~~l~~~L-  148 (822)
T COG0653          80 RHFDVQLLGG--IVLHLGDIAEMRTGEGKTLVATLPAYLNALA--------GKGVHVVTVNDYLARRDAEWMGPLYEFL-  148 (822)
T ss_pred             ChhhHHHhhh--hhhcCCceeeeecCCchHHHHHHHHHHHhcC--------CCCcEEeeehHHhhhhCHHHHHHHHHHc-
Confidence            4555554444  3344457789999999999999888766544        5668899999899998888888888776 


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-h--------CC-
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-D--------MG-  285 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~--------~~-  285 (503)
                      ++.+++...+....+....  ..++|.++|-..| .+.+.-+      ......+.+.|+||++-++ +        .| 
T Consensus       149 GlsvG~~~~~m~~~ek~~a--Y~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSILIDEARtPLiISG~  226 (822)
T COG0653         149 GLSVGVILAGMSPEEKRAA--YACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSILIDEARTPLIISGP  226 (822)
T ss_pred             CCceeeccCCCChHHHHHH--HhcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhheeeeccccceeeecc
Confidence            6999999988876654443  4589999998776 2222111      1224467889999998522 1        00 


Q ss_pred             ------CHHHHHHHHHhCCCC-----------------------------------------------------------
Q 010709          286 ------FEPQIREVMQNLPDK-----------------------------------------------------------  300 (503)
Q Consensus       286 ------~~~~~~~il~~~~~~-----------------------------------------------------------  300 (503)
                            ....+..+...+...                                                           
T Consensus       227 ~~~~~~~Y~~~~~~v~~l~~~~d~~iDek~k~v~lte~G~~kae~~f~~~~Ly~~en~~~~h~~~~alrA~~l~~~D~dY  306 (822)
T COG0653         227 AEDSSELYKKVDDLVRLLSEDEDFTIDEKSKNVSLTESGLEKAEELLGIENLYDLENVNLVHHLNQALRAHILFFRDVDY  306 (822)
T ss_pred             cccCchHHHHHHHHHHHhccccceeecchhcccccchhhHHHHHHHhCcccccchhhHHHHhhHHHHHHHHHHhhcCCee
Confidence                  111222222111100                                                           


Q ss_pred             ----C------------------------------------------------------cEEEEEeeCCHHHHHHHHHhc
Q 010709          301 ----H------------------------------------------------------QTLLFSATMPVEIEALAQEYL  322 (503)
Q Consensus       301 ----~------------------------------------------------------q~i~~SAT~~~~~~~~~~~~~  322 (503)
                          -                                                      ++.+||+|...+-..+..-|.
T Consensus       307 IVrd~ev~IvD~ftGR~m~gRr~s~GLhQAiEAKEgv~i~~e~~tlatITfQn~fR~y~kl~gmTGTa~te~~EF~~iY~  386 (822)
T COG0653         307 IVRDGEVVIVDEFTGRMMEGRRWSDGLHQAIEAKEGVEIQEENQTLATITFQNLFRLYPKLAGMTGTADTEEEEFDVIYG  386 (822)
T ss_pred             EEecCeEEEEecccCCcccCcCCCchhHHHHHHhcCCcccccceeehhhhHHHHHhhhhhhcCCCCcchhhhhhhhhccC
Confidence                0                                                      111222222111111111111


Q ss_pred             CCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEE
Q 010709          323 TDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV  402 (503)
Q Consensus       323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~  402 (503)
                      -+ +.+........ ..-..-.......+|....+..+......       +.|+||-..+.+..+.+.+.|.+.|++..
T Consensus       387 l~-vv~iPTnrp~~-R~D~~D~vy~t~~~K~~Aiv~~I~~~~~~-------gqPvLvgT~sie~SE~ls~~L~~~~i~h~  457 (822)
T COG0653         387 LD-VVVIPTNRPII-RLDEPDLVYKTEEEKFKAIVEDIKERHEK-------GQPVLVGTVSIEKSELLSKLLRKAGIPHN  457 (822)
T ss_pred             Cc-eeeccCCCccc-CCCCccccccchHHHHHHHHHHHHHHHhc-------CCCEEEcCcceecchhHHHHHHhcCCCce
Confidence            11 11111111111 11111223335567888888887776543       44799999999999999999999999988


Q ss_pred             EEcCCCCHHHHHHHHHHHhcCC-CcEEEEccccccCCCCCCCC-----------EEEEccCCCChhHHHHhhCcceeeee
Q 010709          403 ALHGGRNQSDRESALRDFRNGS-TNILVATDVASRGLDVMGVA-----------HVVNLDLPKVLLAASESLCTTSFNIT  470 (503)
Q Consensus       403 ~lh~~~~~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip~v~-----------~VI~~~~p~s~~~~~Qr~GR~gR~~~  470 (503)
                      .+.......+-..+-+   .|. -.|-|||++++||-||.--.           +||-...-.|..-=.|--||+||.. 
T Consensus       458 VLNAk~h~~EA~Iia~---AG~~gaVTiATNMAGRGTDIkLg~~~~~V~~lGGL~VIgTERhESRRIDnQLRGRsGRQG-  533 (822)
T COG0653         458 VLNAKNHAREAEIIAQ---AGQPGAVTIATNMAGRGTDIKLGGNPEFVMELGGLHVIGTERHESRRIDNQLRGRAGRQG-  533 (822)
T ss_pred             eeccccHHHHHHHHhh---cCCCCccccccccccCCcccccCCCHHHHHHhCCcEEEecccchhhHHHHHhhcccccCC-
Confidence            8887776444443333   343 35789999999999987322           4555555666655568889999874 


Q ss_pred             eccCchhhhhhHHHHHHHHHHH
Q 010709          471 TNLDGDMKKLEFCLILAITVLL  492 (503)
Q Consensus       471 ~~~~~~~~~~~~~~~~~~~~~~  492 (503)
                           +...-.++..++|++..
T Consensus       534 -----DpG~S~F~lSleD~L~r  550 (822)
T COG0653         534 -----DPGSSRFYLSLEDDLMR  550 (822)
T ss_pred             -----CcchhhhhhhhHHHHHH
Confidence                 34445556666666543

>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=98.98  E-value=2e-08  Score=92.60  Aligned_cols=129  Identities=26%  Similarity=0.344  Sum_probs=95.2

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      -..|++.|..+.-.+.+|+  |+...||-|||++..+|+....+.        |..|-|++.+..||..=++.+..+...
T Consensus        75 g~~p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~--------G~~V~vvT~NdyLA~RD~~~~~~~y~~  144 (266)
T PF07517_consen   75 GLRPYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ--------GKGVHVVTSNDYLAKRDAEEMRPFYEF  144 (266)
T ss_dssp             S----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT--------SS-EEEEESSHHHHHHHHHHHHHHHHH
T ss_pred             CCcccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh--------cCCcEEEeccHHHhhccHHHHHHHHHH
Confidence            3479999999998886665  999999999999888777766554        677999999999999999999999887


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHH-HHHHcC----C--CCCCCccEEEecchhHHh
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFL-DHLQQG----N--TSLSRVSFVILDEADRML  282 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~-~~l~~~----~--~~l~~~~~vViDEaH~l~  282 (503)
                      + ++.++++.++....+....  ..++|+++|...+. +.+...    .  .....+.++||||+|.++
T Consensus       145 L-Glsv~~~~~~~~~~~r~~~--Y~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  145 L-GLSVGIITSDMSSEERREA--YAADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             T-T--EEEEETTTEHHHHHHH--HHSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             h-hhccccCccccCHHHHHHH--HhCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            7 6999999998876543332  34789999998884 333321    1  125678999999999754

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 ....

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

Probab=98.79  E-value=2e-09  Score=112.00  Aligned_cols=230  Identities=17%  Similarity=0.216  Sum_probs=141.8

Q ss_pred             CCcHHHHHHHHHHhc-CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          143 RPTSIQAQAMPVALS-GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~-~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ...|.|.+.+..+.+ ..++++-+|||+|||++|.+.++......+      +.++++++|..+|+..-.+.+...... 
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~~p------~~kvvyIap~kalvker~~Dw~~r~~~-  999 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSYYP------GSKVVYIAPDKALVKERSDDWSKRDEL-  999 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhccCC------CccEEEEcCCchhhcccccchhhhccc-
Confidence            345566666666554 356999999999999999988887665543      578999999999988877777765533 


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc--CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh---
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ--GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN---  296 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~--~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~---  296 (503)
                      +++++.-+.|+....-  ..+ ..++++|+||++.......  ..-.+++++.+|+||.|.+ +.++++.++.+...   
T Consensus      1000 ~g~k~ie~tgd~~pd~--~~v-~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hll-g~~rgPVle~ivsr~n~ 1075 (1230)
T KOG0952|consen 1000 PGIKVIELTGDVTPDV--KAV-READIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLL-GEDRGPVLEVIVSRMNY 1075 (1230)
T ss_pred             CCceeEeccCccCCCh--hhe-ecCceEEcccccccCccccccchhhhccccceeecccccc-cCCCcceEEEEeecccc
Confidence            3677887877765541  112 3489999999999776663  3456889999999999955 44455544444332   


Q ss_pred             ----CCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCC-ceEEEEEEcChhhHHHHHHHHHHHHHHhhhccC
Q 010709          297 ----LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTA-NVIQILEKVSENEKVDRLLALLVEEAFLAEKSC  371 (503)
Q Consensus       297 ----~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~  371 (503)
                          ..+.+|++++|.-+ .+..++ .++++.+..  .+......+ .....+...+. .-.--....+.+...+..+..
T Consensus      1076 ~s~~t~~~vr~~glsta~-~na~dl-a~wl~~~~~--~nf~~svrpvp~~~~i~gfp~-~~~cprm~smnkpa~qaik~~ 1150 (1230)
T KOG0952|consen 1076 ISSQTEEPVRYLGLSTAL-ANANDL-ADWLNIKDM--YNFRPSVRPVPLEVHIDGFPG-QHYCPRMMSMNKPAFQAIKTH 1150 (1230)
T ss_pred             CccccCcchhhhhHhhhh-hccHHH-HHHhCCCCc--CCCCcccccCCceEeecCCCc-hhcchhhhhcccHHHHHHhcC
Confidence                23456677766444 233333 334433222  122121111 22223333332 111111112233445555666


Q ss_pred             CCCCcEEEEEcchhhHH
Q 010709          372 HPFPLTIVFVERKTRCD  388 (503)
Q Consensus       372 ~~~~~~lIF~~~~~~~~  388 (503)
                      .|..++|||+.+++.-.
T Consensus      1151 sp~~p~lifv~srrqtr 1167 (1230)
T KOG0952|consen 1151 SPIKPVLIFVSSRRQTR 1167 (1230)
T ss_pred             CCCCceEEEeecccccc
Confidence            88899999999977643

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

Probab=98.77  E-value=6.9e-08  Score=102.76  Aligned_cols=144  Identities=17%  Similarity=0.248  Sum_probs=86.4

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH-----HHhcc-CCC--ceEEEEE
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK-----ALSRS-LDS--FKTAIVV  230 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~-----~~~~~-~~~--~~~~~~~  230 (503)
                      .++.+.++||+|||.+|+-.++......+      ..++||+||+.++...+...+.     .++.. ..+  +....+.
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~~~------~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~  133 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQKYG------LFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVIN  133 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHHcC------CcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEe
Confidence            36899999999999999766655443332      4679999999998887775554     22221 112  3333333


Q ss_pred             CCc-------cHHHHHHHhh-------CCCcEEEECcHHHHHHHH-cCC----------CCCCCc----cEEEecchhHH
Q 010709          231 GGT-------NIAEQRSELR-------GGVSIVVATPGRFLDHLQ-QGN----------TSLSRV----SFVILDEADRM  281 (503)
Q Consensus       231 ~~~-------~~~~~~~~~~-------~~~~Ilv~Tp~~l~~~l~-~~~----------~~l~~~----~~vViDEaH~l  281 (503)
                      ++.       ......+.+.       +...|+|+|.+.|..... +..          ..+..+    -+||+||.|++
T Consensus       134 S~k~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~  213 (986)
T PRK15483        134 AGDKKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRF  213 (986)
T ss_pred             cCcccccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCC
Confidence            322       1122222222       147899999999865322 100          111111    27999999987


Q ss_pred             hhCCCHHHHHHHHHhCCCCCcEEEEEeeCCH
Q 010709          282 LDMGFEPQIREVMQNLPDKHQTLLFSATMPV  312 (503)
Q Consensus       282 ~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  312 (503)
                      -..  ...+..+ ..++|.+ ++.+|||.+.
T Consensus       214 ~~~--~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        214 PRD--NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             Ccc--hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            442  3345555 6666555 6779999976

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=98.73  E-value=5.5e-07  Score=92.54  Aligned_cols=55  Identities=7%  Similarity=-0.007  Sum_probs=48.1

Q ss_pred             CCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeeeeeccCchhh
Q 010709          424 STNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNITTNLDGDMK  478 (503)
Q Consensus       424 ~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~~~~~~~~~  478 (503)
                      -.+.+++-.++-+|.|=|+|=.++-+....|..+-.|.+||.=|.-......++.
T Consensus       483 plRFIFS~waLrEGWDNPNVFtIckL~~S~SeiSK~QeVGRGLRLaVNe~G~RV~  537 (985)
T COG3587         483 PLRFIFSKWALREGWDNPNVFTICKLRSSGSEISKLQEVGRGLRLAVNENGERVT  537 (985)
T ss_pred             cceeeeehhHHhhcCCCCCeeEEEEecCCCcchHHHHHhccceeeeeccccceec
Confidence            4789999999999999999999999999999999999999988876666554444

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=98.71  E-value=2e-07  Score=99.16  Aligned_cols=70  Identities=16%  Similarity=0.097  Sum_probs=58.2

Q ss_pred             hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       242 ~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      +.....|+++||..|..-+..+.+.+..+..|||||||++.+..-...+.++.+..++..-+.+|||.|.
T Consensus         4 ly~~ggi~~~T~rIl~~DlL~~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~   73 (814)
T TIGR00596         4 VYLEGGIFSITSRILVVDLLTGIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPE   73 (814)
T ss_pred             HhhcCCEEEEechhhHhHHhcCCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCc
Confidence            3455789999999998888888999999999999999999877666667777777666666888888883

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

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

Probab=98.58  E-value=3.1e-07  Score=82.13  Aligned_cols=123  Identities=21%  Similarity=0.302  Sum_probs=72.8

Q ss_pred             CCcHHHHHHHHHHhcCCC--eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          143 RPTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~--vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ++++-|.+++..++.+++  +++.|+.|+|||... ..+...+...       +.++++++||...+..+.+...     
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~~-------g~~v~~~apT~~Aa~~L~~~~~-----   67 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEAA-------GKRVIGLAPTNKAAKELREKTG-----   67 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHHT-------T--EEEEESSHHHHHHHHHHHT-----
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHhC-------CCeEEEECCcHHHHHHHHHhhC-----
Confidence            367889999999976543  788899999999753 3344444332       5779999999988776555421     


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC----CCCCCccEEEecchhHHhhCCCHHHHHHHHHh
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN----TSLSRVSFVILDEADRMLDMGFEPQIREVMQN  296 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~----~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~  296 (503)
                         +.                        ..|...++.......    ..+...++||||||-.+.    ...+..++..
T Consensus        68 ---~~------------------------a~Ti~~~l~~~~~~~~~~~~~~~~~~vliVDEasmv~----~~~~~~ll~~  116 (196)
T PF13604_consen   68 ---IE------------------------AQTIHSFLYRIPNGDDEGRPELPKKDVLIVDEASMVD----SRQLARLLRL  116 (196)
T ss_dssp             ---S-------------------------EEEHHHHTTEECCEECCSSCC-TSTSEEEESSGGG-B----HHHHHHHHHH
T ss_pred             ---cc------------------------hhhHHHHHhcCCcccccccccCCcccEEEEecccccC----HHHHHHHHHH
Confidence               11                        122222221111110    115567899999999654    4567778887


Q ss_pred             CCC-CCcEEEEEee
Q 010709          297 LPD-KHQTLLFSAT  309 (503)
Q Consensus       297 ~~~-~~q~i~~SAT  309 (503)
                      .+. ..++|++--+
T Consensus       117 ~~~~~~klilvGD~  130 (196)
T PF13604_consen  117 AKKSGAKLILVGDP  130 (196)
T ss_dssp             S-T-T-EEEEEE-T
T ss_pred             HHhcCCEEEEECCc
Confidence            766 6666666543

>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]

Probab=98.50  E-value=2e-05  Score=80.22  Aligned_cols=93  Identities=18%  Similarity=0.273  Sum_probs=72.0

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCC------------------CeEEEEcCCCCHHHHHHHHHHHhcCC---CcEEEEccc
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEG------------------LHAVALHGGRNQSDRESALRDFRNGS---TNILVATDV  433 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~------------------~~v~~lh~~~~~~~r~~~~~~f~~g~---~~vLvaT~~  433 (503)
                      .++|||.......+.+.+.|.+..                  .....+.|..+..+|.+.+++|.+.-   --++++|.+
T Consensus       720 ~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~a~~rekLinqfN~e~~lsWlfllstra  799 (1387)
T KOG1016|consen  720 EKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTSAADREKLINQFNSEPGLSWLFLLSTRA  799 (1387)
T ss_pred             ceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcccchHHHHHHhccCCCCceeeeeehhcc
Confidence            457888888888888888886531                  23456788889999999999998632   347889999


Q ss_pred             cccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          434 ASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       434 ~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      ...|||+=+.+.+|.||.-++..--.|.+.|+-|
T Consensus       800 g~lGinLIsanr~~ifda~wnpchdaqavcRvyr  833 (1387)
T KOG1016|consen  800 GSLGINLISANRCIIFDACWNPCHDAQAVCRVYR  833 (1387)
T ss_pred             ccccceeeccceEEEEEeecCccccchhhhhhhh
Confidence            9999999988899999988887666665555443

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

Probab=98.49  E-value=1e-06  Score=81.46  Aligned_cols=72  Identities=24%  Similarity=0.328  Sum_probs=50.5

Q ss_pred             CcHHHHHHHHHHhcCCC-eEEEccCCCchhHHhHHHHHHHHHhc-CCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          144 PTSIQAQAMPVALSGRD-LLGCAETGSGKTAAFTIPMIQHCVAQ-TPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~-~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      +.+.|.+|+..++.... .+|.||+|+|||... ..++..+... .......+.++|+++|+...+..+.+.+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l-~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTL-ASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHH-HHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHH-HHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            56789999999998888 999999999999653 3444444210 000123468899999999999999988877

>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=98.47  E-value=8.9e-07  Score=78.47  Aligned_cols=142  Identities=15%  Similarity=0.258  Sum_probs=72.5

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH-------HHHH
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI-------EKEV  214 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~-------~~~~  214 (503)
                      ...+..|..++.++.+.+-+++.||.|+|||+.++..++..+...      ...+++|+-|..+....+       .+.+
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g------~~~kiii~Rp~v~~~~~lGflpG~~~eK~   76 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG------EYDKIIITRPPVEAGEDLGFLPGDLEEKM   76 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT------S-SEEEEEE-S--TT----SS--------
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC------CCcEEEEEecCCCCccccccCCCCHHHHH
Confidence            345778999999999777799999999999998877777766542      346678887876532111       1111


Q ss_pred             HHHhcc----CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHH
Q 010709          215 KALSRS----LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQI  290 (503)
Q Consensus       215 ~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~  290 (503)
                      ..+...    +..+.     +....    ..+.....|-+.....+.     + ..+. -.+||+|||+.+.    ..++
T Consensus        77 ~p~~~p~~d~l~~~~-----~~~~~----~~~~~~~~Ie~~~~~~iR-----G-rt~~-~~~iIvDEaQN~t----~~~~  136 (205)
T PF02562_consen   77 EPYLRPIYDALEELF-----GKEKL----EELIQNGKIEIEPLAFIR-----G-RTFD-NAFIIVDEAQNLT----PEEL  136 (205)
T ss_dssp             -TTTHHHHHHHTTTS------TTCH----HHHHHTTSEEEEEGGGGT-----T---B--SEEEEE-SGGG------HHHH
T ss_pred             HHHHHHHHHHHHHHh-----ChHhH----HHHhhcCeEEEEehhhhc-----C-cccc-ceEEEEecccCCC----HHHH
Confidence            111100    00000     11111    111122344444433221     1 1122 3799999999765    6788


Q ss_pred             HHHHHhCCCCCcEEEEEee
Q 010709          291 REVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       291 ~~il~~~~~~~q~i~~SAT  309 (503)
                      ..++.++..+.+++++.-.
T Consensus       137 k~ilTR~g~~skii~~GD~  155 (205)
T PF02562_consen  137 KMILTRIGEGSKIIITGDP  155 (205)
T ss_dssp             HHHHTTB-TT-EEEEEE--
T ss_pred             HHHHcccCCCcEEEEecCc
Confidence            9999999988988876543

; GO: 0005524 ATP binding; PDB: 3B85_A.

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

Probab=98.31  E-value=2.7e-06  Score=84.68  Aligned_cols=66  Identities=27%  Similarity=0.384  Sum_probs=53.0

Q ss_pred             CCCcHHHHHHHHHHhcCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALSGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK  215 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~  215 (503)
                      ..+.+-|.+|+....+.++ .+|.||+|+|||... .-++..+..+       +.++|+.+||.+.+.-+.+++.
T Consensus       184 ~~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~Tl-vEiI~qlvk~-------~k~VLVcaPSn~AVdNiverl~  250 (649)
T KOG1803|consen  184 KNLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTL-VEIISQLVKQ-------KKRVLVCAPSNVAVDNIVERLT  250 (649)
T ss_pred             ccccHHHHHHHHHHhccCCceEeeCCCCCCceeeH-HHHHHHHHHc-------CCeEEEEcCchHHHHHHHHHhc
Confidence            4567779999999998876 899999999999875 4455555554       6889999999998888877543

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=98.27  E-value=1.2e-05  Score=79.68  Aligned_cols=144  Identities=22%  Similarity=0.241  Sum_probs=71.8

Q ss_pred             EEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH----HH
Q 010709          163 GCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA----EQ  238 (503)
Q Consensus       163 i~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~  238 (503)
                      ..++||||||++....+| ++...+      ....|+.|..-..+......+..-...---+.-.+.+++....    ..
T Consensus         2 f~matgsgkt~~ma~lil-~~y~kg------yr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~   74 (812)
T COG3421           2 FEMATGSGKTLVMAGLIL-ECYKKG------YRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNN   74 (812)
T ss_pred             cccccCCChhhHHHHHHH-HHHHhc------hhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecc
Confidence            457899999997644444 333321      3446777766555444433222110000000111111221110    11


Q ss_pred             HHHhhCCCcEEEECcHHHHHHHHcCC---C---CCCCccEE-EecchhHHhhCC---------CHHHHHHHHH-hC--CC
Q 010709          239 RSELRGGVSIVVATPGRFLDHLQQGN---T---SLSRVSFV-ILDEADRMLDMG---------FEPQIREVMQ-NL--PD  299 (503)
Q Consensus       239 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~---~---~l~~~~~v-ViDEaH~l~~~~---------~~~~~~~il~-~~--~~  299 (503)
                      ......+..|+++|.+.|...+.+..   .   .+.+.++| +-||||++-...         -...|+..+. .+  .+
T Consensus        75 fsehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~~nk  154 (812)
T COG3421          75 FSEHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALEQNK  154 (812)
T ss_pred             cCccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHhcCC
Confidence            11234567899999999977665532   2   34455554 559999875321         1122222221 11  33


Q ss_pred             CCcEEEEEeeCCHH
Q 010709          300 KHQTLLFSATMPVE  313 (503)
Q Consensus       300 ~~q~i~~SAT~~~~  313 (503)
                      +.-++.+|||.|.+
T Consensus       155 d~~~lef~at~~k~  168 (812)
T COG3421         155 DNLLLEFSATIPKE  168 (812)
T ss_pred             CceeehhhhcCCcc
Confidence            44467789999843

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

Probab=98.27  E-value=2.2e-05  Score=78.78  Aligned_cols=77  Identities=19%  Similarity=0.222  Sum_probs=63.4

Q ss_pred             HHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          135 DIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       135 ~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      .+...++.++..-|..|+.+++++.-.||.||+|+|||... ..++.++..+      .+..+|+++|+...+.|+++.+
T Consensus       402 ~~s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvts-a~IVyhl~~~------~~~~VLvcApSNiAVDqLaeKI  474 (935)
T KOG1802|consen  402 RFSVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ------HAGPVLVCAPSNIAVDQLAEKI  474 (935)
T ss_pred             hhcCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehh-HHHHHHHHHh------cCCceEEEcccchhHHHHHHHH
Confidence            44456778889999999999999999999999999999875 4455555554      2566999999999999999999


Q ss_pred             HHHh
Q 010709          215 KALS  218 (503)
Q Consensus       215 ~~~~  218 (503)
                      .+-+
T Consensus       475 h~tg  478 (935)
T KOG1802|consen  475 HKTG  478 (935)
T ss_pred             HhcC
Confidence            8765

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

Probab=98.26  E-value=1.6e-05  Score=73.72  Aligned_cols=160  Identities=16%  Similarity=0.188  Sum_probs=101.1

Q ss_pred             CCcHHHHHHHHHHh----------cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVAL----------SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEK  212 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----------~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~  212 (503)
                      .+...|.+++-...          .+.-.++-..||.||--+..--++..++.-       .++.|++..+..|-....+
T Consensus        37 ~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G-------r~r~vwvS~s~dL~~Da~R  109 (303)
T PF13872_consen   37 LLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRG-------RKRAVWVSVSNDLKYDAER  109 (303)
T ss_pred             cccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcC-------CCceEEEECChhhhhHHHH
Confidence            46777888875543          123489999999999986654455554441       3568999999999999999


Q ss_pred             HHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC---CCCC--------CC-ccEEEecchhH
Q 010709          213 EVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG---NTSL--------SR-VSFVILDEADR  280 (503)
Q Consensus       213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~---~~~l--------~~-~~~vViDEaH~  280 (503)
                      .++.++...  +.+..+..-.. .   ....-...|+++|+..|...-...   ...+        .+ =.+||+||||+
T Consensus       110 Dl~DIG~~~--i~v~~l~~~~~-~---~~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~  183 (303)
T PF13872_consen  110 DLRDIGADN--IPVHPLNKFKY-G---DIIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHK  183 (303)
T ss_pred             HHHHhCCCc--ccceechhhcc-C---cCCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchh
Confidence            999887542  22222211000 0   001224579999999987765321   1111        11 24899999998


Q ss_pred             HhhCCC--------HHHHHHHHHhCCCCCcEEEEEeeCCHHHHH
Q 010709          281 MLDMGF--------EPQIREVMQNLPDKHQTLLFSATMPVEIEA  316 (503)
Q Consensus       281 l~~~~~--------~~~~~~il~~~~~~~q~i~~SAT~~~~~~~  316 (503)
                      +.+..-        +..+..+..++|. -+++.+|||-..+.++
T Consensus       184 akn~~~~~~~~sk~g~avl~LQ~~LP~-ARvvY~SATgasep~N  226 (303)
T PF13872_consen  184 AKNLSSGSKKPSKTGIAVLELQNRLPN-ARVVYASATGASEPRN  226 (303)
T ss_pred             cCCCCccCccccHHHHHHHHHHHhCCC-CcEEEecccccCCCce
Confidence            766532        2345556666754 4599999998555443

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

Probab=98.20  E-value=8.2e-06  Score=80.24  Aligned_cols=108  Identities=18%  Similarity=0.297  Sum_probs=68.6

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR  239 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (503)
                      .++|.|..|+|||+.+ +-++..+.     ....+..++++++...|...+.+.+..-...                   
T Consensus         3 v~~I~G~aGTGKTvla-~~l~~~l~-----~~~~~~~~~~l~~n~~l~~~l~~~l~~~~~~-------------------   57 (352)
T PF09848_consen    3 VILITGGAGTGKTVLA-LNLAKELQ-----NSEEGKKVLYLCGNHPLRNKLREQLAKKYNP-------------------   57 (352)
T ss_pred             EEEEEecCCcCHHHHH-HHHHHHhh-----ccccCCceEEEEecchHHHHHHHHHhhhccc-------------------
Confidence            4799999999999865 33444431     1123677899999999988777777553200                   


Q ss_pred             HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-------CHHHHHHHHHh
Q 010709          240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-------FEPQIREVMQN  296 (503)
Q Consensus       240 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-------~~~~~~~il~~  296 (503)
                          ......+..+..+.+.+.........+++|||||||++...+       ....+..+++.
T Consensus        58 ----~~~~~~~~~~~~~i~~~~~~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   58 ----KLKKSDFRKPTSFINNYSESDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             ----chhhhhhhhhHHHHhhcccccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence                001223444444444333223456789999999999998731       24566666666

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.19  E-value=1.7e-05  Score=82.65  Aligned_cols=142  Identities=20%  Similarity=0.287  Sum_probs=87.3

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCc
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSF  224 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~  224 (503)
                      .++|+.|+...+.++-++|.|++|+|||++. ..++..+....   .....++++++||...|..+.+.+........ .
T Consensus       154 ~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v-~~ll~~l~~~~---~~~~~~i~l~APTgkAA~rL~e~~~~~~~~~~-~  228 (615)
T PRK10875        154 VDWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQLA---DGERCRIRLAAPTGKAAARLTESLGKALRQLP-L  228 (615)
T ss_pred             CHHHHHHHHHHhcCCeEEEEeCCCCCHHHHH-HHHHHHHHHhc---CCCCcEEEEECCcHHHHHHHHHHHHhhhhccc-c
Confidence            5899999999999889999999999999864 33444443321   11235688889999988888877765442221 0


Q ss_pred             eEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc------CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC
Q 010709          225 KTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ------GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP  298 (503)
Q Consensus       225 ~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~------~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~  298 (503)
                      .          ...    ......-..|..+|+.....      +....-.+++|||||+-.+ +   ...+..++..++
T Consensus       229 ~----------~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv-d---~~lm~~ll~al~  290 (615)
T PRK10875        229 T----------DEQ----KKRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV-D---LPMMARLIDALP  290 (615)
T ss_pred             c----------hhh----hhcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc-c---HHHHHHHHHhcc
Confidence            0          000    00001112233333221111      1112335689999999843 2   556778888899


Q ss_pred             CCCcEEEEEee
Q 010709          299 DKHQTLLFSAT  309 (503)
Q Consensus       299 ~~~q~i~~SAT  309 (503)
                      +..++|++.-.
T Consensus       291 ~~~rlIlvGD~  301 (615)
T PRK10875        291 PHARVIFLGDR  301 (615)
T ss_pred             cCCEEEEecch
Confidence            88888887543

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

Probab=98.17  E-value=4.9e-06  Score=86.81  Aligned_cols=93  Identities=16%  Similarity=0.183  Sum_probs=78.8

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCC-Cc-EEEEccccccCCCCCCCCEEEEccCC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGS-TN-ILVATDVASRGLDVMGVAHVVNLDLP  452 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~-~~-vLvaT~~~~~Gldip~v~~VI~~~~p  452 (503)
                      ++++||++-...+..+...|...++....+.|.|+...|.+.+..|..+. .. .+++..+...|+++..+.+|+..|+-
T Consensus       540 ~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~~~~~r~~s~~~~~~~~~~~vll~Slkag~~glnlt~a~~v~~~d~~  619 (674)
T KOG1001|consen  540 PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPCDPLVTALLMSLKAGKVGLNLTAASHVLLMDPW  619 (674)
T ss_pred             CceeeehhHHHHHHHhhhhhhhcccccchhhhhhHHHHHHhhhcccccCccHHHHHHHHHHhhhhhchhhhhHHHhhchh
Confidence            48999999999999999999988999999999999999999999998543 23 45677999999999999999999999


Q ss_pred             CChhHHHHhhCccee
Q 010709          453 KVLLAASESLCTTSF  467 (503)
Q Consensus       453 ~s~~~~~Qr~GR~gR  467 (503)
                      +++..-.|-+-|+.|
T Consensus       620 wnp~~eeQaidR~hr  634 (674)
T KOG1001|consen  620 WNPAVEEQAIDRAHR  634 (674)
T ss_pred             cChHHHHHHHHHHHH
Confidence            888665554444433

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=98.17  E-value=2.4e-05  Score=81.29  Aligned_cols=142  Identities=21%  Similarity=0.291  Sum_probs=87.2

Q ss_pred             HHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCce
Q 010709          146 SIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFK  225 (503)
Q Consensus       146 ~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~  225 (503)
                      ++|+.++..++.++-++|.|+.|+|||+.. ..++..+......  ..+.++++++||-..|..+.+.+......+.   
T Consensus       148 ~~Qk~A~~~al~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~~~--~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~---  221 (586)
T TIGR01447       148 NWQKVAVALALKSNFSLITGGPGTGKTTTV-ARLLLALVKQSPK--QGKLRIALAAPTGKAAARLAESLRKAVKNLA---  221 (586)
T ss_pred             HHHHHHHHHHhhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhccc--cCCCcEEEECCcHHHHHHHHHHHHhhhcccc---
Confidence            789999999999999999999999999864 4444444332110  0135799999999888887777655432211   


Q ss_pred             EEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc------CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC
Q 010709          226 TAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ------GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD  299 (503)
Q Consensus       226 ~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~------~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~  299 (503)
                      ..        ..    ......+-..|..+|+.....      .......+++||||||=++ +   ...+..++..+++
T Consensus       222 ~~--------~~----~~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMv-d---~~l~~~ll~al~~  285 (586)
T TIGR01447       222 AA--------EA----LIAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMV-D---LPLMAKLLKALPP  285 (586)
T ss_pred             cc--------hh----hhhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccC-C---HHHHHHHHHhcCC
Confidence            00        00    000011123343333322110      1112335789999999843 2   4567788888888


Q ss_pred             CCcEEEEEee
Q 010709          300 KHQTLLFSAT  309 (503)
Q Consensus       300 ~~q~i~~SAT  309 (503)
                      ..++|++.-.
T Consensus       286 ~~rlIlvGD~  295 (586)
T TIGR01447       286 NTKLILLGDK  295 (586)
T ss_pred             CCEEEEECCh
Confidence            8888876433

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.

>PRK10536 hypothetical protein; Provisional

Probab=98.15  E-value=5.8e-05  Score=68.91  Aligned_cols=147  Identities=18%  Similarity=0.204  Sum_probs=80.6

Q ss_pred             CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH-------HH
Q 010709          139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ-------IE  211 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q-------~~  211 (503)
                      .++...+..|...+.++.++..+++.||+|+|||+.+....+..+...      .-.+++|.=|+.+....       ..
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~------~~~kIiI~RP~v~~ge~LGfLPG~~~  128 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK------DVDRIIVTRPVLQADEDLGFLPGDIA  128 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC------CeeEEEEeCCCCCchhhhCcCCCCHH
Confidence            455667888999999888877899999999999987755555444331      13445555576542211       12


Q ss_pred             HHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHH
Q 010709          212 KEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQI  290 (503)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~  290 (503)
                      +.+..|...+-+.- ..+.+......   .+. ..-.|-|....    ++. +. .+ +-++||+|||+.+-    ...+
T Consensus       129 eK~~p~~~pi~D~L-~~~~~~~~~~~---~~~~~~~~Iei~~l~----ymR-Gr-tl-~~~~vIvDEaqn~~----~~~~  193 (262)
T PRK10536        129 EKFAPYFRPVYDVL-VRRLGASFMQY---CLRPEIGKVEIAPFA----YMR-GR-TF-ENAVVILDEAQNVT----AAQM  193 (262)
T ss_pred             HHHHHHHHHHHHHH-HHHhChHHHHH---HHHhccCcEEEecHH----Hhc-CC-cc-cCCEEEEechhcCC----HHHH
Confidence            22222221110000 00011111111   111 12234444321    222 11 22 23799999999764    5778


Q ss_pred             HHHHHhCCCCCcEEEE
Q 010709          291 REVMQNLPDKHQTLLF  306 (503)
Q Consensus       291 ~~il~~~~~~~q~i~~  306 (503)
                      ..++.++..+.++|++
T Consensus       194 k~~ltR~g~~sk~v~~  209 (262)
T PRK10536        194 KMFLTRLGENVTVIVN  209 (262)
T ss_pred             HHHHhhcCCCCEEEEe
Confidence            8889999888877764

>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=98.09  E-value=6.3e-05  Score=67.37  Aligned_cols=128  Identities=21%  Similarity=0.288  Sum_probs=82.6

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhc---CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALS---GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~---~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      .|+....+.+++=++..  -...++.|.+....+.+   |++.+...-+|.|||.+. +|++...+..+      ..-+.
T Consensus         4 ~w~p~~~P~wLl~E~e~--~iliR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsVI-~Pmla~~LAdg------~~Lvr   74 (229)
T PF12340_consen    4 NWDPMEYPDWLLFEIES--NILIRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSVI-VPMLALALADG------SRLVR   74 (229)
T ss_pred             CCCchhChHHHHHHHHc--CceeeHHHHHHHHHHhCCCCCCCeEeeecccCCccchH-HHHHHHHHcCC------CcEEE
Confidence            35555566777655543  34678899999988874   578999999999999974 99999888752      34566


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEE-EC-CccH--H--HHH----HHhhCCCcEEEECcHHHHHH
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIV-VG-GTNI--A--EQR----SELRGGVSIVVATPGRFLDH  259 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~-~~-~~~~--~--~~~----~~~~~~~~Ilv~Tp~~l~~~  259 (503)
                      +++|. +|..|..+.++.-....-+-.+..+ +. ....  .  ...    ........|+++||+.++.+
T Consensus        75 viVpk-~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf  144 (229)
T PF12340_consen   75 VIVPK-ALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSF  144 (229)
T ss_pred             EEcCH-HHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHH
Confidence            77776 6889998888755433322222211 11 1111  1  111    12224567999999988543

There are two conserved sequence motifs: LLE and NMG.

>PF13245 AAA_19: Part of AAA domain

Probab=98.06  E-value=2.3e-05  Score=57.83  Aligned_cols=60  Identities=32%  Similarity=0.456  Sum_probs=40.7

Q ss_pred             HHHHHhcCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          151 AMPVALSGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       151 ~i~~i~~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      ++...+.+.. ++|.||+|+|||... +..+.++....  ... +.++++++|++..+..+.+.+
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~-~~~i~~l~~~~--~~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTL-AARIAELLAAR--ADP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHH-HHHHHHHHHHh--cCC-CCeEEEECCCHHHHHHHHHHH
Confidence            4443334444 667999999999765 44444444321  112 577999999999999888877

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=98.04  E-value=5.7e-05  Score=80.86  Aligned_cols=126  Identities=21%  Similarity=0.189  Sum_probs=78.4

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..+++.|.+|+..+..++.++|.|+.|+|||+.. -.++..+....     ....+++++||-..|..+.+..       
T Consensus       322 ~~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~-----~~~~v~l~ApTg~AA~~L~e~~-------  388 (720)
T TIGR01448       322 KGLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELG-----GLLPVGLAAPTGRAAKRLGEVT-------  388 (720)
T ss_pred             CCCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcC-----CCceEEEEeCchHHHHHHHHhc-------
Confidence            4789999999999998888999999999999853 33343333221     1156888899987776544321       


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-----CCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-----GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN  296 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-----~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~  296 (503)
                       +...                        .|..+++.....     ..-.....++||||||+.+.    ...+..++..
T Consensus       389 -g~~a------------------------~Tih~lL~~~~~~~~~~~~~~~~~~~llIvDEaSMvd----~~~~~~Ll~~  439 (720)
T TIGR01448       389 -GLTA------------------------STIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMD----TWLALSLLAA  439 (720)
T ss_pred             -CCcc------------------------ccHHHHhhccCCccchhhhhccccCCEEEEeccccCC----HHHHHHHHHh
Confidence             0100                        011111110000     00112357899999999653    4456777888


Q ss_pred             CCCCCcEEEEEee
Q 010709          297 LPDKHQTLLFSAT  309 (503)
Q Consensus       297 ~~~~~q~i~~SAT  309 (503)
                      ++...++|++.-+
T Consensus       440 ~~~~~rlilvGD~  452 (720)
T TIGR01448       440 LPDHARLLLVGDT  452 (720)
T ss_pred             CCCCCEEEEECcc
Confidence            8888888876443

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.

>TIGR00376 DNA helicase, putative

Probab=98.00  E-value=6.4e-05  Score=79.24  Aligned_cols=67  Identities=25%  Similarity=0.338  Sum_probs=54.0

Q ss_pred             CCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      ..+.+.|.+|+..++.. ..++|.||+|+|||... ..++..+...       +.++|+++||...+.++.+.+..
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-VELIRQLVKR-------GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHH-HHHHHHHHHc-------CCCEEEEcCcHHHHHHHHHHHHh
Confidence            46789999999998876 45899999999999764 4445554443       56899999999999999888876

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.

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

Probab=97.93  E-value=8e-06  Score=71.02  Aligned_cols=79  Identities=25%  Similarity=0.317  Sum_probs=58.6

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHCCC--eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc--ccccCCCCCC--CCEE
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAEGL--HAVALHGGRNQSDRESALRDFRNGSTNILVATD--VASRGLDVMG--VAHV  446 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~~~--~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~--~~~~Gldip~--v~~V  446 (503)
                      .++.+|||+++....+.+.+.+.....  ....+..  ...++..+++.|++++..||+++.  .+.+|+|+|+  ++.|
T Consensus         8 ~~g~~lv~f~Sy~~l~~~~~~~~~~~~~~~~~v~~q--~~~~~~~~l~~~~~~~~~il~~v~~g~~~EGiD~~~~~~r~v   85 (167)
T PF13307_consen    8 VPGGVLVFFPSYRRLEKVYERLKERLEEKGIPVFVQ--GSKSRDELLEEFKRGEGAILLAVAGGSFSEGIDFPGDLLRAV   85 (167)
T ss_dssp             CSSEEEEEESSHHHHHHHHTT-TSS-E-ETSCEEES--TCCHHHHHHHHHCCSSSEEEEEETTSCCGSSS--ECESEEEE
T ss_pred             CCCCEEEEeCCHHHHHHHHHHHHhhcccccceeeec--CcchHHHHHHHHHhccCeEEEEEecccEEEeecCCCchhhee
Confidence            346799999999999999999976532  1122222  245778999999999999999998  9999999996  7899


Q ss_pred             EEccCCC
Q 010709          447 VNLDLPK  453 (503)
Q Consensus       447 I~~~~p~  453 (503)
                      |..++|-
T Consensus        86 ii~glPf   92 (167)
T PF13307_consen   86 IIVGLPF   92 (167)
T ss_dssp             EEES---
T ss_pred             eecCCCC
Confidence            9999883

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

Probab=97.79  E-value=0.0002  Score=67.49  Aligned_cols=144  Identities=15%  Similarity=0.198  Sum_probs=88.7

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCC--eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH-----
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI-----  210 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~--vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~-----  210 (503)
                      ..|+..-...|.-|+..++.-.-  |.+.|+.|+|||+.++.+.+...+.++.     ..++|+.=|+..+.+.+     
T Consensus       223 vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~-----y~KiiVtRp~vpvG~dIGfLPG  297 (436)
T COG1875         223 VWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKR-----YRKIIVTRPTVPVGEDIGFLPG  297 (436)
T ss_pred             hhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhh-----hceEEEecCCcCcccccCcCCC
Confidence            45777777888889998886543  8899999999999888888887776532     35566666876654332     


Q ss_pred             --HHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCC----------ccEEEecch
Q 010709          211 --EKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSR----------VSFVILDEA  278 (503)
Q Consensus       211 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~----------~~~vViDEa  278 (503)
                        .+.+..|++..              .+....+..   .-=++.+.+...+.+..+.+..          =.+||||||
T Consensus       298 ~eEeKm~PWmq~i--------------~DnLE~L~~---~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEa  360 (436)
T COG1875         298 TEEEKMGPWMQAI--------------FDNLEVLFS---PNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEA  360 (436)
T ss_pred             chhhhccchHHHH--------------HhHHHHHhc---ccccchHHHHHHHhccceeeeeeeeecccccccceEEEehh
Confidence              11111111110              011111111   1111234454444444332211          148999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      +.+-    ..++..++.+..+..++|++.
T Consensus       361 QNLT----pheikTiltR~G~GsKIVl~g  385 (436)
T COG1875         361 QNLT----PHELKTILTRAGEGSKIVLTG  385 (436)
T ss_pred             hccC----HHHHHHHHHhccCCCEEEEcC
Confidence            9774    678999999999999888754

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

Probab=97.76  E-value=0.00013  Score=76.57  Aligned_cols=141  Identities=24%  Similarity=0.200  Sum_probs=85.9

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          126 MCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       126 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      ..+.|...+.    ....+...|++|+-.++..+| .+|.|=+|+|||+.. ..++..+...       |+++|+.+-|-
T Consensus       656 ~~~~p~~~~~----~~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI-~~LIkiL~~~-------gkkVLLtsyTh  723 (1100)
T KOG1805|consen  656 KVLIPKIKKI----ILLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTI-SLLIKILVAL-------GKKVLLTSYTH  723 (1100)
T ss_pred             cccCchhhHH----HHhhcCHHHHHHHHHHHhccchheeecCCCCCchhhH-HHHHHHHHHc-------CCeEEEEehhh
Confidence            3455555543    334677889999999998887 899999999999864 3344444443       68899999998


Q ss_pred             HHHHHHHHHHHHHhccCC----------CceEEEEECCccH--HHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccE
Q 010709          205 ELAQQIEKEVKALSRSLD----------SFKTAIVVGGTNI--AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSF  272 (503)
Q Consensus       205 ~La~q~~~~~~~~~~~~~----------~~~~~~~~~~~~~--~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~  272 (503)
                      ..+..+.-.++.+.-.+-          .+.-.+...+.+.  -......-+.+.|+.+|---+.+.    -+..+.+++
T Consensus       724 sAVDNILiKL~~~~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~p----lf~~R~FD~  799 (1100)
T KOG1805|consen  724 SAVDNILIKLKGFGIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHP----LFVNRQFDY  799 (1100)
T ss_pred             HHHHHHHHHHhccCcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCch----hhhccccCE
Confidence            877777666665542110          0000000111111  111223335677888884333322    245667999


Q ss_pred             EEecchhHHh
Q 010709          273 VILDEADRML  282 (503)
Q Consensus       273 vViDEaH~l~  282 (503)
                      +|||||-.+.
T Consensus       800 cIiDEASQI~  809 (1100)
T KOG1805|consen  800 CIIDEASQIL  809 (1100)
T ss_pred             EEEccccccc
Confidence            9999998643

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

Probab=97.76  E-value=0.00025  Score=73.88  Aligned_cols=77  Identities=19%  Similarity=0.261  Sum_probs=47.7

Q ss_pred             cEEEEEcchhhHHHHHHHHHHCC-------CeEEEEcCCCCHHHHHHHHHHHhc--------CCCcEEEEccccccCCCC
Q 010709          376 LTIVFVERKTRCDEVSEALVAEG-------LHAVALHGGRNQSDRESALRDFRN--------GSTNILVATDVASRGLDV  440 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~~~-------~~v~~lh~~~~~~~r~~~~~~f~~--------g~~~vLvaT~~~~~Gldi  440 (503)
                      ..|||+++....+.+..++...+       ++-+ +..=.+..+-.+++..|.+        |..-..||-...++|+|+
T Consensus       563 G~L~FfPSY~vmdk~~tfw~~~~~we~~~~vk~l-~vEPr~k~~f~e~m~~y~~~i~~pes~ga~~~aVcRGKVSEGlDF  641 (945)
T KOG1132|consen  563 GLLIFFPSYPVMDKLITFWQNRGLWERMEKVKKL-VVEPRSKSEFTEVMSRYYNAIADPESSGAVFFAVCRGKVSEGLDF  641 (945)
T ss_pred             ceEEeccchHHHHHHHHHHHcchHHHHhhcccCc-eeccCCccchHHHHHHHHHHhhCccccceEEEEEecccccCCCCc
Confidence            38999999988888866665432       1111 1111122333344444432        233455666889999999


Q ss_pred             CC--CCEEEEccCCC
Q 010709          441 MG--VAHVVNLDLPK  453 (503)
Q Consensus       441 p~--v~~VI~~~~p~  453 (503)
                      .+  .+.||..|+|.
T Consensus       642 sD~~~RaVI~tGlPy  656 (945)
T KOG1132|consen  642 SDDNGRAVIITGLPY  656 (945)
T ss_pred             cccCCceeEEecCCC
Confidence            85  67899999874

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.70  E-value=0.00032  Score=76.63  Aligned_cols=123  Identities=20%  Similarity=0.200  Sum_probs=75.7

Q ss_pred             CCcHHHHHHHHHHhcCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          143 RPTSIQAQAMPVALSGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      .+++-|.+++..++.+++ ++|.|..|+|||+.  +-.+..++..      .|.+++.++||-..|..+.+.       .
T Consensus       346 ~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~--l~~~~~~~e~------~G~~V~~~ApTGkAA~~L~e~-------t  410 (988)
T PRK13889        346 VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM--LGVAREAWEA------AGYEVRGAALSGIAAENLEGG-------S  410 (988)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH--HHHHHHHHHH------cCCeEEEecCcHHHHHHHhhc-------c
Confidence            689999999999998665 89999999999985  3333333332      267799999997666543321       0


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDK  300 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~  300 (503)
                       ++..                        .|...|..-...+...+...++|||||+-.+.    ...+..++... +..
T Consensus       411 -Gi~a------------------------~TI~sll~~~~~~~~~l~~~~vlIVDEASMv~----~~~m~~LL~~a~~~g  461 (988)
T PRK13889        411 -GIAS------------------------RTIASLEHGWGQGRDLLTSRDVLVIDEAGMVG----TRQLERVLSHAADAG  461 (988)
T ss_pred             -Ccch------------------------hhHHHHHhhhcccccccccCcEEEEECcccCC----HHHHHHHHHhhhhCC
Confidence             1110                        12222221112223346677899999998543    33455666543 456


Q ss_pred             CcEEEEEee
Q 010709          301 HQTLLFSAT  309 (503)
Q Consensus       301 ~q~i~~SAT  309 (503)
                      .++|++.=+
T Consensus       462 arvVLVGD~  470 (988)
T PRK13889        462 AKVVLVGDP  470 (988)
T ss_pred             CEEEEECCH
Confidence            677776544

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.66  E-value=0.00044  Score=74.48  Aligned_cols=122  Identities=16%  Similarity=0.181  Sum_probs=73.7

Q ss_pred             CCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          142 TRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ..+++-|.+|+..++.+ +-++|.|+.|+|||+..  -.+...+..      .+..+++++||--.+..+.+..      
T Consensus       351 ~~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll--~~i~~~~~~------~g~~V~~~ApTg~Aa~~L~~~~------  416 (744)
T TIGR02768       351 YRLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML--KAAREAWEA------AGYRVIGAALSGKAAEGLQAES------  416 (744)
T ss_pred             CCCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH--HHHHHHHHh------CCCeEEEEeCcHHHHHHHHhcc------
Confidence            35889999999999875 45899999999999753  333333332      2577999999977665543211      


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CC
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PD  299 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~  299 (503)
                        ++..                        .|..++.....+....+...++||||||-.+.    ...+..++... ..
T Consensus       417 --g~~a------------------------~Ti~~~~~~~~~~~~~~~~~~llIvDEasMv~----~~~~~~Ll~~~~~~  466 (744)
T TIGR02768       417 --GIES------------------------RTLASLEYAWANGRDLLSDKDVLVIDEAGMVG----SRQMARVLKEAEEA  466 (744)
T ss_pred             --CCce------------------------eeHHHHHhhhccCcccCCCCcEEEEECcccCC----HHHHHHHHHHHHhc
Confidence              1111                        12222211122223345678999999998543    23344555532 34


Q ss_pred             CCcEEEEE
Q 010709          300 KHQTLLFS  307 (503)
Q Consensus       300 ~~q~i~~S  307 (503)
                      ..++|++.
T Consensus       467 ~~kliLVG  474 (744)
T TIGR02768       467 GAKVVLVG  474 (744)
T ss_pred             CCEEEEEC
Confidence            56666664

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.

>PRK04296 thymidine kinase; Provisional

Probab=97.58  E-value=0.00013  Score=64.95  Aligned_cols=36  Identities=19%  Similarity=0.250  Sum_probs=24.5

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      .-.++.||+|+|||+.. +-++......       +.+++++-|
T Consensus         3 ~i~litG~~GsGKTT~~-l~~~~~~~~~-------g~~v~i~k~   38 (190)
T PRK04296          3 KLEFIYGAMNSGKSTEL-LQRAYNYEER-------GMKVLVFKP   38 (190)
T ss_pred             EEEEEECCCCCHHHHHH-HHHHHHHHHc-------CCeEEEEec
Confidence            34789999999999865 3344443332       567888766

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.56  E-value=0.00031  Score=58.28  Aligned_cols=19  Identities=42%  Similarity=0.441  Sum_probs=12.7

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      +++.++|.|++|+|||...
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            3456999999999999854

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.54  E-value=0.0011  Score=65.13  Aligned_cols=130  Identities=12%  Similarity=0.164  Sum_probs=70.0

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA  236 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (503)
                      +.++++||||+|||++..- +..++....   ...+.++.++.  +.|.-+..+   ++.++..+ ++.+.         
T Consensus       175 ~vi~lvGptGvGKTTT~aK-LA~~~~~~~---~~~g~~V~lit~Dt~R~aa~eQ---L~~~a~~l-gvpv~---------  237 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAK-LAAIYGINS---DDKSLNIKIITIDNYRIGAKKQ---IQTYGDIM-GIPVK---------  237 (388)
T ss_pred             eEEEEECCCCCCHHHHHHH-HHHHHHhhh---ccCCCeEEEEeccCccHHHHHH---HHHHhhcC-CcceE---------
Confidence            4589999999999986532 222222110   01234455554  445544433   44444322 23221         


Q ss_pred             HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-CHHHHHHHHHhCCCC-CcEEEEEeeCCH-H
Q 010709          237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-FEPQIREVMQNLPDK-HQTLLFSATMPV-E  313 (503)
Q Consensus       237 ~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-~~~~~~~il~~~~~~-~q~i~~SAT~~~-~  313 (503)
                                  .+.++..+...+..    +.++++|+||++.++.... ....+.+++....++ -.++.+|||... .
T Consensus       238 ------------~~~~~~~l~~~L~~----~~~~DlVLIDTaGr~~~~~~~l~el~~~l~~~~~~~e~~LVlsat~~~~~  301 (388)
T PRK12723        238 ------------AIESFKDLKEEITQ----SKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRDAEFHLAVSSTTKTSD  301 (388)
T ss_pred             ------------eeCcHHHHHHHHHH----hCCCCEEEEcCCCCCccCHHHHHHHHHHHHhcCCCCeEEEEEcCCCCHHH
Confidence                        11234444444432    3578999999999764221 234555666655443 356888999853 4


Q ss_pred             HHHHHHHh
Q 010709          314 IEALAQEY  321 (503)
Q Consensus       314 ~~~~~~~~  321 (503)
                      +...+..|
T Consensus       302 ~~~~~~~~  309 (388)
T PRK12723        302 VKEIFHQF  309 (388)
T ss_pred             HHHHHHHh
Confidence            55555655

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.49  E-value=0.0019  Score=71.26  Aligned_cols=124  Identities=19%  Similarity=0.197  Sum_probs=76.1

Q ss_pred             CCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          142 TRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ..+++-|.+++..+..+ +-++|.|+.|+|||+.. -++.. .+..      .|.+++.++||-..|..+.+.    .  
T Consensus       380 ~~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~-~~e~------~G~~V~g~ApTgkAA~~L~e~----~--  445 (1102)
T PRK13826        380 ARLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAARE-AWEA------AGYRVVGGALAGKAAEGLEKE----A--  445 (1102)
T ss_pred             CCCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHH-HHHH------cCCeEEEEcCcHHHHHHHHHh----h--
Confidence            46899999999988643 45999999999999853 33333 3332      267799999997666544321    1  


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC-C
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP-D  299 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~-~  299 (503)
                        ++..                        .|...++.....+...+..-++||||||..+.    ...+..++.... .
T Consensus       446 --Gi~a------------------------~TIas~ll~~~~~~~~l~~~~vlVIDEAsMv~----~~~m~~Ll~~~~~~  495 (1102)
T PRK13826        446 --GIQS------------------------RTLSSWELRWNQGRDQLDNKTVFVLDEAGMVA----SRQMALFVEAVTRA  495 (1102)
T ss_pred             --CCCe------------------------eeHHHHHhhhccCccCCCCCcEEEEECcccCC----HHHHHHHHHHHHhc
Confidence              1211                        12222211111222345667899999999543    445566666654 4


Q ss_pred             CCcEEEEEee
Q 010709          300 KHQTLLFSAT  309 (503)
Q Consensus       300 ~~q~i~~SAT  309 (503)
                      ..++|++.-+
T Consensus       496 garvVLVGD~  505 (1102)
T PRK13826        496 GAKLVLVGDP  505 (1102)
T ss_pred             CCEEEEECCH
Confidence            6677776544

>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=97.46  E-value=0.00039  Score=67.33  Aligned_cols=123  Identities=23%  Similarity=0.181  Sum_probs=74.3

Q ss_pred             CcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCC
Q 010709          144 PTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS  223 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~  223 (503)
                      +++-|.+++..  ..++++|.|..|||||.+.+.-+. +++....   ....++|++++|+..+..+.+++...+.... 
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~-~ll~~~~---~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~-   73 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIA-YLLYEGG---VPPERILVLTFTNAAAQEMRERIRELLEEEQ-   73 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHH-HHHHTSS---STGGGEEEEESSHHHHHHHHHHHHHHHHHCC-
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHH-Hhhcccc---CChHHheecccCHHHHHHHHHHHHHhcCccc-
Confidence            46779898888  677899999999999997644443 4444321   2356799999999999999999988764321 


Q ss_pred             ceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCC--CCccEEEecchh
Q 010709          224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSL--SRVSFVILDEAD  279 (503)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l--~~~~~vViDEaH  279 (503)
                      ..      ................+.|+|...+...+.+.....  -.-.+-++|+..
T Consensus        74 ~~------~~~~~~~~~~~~~~~~~~i~T~hsf~~~ll~~~~~~~~~~~~~~i~~~~~  125 (315)
T PF00580_consen   74 QE------SSDNERLRRQLSNIDRIYISTFHSFCYRLLREYGYEIGIDPNFEILDEEE  125 (315)
T ss_dssp             HC------CTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHH
T ss_pred             cc------ccccccccccccccchheeehhhhhhhhhhhhhhhhhhccccceeecchh
Confidence            00      000001111222335678999888765554322111  122456777776

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 ....

>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=97.45  E-value=0.0016  Score=54.81  Aligned_cols=17  Identities=35%  Similarity=0.516  Sum_probs=15.0

Q ss_pred             CCCeEEEccCCCchhHH
Q 010709          158 GRDLLGCAETGSGKTAA  174 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~  174 (503)
                      ++.+++.||+|+|||..
T Consensus        19 ~~~v~i~G~~G~GKT~l   35 (151)
T cd00009          19 PKNLLLYGPPGTGKTTL   35 (151)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            56799999999999974

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.

>PRK06526 transposase; Provisional

Probab=97.38  E-value=0.00076  Score=62.68  Aligned_cols=23  Identities=17%  Similarity=0.193  Sum_probs=18.9

Q ss_pred             HHHhcCCCeEEEccCCCchhHHh
Q 010709          153 PVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       153 ~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      .++..+.+++++||+|+|||..+
T Consensus        93 ~fi~~~~nlll~Gp~GtGKThLa  115 (254)
T PRK06526         93 DFVTGKENVVFLGPPGTGKTHLA  115 (254)
T ss_pred             chhhcCceEEEEeCCCCchHHHH
Confidence            44556788999999999999754

>PRK08181 transposase; Validated

Probab=97.34  E-value=0.0035  Score=58.63  Aligned_cols=121  Identities=17%  Similarity=0.173  Sum_probs=63.2

Q ss_pred             cHHHHHHH----HHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          145 TSIQAQAM----PVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       145 ~~~Q~~~i----~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      ...|..++    .++..+++++++||+|+|||..+ ..+...+...       +..++++. ..+|..++......    
T Consensus        89 ~~~~~~~L~~~~~~~~~~~nlll~Gp~GtGKTHLa-~Aia~~a~~~-------g~~v~f~~-~~~L~~~l~~a~~~----  155 (269)
T PRK08181         89 SKAQVMAIAAGDSWLAKGANLLLFGPPGGGKSHLA-AAIGLALIEN-------GWRVLFTR-TTDLVQKLQVARRE----  155 (269)
T ss_pred             CHHHHHHHHHHHHHHhcCceEEEEecCCCcHHHHH-HHHHHHHHHc-------CCceeeee-HHHHHHHHHHHHhC----
Confidence            34454444    23447788999999999999643 2233333332       34455543 34555443211000    


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-CHHHHHHHHHhCCC
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-FEPQIREVMQNLPD  299 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-~~~~~~~il~~~~~  299 (503)
                                                    .+...+++.       +.++++|||||.+...... ....+..++.....
T Consensus       156 ------------------------------~~~~~~l~~-------l~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~  198 (269)
T PRK08181        156 ------------------------------LQLESAIAK-------LDKFDLLILDDLAYVTKDQAETSVLFELISARYE  198 (269)
T ss_pred             ------------------------------CcHHHHHHH-------HhcCCEEEEeccccccCCHHHHHHHHHHHHHHHh
Confidence                                          011122222       3457899999998653332 22345566655433


Q ss_pred             CCcEEEEEeeCCHHHH
Q 010709          300 KHQTLLFSATMPVEIE  315 (503)
Q Consensus       300 ~~q~i~~SAT~~~~~~  315 (503)
                      ...+|+.|-..+.+..
T Consensus       199 ~~s~IiTSN~~~~~w~  214 (269)
T PRK08181        199 RRSILITANQPFGEWN  214 (269)
T ss_pred             CCCEEEEcCCCHHHHH
Confidence            4456665655544433

>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=97.33  E-value=0.00098  Score=59.40  Aligned_cols=54  Identities=22%  Similarity=0.282  Sum_probs=34.1

Q ss_pred             CCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh
Q 010709          268 SRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                      +++++|+||-+-+.... .....+.+++....+..-++.++||...+....+..+
T Consensus        82 ~~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~~  136 (196)
T PF00448_consen   82 KGYDLVLIDTAGRSPRDEELLEELKKLLEALNPDEVHLVLSATMGQEDLEQALAF  136 (196)
T ss_dssp             TTSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSSSEEEEEEEGGGGGHHHHHHHHH
T ss_pred             cCCCEEEEecCCcchhhHHHHHHHHHHhhhcCCccceEEEecccChHHHHHHHHH
Confidence            45789999988643211 2345566777776666668889999976544444444

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 ....

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=97.33  E-value=0.03  Score=66.60  Aligned_cols=237  Identities=13%  Similarity=0.189  Sum_probs=123.6

Q ss_pred             CCcHHHHHHHHHHhcCC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          143 RPTSIQAQAMPVALSGR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      .+++-|.+++..++..+  -.+|.|+.|+|||..  +-.+..+...      .|..+++++||-..+..+.+........
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~--l~~l~~~~~~------~G~~V~~lAPTgrAA~~L~e~~g~~A~T  500 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEI--AQLLLHLASE------QGYEIQIITAGSLSAQELRQKIPRLAST  500 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHH--HHHHHHHHHh------cCCeEEEEeCCHHHHHHHHHHhcchhhh
Confidence            57889999999998764  499999999999975  3333333332      3678999999987776665543211100


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CC
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PD  299 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~  299 (503)
                                    .......+..  ..-..|...++    .....+..-++||||||-.+.    ...+..++... +.
T Consensus       501 --------------i~~~l~~l~~--~~~~~tv~~fl----~~~~~l~~~~vlIVDEAsMl~----~~~~~~Ll~~a~~~  556 (1960)
T TIGR02760       501 --------------FITWVKNLFN--DDQDHTVQGLL----DKSSPFSNKDIFVVDEANKLS----NNELLKLIDKAEQH  556 (1960)
T ss_pred             --------------HHHHHHhhcc--cccchhHHHhh----cccCCCCCCCEEEEECCCCCC----HHHHHHHHHHHhhc
Confidence                          0011111111  01122222332    223345677899999999553    44566777655 45


Q ss_pred             CCcEEEEEeeC-------CHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCC
Q 010709          300 KHQTLLFSATM-------PVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCH  372 (503)
Q Consensus       300 ~~q~i~~SAT~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~  372 (503)
                      ..++|++.-+-       ...+. .+... +-+. +...........+  .+.......+...+...+....       .
T Consensus       557 garvVlvGD~~QL~sV~aG~~f~-~L~~~-gv~t-~~l~~i~rq~~~v--~i~~~~~~~r~~~ia~~y~~L~-------~  624 (1960)
T TIGR02760       557 NSKLILLNDSAQRQGMSAGSAID-LLKEG-GVTT-YAWVDTKQQKASV--EISEAVDKLRVDYIASAWLDLT-------P  624 (1960)
T ss_pred             CCEEEEEcChhhcCccccchHHH-HHHHC-CCcE-EEeecccccCcce--eeeccCchHHHHHHHHHHHhcc-------c
Confidence            77888775542       12233 33332 1122 2222211111111  1122222233333333222211       1


Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHH----CC------CeEEEEcC-CCCHHHHHHHHHHHhcCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVA----EG------LHAVALHG-GRNQSDRESALRDFRNGS  424 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~----~~------~~v~~lh~-~~~~~~r~~~~~~f~~g~  424 (503)
                      ...+++|+..+..+...|....+.    .|      +....+.. .++..++. ....|+.|.
T Consensus       625 ~r~~tliv~~t~~dr~~Ln~~iR~~L~~~G~L~~~~~~~~~L~p~~lt~~e~r-~~~~Yr~Gd  686 (1960)
T TIGR02760       625 DRQNSQVLATTHREQQDLTQIIRNALKQEGQLSRQEVTVPTLKPVNLTGIQRR-NAAHYKQGM  686 (1960)
T ss_pred             ccCceEEEcCCcHHHHHHHHHHHHHHHHcCCcCCCceEEEEeccCCCCHHHHh-hHhhcCCCC
Confidence            223489999998887777666653    22      22333332 56666666 336666654

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=97.30  E-value=0.0024  Score=61.68  Aligned_cols=55  Identities=15%  Similarity=0.198  Sum_probs=40.2

Q ss_pred             CCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhc
Q 010709          268 SRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYL  322 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~  322 (503)
                      .++++|+||.+.++-.. .....+..+.+...++..++.++||...+....++.|.
T Consensus       221 ~~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~pd~~iLVl~a~~g~d~~~~a~~f~  276 (336)
T PRK14974        221 RGIDVVLIDTAGRMHTDANLMDELKKIVRVTKPDLVIFVGDALAGNDAVEQAREFN  276 (336)
T ss_pred             CCCCEEEEECCCccCCcHHHHHHHHHHHHhhCCceEEEeeccccchhHHHHHHHHH
Confidence            35689999999976432 35566777777777777788999998776666666654

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

Probab=97.28  E-value=0.0011  Score=65.52  Aligned_cols=67  Identities=22%  Similarity=0.275  Sum_probs=46.9

Q ss_pred             CcHHHHHHHHHH------hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH--HHHHH
Q 010709          144 PTSIQAQAMPVA------LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI--EKEVK  215 (503)
Q Consensus       144 ~~~~Q~~~i~~i------~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~--~~~~~  215 (503)
                      +++-|+.++..+      .++..+.+.|+-|+|||..  +-.+......      .+..+++++||-..|..+  -..++
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l--~~~i~~~~~~------~~~~~~~~a~tg~AA~~i~~G~T~h   73 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFL--IKAIIDYLRS------RGKKVLVTAPTGIAAFNIPGGRTIH   73 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHH--HHHHHHHhcc------ccceEEEecchHHHHHhccCCcchH
Confidence            566789998887      5677899999999999974  4344433332      357799999998777655  24444


Q ss_pred             HHh
Q 010709          216 ALS  218 (503)
Q Consensus       216 ~~~  218 (503)
                      .++
T Consensus        74 s~f   76 (364)
T PF05970_consen   74 SFF   76 (364)
T ss_pred             Hhc
Confidence            443

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>KOG0383 consensus Predicted helicase [General function prediction only]

Probab=97.27  E-value=4.6e-05  Score=78.83  Aligned_cols=64  Identities=19%  Similarity=0.263  Sum_probs=55.3

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhc---CCCcEEEEccccccC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRN---GSTNILVATDVASRG  437 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~---g~~~vLvaT~~~~~G  437 (503)
                      ..++++||..-....+.+.+++...+ ....+.|.....+|+..++.|..   .....|++|.+.+.|
T Consensus       630 ~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~~~~rq~ai~~~n~~~~~~~cfllstra~g~g  696 (696)
T KOG0383|consen  630 SGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPITGPERQAAIDRFNAPGSNQFCFLLSTRAGGLG  696 (696)
T ss_pred             cchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCccchhhhhhccccCCCCccceEEEeecccccCC
Confidence            34569999999999999999999888 88889999999999999999983   346688999988765

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.23  E-value=0.0023  Score=62.46  Aligned_cols=128  Identities=20%  Similarity=0.235  Sum_probs=62.8

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHH-hcCCCCCCCCCeEEEEc-cc-HHHHHHHHHHHHHHhccCCCceEEEEECCcc
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCV-AQTPVGRGDGPLALVLA-PT-RELAQQIEKEVKALSRSLDSFKTAIVVGGTN  234 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~-~~~~~~~~~~~~~lil~-Pt-r~La~q~~~~~~~~~~~~~~~~~~~~~~~~~  234 (503)
                      ++.++++||||+|||+.... +..... .++      ..++.+++ .+ |.-+.   +.++.|+... ++.+.       
T Consensus       137 g~ii~lvGptGvGKTTtiak-LA~~~~~~~G------~~~V~lit~D~~R~ga~---EqL~~~a~~~-gv~~~-------  198 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAK-LAARCVMRFG------ASKVALLTTDSYRIGGH---EQLRIFGKIL-GVPVH-------  198 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHH-HHHHHHHhcC------CCeEEEEecccccccHH---HHHHHHHHHc-CCceE-------
Confidence            56799999999999986532 222222 211      12344443 22 22222   3344444322 12222       


Q ss_pred             HHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC-CHHHHHHHHHhCCCCCcEEEEEeeCCHH
Q 010709          235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-FEPQIREVMQNLPDKHQTLLFSATMPVE  313 (503)
Q Consensus       235 ~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~  313 (503)
                                    .+.+++.+...+.+    +.+.++|+||.+-+.-... ....+..+.....+...++.+|||...+
T Consensus       199 --------------~~~~~~~l~~~l~~----l~~~DlVLIDTaG~~~~d~~l~e~La~L~~~~~~~~~lLVLsAts~~~  260 (374)
T PRK14722        199 --------------AVKDGGDLQLALAE----LRNKHMVLIDTIGMSQRDRTVSDQIAMLHGADTPVQRLLLLNATSHGD  260 (374)
T ss_pred             --------------ecCCcccHHHHHHH----hcCCCEEEEcCCCCCcccHHHHHHHHHHhccCCCCeEEEEecCccChH
Confidence                          23344444443332    4567899999996432111 1122222222223334578889998544


Q ss_pred             -HHHHHHHh
Q 010709          314 -IEALAQEY  321 (503)
Q Consensus       314 -~~~~~~~~  321 (503)
                       +...++.|
T Consensus       261 ~l~evi~~f  269 (374)
T PRK14722        261 TLNEVVQAY  269 (374)
T ss_pred             HHHHHHHHH
Confidence             44455555

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.18  E-value=0.0052  Score=59.80  Aligned_cols=129  Identities=18%  Similarity=0.252  Sum_probs=68.8

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccH-HHHHHHHHHHHHHhccCCCceEEEEECCccH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTR-ELAQQIEKEVKALSRSLDSFKTAIVVGGTNI  235 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr-~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (503)
                      +.+.++||||+|||+.... +...+...       +.++.++.  |.| ..+.|+.    .++... ++.+         
T Consensus       242 ~vI~LVGptGvGKTTTiaK-LA~~L~~~-------GkkVglI~aDt~RiaAvEQLk----~yae~l-gipv---------  299 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAK-MAWQFHGK-------KKTVGFITTDHSRIGTVQQLQ----DYVKTI-GFEV---------  299 (436)
T ss_pred             cEEEEECCCCCcHHHHHHH-HHHHHHHc-------CCcEEEEecCCcchHHHHHHH----HHhhhc-CCcE---------
Confidence            4588999999999986433 22222222       34455444  444 3333433    333211 1211         


Q ss_pred             HHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCC-HH
Q 010709          236 AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMP-VE  313 (503)
Q Consensus       236 ~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~-~~  313 (503)
                                  +...+|..+.+.+..-. ...++++|+||-+=+.... .....+.+++....+..-++.+|||.. .+
T Consensus       300 ------------~v~~d~~~L~~aL~~lk-~~~~~DvVLIDTaGRs~kd~~lm~EL~~~lk~~~PdevlLVLsATtk~~d  366 (436)
T PRK11889        300 ------------IAVRDEAAMTRALTYFK-EEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSKD  366 (436)
T ss_pred             ------------EecCCHHHHHHHHHHHH-hccCCCEEEEeCccccCcCHHHHHHHHHHHhhcCCCeEEEEECCccChHH
Confidence                        12335666655554311 1125789999988664322 123445555555555544677898764 45


Q ss_pred             HHHHHHHhc
Q 010709          314 IEALAQEYL  322 (503)
Q Consensus       314 ~~~~~~~~~  322 (503)
                      +...++.|-
T Consensus       367 ~~~i~~~F~  375 (436)
T PRK11889        367 MIEIITNFK  375 (436)
T ss_pred             HHHHHHHhc
Confidence            566776664

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.17  E-value=0.0059  Score=61.27  Aligned_cols=128  Identities=17%  Similarity=0.239  Sum_probs=65.9

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHH-hcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHHhccCCCceEEEEECCcc
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCV-AQTPVGRGDGPLALVLA--PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN  234 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~-~~~~~~~~~~~~~lil~--Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~  234 (503)
                      ++.++++||||+|||+...- +...+. ..      .+.++.++.  |.|.-+.   +.++.++... ++.+        
T Consensus       221 ~~~i~~vGptGvGKTTt~~k-LA~~~~~~~------~g~~V~li~~D~~r~~a~---eqL~~~a~~~-~vp~--------  281 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAK-LAARYALLY------GKKKVALITLDTYRIGAV---EQLKTYAKIM-GIPV--------  281 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHH-HHHHHHHhc------CCCeEEEEECCccHHHHH---HHHHHHHHHh-CCce--------
Confidence            45689999999999986532 222222 11      134455544  4443332   3333333221 1221        


Q ss_pred             HHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHh-CCCCCcEEEEEeeCCH
Q 010709          235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQN-LPDKHQTLLFSATMPV  312 (503)
Q Consensus       235 ~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~-~~~~~q~i~~SAT~~~  312 (503)
                                   ..+.++..+...+..    +.++++|+||.+-+.... .....+..++.. ..+....++++||...
T Consensus       282 -------------~~~~~~~~l~~~l~~----~~~~DlVlIDt~G~~~~d~~~~~~L~~ll~~~~~~~~~~LVl~a~~~~  344 (424)
T PRK05703        282 -------------EVVYDPKELAKALEQ----LRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVLSATTKY  344 (424)
T ss_pred             -------------EccCCHHhHHHHHHH----hCCCCEEEEeCCCCCCCCHHHHHHHHHHHhccCCCCeEEEEEECCCCH
Confidence                         112344445454443    346899999988542211 123345555552 2233447888998864


Q ss_pred             -HHHHHHHHh
Q 010709          313 -EIEALAQEY  321 (503)
Q Consensus       313 -~~~~~~~~~  321 (503)
                       .+...+..|
T Consensus       345 ~~l~~~~~~f  354 (424)
T PRK05703        345 EDLKDIYKHF  354 (424)
T ss_pred             HHHHHHHHHh
Confidence             555555555

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.07  E-value=0.0011  Score=55.30  Aligned_cols=41  Identities=22%  Similarity=0.249  Sum_probs=24.9

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      +..+++.||+|+|||+...  .+.......      +..++++.+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~--~l~~~~~~~------~~~~~~~~~~~~~   42 (148)
T smart00382        2 GEVILIVGPPGSGKTTLAR--ALARELGPP------GGGVIYIDGEDIL   42 (148)
T ss_pred             CCEEEEECCCCCcHHHHHH--HHHhccCCC------CCCEEEECCEEcc
Confidence            4569999999999998532  232222211      1246777766543

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=97.03  E-value=0.0017  Score=59.81  Aligned_cols=44  Identities=23%  Similarity=0.371  Sum_probs=28.0

Q ss_pred             CccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCH
Q 010709          269 RVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPV  312 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~  312 (503)
                      +++++|||++|.+.+. .+...+..++..+....+.++++++.++
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            5678999999976543 3345566777665543345666666533

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.01  E-value=0.0019  Score=59.20  Aligned_cols=86  Identities=27%  Similarity=0.376  Sum_probs=65.5

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCc-cHHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCc
Q 010709          193 DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT-NIAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRV  270 (503)
Q Consensus       193 ~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~  270 (503)
                      ..|.+|||+..-.-|..+.+.++.+..  .+..+.-++... ...++...+. ..++|.||||+|+..++..+.+.++++
T Consensus       125 gsP~~lvvs~SalRa~dl~R~l~~~~~--k~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~~~L~l~~l  202 (252)
T PF14617_consen  125 GSPHVLVVSSSALRAADLIRALRSFKG--KDCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLENGALSLSNL  202 (252)
T ss_pred             CCCEEEEEcchHHHHHHHHHHHHhhcc--CCchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHcCCCCcccC
Confidence            358899999887667777777777631  123444455554 5566666665 478999999999999999999999999


Q ss_pred             cEEEecchhH
Q 010709          271 SFVILDEADR  280 (503)
Q Consensus       271 ~~vViDEaH~  280 (503)
                      .+||||--|.
T Consensus       203 ~~ivlD~s~~  212 (252)
T PF14617_consen  203 KRIVLDWSYL  212 (252)
T ss_pred             eEEEEcCCcc
Confidence            9999998773

>TIGR01075 uvrD DNA helicase II

Probab=96.95  E-value=0.0054  Score=66.43  Aligned_cols=71  Identities=21%  Similarity=0.209  Sum_probs=54.6

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..+++-|.+++..  ....++|.|..|||||.+. ..-+.+++....   -...++|+++-|+..|..+.+++.++.
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L-~~Ria~Li~~~~---v~p~~IL~lTFTnkAA~em~~Rl~~~~   73 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVL-THRIAWLLSVEN---ASPHSIMAVTFTNKAAAEMRHRIGALL   73 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHH-HHHHHHHHHcCC---CCHHHeEeeeccHHHHHHHHHHHHHHh
Confidence            3578899998865  3567999999999999875 444555555321   234679999999999999999998875

Designed to identify uvrD members of the uvrD/rep subfamily.

>PRK08084 DNA replication initiation factor; Provisional

Probab=96.91  E-value=0.0027  Score=58.60  Aligned_cols=44  Identities=16%  Similarity=0.277  Sum_probs=24.8

Q ss_pred             ccEEEecchhHHhhC-CCHHHHHHHHHhCCC--CCcEEEEEeeCCHH
Q 010709          270 VSFVILDEADRMLDM-GFEPQIREVMQNLPD--KHQTLLFSATMPVE  313 (503)
Q Consensus       270 ~~~vViDEaH~l~~~-~~~~~~~~il~~~~~--~~q~i~~SAT~~~~  313 (503)
                      +++|+|||+|.+... .....+..++..+..  ..++++.|..+|..
T Consensus        98 ~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~  144 (235)
T PRK08084         98 LSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQ  144 (235)
T ss_pred             CCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHH
Confidence            478999999987543 234445555544322  33555544444444

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.91  E-value=0.0055  Score=66.32  Aligned_cols=70  Identities=19%  Similarity=0.196  Sum_probs=53.8

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .+++-|.+++..  ....++|.|..|||||.+. +.-+.+++....   -...++|+|+-|+..|..+.+++.++.
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl-~~Ria~Li~~~~---v~p~~IL~lTFT~kAA~Em~~Rl~~~~   78 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVL-VHRIAWLMQVEN---ASPYSIMAVTFTNKAAAEMRHRIEQLL   78 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHH-HHHHHHHHHcCC---CChhHeEeeeccHHHHHHHHHHHHHHh
Confidence            588899999875  3467999999999999875 444555554321   234679999999999999999998875

>smart00492 HELICc3 helicase superfamily c-terminal domain

Probab=96.90  E-value=0.0058  Score=51.20  Aligned_cols=67  Identities=22%  Similarity=0.336  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHCCC------eEEEEcCCCCHHHHHHHHHHHhcCC-CcEEEEccccccCCCCCC--CCEEEEccCCC
Q 010709          387 CDEVSEALVAEGL------HAVALHGGRNQSDRESALRDFRNGS-TNILVATDVASRGLDVMG--VAHVVNLDLPK  453 (503)
Q Consensus       387 ~~~l~~~L~~~~~------~v~~lh~~~~~~~r~~~~~~f~~g~-~~vLvaT~~~~~Gldip~--v~~VI~~~~p~  453 (503)
                      .+.++..+...+.      .-..+.-+....+...+++.|++.. ..||+++.-+++|+|+|+  ++.||..++|-
T Consensus         4 m~~v~~~~~~~~~~~~l~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~iL~~~~~~~EGiD~~g~~~r~vii~glPf   79 (141)
T smart00492        4 MESFVQYWKENGILENINKNLLLLVQGEDGKETGKLLEKYVEACENAILLATARFSEGVDFPGDYLRAVIIDGLPF   79 (141)
T ss_pred             HHHHHHHHHHcCchhhHhcCCeEEEeCCChhHHHHHHHHHHHcCCCEEEEEccceecceecCCCCeeEEEEEecCC
Confidence            3455555555443      2233444555666788999998754 379999988999999997  67899999874

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

Probab=96.90  E-value=0.0057  Score=60.35  Aligned_cols=81  Identities=17%  Similarity=0.257  Sum_probs=51.3

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCC--eE----EEEcCCCCHHHHHHHHHHHh----cCCCcEEE--EccccccCCCCCC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGL--HA----VALHGGRNQSDRESALRDFR----NGSTNILV--ATDVASRGLDVMG  442 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~--~v----~~lh~~~~~~~r~~~~~~f~----~g~~~vLv--aT~~~~~Gldip~  442 (503)
                      +.++.|+++.-..+.++......|+  ++    ..+-+.-...+-.-.+..++    .|.-.||+  |-.-.++|+|+.+
T Consensus       531 dG~v~ff~sylYmesiv~~w~~~gil~ei~k~KL~fIetpD~~ETs~al~ny~~aC~~gRGavl~sVargkVsEgidF~h  610 (755)
T KOG1131|consen  531 DGIVCFFPSYLYMESIVSRWYEQGILDEIMKYKLLFIETPDFRETSLALANYRYACDNGRGAVLLSVARGKVSEGIDFDH  610 (755)
T ss_pred             CceEEEEehHHHHHHHHHHHHHHhHHHHHhhCceEEEeCCchhhhHHHHHHHHHHhcCCCCceEEEEecCccccCccccc
Confidence            4578888887777777776666553  11    22333333333344455443    45556665  4477889999987


Q ss_pred             CC--EEEEccCCCCh
Q 010709          443 VA--HVVNLDLPKVL  455 (503)
Q Consensus       443 v~--~VI~~~~p~s~  455 (503)
                      -.  .||+++.|...
T Consensus       611 hyGR~ViM~gIP~qy  625 (755)
T KOG1131|consen  611 HYGREVIMEGIPYQY  625 (755)
T ss_pred             ccCceEEEEeccchh
Confidence            54  89999999643

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

Probab=96.87  E-value=0.02  Score=53.04  Aligned_cols=53  Identities=25%  Similarity=0.295  Sum_probs=36.5

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhc
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQ  186 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~  186 (503)
                      ..|..+.+|+++++++-+.+.+..                  ...=++|.||||||||+. +..++.++...
T Consensus       100 ~Ip~~i~~~e~LglP~i~~~~~~~------------------~~GLILVTGpTGSGKSTT-lAamId~iN~~  152 (353)
T COG2805         100 LIPSKIPTLEELGLPPIVRELAES------------------PRGLILVTGPTGSGKSTT-LAAMIDYINKH  152 (353)
T ss_pred             ccCccCCCHHHcCCCHHHHHHHhC------------------CCceEEEeCCCCCcHHHH-HHHHHHHHhcc
Confidence            556777778888777665542210                  222399999999999987 47788876654

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

Probab=96.85  E-value=0.0039  Score=67.72  Aligned_cols=154  Identities=18%  Similarity=0.113  Sum_probs=92.1

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcC----------CCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceE
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQT----------PVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKT  226 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~----------~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~  226 (503)
                      .|+++++.-..|.|||.+-+.-.+...-...          ......-+..|||+|. ++..||.+++.......  +++
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~~--lKv  449 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISSL--LKV  449 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhcccc--ceE
Confidence            3567899999999999876544433211100          0011123568999998 67788999998876542  577


Q ss_pred             EEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC--C----------------C--CCccEEEecchhHHhhCCC
Q 010709          227 AIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT--S----------------L--SRVSFVILDEADRMLDMGF  286 (503)
Q Consensus       227 ~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~--~----------------l--~~~~~vViDEaH~l~~~~~  286 (503)
                      ..+.|-....-.....--.+|||++|+..|...+.....  .                |  -.+=-|++|||+.+ .. -
T Consensus       450 ~~Y~Girk~~~~~~~el~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMv-es-s  527 (1394)
T KOG0298|consen  450 LLYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMV-ES-S  527 (1394)
T ss_pred             EEEechhhhcccCchhhhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhh-cc-h
Confidence            777764322111111123589999999999777754311  0                0  01124899999954 33 2


Q ss_pred             HHHHHHHHHhCCCCCcEEEEEeeCCHHHHH
Q 010709          287 EPQIREVMQNLPDKHQTLLFSATMPVEIEA  316 (503)
Q Consensus       287 ~~~~~~il~~~~~~~q~i~~SAT~~~~~~~  316 (503)
                      .....+.+.+++.. -.=++|+||-..+.+
T Consensus       528 sS~~a~M~~rL~~i-n~W~VTGTPiq~Idd  556 (1394)
T KOG0298|consen  528 SSAAAEMVRRLHAI-NRWCVTGTPIQKIDD  556 (1394)
T ss_pred             HHHHHHHHHHhhhh-ceeeecCCchhhhhh
Confidence            44455555555432 357889997444433

>PRK06893 DNA replication initiation factor; Validated

Probab=96.85  E-value=0.0032  Score=57.87  Aligned_cols=45  Identities=20%  Similarity=0.327  Sum_probs=28.1

Q ss_pred             CCccEEEecchhHHhhC-CCHHHHHHHHHhCCC-CCcEEEEEeeCCH
Q 010709          268 SRVSFVILDEADRMLDM-GFEPQIREVMQNLPD-KHQTLLFSATMPV  312 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~-~~q~i~~SAT~~~  312 (503)
                      .+.++|||||+|.+.+. .+...+..++..... ..+++++|++.++
T Consensus        90 ~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p  136 (229)
T PRK06893         90 EQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSP  136 (229)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCCh
Confidence            46789999999987543 233445555555433 3456677777543

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.75  E-value=0.015  Score=61.96  Aligned_cols=72  Identities=24%  Similarity=0.274  Sum_probs=54.0

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      -..+++-|++++..  ...+++|.|..|||||.+. +.-+.+++...   ...+..+|+++.++..|..+.+++....
T Consensus       194 ~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl-~~r~ayLl~~~---~~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        194 SSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVL-VARAGWLLARG---QAQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             CCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHH-HHHHHHHHHhC---CCCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            35689999998864  3356899999999999875 44555555432   1234679999999999999999887755

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.75  E-value=0.0066  Score=55.69  Aligned_cols=19  Identities=37%  Similarity=0.440  Sum_probs=15.7

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .+..+++.||+|+|||..+
T Consensus        37 ~~~~lll~G~~G~GKT~la   55 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLL   55 (226)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3457999999999999754

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.

>PF13173 AAA_14: AAA domain

Probab=96.68  E-value=0.021  Score=47.10  Aligned_cols=38  Identities=16%  Similarity=0.345  Sum_probs=25.6

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      +-.+|+|||+|++-+  +...+..+.... ++.++++.+..
T Consensus        61 ~~~~i~iDEiq~~~~--~~~~lk~l~d~~-~~~~ii~tgS~   98 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPD--WEDALKFLVDNG-PNIKIILTGSS   98 (128)
T ss_pred             CCcEEEEehhhhhcc--HHHHHHHHHHhc-cCceEEEEccc
Confidence            567899999998753  466666776654 45666654443

>PRK06921 hypothetical protein; Provisional

Probab=96.66  E-value=0.037  Score=51.97  Aligned_cols=43  Identities=19%  Similarity=0.138  Sum_probs=25.5

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      ++++++.|++|+|||..+ ..+...+...      .+..++++.. .++..
T Consensus       117 ~~~l~l~G~~G~GKThLa-~aia~~l~~~------~g~~v~y~~~-~~l~~  159 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLL-TAAANELMRK------KGVPVLYFPF-VEGFG  159 (266)
T ss_pred             CCeEEEECCCCCcHHHHH-HHHHHHHhhh------cCceEEEEEH-HHHHH
Confidence            567999999999999643 3334443332      1345666553 34433

>smart00491 HELICc2 helicase superfamily c-terminal domain

Probab=96.66  E-value=0.0071  Score=50.75  Aligned_cols=67  Identities=19%  Similarity=0.354  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHCCC---eEEEEcCCCCHHHHHHHHHHHhcCCC---cEEEEccc--cccCCCCCC--CCEEEEccCCC
Q 010709          387 CDEVSEALVAEGL---HAVALHGGRNQSDRESALRDFRNGST---NILVATDV--ASRGLDVMG--VAHVVNLDLPK  453 (503)
Q Consensus       387 ~~~l~~~L~~~~~---~v~~lh~~~~~~~r~~~~~~f~~g~~---~vLvaT~~--~~~Gldip~--v~~VI~~~~p~  453 (503)
                      .+.+++.+...+.   ....+.-+....+...+++.|++...   .||+++.-  +++|||+|+  ++.||..++|-
T Consensus         4 m~~v~~~~~~~~~~~~~~~i~~e~~~~~~~~~~l~~f~~~~~~~g~iL~~v~~G~~~EGiD~~g~~~r~vii~glPf   80 (142)
T smart00491        4 LEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDFPDDLGRAVIIVGIPF   80 (142)
T ss_pred             HHHHHHHHHhcCccccCceEEEECCCCchHHHHHHHHHHhcCCCCEEEEEEeCCeeecceecCCCccEEEEEEecCC
Confidence            4556666665443   12223333333355788888987543   68988876  999999997  68999999873

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.62  E-value=0.034  Score=59.41  Aligned_cols=22  Identities=36%  Similarity=0.400  Sum_probs=15.9

Q ss_pred             eEEEccCCCchhHHhHHHHHHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      +.|.|+||+|||++. -.++..+
T Consensus       784 LYIyG~PGTGKTATV-K~VLrEL  805 (1164)
T PTZ00112        784 LYISGMPGTGKTATV-YSVIQLL  805 (1164)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHH
Confidence            359999999999875 3344443

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.61  E-value=0.015  Score=66.55  Aligned_cols=65  Identities=23%  Similarity=0.237  Sum_probs=45.2

Q ss_pred             CCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q 010709          143 RPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIE  211 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~  211 (503)
                      .+++-|.+++..++.+  +-++|.|..|+|||+.. -.++..+...   ....+..++.++||-..+..+.
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l-~~i~~~~~~l---~e~~g~~V~glAPTgkAa~~L~  901 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQF-RAVMSAVNML---PESERPRVVGLGPTHRAVGEMR  901 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHH-HHHHHHHHHH---hhccCceEEEEechHHHHHHHH
Confidence            6899999999999965  55999999999999853 2222222111   0113567888999987766553

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.61  E-value=0.031  Score=47.96  Aligned_cols=36  Identities=22%  Similarity=0.231  Sum_probs=22.2

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      +++.|++|+|||..... +......       .+..++++....
T Consensus         2 ~~i~G~~G~GKT~l~~~-i~~~~~~-------~~~~v~~~~~e~   37 (165)
T cd01120           2 ILVFGPTGSGKTTLALQ-LALNIAT-------KGGKVVYVDIEE   37 (165)
T ss_pred             eeEeCCCCCCHHHHHHH-HHHHHHh-------cCCEEEEEECCc
Confidence            68999999999985422 2222222       245677766543

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.61  E-value=0.046  Score=55.55  Aligned_cols=129  Identities=16%  Similarity=0.221  Sum_probs=61.8

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHHhccCCCceEEEEECCcc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN  234 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~  234 (503)
                      .|+.+.++||||+|||+....-+. .+...     ..+.++.++.  +.|..+.   +.++.++... ++.+..      
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa-~la~~-----~~gkkVaLIdtDtyRigA~---EQLk~ya~iL-gv~v~~------  412 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQ-RFAAQ-----HAPRDVALVTTDTQRVGGR---EQLHSYGRQL-GIAVHE------  412 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH-HHHHh-----cCCCceEEEecccccccHH---HHHHHhhccc-CceeEe------
Confidence            456788999999999985432222 22221     1123344443  3343332   2233333221 121110      


Q ss_pred             HHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCC-H
Q 010709          235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMP-V  312 (503)
Q Consensus       235 ~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~-~  312 (503)
                                     +.+++.+...+.+    +.++++|+||.+-+.... .....+..+... .....+++++++.. .
T Consensus       413 ---------------a~d~~~L~~aL~~----l~~~DLVLIDTaG~s~~D~~l~eeL~~L~aa-~~~a~lLVLpAtss~~  472 (559)
T PRK12727        413 ---------------ADSAESLLDLLER----LRDYKLVLIDTAGMGQRDRALAAQLNWLRAA-RQVTSLLVLPANAHFS  472 (559)
T ss_pred             ---------------cCcHHHHHHHHHH----hccCCEEEecCCCcchhhHHHHHHHHHHHHh-hcCCcEEEEECCCChh
Confidence                           1133444444443    346889999999743211 111122222222 23345778888874 3


Q ss_pred             HHHHHHHHh
Q 010709          313 EIEALAQEY  321 (503)
Q Consensus       313 ~~~~~~~~~  321 (503)
                      ++...++.|
T Consensus       473 Dl~eii~~f  481 (559)
T PRK12727        473 DLDEVVRRF  481 (559)
T ss_pred             HHHHHHHHH
Confidence            555555554

>PRK08727 hypothetical protein; Validated

Probab=96.60  E-value=0.004  Score=57.32  Aligned_cols=47  Identities=17%  Similarity=0.130  Sum_probs=26.4

Q ss_pred             CCccEEEecchhHHhhCC-CHHHHHHHHHhCCC-CCcEEEEEeeCCHHH
Q 010709          268 SRVSFVILDEADRMLDMG-FEPQIREVMQNLPD-KHQTLLFSATMPVEI  314 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~-~~~~~~~il~~~~~-~~q~i~~SAT~~~~~  314 (503)
                      .++++|||||+|.+.... ....+..++..... ..++|+.|-..|..+
T Consensus        92 ~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l  140 (233)
T PRK08727         92 EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGL  140 (233)
T ss_pred             hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhh
Confidence            345799999999775432 22334445444322 344555555555554

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.58  E-value=0.031  Score=52.35  Aligned_cols=130  Identities=18%  Similarity=0.225  Sum_probs=69.2

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccH-HHHHHHHHHHHHHhccCCCceEEEEECCcc
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTR-ELAQQIEKEVKALSRSLDSFKTAIVVGGTN  234 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr-~La~q~~~~~~~~~~~~~~~~~~~~~~~~~  234 (503)
                      +..+.++|++|+|||+.+..  +......      .+.++.++.  +.| ..+.|+......+     ++.+.       
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~--l~~~l~~------~~~~v~~i~~D~~ri~~~~ql~~~~~~~-----~~~~~-------  134 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAK--MAWQFHG------KKKTVGFITTDHSRIGTVQQLQDYVKTI-----GFEVI-------  134 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHH--HHHHHHH------cCCeEEEEecCCCCHHHHHHHHHHhhhc-----CceEE-------
Confidence            35699999999999985543  2222221      134444444  333 4555554333221     12211       


Q ss_pred             HHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCC-H
Q 010709          235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMP-V  312 (503)
Q Consensus       235 ~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~-~  312 (503)
                                    ...++..+.+.+..- ....++++||||-+=+.-.. .....+..++....+..-++.+|||.. .
T Consensus       135 --------------~~~~~~~l~~~l~~l-~~~~~~D~ViIDt~Gr~~~~~~~l~el~~~~~~~~~~~~~LVl~a~~~~~  199 (270)
T PRK06731        135 --------------AVRDEAAMTRALTYF-KEEARVDYILIDTAGKNYRASETVEEMIETMGQVEPDYICLTLSASMKSK  199 (270)
T ss_pred             --------------ecCCHHHHHHHHHHH-HhcCCCCEEEEECCCCCcCCHHHHHHHHHHHhhhCCCeEEEEEcCccCHH
Confidence                          112444444433320 11246789999998654221 123445555555555555777999864 4


Q ss_pred             HHHHHHHHhc
Q 010709          313 EIEALAQEYL  322 (503)
Q Consensus       313 ~~~~~~~~~~  322 (503)
                      +....++.|-
T Consensus       200 d~~~~~~~f~  209 (270)
T PRK06731        200 DMIEIITNFK  209 (270)
T ss_pred             HHHHHHHHhC
Confidence            6667777763

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.58  E-value=0.027  Score=51.95  Aligned_cols=48  Identities=21%  Similarity=0.344  Sum_probs=26.4

Q ss_pred             CCCccEEEecchhHHhhCCCHH-HHHHHHHhC-CCCCcEEEEEeeCCHHH
Q 010709          267 LSRVSFVILDEADRMLDMGFEP-QIREVMQNL-PDKHQTLLFSATMPVEI  314 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~-~~~~il~~~-~~~~q~i~~SAT~~~~~  314 (503)
                      +.++++|||||++......+.. .+..++... .....+++.|---+.++
T Consensus       160 l~~~dlLvIDDig~~~~s~~~~~~l~~Ii~~Ry~~~~~tiitSNl~~~~l  209 (244)
T PRK07952        160 LSNVDLLVIDEIGVQTESRYEKVIINQIVDRRSSSKRPTGMLTNSNMEEM  209 (244)
T ss_pred             hccCCEEEEeCCCCCCCCHHHHHHHHHHHHHHHhCCCCEEEeCCCCHHHH
Confidence            3468899999999654333333 344555543 22344555554433333

>PHA02533 17 large terminase protein; Provisional

Probab=96.57  E-value=0.019  Score=59.31  Aligned_cols=149  Identities=15%  Similarity=0.132  Sum_probs=84.9

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|.|+|...+..+..++-.++..+=..|||.+....++......      .+..+++++|++.-|..+.+.++......+
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~------~~~~v~i~A~~~~QA~~vF~~ik~~ie~~P  132 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN------KDKNVGILAHKASMAAEVLDRTKQAIELLP  132 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC------CCCEEEEEeCCHHHHHHHHHHHHHHHHhCH
Confidence            57899999998876566677888889999987654444443332      246899999999999988888886655432


Q ss_pred             Cc-eEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC--
Q 010709          223 SF-KTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD--  299 (503)
Q Consensus       223 ~~-~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~--  299 (503)
                      .+ ...+.....    ....+.++..|.+.|.+.       ....-....++|+||+|.+-+  +...+..+...+..  
T Consensus       133 ~l~~~~i~~~~~----~~I~l~NGS~I~~lss~~-------~t~rG~~~~~liiDE~a~~~~--~~e~~~ai~p~lasg~  199 (534)
T PHA02533        133 DFLQPGIVEWNK----GSIELENGSKIGAYASSP-------DAVRGNSFAMIYIDECAFIPN--FIDFWLAIQPVISSGR  199 (534)
T ss_pred             HHhhcceeecCc----cEEEeCCCCEEEEEeCCC-------CccCCCCCceEEEeccccCCC--HHHHHHHHHHHHHcCC
Confidence            21 111111000    001123455665554221       111223467899999996532  23333333333322  


Q ss_pred             CCcEEEEEeeC
Q 010709          300 KHQTLLFSATM  310 (503)
Q Consensus       300 ~~q~i~~SAT~  310 (503)
                      ..+++.+|++.
T Consensus       200 ~~r~iiiSTp~  210 (534)
T PHA02533        200 SSKIIITSTPN  210 (534)
T ss_pred             CceEEEEECCC
Confidence            23455555443

>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=96.56  E-value=0.03  Score=49.51  Aligned_cols=49  Identities=20%  Similarity=0.233  Sum_probs=30.8

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ++|.|++|+|||+..+-.+. .....       +.+++|+... +-..++.+.+..++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~-~~~~~-------g~~v~~~s~e-~~~~~~~~~~~~~g   50 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLY-AGLAR-------GEPGLYVTLE-ESPEELIENAESLG   50 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHH-HHHHC-------CCcEEEEECC-CCHHHHHHHHHHcC
Confidence            68999999999985433222 22222       5667877643 45566666666553

A related protein is found in archaea.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.56  E-value=0.018  Score=55.72  Aligned_cols=42  Identities=14%  Similarity=0.008  Sum_probs=30.6

Q ss_pred             CcHHHHHHHHHHhcCC----CeEEEccCCCchhHHhHHHHHHHHHhc
Q 010709          144 PTSIQAQAMPVALSGR----DLLGCAETGSGKTAAFTIPMIQHCVAQ  186 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~----~vii~~~TGsGKTl~~~lp~l~~~~~~  186 (503)
                      .+|||...|..+...+    -.+++||.|.|||..+ ..+...+.+.
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A-~~~A~~llC~   49 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALA-ERLAAALLCE   49 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHH-HHHHHHHcCC
Confidence            4788999998887543    3889999999999865 3344455543

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.55  E-value=0.02  Score=66.50  Aligned_cols=66  Identities=21%  Similarity=0.204  Sum_probs=46.0

Q ss_pred             CCCcHHHHHHHHHHhcCC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALSGR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIE  211 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~  211 (503)
                      ..+++.|.+++..++.+.  -++|.|..|+|||+.. -.++..+...   ....+..++.++||--.|..+.
T Consensus       966 ~~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l---~~~~~~~V~glAPTgrAAk~L~ 1033 (1747)
T PRK13709        966 EGLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTL---PESERPRVVGLGPTHRAVGEMR 1033 (1747)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHh---hcccCceEEEECCcHHHHHHHH
Confidence            368999999999999764  4999999999999853 3333332211   0112466888999987766543

>PRK08116 hypothetical protein; Validated

Probab=96.53  E-value=0.048  Score=51.30  Aligned_cols=48  Identities=13%  Similarity=0.184  Sum_probs=26.6

Q ss_pred             CCccEEEecchhHHhhCC-CHHHHHHHHHhC-CCCCcEEEEEeeCCHHHH
Q 010709          268 SRVSFVILDEADRMLDMG-FEPQIREVMQNL-PDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~-~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~  315 (503)
                      .+.++|||||++...... ....+..++... .....+|+.|-..+.++.
T Consensus       177 ~~~dlLviDDlg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~~~eL~  226 (268)
T PRK08116        177 VNADLLILDDLGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLSLEELK  226 (268)
T ss_pred             cCCCEEEEecccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHH
Confidence            457899999996321111 233455555543 334556666665555544

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.50  E-value=0.014  Score=54.15  Aligned_cols=45  Identities=20%  Similarity=0.356  Sum_probs=33.4

Q ss_pred             CCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          265 TSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       265 ~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      .....++.+|+||||.|... -...+++.+.......++++...-+
T Consensus       125 ~~~~~fKiiIlDEcdsmtsd-aq~aLrr~mE~~s~~trFiLIcnyl  169 (346)
T KOG0989|consen  125 YPCPPFKIIILDECDSMTSD-AQAALRRTMEDFSRTTRFILICNYL  169 (346)
T ss_pred             CCCCcceEEEEechhhhhHH-HHHHHHHHHhccccceEEEEEcCCh
Confidence            34567899999999987543 3556778888877777788777665

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=96.49  E-value=0.034  Score=53.45  Aligned_cols=144  Identities=19%  Similarity=0.217  Sum_probs=74.0

Q ss_pred             CCCcHHHHHHHHHHh----cCC---CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVAL----SGR---DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~----~~~---~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      ..++|||..++..+.    .|+   -.++.||.|.||+..+ ..+...+++.....   .+    -++.       .+.+
T Consensus         3 ~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA-~~lA~~LlC~~~~~---~~----~c~~-------c~~~   67 (319)
T PRK08769          3 SAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVA-LALAEHVLASGPDP---AA----AQRT-------RQLI   67 (319)
T ss_pred             ccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHH-HHHHHHHhCCCCCC---CC----cchH-------HHHH
Confidence            467899999998765    333   3899999999999865 44555555542110   00    0111       1111


Q ss_pred             HHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHH
Q 010709          215 KALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVM  294 (503)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il  294 (503)
                      ..  ..++++.+.....+....      .....|.|--.-.+.+.+.. .-.....+++|||+||.|... -.+.+.+++
T Consensus        68 ~~--g~HPD~~~i~~~p~~~~~------k~~~~I~idqIR~l~~~~~~-~p~~g~~kV~iI~~ae~m~~~-AaNaLLKtL  137 (319)
T PRK08769         68 AA--GTHPDLQLVSFIPNRTGD------KLRTEIVIEQVREISQKLAL-TPQYGIAQVVIVDPADAINRA-ACNALLKTL  137 (319)
T ss_pred             hc--CCCCCEEEEecCCCcccc------cccccccHHHHHHHHHHHhh-CcccCCcEEEEeccHhhhCHH-HHHHHHHHh
Confidence            11  122344333211110000      00011222111122222222 123457899999999988533 456677777


Q ss_pred             HhCCCCCcEEEEEeeC
Q 010709          295 QNLPDKHQTLLFSATM  310 (503)
Q Consensus       295 ~~~~~~~q~i~~SAT~  310 (503)
                      ..-+++..+|++|..+
T Consensus       138 EEPp~~~~fiL~~~~~  153 (319)
T PRK08769        138 EEPSPGRYLWLISAQP  153 (319)
T ss_pred             hCCCCCCeEEEEECCh
Confidence            7767777666666544

>PRK12377 putative replication protein; Provisional

Probab=96.48  E-value=0.026  Score=52.22  Aligned_cols=45  Identities=13%  Similarity=0.265  Sum_probs=26.9

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIE  211 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~  211 (503)
                      ..++++.|++|+|||..+ .++...+...       +..+++ ++..+|..++.
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~~-------g~~v~~-i~~~~l~~~l~  145 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLAK-------GRSVIV-VTVPDVMSRLH  145 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHc-------CCCeEE-EEHHHHHHHHH
Confidence            357999999999999743 3344444432       344444 34445655443

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=96.40  E-value=0.012  Score=54.69  Aligned_cols=49  Identities=18%  Similarity=0.295  Sum_probs=31.8

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      .++++++.|++|+|||..+ .++-..+...       |.. ++.+++.+++.++...+
T Consensus       104 ~~~nl~l~G~~G~GKThLa-~Ai~~~l~~~-------g~s-v~f~~~~el~~~Lk~~~  152 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLA-IAIGNELLKA-------GIS-VLFITAPDLLSKLKAAF  152 (254)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHHc-------CCe-EEEEEHHHHHHHHHHHH
Confidence            6778999999999999754 3344444432       333 55556667776655544

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=96.34  E-value=0.043  Score=57.88  Aligned_cols=156  Identities=21%  Similarity=0.268  Sum_probs=88.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      .++..-..+.....+.+..-|.+.+..+++.+  -+++.|.=|=|||.+.-+.+. .+....     ....++|++|+.+
T Consensus       199 ~~~~~~~~l~~l~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~-~~~~~~-----~~~~iiVTAP~~~  272 (758)
T COG1444         199 LDPVFPRELYELCLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALA-AAARLA-----GSVRIIVTAPTPA  272 (758)
T ss_pred             CCCCCCHHHhhhhcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHH-HHHHhc-----CCceEEEeCCCHH
Confidence            33333445555555556555556666666554  489999999999987655442 222211     0346899999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       206 La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      -++.+.+.+.+-+...+ ++..........  ..........|-+..|....          ..-++||||||=.+-   
T Consensus       273 nv~~Lf~fa~~~l~~lg-~~~~v~~d~~g~--~~~~~~~~~~i~y~~P~~a~----------~~~DllvVDEAAaIp---  336 (758)
T COG1444         273 NVQTLFEFAGKGLEFLG-YKRKVAPDALGE--IREVSGDGFRIEYVPPDDAQ----------EEADLLVVDEAAAIP---  336 (758)
T ss_pred             HHHHHHHHHHHhHHHhC-Cccccccccccc--eeeecCCceeEEeeCcchhc----------ccCCEEEEehhhcCC---
Confidence            88877766655444331 221111111000  00000112334455554432          126799999997543   


Q ss_pred             CHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          286 FEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       286 ~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                       .+.+.+++..++    .++||.|+
T Consensus       337 -lplL~~l~~~~~----rv~~sTTI  356 (758)
T COG1444         337 -LPLLHKLLRRFP----RVLFSTTI  356 (758)
T ss_pred             -hHHHHHHHhhcC----ceEEEeee
Confidence             566777777654    68899998

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.34  E-value=0.061  Score=55.92  Aligned_cols=153  Identities=13%  Similarity=0.139  Sum_probs=81.8

Q ss_pred             CCCCCcHHHHHHHHHHh---cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          140 EYTRPTSIQAQAMPVAL---SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~---~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      +...|.|.=.+-+..+.   ..+-.++.+|=|.|||.+..+.+. .+...      .+.+++|++|...-+.++.+.++.
T Consensus       166 np~~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~-~La~f------~Gi~IlvTAH~~~ts~evF~rv~~  238 (752)
T PHA03333        166 NPEAPSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILA-AMISF------LEIDIVVQAQRKTMCLTLYNRVET  238 (752)
T ss_pred             CcCCCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHH-HHHHh------cCCeEEEECCChhhHHHHHHHHHH
Confidence            33344555555555444   455688899999999987544333 33332      256799999999999998888887


Q ss_pred             HhccCC-------CceEEEEECCccHHHHH--HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCC
Q 010709          217 LSRSLD-------SFKTAIVVGGTNIAEQR--SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGF  286 (503)
Q Consensus       217 ~~~~~~-------~~~~~~~~~~~~~~~~~--~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~  286 (503)
                      ......       ...+..+.|+...-...  .... ++..|.+++-.       .+...-..++++|+|||+.+-.   
T Consensus       239 ~le~lg~~~~fp~~~~iv~vkgg~E~I~f~~p~gak~G~sti~F~Ars-------~~s~RG~~~DLLIVDEAAfI~~---  308 (752)
T PHA03333        239 VVHAYQHKPWFPEEFKIVTLKGTDENLEYISDPAAKEGKTTAHFLASS-------PNAARGQNPDLVIVDEAAFVNP---  308 (752)
T ss_pred             HHHHhccccccCCCceEEEeeCCeeEEEEecCcccccCcceeEEeccc-------CCCcCCCCCCEEEEECcccCCH---
Confidence            775321       11122222222100000  0000 01233333211       1222334678999999996542   


Q ss_pred             HHHHHHHHHhCC-CCCcEEEEEeeC
Q 010709          287 EPQIREVMQNLP-DKHQTLLFSATM  310 (503)
Q Consensus       287 ~~~~~~il~~~~-~~~q~i~~SAT~  310 (503)
                       ..+..++-.+. .+.+++++|.+-
T Consensus       309 -~~l~aIlP~l~~~~~k~IiISS~~  332 (752)
T PHA03333        309 -GALLSVLPLMAVKGTKQIHISSPV  332 (752)
T ss_pred             -HHHHHHHHHHccCCCceEEEeCCC
Confidence             33444444333 345566666664

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=96.33  E-value=0.02  Score=54.28  Aligned_cols=60  Identities=22%  Similarity=0.248  Sum_probs=42.9

Q ss_pred             CCCCCcHHHHHHHHHHhcCC-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          140 EYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~~~~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      .+...++-|...+..+...+ +++++|.||||||+.  +-++.....       ..-++|.+--|.||-.
T Consensus       154 ~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTl--LNal~~~i~-------~~eRvItiEDtaELql  214 (355)
T COG4962         154 IFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTL--LNALSGFID-------SDERVITIEDTAELQL  214 (355)
T ss_pred             HcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHH--HHHHHhcCC-------CcccEEEEeehhhhcc
Confidence            45678888999888877666 899999999999983  333333222       1337888888887743

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.32  E-value=0.047  Score=53.97  Aligned_cols=125  Identities=15%  Similarity=0.167  Sum_probs=62.7

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      -++++||+|+|||+...--+..+....       +.++.++.  +.|..+..+   ++.++... ++....         
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~~~~~~-------G~~V~Lit~Dt~R~aA~eQ---Lk~yAe~l-gvp~~~---------  284 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAKYFLHM-------GKSVSLYTTDNYRIAAIEQ---LKRYADTM-GMPFYP---------  284 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHhc-------CCeEEEecccchhhhHHHH---HHHHHHhc-CCCeee---------
Confidence            478999999999986543322222222       34454444  455554432   33333221 121110         


Q ss_pred             HHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhh-CCCHHHHHHHHHhCC---CCCcEEEEEeeCCH-
Q 010709          238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIREVMQNLP---DKHQTLLFSATMPV-  312 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~-~~~~~~~~~il~~~~---~~~q~i~~SAT~~~-  312 (503)
                                  +..+..+...+.     -.++++|+||=+-+... ......+..++....   +.-.++.++||... 
T Consensus       285 ------------~~~~~~l~~~l~-----~~~~D~VLIDTaGr~~rd~~~l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~  347 (432)
T PRK12724        285 ------------VKDIKKFKETLA-----RDGSELILIDTAGYSHRNLEQLERMQSFYSCFGEKDSVENLLVLSSTSSYH  347 (432)
T ss_pred             ------------hHHHHHHHHHHH-----hCCCCEEEEeCCCCCccCHHHHHHHHHHHHhhcCCCCCeEEEEEeCCCCHH
Confidence                        001222333332     24678999996543311 112344555555442   22357888999876 


Q ss_pred             HHHHHHHHh
Q 010709          313 EIEALAQEY  321 (503)
Q Consensus       313 ~~~~~~~~~  321 (503)
                      ++...++.|
T Consensus       348 ~~~~~~~~f  356 (432)
T PRK12724        348 HTLTVLKAY  356 (432)
T ss_pred             HHHHHHHHh
Confidence            555555554

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=96.32  E-value=0.019  Score=52.67  Aligned_cols=43  Identities=14%  Similarity=0.251  Sum_probs=25.5

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCc-EEEEEeeCCH
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ-TLLFSATMPV  312 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q-~i~~SAT~~~  312 (503)
                      ..++|||||+|.+... ....+..++........ +++++++.++
T Consensus        90 ~~~~liiDdi~~l~~~-~~~~L~~~~~~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903         90 EAELYAVDDVERLDDA-QQIALFNLFNRVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             cCCEEEEeChhhcCch-HHHHHHHHHHHHHHcCCcEEEEeCCCCH
Confidence            4678999999976432 33445555554433333 4677776543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.31  E-value=0.021  Score=57.81  Aligned_cols=50  Identities=12%  Similarity=0.302  Sum_probs=29.5

Q ss_pred             CCccEEEecchhHHhhCC-CHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHH
Q 010709          268 SRVSFVILDEADRMLDMG-FEPQIREVMQNL-PDKHQTLLFSATMPVEIEAL  317 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~-~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~  317 (503)
                      .+.++++|||+|.+.+.. ....+..++..+ ....++|+.|-+.|..+..+
T Consensus       201 ~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l  252 (445)
T PRK12422        201 RNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAM  252 (445)
T ss_pred             ccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhh
Confidence            467899999999876542 234444554433 23455665555556665543

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.31  E-value=0.013  Score=56.50  Aligned_cols=45  Identities=22%  Similarity=0.277  Sum_probs=27.3

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI  210 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~  210 (503)
                      .++++++.|+||+|||..+ ..+...+...       +..|+++. ..+|..+.
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~~~-------g~~V~y~t-~~~l~~~l  226 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELLDR-------GKSVIYRT-ADELIEIL  226 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHHC-------CCeEEEEE-HHHHHHHH
Confidence            3577999999999999743 3344444432       44555544 34454443

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.27  E-value=0.033  Score=56.55  Aligned_cols=109  Identities=13%  Similarity=0.117  Sum_probs=57.1

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR  239 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (503)
                      .+++.|++|+|||... ..+...+...     ..+.+++++.. .++..++...+..-.                     
T Consensus       143 pl~i~G~~G~GKTHLl-~Ai~~~l~~~-----~~~~~v~yv~~-~~f~~~~~~~l~~~~---------------------  194 (450)
T PRK14087        143 PLFIYGESGMGKTHLL-KAAKNYIESN-----FSDLKVSYMSG-DEFARKAVDILQKTH---------------------  194 (450)
T ss_pred             ceEEECCCCCcHHHHH-HHHHHHHHHh-----CCCCeEEEEEH-HHHHHHHHHHHHHhh---------------------
Confidence            4899999999999632 3333333321     12455666655 455554444332100                     


Q ss_pred             HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCC-CCCcEEEEEeeCCHHH
Q 010709          240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLP-DKHQTLLFSATMPVEI  314 (503)
Q Consensus       240 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~~~~  314 (503)
                                    +.+.....    .+.++++|||||+|.+.+. .....+..++..+. ...|+|+.|-..|..+
T Consensus       195 --------------~~~~~~~~----~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l  253 (450)
T PRK14087        195 --------------KEIEQFKN----EICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELL  253 (450)
T ss_pred             --------------hHHHHHHH----HhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHH
Confidence                          11111111    1346789999999976543 23344555555443 2345655555555444

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.26  E-value=0.019  Score=53.92  Aligned_cols=34  Identities=18%  Similarity=0.324  Sum_probs=21.3

Q ss_pred             CCccEEEecchhHHhhCCC--HHHHHHHHHhCCCCC
Q 010709          268 SRVSFVILDEADRMLDMGF--EPQIREVMQNLPDKH  301 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~--~~~~~~il~~~~~~~  301 (503)
                      -+++++||||+|+++....  ...+...++.+.+..
T Consensus       144 ~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL  179 (302)
T PF05621_consen  144 LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNEL  179 (302)
T ss_pred             cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhcc
Confidence            3578999999999865432  233444455554433

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.25  E-value=0.014  Score=62.64  Aligned_cols=70  Identities=23%  Similarity=0.169  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .+++-|.+++..  ....++|.|..|||||.+. +.-+.+++...   +-...++|+++.|+..|..+.+++..+.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL-~~Ria~Li~~~---~v~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVI-TNKIAHLIRGC---GYQARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHH-HHHHHHHHHhc---CCCHHHeeeEechHHHHHHHHHHHHHHh
Confidence            467889998865  3567899999999999875 44455555431   1234679999999999999999998765

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.24  E-value=0.027  Score=54.89  Aligned_cols=132  Identities=17%  Similarity=0.229  Sum_probs=70.3

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc-HHHHHHHHHHHHHHhccCCCceEEEEECCccHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT-RELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA  236 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt-r~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (503)
                      ++.+.++||||.|||+...=-+..+.+..     ......||.+-| |.=|.   ++++.|++-+ ++.+          
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~-----~~~kVaiITtDtYRIGA~---EQLk~Ya~im-~vp~----------  263 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLK-----KKKKVAIITTDTYRIGAV---EQLKTYADIM-GVPL----------  263 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhc-----cCcceEEEEeccchhhHH---HHHHHHHHHh-CCce----------
Confidence            67799999999999986432222222111     123445555543 33322   3344444322 2333          


Q ss_pred             HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCC-HHH
Q 010709          237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMP-VEI  314 (503)
Q Consensus       237 ~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~-~~~  314 (503)
                                 .++-+|.-|...+..    +.++++|.||=+-+--.. .....+..++..-.+---.+.+|||.. .++
T Consensus       264 -----------~vv~~~~el~~ai~~----l~~~d~ILVDTaGrs~~D~~~i~el~~~~~~~~~i~~~Lvlsat~K~~dl  328 (407)
T COG1419         264 -----------EVVYSPKELAEAIEA----LRDCDVILVDTAGRSQYDKEKIEELKELIDVSHSIEVYLVLSATTKYEDL  328 (407)
T ss_pred             -----------EEecCHHHHHHHHHH----hhcCCEEEEeCCCCCccCHHHHHHHHHHHhccccceEEEEEecCcchHHH
Confidence                       234455555555543    566788888877642111 123344555554444444677888874 456


Q ss_pred             HHHHHHhcC
Q 010709          315 EALAQEYLT  323 (503)
Q Consensus       315 ~~~~~~~~~  323 (503)
                      ..++..|-.
T Consensus       329 kei~~~f~~  337 (407)
T COG1419         329 KEIIKQFSL  337 (407)
T ss_pred             HHHHHHhcc
Confidence            666666643

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.21  E-value=0.031  Score=64.10  Aligned_cols=123  Identities=24%  Similarity=0.235  Sum_probs=77.9

Q ss_pred             CcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCC
Q 010709          144 PTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS  223 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~  223 (503)
                      .|+-|.++|..  .+++++|.|..|||||.+..--++..+...     ....++|+|+=|+..|..+.+++.+-....  
T Consensus         2 ~t~~Q~~ai~~--~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-----~~~~~il~~tFt~~aa~e~~~ri~~~l~~~--   72 (1232)
T TIGR02785         2 WTDEQWQAIYT--RGQNILVSASAGSGKTAVLVERIIKKILRG-----VDIDRLLVVTFTNAAAREMKERIEEALQKA--   72 (1232)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcC-----CCHhhEEEEeccHHHHHHHHHHHHHHHHHH--
Confidence            57889999974  688999999999999987655555544321     122469999999999999998888655321  


Q ss_pred             ceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCc--cEEEecchhH
Q 010709          224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRV--SFVILDEADR  280 (503)
Q Consensus       224 ~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~--~~vViDEaH~  280 (503)
                      +.     .........+.+..-...-|+|...++..+.+.....-++  .+=|.||...
T Consensus        73 ~~-----~~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        73 LQ-----QEPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             Hh-----cCchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence            10     0111111222233335667899998876665543222122  3456888774

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.

>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=96.17  E-value=0.062  Score=44.23  Aligned_cols=15  Identities=33%  Similarity=0.417  Sum_probs=12.9

Q ss_pred             eEEEccCCCchhHHh
Q 010709          161 LLGCAETGSGKTAAF  175 (503)
Q Consensus       161 vii~~~TGsGKTl~~  175 (503)
                      +++.||+|+|||..+
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            589999999999743

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 ....

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

Probab=96.17  E-value=0.028  Score=54.22  Aligned_cols=16  Identities=25%  Similarity=0.382  Sum_probs=14.3

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      +.|+.||+|+|||+.+
T Consensus        50 SmIl~GPPG~GKTTlA   65 (436)
T COG2256          50 SMILWGPPGTGKTTLA   65 (436)
T ss_pred             eeEEECCCCCCHHHHH
Confidence            5999999999999854

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=96.16  E-value=0.014  Score=50.68  Aligned_cols=103  Identities=18%  Similarity=0.169  Sum_probs=56.3

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS  240 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (503)
                      .+++||++||||.-.+.-+-.+ ..       .+.++++..|...--         +..    -.+.... |.       
T Consensus         7 ~~i~gpM~SGKT~eLl~r~~~~-~~-------~g~~v~vfkp~iD~R---------~~~----~~V~Sr~-G~-------   57 (201)
T COG1435           7 EFIYGPMFSGKTEELLRRARRY-KE-------AGMKVLVFKPAIDTR---------YGV----GKVSSRI-GL-------   57 (201)
T ss_pred             EEEEccCcCcchHHHHHHHHHH-HH-------cCCeEEEEecccccc---------ccc----ceeeecc-CC-------
Confidence            6899999999998543322222 22       256788888864211         110    0111111 11       


Q ss_pred             HhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          241 ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       241 ~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                         ....++|-.+..+.+.+....... .+++|.||||+-+. ......+.++...+
T Consensus        58 ---~~~A~~i~~~~~i~~~i~~~~~~~-~~~~v~IDEaQF~~-~~~v~~l~~lad~l  109 (201)
T COG1435          58 ---SSEAVVIPSDTDIFDEIAALHEKP-PVDCVLIDEAQFFD-EELVYVLNELADRL  109 (201)
T ss_pred             ---cccceecCChHHHHHHHHhcccCC-CcCEEEEehhHhCC-HHHHHHHHHHHhhc
Confidence               113456667777777776533222 28899999999543 32334455555543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=96.15  E-value=0.091  Score=55.62  Aligned_cols=39  Identities=13%  Similarity=0.264  Sum_probs=25.7

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+++++||||+|+|.... .+.+.+++..-++...+|+.+
T Consensus       118 gr~KVIIIDEah~LT~~A-~NALLKtLEEPP~~v~FILaT  156 (830)
T PRK07003        118 ARFKVYMIDEVHMLTNHA-FNAMLKTLEEPPPHVKFILAT  156 (830)
T ss_pred             CCceEEEEeChhhCCHHH-HHHHHHHHHhcCCCeEEEEEE
Confidence            468999999999875432 344556666656566555544

>PTZ00293 thymidine kinase; Provisional

Probab=96.14  E-value=0.039  Score=49.21  Aligned_cols=39  Identities=15%  Similarity=0.138  Sum_probs=25.6

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      |.=-++.||+++|||.-.+- .+......       +.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr-~i~~y~~a-------g~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMR-LVKRFTYS-------EKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHH-HHHHHHHc-------CCceEEEEecc
Confidence            33468899999999975433 33332222       56688888864

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.14  E-value=0.044  Score=55.00  Aligned_cols=52  Identities=17%  Similarity=0.289  Sum_probs=30.6

Q ss_pred             ccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh
Q 010709          270 VSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       270 ~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                      .++||||.+-++... .....+..+.....++.-++.++|+...+....++.|
T Consensus       176 ~DvVIIDTAGr~~~d~~lm~El~~l~~~~~pdevlLVvda~~gq~av~~a~~F  228 (437)
T PRK00771        176 ADVIIVDTAGRHALEEDLIEEMKEIKEAVKPDEVLLVIDATIGQQAKNQAKAF  228 (437)
T ss_pred             CCEEEEECCCcccchHHHHHHHHHHHHHhcccceeEEEeccccHHHHHHHHHH
Confidence            378999988543211 1233445555555566667777888766555555554

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.14  E-value=0.02  Score=56.94  Aligned_cols=32  Identities=16%  Similarity=0.186  Sum_probs=25.4

Q ss_pred             CcHHHHHHHHHHhcCCCeEEEccCCCchhHHh
Q 010709          144 PTSIQAQAMPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      +.......+..+..++++++.||+|+|||..+
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA  211 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVA  211 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHH
Confidence            44455666677778999999999999999754

>PF13871 Helicase_C_4: Helicase_C-like

Probab=96.13  E-value=0.0093  Score=55.46  Aligned_cols=54  Identities=19%  Similarity=0.299  Sum_probs=47.7

Q ss_pred             HHHHHHhcCCCcEEEEccccccCCCCCC--------CCEEEEccCCCChhHHHHhhCcceee
Q 010709          415 SALRDFRNGSTNILVATDVASRGLDVMG--------VAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       415 ~~~~~f~~g~~~vLvaT~~~~~Gldip~--------v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ...+.|.+|+..|+|.++++++|+.+..        -++-|.+.+|++....+|..||+.|+
T Consensus        52 ~e~~~F~~g~k~v~iis~AgstGiSlHAd~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRs  113 (278)
T PF13871_consen   52 AEKQAFMDGEKDVAIISDAGSTGISLHADRRVKNQRRRVHITLELPWSADKAIQQFGRTHRS  113 (278)
T ss_pred             HHHHHHhCCCceEEEEecccccccchhccccCCCCCceEEEEeeCCCCHHHHHHHhcccccc
Confidence            5567899999999999999999999874        24567889999999999999999996

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=96.12  E-value=0.061  Score=56.57  Aligned_cols=38  Identities=16%  Similarity=0.239  Sum_probs=25.3

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF  306 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~  306 (503)
                      .+++++||||+|+|... -.+.+.+.+..-++...+|+.
T Consensus       118 g~~KV~IIDEah~Ls~~-a~NALLKtLEEPp~~v~FIL~  155 (647)
T PRK07994        118 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLA  155 (647)
T ss_pred             CCCEEEEEechHhCCHH-HHHHHHHHHHcCCCCeEEEEe
Confidence            57899999999987543 244555566665555555554

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=96.12  E-value=0.035  Score=59.86  Aligned_cols=70  Identities=19%  Similarity=0.107  Sum_probs=52.3

Q ss_pred             CcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          144 PTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      +++-|.+++..  ...+++|.|..|||||.+. +--+.+++...   .....++|+|+.|+..|.++.+++.+...
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--VTGPCLVLAGAGSGKTRVI-TNKIAYLIQNC---GYKARNIAAVTFTNKAAREMKERVAKTLG   71 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHH-HHHHHHHHHhc---CCCHHHeEEEeccHHHHHHHHHHHHHHhC
Confidence            67789888765  3568999999999999875 44444555421   11346799999999999999999987653

Designed to identify rep members of the uvrD/rep subfamily.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.11  E-value=0.057  Score=53.84  Aligned_cols=43  Identities=21%  Similarity=0.149  Sum_probs=25.3

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQQI  210 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~q~  210 (503)
                      .++++|++|+|||+...  -+...+..      .+.+++++.  +.|..|.++
T Consensus       102 vi~lvG~~GvGKTTtaa--KLA~~l~~------~G~kV~lV~~D~~R~aA~eQ  146 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCT--KLAYYYQR------KGFKPCLVCADTFRAGAFDQ  146 (429)
T ss_pred             EEEEECCCCCCHHHHHH--HHHHHHHH------CCCCEEEEcCcccchhHHHH
Confidence            47899999999997543  22222222      144566655  556544443

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.

>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=96.10  E-value=0.052  Score=46.80  Aligned_cols=43  Identities=16%  Similarity=0.389  Sum_probs=31.2

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      ..++++||||||.|... -...+.+.+..-+....++++|..+.
T Consensus       101 ~~~KviiI~~ad~l~~~-a~NaLLK~LEepp~~~~fiL~t~~~~  143 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEE-AQNALLKTLEEPPENTYFILITNNPS  143 (162)
T ss_dssp             SSSEEEEEETGGGS-HH-HHHHHHHHHHSTTTTEEEEEEES-GG
T ss_pred             CCceEEEeehHhhhhHH-HHHHHHHHhcCCCCCEEEEEEECChH
Confidence            57899999999987533 46677788888777787777666553

...

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.09  E-value=0.036  Score=66.02  Aligned_cols=64  Identities=25%  Similarity=0.285  Sum_probs=45.1

Q ss_pred             CCCcHHHHHHHHHHhcCCC--eEEEccCCCchhHHhHH--HHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTI--PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIE  211 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~--vii~~~TGsGKTl~~~l--p~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~  211 (503)
                      ..+++.|.+|+..++.+.+  ++|.|..|+|||+...-  -.+......      .+..++.++||-..+..+.
T Consensus      1018 ~~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~------~g~~v~glApT~~Aa~~L~ 1085 (1960)
T TIGR02760      1018 ERLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES------EQLQVIGLAPTHEAVGELK 1085 (1960)
T ss_pred             CCCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh------cCCeEEEEeChHHHHHHHH
Confidence            4689999999999987644  78899999999975410  122222221      2567899999987766553

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.

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

Probab=96.09  E-value=0.021  Score=58.67  Aligned_cols=152  Identities=16%  Similarity=0.142  Sum_probs=81.4

Q ss_pred             HHHHHHHHHHh-----cC----CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          146 SIQAQAMPVAL-----SG----RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       146 ~~Q~~~i~~i~-----~~----~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      |+|...+..++     .|    +.+++.-|=|-|||......++..+...    +..+..+++++++++-|..+.+.++.
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~----g~~~~~i~~~A~~~~QA~~~f~~~~~   76 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLD----GEPGAEIYCAANTRDQAKIVFDEAKK   76 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcC----CccCceEEEEeCCHHHHHHHHHHHHH
Confidence            56777777666     22    2488888999999975433333333322    23467899999999999999999988


Q ss_pred             HhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC--CCCCCCccEEEecchhHHhhCCCHHHHHHHH
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG--NTSLSRVSFVILDEADRMLDMGFEPQIREVM  294 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~--~~~l~~~~~vViDEaH~l~~~~~~~~~~~il  294 (503)
                      +....+.+....  ... .   .. . ....|..-..+.+...+...  ...-.+..++|+||+|.+-+......+..-+
T Consensus        77 ~i~~~~~l~~~~--~~~-~---~~-~-~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~i~DE~h~~~~~~~~~~l~~g~  148 (477)
T PF03354_consen   77 MIEASPELRKRK--KPK-I---IK-S-NKKEIEFPKTGSFFKALSSDADSLDGLNPSLAIFDELHAHKDDELYDALESGM  148 (477)
T ss_pred             HHHhChhhccch--hhh-h---hh-h-hceEEEEcCCCcEEEEEecCCCCccCCCCceEEEeCCCCCCCHHHHHHHHhhh
Confidence            876533222100  000 0   00 0 01122222212222222221  1222356899999999765433344444444


Q ss_pred             HhCCCCCcEEEEEee
Q 010709          295 QNLPDKHQTLLFSAT  309 (503)
Q Consensus       295 ~~~~~~~q~i~~SAT  309 (503)
                      ...+.+.-+++.||.
T Consensus       149 ~~r~~pl~~~ISTag  163 (477)
T PF03354_consen  149 GARPNPLIIIISTAG  163 (477)
T ss_pred             ccCCCceEEEEeCCC
Confidence            443333333333443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.06  E-value=0.03  Score=54.25  Aligned_cols=39  Identities=18%  Similarity=0.267  Sum_probs=26.5

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..++|||||+|.+........+..++...+...++|+.+
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~  138 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITA  138 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEc
Confidence            467999999998733323455666777777777666544

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=96.05  E-value=0.05  Score=53.28  Aligned_cols=40  Identities=13%  Similarity=0.297  Sum_probs=26.2

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ....++|||||+|.+... ....+..++...++..++|+.+
T Consensus       123 ~~~~~vlilDe~~~l~~~-~~~~L~~~le~~~~~~~~Il~~  162 (337)
T PRK12402        123 SADYKTILLDNAEALRED-AQQALRRIMEQYSRTCRFIIAT  162 (337)
T ss_pred             CCCCcEEEEeCcccCCHH-HHHHHHHHHHhccCCCeEEEEe
Confidence            345789999999976432 3445666666666666655544

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.05  E-value=0.051  Score=57.88  Aligned_cols=66  Identities=15%  Similarity=0.137  Sum_probs=33.4

Q ss_pred             CcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCC-HHHHHHHHHh
Q 010709          252 TPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMP-VEIEALAQEY  321 (503)
Q Consensus       252 Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~-~~~~~~~~~~  321 (503)
                      +|..+.+.+..    +.++++|+||=+=+.-.. .....+..+.....+...++.++||.. ..+.++++.|
T Consensus       250 ~~~~l~~al~~----~~~~D~VLIDTAGRs~~d~~l~eel~~l~~~~~p~e~~LVLsAt~~~~~l~~i~~~f  317 (767)
T PRK14723        250 DAADLRFALAA----LGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGRPVRRLLLLNAASHGDTLNEVVHAY  317 (767)
T ss_pred             CHHHHHHHHHH----hcCCCEEEEeCCCCCccCHHHHHHHHHHhccCCCCeEEEEECCCCcHHHHHHHHHHH
Confidence            55555555542    345577888777643211 112223333333344455677788764 3344455555

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.05  E-value=0.031  Score=56.63  Aligned_cols=51  Identities=12%  Similarity=0.333  Sum_probs=28.7

Q ss_pred             CccEEEecchhHHhhCC-CHHHHHHHHHhCC-CCCcEEEEEeeCCHHHHHHHH
Q 010709          269 RVSFVILDEADRMLDMG-FEPQIREVMQNLP-DKHQTLLFSATMPVEIEALAQ  319 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~-~~~~~~~il~~~~-~~~q~i~~SAT~~~~~~~~~~  319 (503)
                      +.++|+|||+|.+.+.. ....+..++..+. ...++|+.|...|..+..+..
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~  246 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQD  246 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHH
Confidence            47799999999876542 2233444444332 234555555455555554433

>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=96.05  E-value=0.01  Score=53.97  Aligned_cols=49  Identities=18%  Similarity=0.297  Sum_probs=30.5

Q ss_pred             CCCccEEEecchhHHhhC-CCHHHHHHHHHhCC-CCCcEEEEEeeCCHHHH
Q 010709          267 LSRVSFVILDEADRMLDM-GFEPQIREVMQNLP-DKHQTLLFSATMPVEIE  315 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~~~~~  315 (503)
                      +..+++++||++|.+.+. .....+..++..+. .+.++|+.|...|..+.
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            346889999999987654 23445555555542 34567777767766543

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.

>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=96.01  E-value=0.0026  Score=55.08  Aligned_cols=123  Identities=21%  Similarity=0.293  Sum_probs=52.3

Q ss_pred             EEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHH
Q 010709          162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE  241 (503)
Q Consensus       162 ii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (503)
                      |+.|+=|-|||.+.-+. +..+...      ...+++|.+|+.+-++.+.+.+..-.+... ++.......   ......
T Consensus         1 VltA~RGRGKSa~lGl~-~a~l~~~------~~~~I~vtAP~~~~~~~lf~~~~~~l~~~~-~~~~~~~~~---~~~~~~   69 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLA-AAALIQK------GKIRILVTAPSPENVQTLFEFAEKGLKALG-YKEEKKKRI---GQIIKL   69 (177)
T ss_dssp             -EEE-TTSSHHHHHHHC-CCCSSS-----------EEEE-SS--S-HHHHHCC---------------------------
T ss_pred             CccCCCCCCHHHHHHHH-HHHHHHh------cCceEEEecCCHHHHHHHHHHHHhhccccc-ccccccccc---cccccc
Confidence            57899999999754332 1122221      124699999999888777665544332221 111000000   000001


Q ss_pred             hhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       242 ~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ...+..|-+..|+.+....       ...+++|||||=.+-    .+.+.+++...+    .++||.|.
T Consensus        70 ~~~~~~i~f~~Pd~l~~~~-------~~~DlliVDEAAaIp----~p~L~~ll~~~~----~vv~stTi  123 (177)
T PF05127_consen   70 RFNKQRIEFVAPDELLAEK-------PQADLLIVDEAAAIP----LPLLKQLLRRFP----RVVFSTTI  123 (177)
T ss_dssp             ---CCC--B--HHHHCCT-----------SCEEECTGGGS-----HHHHHHHHCCSS----EEEEEEEB
T ss_pred             ccccceEEEECCHHHHhCc-------CCCCEEEEechhcCC----HHHHHHHHhhCC----EEEEEeec
Confidence            1124667777777765321       235899999997543    455666655543    57778887

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.00  E-value=0.042  Score=56.09  Aligned_cols=47  Identities=17%  Similarity=0.253  Sum_probs=26.2

Q ss_pred             CccEEEecchhHHhhCC-CHHHHHHHHHhC-CCCCcEEEEEeeCCHHHH
Q 010709          269 RVSFVILDEADRMLDMG-FEPQIREVMQNL-PDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~-~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~  315 (503)
                      ++++|||||+|.+.+.. ....+..++..+ ....++++.|...|..+.
T Consensus       211 ~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~  259 (450)
T PRK00149        211 SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELP  259 (450)
T ss_pred             cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHH
Confidence            57799999999875432 223344444433 223455555544554544

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.96  E-value=0.21  Score=42.64  Aligned_cols=54  Identities=22%  Similarity=0.352  Sum_probs=41.9

Q ss_pred             CCCCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHH
Q 010709          266 SLSRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQ  319 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~  319 (503)
                      ....+++||+||+=..++.+  -...+..+++..++..-+|+.+-.+|+.+.+.+.
T Consensus        92 ~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD  147 (159)
T cd00561          92 ASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAAD  147 (159)
T ss_pred             hcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCc
Confidence            35679999999999877766  4567788888888888788877788888776544

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.

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.96  E-value=0.053  Score=52.80  Aligned_cols=18  Identities=33%  Similarity=0.381  Sum_probs=15.1

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++.++++||+|+|||+..
T Consensus       206 ~~ii~lvGptGvGKTTt~  223 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTL  223 (407)
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            456899999999999864

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.95  E-value=0.031  Score=53.68  Aligned_cols=65  Identities=28%  Similarity=0.273  Sum_probs=40.8

Q ss_pred             HHHHHCCCCCCcHHHHHHHHHHh-cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          134 KDIEFHEYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       134 ~~l~~~~~~~~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      ..+...|.  +++.|.+.+..+. .+++++|+|+||||||+.. -.++..+...+     .+.+++.+=.+.||
T Consensus       121 ~~lv~~g~--~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~-----~~~rivtiEd~~El  186 (323)
T PRK13833        121 DDYVTSKI--MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASA-----PEDRLVILEDTAEI  186 (323)
T ss_pred             HHHHHcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCC-----CCceEEEecCCccc
Confidence            44444444  4566777776654 5678999999999999842 44444433221     13456766677776

>PLN03025 replication factor C subunit; Provisional

Probab=95.95  E-value=0.12  Score=50.12  Aligned_cols=41  Identities=29%  Similarity=0.383  Sum_probs=26.2

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      .+.+++||||+|.|... -...+.+.+...++...+++ +++.
T Consensus        98 ~~~kviiiDE~d~lt~~-aq~aL~~~lE~~~~~t~~il-~~n~  138 (319)
T PLN03025         98 GRHKIVILDEADSMTSG-AQQALRRTMEIYSNTTRFAL-ACNT  138 (319)
T ss_pred             CCeEEEEEechhhcCHH-HHHHHHHHHhcccCCceEEE-EeCC
Confidence            35789999999987543 24556666666555555444 4443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.85  E-value=0.013  Score=52.02  Aligned_cols=39  Identities=31%  Similarity=0.427  Sum_probs=26.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF  306 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~  306 (503)
                      ..+.+.||+||||.|-+ |-...+++.+....+..++.+.
T Consensus       111 ~grhKIiILDEADSMT~-gAQQAlRRtMEiyS~ttRFala  149 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTA-GAQQALRRTMEIYSNTTRFALA  149 (333)
T ss_pred             CCceeEEEeeccchhhh-HHHHHHHHHHHHHcccchhhhh
Confidence            46788999999997753 3455677777666555555443

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.84  E-value=0.1  Score=52.99  Aligned_cols=19  Identities=32%  Similarity=0.321  Sum_probs=15.4

Q ss_pred             CCCeEEEccCCCchhHHhH
Q 010709          158 GRDLLGCAETGSGKTAAFT  176 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~  176 (503)
                      |+.+.++||||+|||++..
T Consensus       256 g~Vi~LvGpnGvGKTTTia  274 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTA  274 (484)
T ss_pred             CcEEEEECCCCccHHHHHH
Confidence            3458899999999998643

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.82  E-value=0.11  Score=50.58  Aligned_cols=43  Identities=19%  Similarity=0.183  Sum_probs=29.0

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ...++++|||+||+|... -.+.+.+.+..-++...+|++|.-+
T Consensus       130 ~~~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t~~~  172 (342)
T PRK06964        130 RGGARVVVLYPAEALNVA-AANALLKTLEEPPPGTVFLLVSARI  172 (342)
T ss_pred             cCCceEEEEechhhcCHH-HHHHHHHHhcCCCcCcEEEEEECCh
Confidence            467899999999987533 3556667777656666555555443

>PRK05580 primosome assembly protein PriA; Validated

Probab=95.81  E-value=0.12  Score=55.61  Aligned_cols=73  Identities=16%  Similarity=0.267  Sum_probs=62.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~  448 (503)
                      +++||.++++..+.++.+.|++. +..+..+||+++..+|.+.+....+|+.+|+|+|..+- -+.+.++.+||.
T Consensus       191 ~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal-~~p~~~l~liVv  264 (679)
T PRK05580        191 KQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSAL-FLPFKNLGLIIV  264 (679)
T ss_pred             CeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHh-cccccCCCEEEE
Confidence            46999999999999999999874 78899999999999999999999999999999996432 245667887774

>PRK09183 transposase/IS protein; Provisional

Probab=95.79  E-value=0.059  Score=50.42  Aligned_cols=21  Identities=19%  Similarity=0.208  Sum_probs=17.7

Q ss_pred             HhcCCCeEEEccCCCchhHHh
Q 010709          155 ALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~  175 (503)
                      +..+.++++.||+|+|||..+
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa  119 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLA  119 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHH
Confidence            456788999999999999744

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.78  E-value=0.025  Score=58.59  Aligned_cols=49  Identities=14%  Similarity=0.257  Sum_probs=29.8

Q ss_pred             CCCccEEEecchhHHhhCC-CHHHHHHHHHhCCC-CCcEEEEEeeCCHHHH
Q 010709          267 LSRVSFVILDEADRMLDMG-FEPQIREVMQNLPD-KHQTLLFSATMPVEIE  315 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~-~~~~~~~il~~~~~-~~q~i~~SAT~~~~~~  315 (503)
                      +.++++|||||+|.+.+.. ....+..++..+.. ..++|+.|-..|.++.
T Consensus       375 y~~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~  425 (617)
T PRK14086        375 YREMDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLV  425 (617)
T ss_pred             hhcCCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhh
Confidence            3457899999999775542 23445555555433 4566665555555544

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.78  E-value=0.04  Score=59.23  Aligned_cols=74  Identities=15%  Similarity=0.274  Sum_probs=64.2

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      .+++|.++++.-|.++++.+++.    ++.+..+||+++..+|.++++.+.+|+..|+|+|. .+...+.+.++.+||.
T Consensus       311 ~q~lilaPT~~LA~Q~~~~l~~l~~~~~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~v~~~~l~lvVI  389 (681)
T PRK10917        311 YQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVII  389 (681)
T ss_pred             CeEEEEeccHHHHHHHHHHHHHHHhhcCcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcccchhcccceEEE
Confidence            46999999999999888877653    68999999999999999999999999999999995 5556678888888774

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.78  E-value=0.088  Score=54.24  Aligned_cols=39  Identities=13%  Similarity=0.248  Sum_probs=26.6

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+++++||||+|+|.... .+.+.+.+...++...+|+.+
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            468999999999875432 344556666666666665544

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=95.77  E-value=0.67  Score=48.04  Aligned_cols=163  Identities=18%  Similarity=0.230  Sum_probs=94.2

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcC-CCeEEE----------------eC
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLT-DPVQVK----------------VG  331 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~-~~~~~~----------------~~  331 (503)
                      .++++.+|-|.++         ..++...+   -+++..+|+.+ +.++....+. .|..+.                +-
T Consensus       526 ~lky~lL~pA~~f---------~evv~ear---avvLAGGTMeP-~~e~~e~L~~~~~~~i~~fsc~Hvip~e~il~~vv  592 (821)
T KOG1133|consen  526 TLKYMLLNPAKHF---------AEVVLEAR---AVVLAGGTMEP-VDELREQLFPGCPERISPFSCSHVIPPENILPLVV  592 (821)
T ss_pred             eEEEEecCcHHHH---------HHHHHHhh---eeeecCCcccc-HHHHHHHhcccchhhccceecccccChhheeeeee
Confidence            4688888888763         33333322   37788888843 3444444433 111110                00


Q ss_pred             CCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC-------eEEEE
Q 010709          332 KVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL-------HAVAL  404 (503)
Q Consensus       332 ~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~-------~v~~l  404 (503)
                      ..+.....+...+..-....-++.+...+.+....      -++.+++|+++.+....+.+.+.+.|+       +-+.+
T Consensus       593 ~~gpsg~p~eftf~~R~s~~~l~~l~~~~~nL~~~------VPgGvV~FfPSy~yL~~v~k~w~~~gil~ri~~kK~vF~  666 (821)
T KOG1133|consen  593 SSGPSGQPLEFTFETRESPEMIKDLGSSISNLSNA------VPGGVVCFFPSYAYLGQVRKRWEQNGILARIVGKKKVFY  666 (821)
T ss_pred             ccCCCCCceEEEeeccCChHHHHHHHHHHHHHHhh------CCCcEEEEeccHHHHHHHHHHHHhcchHHHhhccchhhc
Confidence            00111112223333333444555555555443322      236799999999999999999987654       22333


Q ss_pred             cCCCCHHHHHHHHHHHh----cCCCcEEEEc--cccccCCCCCC--CCEEEEccCCC
Q 010709          405 HGGRNQSDRESALRDFR----NGSTNILVAT--DVASRGLDVMG--VAHVVNLDLPK  453 (503)
Q Consensus       405 h~~~~~~~r~~~~~~f~----~g~~~vLvaT--~~~~~Gldip~--v~~VI~~~~p~  453 (503)
                      -...+   -..+++.|.    .|.-.+|+|.  .-+++|||+.+  .+.||.+|+|-
T Consensus       667 E~k~~---~~dvl~~Ya~a~~~g~GaiLlaVVGGKlSEGINF~D~LgRaVvvVGlPy  720 (821)
T KOG1133|consen  667 EPKDT---VEDVLEGYAEAAERGRGAILLAVVGGKLSEGINFSDDLGRAVVVVGLPY  720 (821)
T ss_pred             cCccc---HHHHHHHHHHHhhcCCCeEEEEEeccccccccccccccccEEEEeecCC
Confidence            33333   345666664    4566788777  78899999997  78999999884

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=95.76  E-value=0.034  Score=56.28  Aligned_cols=88  Identities=19%  Similarity=0.204  Sum_probs=55.2

Q ss_pred             HHHHHHHHHCCCCCCcH----HHHHHHHHHh--cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          130 PSIMKDIEFHEYTRPTS----IQAQAMPVAL--SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       130 ~~l~~~l~~~~~~~~~~----~Q~~~i~~i~--~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      +-|...|.+..-..++.    +|.+-=+.+.  .++-+||+|..|||||++++-- +.+++.... +.-.++.|||+.|.
T Consensus       192 EvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHR-vAyLlY~~R-~~l~~k~vlvl~PN  269 (747)
T COG3973         192 EVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHR-VAYLLYGYR-GPLQAKPVLVLGPN  269 (747)
T ss_pred             HHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHH-HHHHHhccc-cccccCceEEEcCc
Confidence            34455666654444433    2444333444  4455999999999999987443 333333211 11234449999999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 010709          204 RELAQQIEKEVKALSR  219 (503)
Q Consensus       204 r~La~q~~~~~~~~~~  219 (503)
                      +.+..-+.+.+-+++.
T Consensus       270 ~vFleYis~VLPeLGe  285 (747)
T COG3973         270 RVFLEYISRVLPELGE  285 (747)
T ss_pred             HHHHHHHHHhchhhcc
Confidence            9999988888888774

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.75  E-value=0.078  Score=51.51  Aligned_cols=40  Identities=20%  Similarity=0.393  Sum_probs=27.5

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ...+++||||||+.|.. +-...+.+.+..-+.+..+++.+
T Consensus       107 ~~~~kviiidead~mt~-~A~nallk~lEep~~~~~~il~~  146 (325)
T COG0470         107 EGGYKVVIIDEADKLTE-DAANALLKTLEEPPKNTRFILIT  146 (325)
T ss_pred             CCCceEEEeCcHHHHhH-HHHHHHHHHhccCCCCeEEEEEc
Confidence            36789999999998754 24555666666666666555544

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=95.74  E-value=0.088  Score=57.26  Aligned_cols=40  Identities=18%  Similarity=0.234  Sum_probs=27.8

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+++++||||+|+|... -.+.+.+++...+....+|+.+
T Consensus       118 ~~~~KV~IIDEad~lt~~-a~NaLLK~LEEpP~~~~fIl~t  157 (824)
T PRK07764        118 ESRYKIFIIDEAHMVTPQ-GFNALLKIVEEPPEHLKFIFAT  157 (824)
T ss_pred             cCCceEEEEechhhcCHH-HHHHHHHHHhCCCCCeEEEEEe
Confidence            357899999999987543 3445666777766666555544

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=95.74  E-value=0.055  Score=58.89  Aligned_cols=72  Identities=25%  Similarity=0.236  Sum_probs=54.3

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      ..+++-|.+++..  ...+++|.|..|||||.+. +--+.+++....   -...++|+++-|+..|..+.+++.++..
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l-~~ria~Li~~~~---i~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVL-THRIAHLIAEKN---VAPWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHH-HHHHHHHHHcCC---CCHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            3578889999875  3567999999999999875 444445554321   1245799999999999999999988754

Designed to identify pcrA members of the uvrD/rep subfamily.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.73  E-value=0.02  Score=53.84  Aligned_cols=17  Identities=24%  Similarity=0.317  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||..+
T Consensus        43 ~~vll~GppGtGKTtlA   59 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVA   59 (261)
T ss_pred             ceEEEEcCCCCCHHHHH
Confidence            46899999999999854

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.72  E-value=0.32  Score=45.79  Aligned_cols=55  Identities=15%  Similarity=0.272  Sum_probs=31.6

Q ss_pred             CCccEEEecchhHHhhC-CCHHHHHHHHHhCC------CCCcEEEEEeeCCHHHHHHHHHhc
Q 010709          268 SRVSFVILDEADRMLDM-GFEPQIREVMQNLP------DKHQTLLFSATMPVEIEALAQEYL  322 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~------~~~q~i~~SAT~~~~~~~~~~~~~  322 (503)
                      .++++||||=+-++... .....+.++....+      +.-.++.++||...+....+..|.
T Consensus       153 ~~~D~ViIDT~G~~~~d~~~~~el~~~~~~~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~f~  214 (272)
T TIGR00064       153 RNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDKDAPDEVLLVLDATTGQNALEQAKVFN  214 (272)
T ss_pred             CCCCEEEEeCCCCCcchHHHHHHHHHHHHHHhcccCCCCceEEEEEECCCCHHHHHHHHHHH
Confidence            45778888877654211 12334455544443      455678889987665444555554

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.

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.72  E-value=0.045  Score=51.73  Aligned_cols=40  Identities=23%  Similarity=0.211  Sum_probs=25.2

Q ss_pred             HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          155 ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      +..|.-+++.|++|+|||+.... +.......      .+..++++.
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~-~~~~~~~~------~g~~vl~iS   66 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLRE-YALDLITQ------HGVRVGTIS   66 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHH-HHHHHHHh------cCceEEEEE
Confidence            34667799999999999974432 22232221      145677776

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>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=95.70  E-value=0.015  Score=52.00  Aligned_cols=16  Identities=31%  Similarity=0.324  Sum_probs=14.0

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      ++++.||+|+|||+.+
T Consensus        52 h~lf~GPPG~GKTTLA   67 (233)
T PF05496_consen   52 HMLFYGPPGLGKTTLA   67 (233)
T ss_dssp             EEEEESSTTSSHHHHH
T ss_pred             eEEEECCCccchhHHH
Confidence            5999999999999843

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.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.68  E-value=0.078  Score=55.25  Aligned_cols=42  Identities=12%  Similarity=0.262  Sum_probs=27.0

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      ..+++++||||+|+|.... .+.+.+.+..-++...+|+.|--
T Consensus       122 ~gr~KViIIDEah~Ls~~A-aNALLKTLEEPP~~v~FILaTte  163 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHA-FNAMLKTLEEPPEHVKFILATTD  163 (700)
T ss_pred             cCCceEEEEEChHhcCHHH-HHHHHHhhccCCCCceEEEEeCC
Confidence            4568999999999875432 23455555555556666665543

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=95.67  E-value=0.057  Score=54.19  Aligned_cols=144  Identities=13%  Similarity=0.240  Sum_probs=79.7

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH-HHHHHHHHHHHHhccCCCceEEEEECCccHHHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE-LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR  239 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~-La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (503)
                      .++.|..|||||.+...-++..++..     ..+.+++++-++.. |...+...+......+. +...........  ..
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~-----~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g-~~~~~~~~~~~~--~i   75 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAIN-----KKQQNILAARKVQNSIRDSVFKDIENLLSIEG-INYEFKKSKSSM--EI   75 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhc-----CCCcEEEEEehhhhHHHHHHHHHHHHHHHHcC-ChhheeecCCcc--EE
Confidence            68899999999998877777776664     12567888888875 66666677765554331 211111111100  00


Q ss_pred             HHhhC-CCcEEEECc-HHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCC--CCcEEEEEeeCCHHHH
Q 010709          240 SELRG-GVSIVVATP-GRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD--KHQTLLFSATMPVEIE  315 (503)
Q Consensus       240 ~~~~~-~~~Ilv~Tp-~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~~~  315 (503)
                       .+.. +..|++..- +...+ +.    ....+.++.+|||..+.    ...+..++..++.  ....+++|.+|+....
T Consensus        76 -~~~~~g~~i~f~g~~d~~~~-ik----~~~~~~~~~idEa~~~~----~~~~~~l~~rlr~~~~~~~i~~t~NP~~~~~  145 (396)
T TIGR01547        76 -KILNTGKKFIFKGLNDKPNK-LK----SGAGIAIIWFEEASQLT----FEDIKELIPRLRETGGKKFIIFSSNPESPLH  145 (396)
T ss_pred             -EecCCCeEEEeecccCChhH-hh----CcceeeeehhhhhhhcC----HHHHHHHHHHhhccCCccEEEEEcCcCCCcc
Confidence             0111 345555443 22211 11    22346899999999764    2345555555542  2224788889865433


Q ss_pred             HHHHHhc
Q 010709          316 ALAQEYL  322 (503)
Q Consensus       316 ~~~~~~~  322 (503)
                      -+.+.|.
T Consensus       146 w~~~~f~  152 (396)
T TIGR01547       146 WVKKRFI  152 (396)
T ss_pred             HHHHHHH
Confidence            3444443

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.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.66  E-value=0.071  Score=53.48  Aligned_cols=17  Identities=29%  Similarity=0.444  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .+++|.||+|+|||...
T Consensus        56 ~~~lI~G~~GtGKT~l~   72 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTV   72 (394)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999854

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=95.66  E-value=0.14  Score=49.68  Aligned_cols=138  Identities=17%  Similarity=0.174  Sum_probs=69.1

Q ss_pred             CcHHHHHHHHHHh----cCC---CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          144 PTSIQAQAMPVAL----SGR---DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       144 ~~~~Q~~~i~~i~----~~~---~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      .+|||...|..+.    .|+   -.++.||.|.||+..+ ..+...+++..+.....-+    .|          ..++.
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA-~~~A~~LlC~~~~~~~~Cg----~C----------~sC~~   67 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALI-YALSRWLMCQQPQGHKSCG----HC----------RGCQL   67 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHH-HHHHHHHcCCCCCCCCCCC----CC----------HHHHH
Confidence            5677888887665    343   3789999999999865 4445555553221110000    11          11222


Q ss_pred             Hhc-cCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          217 LSR-SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       217 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      +.. .++++....-.++.            ..|-|-..-.+.+.+.. .-.....+++|||+||+|-.. -.+.+.+++.
T Consensus        68 ~~~g~HPD~~~i~p~~~~------------~~I~idqiR~l~~~~~~-~~~~g~~kV~iI~~ae~m~~~-AaNaLLKtLE  133 (334)
T PRK07993         68 MQAGTHPDYYTLTPEKGK------------SSLGVDAVREVTEKLYE-HARLGGAKVVWLPDAALLTDA-AANALLKTLE  133 (334)
T ss_pred             HHcCCCCCEEEEeccccc------------ccCCHHHHHHHHHHHhh-ccccCCceEEEEcchHhhCHH-HHHHHHHHhc
Confidence            221 22233322111110            01111111112222222 223467899999999988533 4566667777


Q ss_pred             hCCCCCcEEEEEeeC
Q 010709          296 NLPDKHQTLLFSATM  310 (503)
Q Consensus       296 ~~~~~~q~i~~SAT~  310 (503)
                      .-++...+|++|.-+
T Consensus       134 EPp~~t~fiL~t~~~  148 (334)
T PRK07993        134 EPPENTWFFLACREP  148 (334)
T ss_pred             CCCCCeEEEEEECCh
Confidence            755566555555443

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=95.65  E-value=0.064  Score=53.99  Aligned_cols=47  Identities=17%  Similarity=0.284  Sum_probs=25.7

Q ss_pred             CccEEEecchhHHhhCC-CHHHHHHHHHhC-CCCCcEEEEEeeCCHHHH
Q 010709          269 RVSFVILDEADRMLDMG-FEPQIREVMQNL-PDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~-~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~  315 (503)
                      ++++|||||+|.+.+.. ....+..++..+ ....++|+.|...|..+.
T Consensus       199 ~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~  247 (405)
T TIGR00362       199 SVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELP  247 (405)
T ss_pred             hCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHh
Confidence            36799999999876542 223344444433 234555554444444444

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).

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.63  E-value=0.14  Score=51.71  Aligned_cols=16  Identities=25%  Similarity=0.382  Sum_probs=14.2

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      ++++.||+|+|||+.+
T Consensus        38 ~ilL~GppGtGKTtLA   53 (413)
T PRK13342         38 SMILWGPPGTGKTTLA   53 (413)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            6999999999999854

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.61  E-value=0.17  Score=43.76  Aligned_cols=53  Identities=23%  Similarity=0.370  Sum_probs=41.0

Q ss_pred             CCCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHH
Q 010709          267 LSRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQ  319 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~  319 (503)
                      -..+++||+||+=..++.+  -...+..++...|+..-+|+..-.+|+.+.+.+.
T Consensus        95 ~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD  149 (173)
T TIGR00708        95 DPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELAD  149 (173)
T ss_pred             cCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCc
Confidence            4679999999999888776  3456778888888888777777777887776554

Alternate name: corrinoid adenosyltransferase.

>TIGR00595 priA primosomal protein N'

Probab=95.61  E-value=0.1  Score=53.78  Aligned_cols=73  Identities=19%  Similarity=0.289  Sum_probs=62.0

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~  448 (503)
                      +++||.+++...+.++++.|++. +..+..+||+++..+|.+.+....+|+.+|+|+|..+-. +.++++.+||.
T Consensus        26 ~~vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf-~p~~~l~lIIV   99 (505)
T TIGR00595        26 KSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF-LPFKNLGLIIV   99 (505)
T ss_pred             CeEEEEeCcHHHHHHHHHHHHHHhCCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc-CcccCCCEEEE
Confidence            46999999999999999999864 778999999999999999999999999999999964332 45667787774

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).

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.60  E-value=0.092  Score=46.04  Aligned_cols=146  Identities=18%  Similarity=0.148  Sum_probs=76.7

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA  236 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (503)
                      ....+++..++|.|||.+++- +..+...+       |.+|+++.=.+--..  ..+...+. .+..+...  ..+....
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g-~a~ra~g~-------G~~V~ivQFlKg~~~--~GE~~~l~-~l~~v~~~--~~g~~~~   87 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFG-MALRAVGH-------GKKVGVVQFIKGAWS--TGERNLLE-FGGGVEFH--VMGTGFT   87 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHH-HHHHHHHC-------CCeEEEEEEecCCCc--cCHHHHHh-cCCCcEEE--ECCCCCc
Confidence            556799999999999998754 44444443       677888863331100  01111111 11112221  1111100


Q ss_pred             HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCC--HHHHHHHHHhCCCCCcEEEEEeeCCHHH
Q 010709          237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGF--EPQIREVMQNLPDKHQTLLFSATMPVEI  314 (503)
Q Consensus       237 ~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~~  314 (503)
                      -.    .....--.......++.... .+.-..+++||+||+=..++.++  ...+..++...|+..-+|+..-.+|+.+
T Consensus        88 ~~----~~~~~e~~~~~~~~~~~a~~-~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~L  162 (191)
T PRK05986         88 WE----TQDRERDIAAAREGWEEAKR-MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPREL  162 (191)
T ss_pred             cc----CCCcHHHHHHHHHHHHHHHH-HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHH
Confidence            00    00000000011111222221 22346799999999998888774  4567778888777777777666677777


Q ss_pred             HHHHHH
Q 010709          315 EALAQE  320 (503)
Q Consensus       315 ~~~~~~  320 (503)
                      .+.+..
T Consensus       163 ie~ADl  168 (191)
T PRK05986        163 IEAADL  168 (191)
T ss_pred             HHhCch
Confidence            765543

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=95.59  E-value=0.15  Score=52.41  Aligned_cols=17  Identities=29%  Similarity=0.274  Sum_probs=14.8

Q ss_pred             CeEEEccCCCchhHHhH
Q 010709          160 DLLGCAETGSGKTAAFT  176 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~  176 (503)
                      .++++||.|+|||+.+.
T Consensus        45 a~Lf~Gp~G~GKTT~Ar   61 (507)
T PRK06645         45 GYLLTGIRGVGKTTSAR   61 (507)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            59999999999998653

>PRK10867 signal recognition particle protein; Provisional

Probab=95.54  E-value=0.18  Score=50.65  Aligned_cols=16  Identities=25%  Similarity=0.331  Sum_probs=13.9

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      -++++|++|+|||+..
T Consensus       102 vI~~vG~~GsGKTTta  117 (433)
T PRK10867        102 VIMMVGLQGAGKTTTA  117 (433)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            3889999999999865

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.53  E-value=0.14  Score=53.48  Aligned_cols=39  Identities=13%  Similarity=0.232  Sum_probs=25.6

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+++++||||+|+|... -...+.+++...++...+|+.+
T Consensus       117 gk~KV~IIDEVh~LS~~-A~NALLKtLEEPP~~v~FILaT  155 (702)
T PRK14960        117 GRFKVYLIDEVHMLSTH-SFNALLKTLEEPPEHVKFLFAT  155 (702)
T ss_pred             CCcEEEEEechHhcCHH-HHHHHHHHHhcCCCCcEEEEEE
Confidence            46889999999977543 2345666666655556555433

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=95.53  E-value=0.11  Score=54.61  Aligned_cols=40  Identities=13%  Similarity=0.185  Sum_probs=26.8

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      +.+.++|||||+|.|... -.+.+.+.+...++...+|+.+
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            567899999999987533 2344555566666666666654

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=95.52  E-value=0.2  Score=54.13  Aligned_cols=18  Identities=39%  Similarity=0.399  Sum_probs=15.4

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ..++++.||+|+|||..+
T Consensus       207 ~~n~LLvGppGvGKT~la  224 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_pred             CCCeEEECCCCCCHHHHH
Confidence            457999999999999754

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.50  E-value=0.23  Score=47.71  Aligned_cols=44  Identities=14%  Similarity=0.209  Sum_probs=30.3

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ....++++|||+||+|... -.+.+.+.+..-+++..+|+.|..+
T Consensus       105 ~~~~~kV~iI~~ae~m~~~-AaNaLLKtLEEPp~~t~fiL~t~~~  148 (319)
T PRK06090        105 QLNGYRLFVIEPADAMNES-ASNALLKTLEEPAPNCLFLLVTHNQ  148 (319)
T ss_pred             ccCCceEEEecchhhhCHH-HHHHHHHHhcCCCCCeEEEEEECCh
Confidence            3467899999999988533 4566777777766666555555544

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=95.48  E-value=0.17  Score=48.91  Aligned_cols=41  Identities=17%  Similarity=0.270  Sum_probs=27.7

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEe
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA  308 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SA  308 (503)
                      ....+++|+|++|.|- ......+.+.+...+....+|++|-
T Consensus       111 ~~~~kV~iiEp~~~Ld-~~a~naLLk~LEep~~~~~~Ilvth  151 (325)
T PRK08699        111 RGGLRVILIHPAESMN-LQAANSLLKVLEEPPPQVVFLLVSH  151 (325)
T ss_pred             cCCceEEEEechhhCC-HHHHHHHHHHHHhCcCCCEEEEEeC
Confidence            4678999999999763 3356667777777665554555443

>TIGR00959 ffh signal recognition particle protein

Probab=95.45  E-value=0.18  Score=50.55  Aligned_cols=16  Identities=38%  Similarity=0.409  Sum_probs=14.1

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .++++|++|+|||+..
T Consensus       101 vi~~vG~~GsGKTTta  116 (428)
T TIGR00959       101 VILMVGLQGSGKTTTC  116 (428)
T ss_pred             EEEEECCCCCcHHHHH
Confidence            3889999999999865

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.

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.45  E-value=0.19  Score=46.05  Aligned_cols=53  Identities=13%  Similarity=0.142  Sum_probs=31.6

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|.-+++.|++|+|||+..+ -++......       +.++++++.. +-..+..+.+..++
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~-~~~~~~~~~-------g~~~~yi~~e-~~~~~~~~~~~~~g   75 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQ-RLAYGFLQN-------GYSVSYVSTQ-LTTTEFIKQMMSLG   75 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHH-HHHHHHHhC-------CCcEEEEeCC-CCHHHHHHHHHHhC
Confidence            46679999999999998532 233333332       4567888743 33344444444443

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=95.43  E-value=0.039  Score=58.26  Aligned_cols=42  Identities=17%  Similarity=0.369  Sum_probs=36.3

Q ss_pred             ccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          270 VSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       270 ~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      -=++|+|+.|.+.+......++.++++.|++..+++.|=+-|
T Consensus       130 pl~LVlDDyHli~~~~l~~~l~fLl~~~P~~l~lvv~SR~rP  171 (894)
T COG2909         130 PLYLVLDDYHLISDPALHEALRFLLKHAPENLTLVVTSRSRP  171 (894)
T ss_pred             ceEEEeccccccCcccHHHHHHHHHHhCCCCeEEEEEeccCC
Confidence            348999999998888788889999999999998888887654

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.42  E-value=0.13  Score=55.63  Aligned_cols=38  Identities=16%  Similarity=0.239  Sum_probs=25.4

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF  306 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~  306 (503)
                      .+++++||||||+|... -...+.+++..-++...+|+.
T Consensus       118 gk~KViIIDEAh~LT~e-AqNALLKtLEEPP~~vrFILa  155 (944)
T PRK14949        118 GRFKVYLIDEVHMLSRS-SFNALLKTLEEPPEHVKFLLA  155 (944)
T ss_pred             CCcEEEEEechHhcCHH-HHHHHHHHHhccCCCeEEEEE
Confidence            46899999999987422 344556666665566655554

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=95.41  E-value=0.11  Score=51.89  Aligned_cols=29  Identities=21%  Similarity=0.237  Sum_probs=20.6

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCC
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTP  188 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~  188 (503)
                      -+-+++.||+|+|||+.  .-.+-.++.-+.
T Consensus       256 VKGiLLyGPPGTGKTLi--ARqIGkMLNAre  284 (744)
T KOG0741|consen  256 VKGILLYGPPGTGKTLI--ARQIGKMLNARE  284 (744)
T ss_pred             eeeEEEECCCCCChhHH--HHHHHHHhcCCC
Confidence            35699999999999984  345555555443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.40  E-value=0.13  Score=50.88  Aligned_cols=40  Identities=15%  Similarity=0.238  Sum_probs=24.4

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+.+++||||+|.+.... ...+.+.+...++...+|+.+
T Consensus       117 ~~~~kviIIDEa~~l~~~a-~naLLk~lEe~~~~~~fIl~t  156 (363)
T PRK14961        117 KSRFKVYLIDEVHMLSRHS-FNALLKTLEEPPQHIKFILAT  156 (363)
T ss_pred             cCCceEEEEEChhhcCHHH-HHHHHHHHhcCCCCeEEEEEc
Confidence            3467899999999875432 233445555545555555543

>PF05729 NACHT: NACHT domain

Probab=95.39  E-value=0.16  Score=43.65  Aligned_cols=38  Identities=18%  Similarity=0.359  Sum_probs=22.8

Q ss_pred             EEEecchhHHhhCC-------CHHHHHHHHHh-CCCCCcEEEEEee
Q 010709          272 FVILDEADRMLDMG-------FEPQIREVMQN-LPDKHQTLLFSAT  309 (503)
Q Consensus       272 ~vViDEaH~l~~~~-------~~~~~~~il~~-~~~~~q~i~~SAT  309 (503)
                      ++|||-+|.+....       +...+..++.. .++..++++.|.+
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~  129 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRP  129 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcC
Confidence            49999999876532       22344455554 4556766665543

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.37  E-value=0.23  Score=47.91  Aligned_cols=43  Identities=12%  Similarity=0.116  Sum_probs=29.3

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ....+++|||+||.|... -.+.+.+++..-++...+|+.|..+
T Consensus       105 ~g~~KV~iI~~a~~m~~~-AaNaLLKtLEEPp~~~~fiL~t~~~  147 (325)
T PRK06871        105 QGGNKVVYIQGAERLTEA-AANALLKTLEEPRPNTYFLLQADLS  147 (325)
T ss_pred             cCCceEEEEechhhhCHH-HHHHHHHHhcCCCCCeEEEEEECCh
Confidence            457899999999988533 4566777777766666555555433

>CHL00181 cbbX CbbX; Provisional

Probab=95.35  E-value=0.039  Score=52.42  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=15.7

Q ss_pred             CCCeEEEccCCCchhHHhH
Q 010709          158 GRDLLGCAETGSGKTAAFT  176 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~  176 (503)
                      +.++++.||+|+|||+.+-
T Consensus        59 ~~~ill~G~pGtGKT~lAr   77 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVAL   77 (287)
T ss_pred             CceEEEECCCCCCHHHHHH
Confidence            4468999999999998653

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.32  E-value=0.088  Score=54.92  Aligned_cols=40  Identities=18%  Similarity=0.213  Sum_probs=26.3

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+++++||||+|.|... -.+.+.+.+...++...+|+.+
T Consensus       116 ~~~~KVvIIDEah~Lt~~-A~NALLK~LEEpp~~~~fIL~t  155 (584)
T PRK14952        116 QSRYRIFIVDEAHMVTTA-GFNALLKIVEEPPEHLIFIFAT  155 (584)
T ss_pred             cCCceEEEEECCCcCCHH-HHHHHHHHHhcCCCCeEEEEEe
Confidence            357899999999977543 3344556666656566555544

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=95.32  E-value=0.29  Score=48.66  Aligned_cols=44  Identities=20%  Similarity=0.391  Sum_probs=27.5

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCH
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPV  312 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  312 (503)
                      ..+.+++||||+|+|... ..+.+.+.+..-++... +++.+|-+.
T Consensus       115 ~~~~kViiIDead~m~~~-aanaLLk~LEep~~~~~-fIL~a~~~~  158 (394)
T PRK07940        115 TGRWRIVVIEDADRLTER-AANALLKAVEEPPPRTV-WLLCAPSPE  158 (394)
T ss_pred             cCCcEEEEEechhhcCHH-HHHHHHHHhhcCCCCCe-EEEEECChH
Confidence            457889999999988543 33556666666555554 444444333

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.30  E-value=0.086  Score=50.04  Aligned_cols=17  Identities=29%  Similarity=0.333  Sum_probs=14.5

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.++++||||+|||+..
T Consensus       195 ~vi~~vGptGvGKTTt~  211 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTL  211 (282)
T ss_pred             eEEEEECCCCCCHHHHH
Confidence            45889999999999864

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=95.30  E-value=0.1  Score=51.77  Aligned_cols=24  Identities=25%  Similarity=0.348  Sum_probs=17.5

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      .+++|.||+|+|||... -.++..+
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l   64 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKEL   64 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHH
Confidence            46999999999999754 3344433

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=95.29  E-value=0.14  Score=50.03  Aligned_cols=41  Identities=24%  Similarity=0.263  Sum_probs=27.7

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEe
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA  308 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SA  308 (503)
                      ...+++|||||||.|... -.+.+.+.+...+....+|++|.
T Consensus       139 ~g~~rVviIDeAd~l~~~-aanaLLk~LEEpp~~~~fiLit~  179 (351)
T PRK09112        139 DGNWRIVIIDPADDMNRN-AANAILKTLEEPPARALFILISH  179 (351)
T ss_pred             cCCceEEEEEchhhcCHH-HHHHHHHHHhcCCCCceEEEEEC
Confidence            457899999999987433 34556667776555565566653

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.29  E-value=0.16  Score=52.63  Aligned_cols=40  Identities=15%  Similarity=0.252  Sum_probs=26.0

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+++++||||+|+|.... .+.+.+.+...++...+|+.+
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            4568999999999875432 334555566655566555554

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.28  E-value=0.093  Score=53.21  Aligned_cols=53  Identities=25%  Similarity=0.289  Sum_probs=33.5

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|.-+++.|++|+|||+..+. +......       .+.+++|+.- .+-..|+....+.++
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq-~a~~~a~-------~g~~vlYvs~-Ees~~qi~~ra~rlg  131 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQ-VAARLAA-------AGGKVLYVSG-EESASQIKLRAERLG  131 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHH-HHHHHHh-------cCCeEEEEEc-cccHHHHHHHHHHcC
Confidence            345689999999999984422 2223222       1456888874 345567766666654

>PRK04195 replication factor C large subunit; Provisional

Probab=95.24  E-value=0.09  Score=54.16  Aligned_cols=18  Identities=33%  Similarity=0.372  Sum_probs=15.2

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+.+++.||+|+|||..+
T Consensus        39 ~~~lLL~GppG~GKTtla   56 (482)
T PRK04195         39 KKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            356999999999999754

>PHA00729 NTP-binding motif containing protein

Probab=95.24  E-value=0.1  Score=47.10  Aligned_cols=75  Identities=12%  Similarity=0.213  Sum_probs=38.2

Q ss_pred             CcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-HhhCCCH----HHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHH
Q 010709          246 VSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-MLDMGFE----PQIREVMQNLPDKHQTLLFSATMPVEIEALAQE  320 (503)
Q Consensus       246 ~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-l~~~~~~----~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~  320 (503)
                      ...++.+.+.+.+.+....-...+++++||||+-- +....+.    ..+..+...+....+++.+...-+.++...++.
T Consensus        59 ~~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~~wh~~~~~~yf~L~~aLrSR~~l~il~~ls~edL~~~Lr~  138 (226)
T PHA00729         59 QNSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKYVWYEDYMKTFYKIYALIRTRVSAVIFTTPSPEDLAFYLRE  138 (226)
T ss_pred             CcEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhcccchhhhccchHHHHHHHHHhhCcEEEEecCCHHHHHHHHHh
Confidence            34556666666665543211223467899999421 1111111    112233333344456777776666676666655

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=95.22  E-value=0.23  Score=48.93  Aligned_cols=44  Identities=25%  Similarity=0.277  Sum_probs=28.2

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      .....++|||||+|+|-. .-.+.+.+.+...++...+|++|..+
T Consensus       138 ~~~~~kVviIDead~m~~-~aanaLLK~LEepp~~~~~IL~t~~~  181 (365)
T PRK07471        138 AEGGWRVVIVDTADEMNA-NAANALLKVLEEPPARSLFLLVSHAP  181 (365)
T ss_pred             ccCCCEEEEEechHhcCH-HHHHHHHHHHhcCCCCeEEEEEECCc
Confidence            345788999999997742 23445666666655555555555444

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.22  E-value=0.1  Score=50.06  Aligned_cols=17  Identities=24%  Similarity=0.259  Sum_probs=14.7

Q ss_pred             CCCeEEEccCCCchhHH
Q 010709          158 GRDLLGCAETGSGKTAA  174 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~  174 (503)
                      ++.+++.|++|+|||..
T Consensus       156 ~~gl~L~G~~G~GKThL  172 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYL  172 (306)
T ss_pred             CCeEEEECCCCCCHHHH
Confidence            45799999999999964

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.20  E-value=0.26  Score=50.25  Aligned_cols=40  Identities=13%  Similarity=0.179  Sum_probs=24.9

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+++++||||+|.+.... .+.+.+.+..-++...+|+.+
T Consensus       114 ~~~~KVvIIDEah~Ls~~A-~NaLLK~LEePp~~v~fIlat  153 (491)
T PRK14964        114 SSKFKVYIIDEVHMLSNSA-FNALLKTLEEPAPHVKFILAT  153 (491)
T ss_pred             cCCceEEEEeChHhCCHHH-HHHHHHHHhCCCCCeEEEEEe
Confidence            4578999999999775432 334555555555555444433

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=95.20  E-value=0.43  Score=51.91  Aligned_cols=18  Identities=39%  Similarity=0.374  Sum_probs=15.3

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ..++++.||+|+|||..+
T Consensus       203 ~~n~lL~G~pG~GKT~l~  220 (731)
T TIGR02639       203 KNNPLLVGEPGVGKTAIA  220 (731)
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            357999999999999754

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=95.19  E-value=0.086  Score=48.68  Aligned_cols=53  Identities=15%  Similarity=0.167  Sum_probs=34.3

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|..++|.|++|+|||+..+-.+...+ ..       +.++++++ +.+-..|+.+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~-~~-------ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGL-QM-------GEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHH-Hc-------CCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            456799999999999985543333332 22       55678887 3445556666666654

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.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.19  E-value=0.075  Score=51.19  Aligned_cols=68  Identities=25%  Similarity=0.258  Sum_probs=42.9

Q ss_pred             HHHHHHHHCCCCCCcHHHHHHHHHH-hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          131 SIMKDIEFHEYTRPTSIQAQAMPVA-LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       131 ~l~~~l~~~~~~~~~~~Q~~~i~~i-~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      .-+..+...|.  +.+.|.+.+..+ ..+++++|+|+||+|||+. +-.++..+...     ....+++++-.+.|+
T Consensus       122 ~tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~-----~~~~rivtIEd~~El  190 (319)
T PRK13894        122 FTLDQYVERGI--MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQ-----DPTERVFIIEDTGEI  190 (319)
T ss_pred             CCHHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhc-----CCCceEEEEcCCCcc
Confidence            33455555554  456677777654 4667899999999999974 34444443221     123467777777776

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.16  E-value=0.088  Score=53.11  Aligned_cols=16  Identities=25%  Similarity=0.247  Sum_probs=14.1

Q ss_pred             eEEEccCCCchhHHhH
Q 010709          161 LLGCAETGSGKTAAFT  176 (503)
Q Consensus       161 vii~~~TGsGKTl~~~  176 (503)
                      .+++||.|+|||..+.
T Consensus        43 ~Lf~GP~GtGKTTlAr   58 (484)
T PRK14956         43 YIFFGPRGVGKTTIAR   58 (484)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7999999999998653

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

Probab=95.13  E-value=0.05  Score=56.74  Aligned_cols=126  Identities=16%  Similarity=0.197  Sum_probs=75.9

Q ss_pred             CCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH-HHHHHHhc
Q 010709          143 RPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIE-KEVKALSR  219 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~-~~~~~~~~  219 (503)
                      ..+|+|.+.+.++-..  +.|+++.++-+|||.+. +.++.+.+.+.      ...+|++.||.++|..+. .++..+..
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~-~n~~g~~i~~~------P~~~l~v~Pt~~~a~~~~~~rl~Pmi~   88 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELL-LNWIGYSIDQD------PGPMLYVQPTDDAAKDFSKERLDPMIR   88 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHH-HhhceEEEEeC------CCCEEEEEEcHHHHHHHHHHHHHHHHH
Confidence            5688899999887654  45999999999999854 44555544442      355899999999999876 66777665


Q ss_pred             cCCCceEEEEE---CCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHh
Q 010709          220 SLDSFKTAIVV---GGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRML  282 (503)
Q Consensus       220 ~~~~~~~~~~~---~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~  282 (503)
                      ..+.++-.+.-   ...........+. +..+.++....-      ..+.-..+++|++||++..-
T Consensus        89 ~sp~l~~~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~S~------~~l~s~~~r~~~~DEvD~~p  147 (557)
T PF05876_consen   89 ASPVLRRKLSPSKSRDSGNTILYKRFP-GGFLYLVGANSP------SNLRSRPARYLLLDEVDRYP  147 (557)
T ss_pred             hCHHHHHHhCchhhcccCCchhheecC-CCEEEEEeCCCC------cccccCCcCEEEEechhhcc
Confidence            54333211111   0000011111122 333444432211      12334568899999999874

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 [].

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.12  E-value=0.08  Score=56.47  Aligned_cols=74  Identities=15%  Similarity=0.239  Sum_probs=63.7

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      .+++|.++++.-|.++++.+++.    |+.+..+||+++..+|..+++...+|+..|+|+|. .+...+.+.++.+||.
T Consensus       285 ~qvlilaPT~~LA~Q~~~~~~~l~~~~gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~~~~~~~l~lvVI  363 (630)
T TIGR00643       285 YQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVII  363 (630)
T ss_pred             CcEEEECCHHHHHHHHHHHHHHHhcccCcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhccccccccceEEE
Confidence            46999999999999988877653    78999999999999999999999999999999995 4555677888888774

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=95.08  E-value=0.47  Score=48.42  Aligned_cols=16  Identities=25%  Similarity=0.345  Sum_probs=13.9

Q ss_pred             eEEEccCCCchhHHhH
Q 010709          161 LLGCAETGSGKTAAFT  176 (503)
Q Consensus       161 vii~~~TGsGKTl~~~  176 (503)
                      ++++||+|+|||+.+.
T Consensus        39 ~Lf~GPpGtGKTTlA~   54 (472)
T PRK14962         39 YIFAGPRGTGKTTVAR   54 (472)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            6999999999998653

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.05  E-value=0.41  Score=47.80  Aligned_cols=18  Identities=33%  Similarity=0.287  Sum_probs=15.1

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      |+.+.++||||+|||+..
T Consensus       191 g~vi~lvGpnG~GKTTtl  208 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTT  208 (420)
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            445899999999999854

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.05  E-value=0.36  Score=51.96  Aligned_cols=40  Identities=18%  Similarity=0.229  Sum_probs=24.0

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHH
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVE  313 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  313 (503)
                      +..++||||+|++...    ....++..+. ..++++++||-++.
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            4568999999986422    2233333333 34577777775443

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=95.02  E-value=0.14  Score=50.49  Aligned_cols=48  Identities=15%  Similarity=0.270  Sum_probs=33.3

Q ss_pred             CccEEEecchhHHhhC-CCHHHHHHHHHhCCC-CCcEEEEEeeCCHHHHH
Q 010709          269 RVSFVILDEADRMLDM-GFEPQIREVMQNLPD-KHQTLLFSATMPVEIEA  316 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~-~~q~i~~SAT~~~~~~~  316 (503)
                      ++++++||+++.+.+. .....+-.++..+.. ..|+|+.|..+|.++..
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~  224 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNG  224 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhcc
Confidence            6889999999988765 345555555555543 34788888777777653

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.97  E-value=0.11  Score=49.81  Aligned_cols=66  Identities=23%  Similarity=0.283  Sum_probs=39.9

Q ss_pred             HHHHHHCCCCCCcHHHHHHHHHHh-cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          133 MKDIEFHEYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       133 ~~~l~~~~~~~~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      +..+...|.  +.+.|.+.+..+. .+++++|+|+||||||+.. -.++..+...     ....+++++=...|+
T Consensus       108 l~~l~~~g~--~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~-----~~~~ri~tiEd~~El  174 (299)
T TIGR02782       108 LDDYVEAGI--MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKN-----DPTDRVVIIEDTREL  174 (299)
T ss_pred             HHHHHhcCC--CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhcc-----CCCceEEEECCchhh
Confidence            444444443  3445555555544 5678999999999999843 3344443321     123567777777776

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=94.94  E-value=0.088  Score=50.04  Aligned_cols=18  Identities=22%  Similarity=0.231  Sum_probs=15.5

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      +.++++.||+|+|||+.+
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            457999999999999865

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.

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=94.92  E-value=0.21  Score=51.96  Aligned_cols=133  Identities=20%  Similarity=0.214  Sum_probs=79.8

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC-CCceEEEEECCccHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL-DSFKTAIVVGGTNIA  236 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~  236 (503)
                      .+-.++..|=-.|||.... +++..++..     ..|.++++++|.+..++.+.+++....... ....+..+.| ... 
T Consensus       254 qk~tVflVPRR~GKTwivv-~iI~~ll~s-----~~Gi~IgytAH~~~ts~~vF~eI~~~le~~f~~~~v~~vkG-e~I-  325 (738)
T PHA03368        254 QRATVFLVPRRHGKTWFLV-PLIALALAT-----FRGIKIGYTAHIRKATEPVFEEIGARLRQWFGASRVDHVKG-ETI-  325 (738)
T ss_pred             ccceEEEecccCCchhhHH-HHHHHHHHh-----CCCCEEEEEcCcHHHHHHHHHHHHHHHhhhcchhheeeecC-cEE-
Confidence            4558889999999998653 666655532     136889999999999999999988876432 1111212222 110 


Q ss_pred             HHHHHhhCC--CcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeC
Q 010709          237 EQRSELRGG--VSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATM  310 (503)
Q Consensus       237 ~~~~~~~~~--~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~  310 (503)
                        .-.+.++  ..|.+++.      -..+...-+.++++|||||+.+-.    ..+..++-.+ ..+.++|.+|.|-
T Consensus       326 --~i~f~nG~kstI~FaSa------rntNsiRGqtfDLLIVDEAqFIk~----~al~~ilp~l~~~n~k~I~ISS~N  390 (738)
T PHA03368        326 --SFSFPDGSRSTIVFASS------HNTNGIRGQDFNLLFVDEANFIRP----DAVQTIMGFLNQTNCKIIFVSSTN  390 (738)
T ss_pred             --EEEecCCCccEEEEEec------cCCCCccCCcccEEEEechhhCCH----HHHHHHHHHHhccCccEEEEecCC
Confidence              0011112  24555531      112233445799999999997653    3344444322 2377889998884

>PRK14873 primosome assembly protein PriA; Provisional

Probab=94.91  E-value=0.16  Score=53.89  Aligned_cols=93  Identities=23%  Similarity=0.164  Sum_probs=72.3

Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-C-CeEEEEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-G-LHAVALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-~-~~v~~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                      ..|....++++......       ++.+||.++......++.+.|+.. | -.+..+|++++..+|.+.+....+|+.+|
T Consensus       171 SGKTevyl~~i~~~l~~-------Gk~vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS~l~~~~R~~~w~~~~~G~~~I  243 (665)
T PRK14873        171 EDWARRLAAAAAATLRA-------GRGALVVVPDQRDVDRLEAALRALLGAGDVAVLSAGLGPADRYRRWLAVLRGQARV  243 (665)
T ss_pred             CcHHHHHHHHHHHHHHc-------CCeEEEEecchhhHHHHHHHHHHHcCCCcEEEECCCCCHHHHHHHHHHHhCCCCcE
Confidence            45666666666554432       335999999999999999999865 4 67999999999999999999999999999


Q ss_pred             EEEccccccCCCCCCCCEEEEcc
Q 010709          428 LVATDVASRGLDVMGVAHVVNLD  450 (503)
Q Consensus       428 LvaT~~~~~Gldip~v~~VI~~~  450 (503)
                      +|.|..+- =.-+++...||..+
T Consensus       244 ViGtRSAv-FaP~~~LgLIIvdE  265 (665)
T PRK14873        244 VVGTRSAV-FAPVEDLGLVAIWD  265 (665)
T ss_pred             EEEcceeE-EeccCCCCEEEEEc
Confidence            99996543 23555677777533

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.89  E-value=0.12  Score=54.16  Aligned_cols=40  Identities=15%  Similarity=0.198  Sum_probs=26.1

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+++++||||+|+|... -.+.+.+.+...++...+|+.+
T Consensus       117 ~~~~KVvIIdev~~Lt~~-a~naLLk~LEepp~~~~fIl~t  156 (576)
T PRK14965        117 RSRYKIFIIDEVHMLSTN-AFNALLKTLEEPPPHVKFIFAT  156 (576)
T ss_pred             cCCceEEEEEChhhCCHH-HHHHHHHHHHcCCCCeEEEEEe
Confidence            457899999999977533 2345666666655555555444

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=94.89  E-value=0.47  Score=52.55  Aligned_cols=17  Identities=35%  Similarity=0.399  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      ++.++.||+|+|||...
T Consensus       195 ~n~lL~G~pGvGKT~l~  211 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIV  211 (852)
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            57999999999999754

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.88  E-value=0.38  Score=49.82  Aligned_cols=40  Identities=13%  Similarity=0.194  Sum_probs=26.4

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+.+++||||+|+|... -...+.+.+...++...+|+.+
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            456789999999987543 2345566666655566555544

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.85  E-value=0.16  Score=50.00  Aligned_cols=53  Identities=21%  Similarity=0.288  Sum_probs=32.7

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|.-+++.|++|+|||+..+ -+.......       +.+++|+.-. +-..|+..+...++
T Consensus        81 ~GslvLI~G~pG~GKStLll-q~a~~~a~~-------g~~VlYvs~E-Es~~qi~~Ra~rlg  133 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLL-QVAARLAKR-------GGKVLYVSGE-ESPEQIKLRADRLG  133 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHH-HHHHHHHhc-------CCeEEEEECC-cCHHHHHHHHHHcC
Confidence            34569999999999998442 223332221       4568887654 34556666665554

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.

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

Probab=94.82  E-value=0.072  Score=46.70  Aligned_cols=49  Identities=18%  Similarity=0.373  Sum_probs=27.6

Q ss_pred             HHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q 010709          153 PVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI  210 (503)
Q Consensus       153 ~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~  210 (503)
                      .++.+++++++.|++|+|||..+ ..+...+...       +..++++ ...+|...+
T Consensus        42 ~~~~~~~~l~l~G~~G~GKThLa-~ai~~~~~~~-------g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   42 EFIENGENLILYGPPGTGKTHLA-VAIANEAIRK-------GYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             -S-SC--EEEEEESTTSSHHHHH-HHHHHHHHHT-------T--EEEE-EHHHHHHHH
T ss_pred             CCcccCeEEEEEhhHhHHHHHHH-HHHHHHhccC-------CcceeEe-ecCceeccc
Confidence            33446778999999999999754 3344444443       4455554 444555543

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.

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

Probab=94.82  E-value=0.23  Score=50.32  Aligned_cols=91  Identities=15%  Similarity=0.251  Sum_probs=72.2

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-----cccccC-CCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-----DVASRG-LDVMG  442 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-----~~~~~G-ldip~  442 (503)
                      ..+.+||.+++++.|.++.+.+.+.    ++...+++|+.+...|..-+++    -+.|+|||     +.++.| +|+..
T Consensus       164 ~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~~l~~----gvdiviaTPGRl~d~le~g~~~l~~  239 (519)
T KOG0331|consen  164 DGPIVLVLAPTRELAVQVQAEAREFGKSLRLRSTCVYGGAPKGPQLRDLER----GVDVVIATPGRLIDLLEEGSLNLSR  239 (519)
T ss_pred             CCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccEEEEeCCCCccHHHHHHhc----CCcEEEeCChHHHHHHHcCCccccc
Confidence            3456999999999999999988765    4568999999998877776653    58999999     456665 47788


Q ss_pred             CCEEE--------EccCCCChhHHHHhhCccee
Q 010709          443 VAHVV--------NLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       443 v~~VI--------~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |.++|        +.++-..+...+++++|.-|
T Consensus       240 v~ylVLDEADrMldmGFe~qI~~Il~~i~~~~r  272 (519)
T KOG0331|consen  240 VTYLVLDEADRMLDMGFEPQIRKILSQIPRPDR  272 (519)
T ss_pred             eeEEEeccHHhhhccccHHHHHHHHHhcCCCcc
Confidence            88887        35556677888999999888

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

Probab=94.81  E-value=0.18  Score=50.68  Aligned_cols=41  Identities=22%  Similarity=0.257  Sum_probs=30.8

Q ss_pred             CcHHHHHHHHHHhcCCC--eEEEccCCCchhHHhHHHHHHHHHh
Q 010709          144 PTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       144 ~~~~Q~~~i~~i~~~~~--vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      ..+.|.+.+..+++...  +++.||||||||+.. ..++..+..
T Consensus       242 ~~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTTL-Y~~L~~ln~  284 (500)
T COG2804         242 MSPFQLARLLRLLNRPQGLILVTGPTGSGKTTTL-YAALSELNT  284 (500)
T ss_pred             CCHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHHH-HHHHHHhcC
Confidence            36778888888887665  899999999999863 555655443

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=94.78  E-value=0.39  Score=45.25  Aligned_cols=32  Identities=28%  Similarity=0.317  Sum_probs=21.5

Q ss_pred             CcHHHHHHHHHHh----cCC-CeEEEccCCCchhHHh
Q 010709          144 PTSIQAQAMPVAL----SGR-DLLGCAETGSGKTAAF  175 (503)
Q Consensus       144 ~~~~Q~~~i~~i~----~~~-~vii~~~TGsGKTl~~  175 (503)
                      +++.+.+++..+.    .+. .+++.||+|+|||+..
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~   60 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLI   60 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH
Confidence            4444555655543    333 4899999999999854

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.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=94.78  E-value=0.11  Score=55.25  Aligned_cols=97  Identities=19%  Similarity=0.259  Sum_probs=76.9

Q ss_pred             EEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhc
Q 010709          344 LEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFRN  422 (503)
Q Consensus       344 ~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~~  422 (503)
                      +..+....|....++.+.+....+       +.+||.++-+....++.+.|+.. |.++..+||++++.+|...+.+..+
T Consensus       222 l~GvTGSGKTEvYl~~i~~~L~~G-------kqvLvLVPEI~Ltpq~~~rf~~rFg~~v~vlHS~Ls~~er~~~W~~~~~  294 (730)
T COG1198         222 LDGVTGSGKTEVYLEAIAKVLAQG-------KQVLVLVPEIALTPQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARR  294 (730)
T ss_pred             EeCCCCCcHHHHHHHHHHHHHHcC-------CEEEEEeccccchHHHHHHHHHHhCCChhhhcccCChHHHHHHHHHHhc
Confidence            344566778877777777665443       35999999999999998888765 8899999999999999999999999


Q ss_pred             CCCcEEEEccccccCCCCCCCCEEEE
Q 010709          423 GSTNILVATDVASRGLDVMGVAHVVN  448 (503)
Q Consensus       423 g~~~vLvaT~~~~~Gldip~v~~VI~  448 (503)
                      |+.+|+|.|..+- =.-++++..||.
T Consensus       295 G~~~vVIGtRSAl-F~Pf~~LGLIIv  319 (730)
T COG1198         295 GEARVVIGTRSAL-FLPFKNLGLIIV  319 (730)
T ss_pred             CCceEEEEechhh-cCchhhccEEEE
Confidence            9999999996432 234556666664

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=94.76  E-value=0.22  Score=55.04  Aligned_cols=74  Identities=14%  Similarity=0.228  Sum_probs=64.3

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      .+++|.++++..|.+.++.+++.    ++.+..++|..+..++.++++.+.+|+.+|+|+|. ++...+.+.++.+||.
T Consensus       501 ~qvlvLvPT~~LA~Q~~~~f~~~~~~~~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~ll~~~v~f~~L~llVI  579 (926)
T TIGR00580       501 KQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLII  579 (926)
T ss_pred             CeEEEEeCcHHHHHHHHHHHHHHhccCCcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHHhhCCCCcccCCEEEe
Confidence            46999999999999999888763    67888999999999999999999999999999995 5556788888888774

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.

>COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.68  E-value=0.79  Score=41.97  Aligned_cols=22  Identities=32%  Similarity=0.404  Sum_probs=17.3

Q ss_pred             CeEEEccCCCchhHHhHHHHHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQH  182 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~  182 (503)
                      =+|++|+|||||++.. ..++.+
T Consensus       129 LviiVGaTGSGKSTtm-AaMi~y  150 (375)
T COG5008         129 LVIIVGATGSGKSTTM-AAMIGY  150 (375)
T ss_pred             eEEEECCCCCCchhhH-HHHhcc
Confidence            3999999999999864 555554

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

Probab=94.68  E-value=0.76  Score=45.26  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=20.2

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                      ....-+||+||++.|.+..- ..+..+++..
T Consensus       121 ~~~~~IvvLDEid~L~~~~~-~~LY~L~r~~  150 (366)
T COG1474         121 KGKTVIVILDEVDALVDKDG-EVLYSLLRAP  150 (366)
T ss_pred             cCCeEEEEEcchhhhccccc-hHHHHHHhhc
Confidence            34566899999999987743 4455555443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=94.68  E-value=0.53  Score=41.65  Aligned_cols=38  Identities=21%  Similarity=0.325  Sum_probs=22.7

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLL  305 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~  305 (503)
                      ....++|||||+|++... ....+.+.+...++...+|+
T Consensus        94 ~~~~kviiide~~~l~~~-~~~~Ll~~le~~~~~~~~il  131 (188)
T TIGR00678        94 ESGRRVVIIEDAERMNEA-AANALLKTLEEPPPNTLFIL  131 (188)
T ss_pred             cCCeEEEEEechhhhCHH-HHHHHHHHhcCCCCCeEEEE
Confidence            467889999999987532 23334445544343443333

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.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.67  E-value=0.31  Score=51.49  Aligned_cols=41  Identities=17%  Similarity=0.297  Sum_probs=23.5

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      +.+.++|||||+|.|... -...+.+.+...++.. ++++.++
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            457899999999977532 2233444444444444 3334333

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.67  E-value=0.053  Score=52.70  Aligned_cols=45  Identities=27%  Similarity=0.330  Sum_probs=29.2

Q ss_pred             HHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          154 VALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       154 ~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      ++..+++++|+|+||||||+.. -.++..+ .       ...+++.+=.+.||.
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll-~aLl~~i-~-------~~~rivtiEd~~El~  202 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMS-KTLISAI-P-------PQERLITIEDTLELV  202 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHH-HHHHccc-C-------CCCCEEEECCCcccc
Confidence            3446789999999999999842 3333322 1       134567766777663

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=94.67  E-value=0.76  Score=44.36  Aligned_cols=55  Identities=15%  Similarity=0.292  Sum_probs=30.6

Q ss_pred             CCccEEEecchhHHhhC-CCHHHHHHHHHhC------CCCCcEEEEEeeCCHHHHHHHHHhc
Q 010709          268 SRVSFVILDEADRMLDM-GFEPQIREVMQNL------PDKHQTLLFSATMPVEIEALAQEYL  322 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~-~~~~~~~~il~~~------~~~~q~i~~SAT~~~~~~~~~~~~~  322 (503)
                      .++++||||=+-++-.. .....+.++.+..      .+...++.++||...+.-..+..|.
T Consensus       195 ~~~D~ViIDTaGr~~~~~~l~~eL~~~~~v~~~~~~~~p~~~~LVl~a~~g~~~~~~a~~f~  256 (318)
T PRK10416        195 RGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQAKAFH  256 (318)
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHHHHHHhhhcCCCCceEEEEEECCCChHHHHHHHHHH
Confidence            56788999888754322 1223344443321      2334578889997655444455553

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=94.66  E-value=0.4  Score=45.83  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +-|++.||+|+|||+.+
T Consensus       186 KGVLLYGPPGTGKTLLA  202 (406)
T COG1222         186 KGVLLYGPPGTGKTLLA  202 (406)
T ss_pred             CceEeeCCCCCcHHHHH
Confidence            56999999999999844

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.64  E-value=0.25  Score=51.89  Aligned_cols=40  Identities=13%  Similarity=0.252  Sum_probs=23.8

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+++++||||+|+|.... .+.+.+.+...+....+|+.+
T Consensus       122 ~g~~KV~IIDEvh~Ls~~a-~NaLLKtLEEPP~~~~fIL~T  161 (618)
T PRK14951        122 QGRFKVFMIDEVHMLTNTA-FNAMLKTLEEPPEYLKFVLAT  161 (618)
T ss_pred             cCCceEEEEEChhhCCHHH-HHHHHHhcccCCCCeEEEEEE
Confidence            3568999999999875432 223444444444455454443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.61  E-value=0.17  Score=52.00  Aligned_cols=24  Identities=21%  Similarity=0.157  Sum_probs=17.2

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHh
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      ++++||.|+|||+.+. .+...+..
T Consensus        39 ~Lf~GppGtGKTTlA~-~lA~~l~c   62 (504)
T PRK14963         39 YLFSGPRGVGKTTTAR-LIAMAVNC   62 (504)
T ss_pred             EEEECCCCCCHHHHHH-HHHHHHhc
Confidence            5999999999998753 34444433

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

Probab=94.59  E-value=0.48  Score=40.95  Aligned_cols=54  Identities=28%  Similarity=0.476  Sum_probs=35.4

Q ss_pred             CCCCccEEEecchhHHhhCCC--HHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHH
Q 010709          266 SLSRVSFVILDEADRMLDMGF--EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQ  319 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~  319 (503)
                      .-..+++||+||+-..++.++  ...+..++...++..-+|+.--.+|+.+.+.+.
T Consensus        93 ~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~AD  148 (172)
T PF02572_consen   93 SSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAAD  148 (172)
T ss_dssp             T-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-S
T ss_pred             hCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCC
Confidence            346799999999998888774  456778888777778777776677777766544

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=94.58  E-value=0.1  Score=51.27  Aligned_cols=28  Identities=39%  Similarity=0.540  Sum_probs=20.2

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      .+..++|+||||||||+.. ..++.++..
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~~  175 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCGE  175 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            3456999999999999853 455555543

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).

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

Probab=94.53  E-value=0.028  Score=63.89  Aligned_cols=92  Identities=23%  Similarity=0.256  Sum_probs=76.5

Q ss_pred             EEEEEcchhhHHHHHHHHHHCC-CeEEEEcCCCC-----------HHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCC
Q 010709          377 TIVFVERKTRCDEVSEALVAEG-LHAVALHGGRN-----------QSDRESALRDFRNGSTNILVATDVASRGLDVMGVA  444 (503)
Q Consensus       377 ~lIF~~~~~~~~~l~~~L~~~~-~~v~~lh~~~~-----------~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~  444 (503)
                      .++|++.+..+..+.+.++... ..+..+.|.+.           +..+.+++..|.....++|++|.++..|+|++.++
T Consensus       295 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~k~~~~~~~~~~~~vl~~~~~~~ln~L~~~~~~~e~~d~~~~~  374 (1606)
T KOG0701|consen  295 GIIFVDQRYTAYVLLELLREIFSNDPLFVTGASGANLWKSFKNELELRQAEVLRRFHFHELNLLIATSVLEEGVDVPKCN  374 (1606)
T ss_pred             heeecccchHHHHHHHHHHHhhccCcceeeccccCccchhhHHHHHhhhHHHHHHHhhhhhhHHHHHHHHHhhcchhhhh
Confidence            6999999999988888887652 23333444333           23478899999999999999999999999999999


Q ss_pred             EEEEccCCCChhHHHHhhCcceee
Q 010709          445 HVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       445 ~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .|+.++.|.....|+|+.||+-+.
T Consensus       375 ~~~~~~~~~~~~~~vq~~~r~~~~  398 (1606)
T KOG0701|consen  375 LVVLFDAPTYYRSYVQKKGRARAA  398 (1606)
T ss_pred             hheeccCcchHHHHHHhhcccccc
Confidence            999999999999999999997663

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=94.49  E-value=0.11  Score=50.97  Aligned_cols=26  Identities=23%  Similarity=0.313  Sum_probs=19.0

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      .+.-++|+||||||||+.. ..++.++
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i  158 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIREL  158 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHH
Confidence            4566999999999999853 3344444

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.

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=94.48  E-value=0.11  Score=51.40  Aligned_cols=130  Identities=14%  Similarity=0.020  Sum_probs=71.8

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC---
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL---  221 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~---  221 (503)
                      ...|..+.-..-.|+- .|.|=.|||||...  ++-...+..    .+..-++++.+=|+.|+.++...+.+++-..   
T Consensus       164 D~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~L--a~Kaa~lh~----knPd~~I~~Tfftk~L~s~~r~lv~~F~f~~~e~  236 (660)
T COG3972         164 DTDQTKAAFQSGFGKQ-RIRGLAGSGKTELL--AHKAAELHS----KNPDSRIAFTFFTKILASTMRTLVPEFFFMRVEK  236 (660)
T ss_pred             cchhheeeeecCCchh-hhhcccCCCchhHH--HHHHHHHhc----CCCCceEEEEeehHHHHHHHHHHHHHHHHHHhhc
Confidence            3346665544444544 56788899999743  222222222    1235679999999999999999888876321   


Q ss_pred             ----CCceEEEEECCccHHHHHH---HhhCCCcEEEECc----HHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          222 ----DSFKTAIVVGGTNIAEQRS---ELRGGVSIVVATP----GRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       222 ----~~~~~~~~~~~~~~~~~~~---~~~~~~~Ilv~Tp----~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                          +.+-+..-.||........   .......+-++--    ..++..+.+..-...-+++|.|||++-+
T Consensus       237 ~pdW~~~l~~h~wgG~t~~g~y~~~~~~~~~~~~~fsg~g~~F~~aC~eli~~~~~~~~yD~ilIDE~QDF  307 (660)
T COG3972         237 QPDWGTKLFCHNWGGLTKEGFYGMYRYICHYYEIPFSGFGNGFDAACKELIADINNKKAYDYILIDESQDF  307 (660)
T ss_pred             CCCccceEEEeccCCCCCCcchHHHHHHhcccccccCCCCcchHHHHHHHHHhhhccccccEEEecccccC
Confidence                1122333344544332222   2222222222211    1223333333334677999999999853

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=94.46  E-value=0.25  Score=51.69  Aligned_cols=42  Identities=12%  Similarity=0.199  Sum_probs=23.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ..+++++||||+|.|.... ...+.+.+...+... ++++.+|-
T Consensus       117 ~~~~kViIIDE~~~Lt~~a-~naLLKtLEepp~~~-ifIlatt~  158 (559)
T PRK05563        117 EAKYKVYIIDEVHMLSTGA-FNALLKTLEEPPAHV-IFILATTE  158 (559)
T ss_pred             cCCeEEEEEECcccCCHHH-HHHHHHHhcCCCCCe-EEEEEeCC
Confidence            4578999999999775322 223444444434344 33333443

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

Probab=94.44  E-value=0.15  Score=46.65  Aligned_cols=54  Identities=20%  Similarity=0.206  Sum_probs=31.4

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|..++|.|++|+|||+-.+-.+...+...       +.++++++-. +-..++.+.++.++
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~-------ge~vlyvs~e-e~~~~l~~~~~s~g   71 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF-------GEKVLYVSFE-EPPEELIENMKSFG   71 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH-------T--EEEEESS-S-HHHHHHHHHTTT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc-------CCcEEEEEec-CCHHHHHHHHHHcC
Confidence            455699999999999975544344443331       3457777732 33355555555543

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 ....

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.37  E-value=0.36  Score=50.51  Aligned_cols=17  Identities=29%  Similarity=0.276  Sum_probs=14.6

Q ss_pred             CeEEEccCCCchhHHhH
Q 010709          160 DLLGCAETGSGKTAAFT  176 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~  176 (503)
                      .+|+.||.|+|||+++.
T Consensus        40 a~Lf~GPpG~GKTtiAr   56 (624)
T PRK14959         40 AYLFSGTRGVGKTTIAR   56 (624)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            38899999999998764

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=94.37  E-value=0.14  Score=49.64  Aligned_cols=43  Identities=19%  Similarity=0.256  Sum_probs=27.6

Q ss_pred             HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          155 ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      +..+++++|+|+||||||+. +-.++.++-        ...+++.+=-+.|+
T Consensus       157 v~~~~nili~G~tgSGKTTl-l~aL~~~ip--------~~~ri~tiEd~~El  199 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTF-TNAALREIP--------AIERLITVEDAREI  199 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHH-HHHHHhhCC--------CCCeEEEecCCCcc
Confidence            44678999999999999984 233443321        13456665555555

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=94.34  E-value=0.72  Score=47.51  Aligned_cols=129  Identities=19%  Similarity=0.192  Sum_probs=77.6

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc-cCCCceEEEEECCccHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR-SLDSFKTAIVVGGTNIA  236 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~-~~~~~~~~~~~~~~~~~  236 (503)
                      .+-.+.--|=-.|||. +++|++..++..     -.|-++.|+++.+-.++-+.+++..-+. .++.-.+...-+     
T Consensus       202 QkaTVFLVPRRHGKTW-f~VpiIsllL~s-----~~gI~IGYvAHqKhvs~~Vf~EI~~~lrrwF~~~~vi~~k~-----  270 (668)
T PHA03372        202 QKATVFLVPRRHGKTW-FIIPIISFLLKN-----IIGISIGYVAHQKHVSQFVLKEVEFRCRRMFPRKHTIENKD-----  270 (668)
T ss_pred             ccceEEEecccCCcee-hHHHHHHHHHHh-----hcCceEEEEeeHHHHHHHHHHHHHHHHhhhcCccceeeecC-----
Confidence            3456777899999997 578898888773     2478899999999777766655543221 111111111111     


Q ss_pred             HHHHHhhCCCcEEEECcHH-----HHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeC
Q 010709          237 EQRSELRGGVSIVVATPGR-----FLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATM  310 (503)
Q Consensus       237 ~~~~~~~~~~~Ilv~Tp~~-----l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~  310 (503)
                               --|.+.-|+.     +......+...-+.+.++++||||-+.    ...+..++-.+ .++.++|..|.|-
T Consensus       271 ---------~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI~----~~a~~tilgfm~q~~~KiIfISS~N  337 (668)
T PHA03372        271 ---------NVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFIK----KDAFNTILGFLAQNTTKIIFISSTN  337 (668)
T ss_pred             ---------cEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhccC----HHHHHHhhhhhcccCceEEEEeCCC
Confidence                     1233322221     111222334566789999999999543    33455555544 3577888888773

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=94.29  E-value=0.26  Score=45.59  Aligned_cols=46  Identities=22%  Similarity=0.280  Sum_probs=28.3

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc---ccHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA---PTRELAQQ  209 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~---Ptr~La~q  209 (503)
                      .|.-++|+|++|+|||...+- ++......      .+..++++.   |..+++..
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~-~~~~~~~~------~g~~vly~s~E~~~~~~~~r   60 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALN-IAENIAKK------QGKPVLFFSLEMSKEQLLQR   60 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHH-HHHHHHHh------CCCceEEEeCCCCHHHHHHH
Confidence            556699999999999975433 33333332      145577777   34444443

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.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=94.25  E-value=0.19  Score=52.99  Aligned_cols=40  Identities=13%  Similarity=0.211  Sum_probs=26.1

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      +.+++++||||+|.|... -...+.+.+...+....+|+.+
T Consensus       117 ~gk~KVIIIDEad~Ls~~-A~NALLKtLEEPp~~v~fILaT  156 (709)
T PRK08691        117 AGKYKVYIIDEVHMLSKS-AFNAMLKTLEEPPEHVKFILAT  156 (709)
T ss_pred             hCCcEEEEEECccccCHH-HHHHHHHHHHhCCCCcEEEEEe
Confidence            457899999999976532 2334566666656666565544

>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=94.24  E-value=0.52  Score=46.30  Aligned_cols=47  Identities=13%  Similarity=0.174  Sum_probs=29.6

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHH
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~  315 (503)
                      ++..+|.+||+| +-+-+-.-.+.+++..+ ....-+|+.|-++|.++.
T Consensus       126 ~~~~lLcfDEF~-V~DiaDAmil~rLf~~l~~~gvvlVaTSN~~P~~Ly  173 (362)
T PF03969_consen  126 KESRLLCFDEFQ-VTDIADAMILKRLFEALFKRGVVLVATSNRPPEDLY  173 (362)
T ss_pred             hcCCEEEEeeee-ccchhHHHHHHHHHHHHHHCCCEEEecCCCChHHHc
Confidence            356799999999 32332233345555443 456677888888877654

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

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

Probab=94.24  E-value=1.6  Score=37.86  Aligned_cols=54  Identities=17%  Similarity=0.283  Sum_probs=29.6

Q ss_pred             CCccEEEecchhHHh-hCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh
Q 010709          268 SRVSFVILDEADRML-DMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       268 ~~~~~vViDEaH~l~-~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                      .+.++||+|...... +......+..+.....+..-++.+.|.-..+....+..+
T Consensus        81 ~~~d~viiDt~g~~~~~~~~l~~l~~l~~~~~~~~~~lVv~~~~~~~~~~~~~~~  135 (173)
T cd03115          81 ENFDVVIVDTAGRLQIDENLMEELKKIKRVVKPDEVLLVVDAMTGQDAVNQAKAF  135 (173)
T ss_pred             CCCCEEEEECcccchhhHHHHHHHHHHHhhcCCCeEEEEEECCCChHHHHHHHHH
Confidence            467789999988542 111233344444433445556667776555544455444

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.24  E-value=0.35  Score=44.36  Aligned_cols=52  Identities=17%  Similarity=0.172  Sum_probs=29.9

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .|..+++.|++|+|||+.+...+. .....       +..++++.- .+...++.+..+.+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~-~~~~~-------g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAY-KGLRD-------GDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHH-HHHhc-------CCeEEEEEc-cCCHHHHHHHHHHh
Confidence            456799999999999975433222 22222       345677663 23334444444444

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.

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.21  E-value=0.47  Score=47.56  Aligned_cols=42  Identities=17%  Similarity=0.210  Sum_probs=23.9

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      .+.+.+++||||+|++.... ...+.+.+...++...+| +.++
T Consensus       124 ~~~~~kvvIIdea~~l~~~~-~~~LLk~LEep~~~t~~I-l~t~  165 (397)
T PRK14955        124 QKGRYRVYIIDEVHMLSIAA-FNAFLKTLEEPPPHAIFI-FATT  165 (397)
T ss_pred             hcCCeEEEEEeChhhCCHHH-HHHHHHHHhcCCCCeEEE-EEeC
Confidence            35678999999999875321 223444444444444333 4434

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.20  E-value=0.45  Score=45.96  Aligned_cols=16  Identities=31%  Similarity=0.484  Sum_probs=14.2

Q ss_pred             CCeEEEccCCCchhHH
Q 010709          159 RDLLGCAETGSGKTAA  174 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~  174 (503)
                      +.++..||+|+|||+.
T Consensus       246 kgvLm~GPPGTGKTlL  261 (491)
T KOG0738|consen  246 KGVLMVGPPGTGKTLL  261 (491)
T ss_pred             ceeeeeCCCCCcHHHH
Confidence            5699999999999973

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=94.17  E-value=0.071  Score=54.83  Aligned_cols=43  Identities=21%  Similarity=0.215  Sum_probs=35.1

Q ss_pred             CCCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCV  184 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~  184 (503)
                      -+|+.+|.+.+..++    .|+-.|.-+|||+|||+..+=..+.++.
T Consensus        14 y~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~   60 (821)
T KOG1133|consen   14 YTPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLR   60 (821)
T ss_pred             CCchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHH
Confidence            379999999887765    6888999999999999877666666544

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=94.16  E-value=0.75  Score=50.73  Aligned_cols=28  Identities=21%  Similarity=0.324  Sum_probs=20.4

Q ss_pred             HHHHHHHHhc------CCCeEEEccCCCchhHHh
Q 010709          148 QAQAMPVALS------GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       148 Q~~~i~~i~~------~~~vii~~~TGsGKTl~~  175 (503)
                      |..-+..+++      ..++++.||.|+|||...
T Consensus       192 r~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       192 RDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHH
Confidence            5555655542      347999999999999754

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=94.15  E-value=0.79  Score=50.69  Aligned_cols=17  Identities=35%  Similarity=0.399  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +++++.||+|+|||...
T Consensus       200 ~n~lL~G~pGvGKT~l~  216 (857)
T PRK10865        200 NNPVLIGEPGVGKTAIV  216 (857)
T ss_pred             CceEEECCCCCCHHHHH
Confidence            47999999999999754

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=94.14  E-value=0.68  Score=44.81  Aligned_cols=38  Identities=21%  Similarity=0.343  Sum_probs=24.9

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..++|+|||+|.+... ....+..++...++...+|+.+
T Consensus       102 ~~~vviiDe~~~l~~~-~~~~L~~~le~~~~~~~lIl~~  139 (319)
T PRK00440        102 PFKIIFLDEADNLTSD-AQQALRRTMEMYSQNTRFILSC  139 (319)
T ss_pred             CceEEEEeCcccCCHH-HHHHHHHHHhcCCCCCeEEEEe
Confidence            4679999999977432 2345666666666666666544

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=94.12  E-value=1  Score=39.02  Aligned_cols=53  Identities=28%  Similarity=0.498  Sum_probs=41.0

Q ss_pred             CCCccEEEecchhHHhhCCC--HHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHH
Q 010709          267 LSRVSFVILDEADRMLDMGF--EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQ  319 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~  319 (503)
                      -..+++||+||+-..++.++  ...+..+++..|+..-+|+..-.+|+.+.+.+.
T Consensus       113 ~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~AD  167 (178)
T PRK07414        113 EGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIAD  167 (178)
T ss_pred             CCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCC
Confidence            46789999999998888774  456778888888887777777777877766543

>CHL00095 clpC Clp protease ATP binding subunit

Probab=94.10  E-value=0.73  Score=50.85  Aligned_cols=18  Identities=33%  Similarity=0.331  Sum_probs=15.4

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+++++.||+|+|||..+
T Consensus       200 ~~n~lL~G~pGvGKTal~  217 (821)
T CHL00095        200 KNNPILIGEPGVGKTAIA  217 (821)
T ss_pred             cCCeEEECCCCCCHHHHH
Confidence            357999999999999854

>PRK10689 transcription-repair coupling factor; Provisional

Probab=94.08  E-value=0.22  Score=56.48  Aligned_cols=75  Identities=12%  Similarity=0.164  Sum_probs=63.2

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      ..+++|.++++..|.++++.+.+.    ++.+..++++.+..++.++++.+.+|..+|||+|. .+...+.+.++.+||.
T Consensus       649 g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~~v~~~~L~lLVI  728 (1147)
T PRK10689        649 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIV  728 (1147)
T ss_pred             CCeEEEEeCcHHHHHHHHHHHHHhhccCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhCCCCHhhCCEEEE
Confidence            346999999999999999988753    46788899999999999999999999999999994 5555677778888773

>PRK06904 replicative DNA helicase; Validated

Probab=94.05  E-value=0.62  Score=47.67  Aligned_cols=114  Identities=14%  Similarity=0.149  Sum_probs=52.7

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEE-EC-CccH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIV-VG-GTNI  235 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~-~~-~~~~  235 (503)
                      |.=+||.|.||.|||.-+ +-+.......      .+..++|...- --..|+..++-....   ++....+ .| ....
T Consensus       221 G~LiiIaarPg~GKTafa-lnia~~~a~~------~g~~Vl~fSlE-Ms~~ql~~Rlla~~s---~v~~~~i~~g~~l~~  289 (472)
T PRK06904        221 SDLIIVAARPSMGKTTFA-MNLCENAAMA------SEKPVLVFSLE-MPAEQIMMRMLASLS---RVDQTKIRTGQNLDQ  289 (472)
T ss_pred             CcEEEEEeCCCCChHHHH-HHHHHHHHHh------cCCeEEEEecc-CCHHHHHHHHHHhhC---CCCHHHhccCCCCCH
Confidence            344899999999999744 4344433321      13456666432 223344433332221   1222111 22 1222


Q ss_pred             HHH------HHHhhCCCcEEEE-----CcHHHHHHHHcCCCCCCCccEEEecchhHHh
Q 010709          236 AEQ------RSELRGGVSIVVA-----TPGRFLDHLQQGNTSLSRVSFVILDEADRML  282 (503)
Q Consensus       236 ~~~------~~~~~~~~~Ilv~-----Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~  282 (503)
                      .+.      ...+.....+.|-     |+..+...+.+.......+++||||=.+.+.
T Consensus       290 ~e~~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~  347 (472)
T PRK06904        290 QDWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRENGGLSLIMVDYLQLMR  347 (472)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHHhCCCCCEEEEecHHhcC
Confidence            221      1122223445553     3444433332211112358899999998664

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=93.99  E-value=0.14  Score=55.28  Aligned_cols=61  Identities=23%  Similarity=0.270  Sum_probs=51.4

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHCC-----CeEEE-EcCCCCHHHHHHHHHHHhcCCCcEEEEcccc
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAEG-----LHAVA-LHGGRNQSDRESALRDFRNGSTNILVATDVA  434 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~~-----~~v~~-lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~  434 (503)
                      ++++++.++|..-+.+.++.|.+..     +.+.. +||.++.+++.+.+++|.+|..+|||+|..+
T Consensus       125 gkr~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~F  191 (1187)
T COG1110         125 GKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQF  191 (1187)
T ss_pred             CCeEEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHH
Confidence            3569999999999999888887642     44333 9999999999999999999999999999654

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

Probab=93.96  E-value=0.15  Score=47.15  Aligned_cols=16  Identities=31%  Similarity=0.314  Sum_probs=14.0

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      ++++.||+|.|||+.+
T Consensus        54 HvLl~GPPGlGKTTLA   69 (332)
T COG2255          54 HVLLFGPPGLGKTTLA   69 (332)
T ss_pred             eEEeeCCCCCcHHHHH
Confidence            5999999999999743

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=93.83  E-value=0.38  Score=48.67  Aligned_cols=39  Identities=18%  Similarity=0.294  Sum_probs=24.3

Q ss_pred             hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      ..|.-++|.|++|.|||... +-+.......      .+..++++.
T Consensus       192 ~~g~liviag~pg~GKT~~a-l~ia~~~a~~------~g~~v~~fS  230 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKTTLA-LNIAENVALR------EGKPVLFFS  230 (421)
T ss_pred             CCCceEEEEeCCCCCHHHHH-HHHHHHHHHh------CCCcEEEEE
Confidence            34556999999999999754 3343333211      144567775

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=93.82  E-value=1.1  Score=41.33  Aligned_cols=53  Identities=13%  Similarity=0.157  Sum_probs=31.0

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|.-+++.|++|+|||+.....+... ..       ++.+++++.=-. -..++.+.+..++
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~-~~-------~g~~~~y~~~e~-~~~~~~~~~~~~g   76 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGA-LK-------QGKKVYVITTEN-TSKSYLKQMESVK   76 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHH-Hh-------CCCEEEEEEcCC-CHHHHHHHHHHCC
Confidence            34569999999999997543322222 22       256677776433 2344555555553

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.77  E-value=1.5  Score=40.88  Aligned_cols=124  Identities=15%  Similarity=0.280  Sum_probs=68.2

Q ss_pred             HHHhcCC-----CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEE
Q 010709          153 PVALSGR-----DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA  227 (503)
Q Consensus       153 ~~i~~~~-----~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~  227 (503)
                      |.+..|+     -+++.||+|+||+.  +.-++.....          ...+-+.+..|+..|.-+-.++.+        
T Consensus       156 PqlFtGkR~PwrgiLLyGPPGTGKSY--LAKAVATEAn----------STFFSvSSSDLvSKWmGESEkLVk--------  215 (439)
T KOG0739|consen  156 PQLFTGKRKPWRGILLYGPPGTGKSY--LAKAVATEAN----------STFFSVSSSDLVSKWMGESEKLVK--------  215 (439)
T ss_pred             hhhhcCCCCcceeEEEeCCCCCcHHH--HHHHHHhhcC----------CceEEeehHHHHHHHhccHHHHHH--------
Confidence            4556664     38999999999994  4444433222          257777777887766544444331        


Q ss_pred             EEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC---CHHHHHHH----HHhCC--
Q 010709          228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG---FEPQIREV----MQNLP--  298 (503)
Q Consensus       228 ~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~---~~~~~~~i----l~~~~--  298 (503)
                                                 .|..+...     .+-+.|.|||+|.+.+..   -...-++|    +-+++  
T Consensus       216 ---------------------------nLFemARe-----~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGV  263 (439)
T KOG0739|consen  216 ---------------------------NLFEMARE-----NKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGV  263 (439)
T ss_pred             ---------------------------HHHHHHHh-----cCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhcc
Confidence                                       12222222     245789999999776542   11222222    33332  


Q ss_pred             --CCCcEEEEEeeCCH-HHHHHHHHhcCCCeEE
Q 010709          299 --DKHQTLLFSATMPV-EIEALAQEYLTDPVQV  328 (503)
Q Consensus       299 --~~~q~i~~SAT~~~-~~~~~~~~~~~~~~~~  328 (503)
                        .+--++.+.||-.+ .+..-+++-+...+.+
T Consensus       264 G~d~~gvLVLgATNiPw~LDsAIRRRFekRIYI  296 (439)
T KOG0739|consen  264 GNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYI  296 (439)
T ss_pred             ccCCCceEEEecCCCchhHHHHHHHHhhcceec
Confidence              23457888888533 3343444444444333

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=93.70  E-value=1.4  Score=42.08  Aligned_cols=129  Identities=19%  Similarity=0.247  Sum_probs=69.0

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc-c-cHHHHHHHHHHHHHHhccCCCceEEE-EECCccHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA-P-TRELAQQIEKEVKALSRSLDSFKTAI-VVGGTNIAE  237 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~-P-tr~La~q~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  237 (503)
                      ++++|-.|+|||+.  +.=|.+.+..      .|.++++.+ - -|+-|..+.+.+.+-   . ++.+.. -+|+.+.. 
T Consensus       142 il~vGVNG~GKTTT--IaKLA~~l~~------~g~~VllaA~DTFRAaAiEQL~~w~er---~-gv~vI~~~~G~DpAa-  208 (340)
T COG0552         142 ILFVGVNGVGKTTT--IAKLAKYLKQ------QGKSVLLAAGDTFRAAAIEQLEVWGER---L-GVPVISGKEGADPAA-  208 (340)
T ss_pred             EEEEecCCCchHhH--HHHHHHHHHH------CCCeEEEEecchHHHHHHHHHHHHHHH---h-CCeEEccCCCCCcHH-
Confidence            88999999999986  3344444443      266677766 2 455544333333322   2 233322 12222211 


Q ss_pred             HHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCC------cEEEEEeeC
Q 010709          238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKH------QTLLFSATM  310 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~------q~i~~SAT~  310 (503)
                                       ...+-++.  -.-+++++|++|=|-||-+. +....+.++.+-+.+..      -++.+=||.
T Consensus       209 -----------------VafDAi~~--Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~llvlDAtt  269 (340)
T COG0552         209 -----------------VAFDAIQA--AKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATT  269 (340)
T ss_pred             -----------------HHHHHHHH--HHHcCCCEEEEeCcccccCchhHHHHHHHHHHHhccccCCCCceEEEEEEccc
Confidence                             12222222  12346777888877776544 34556666666655433      244448888


Q ss_pred             CHHHHHHHHHh
Q 010709          311 PVEIEALAQEY  321 (503)
Q Consensus       311 ~~~~~~~~~~~  321 (503)
                      ..+--.-++.|
T Consensus       270 Gqnal~QAk~F  280 (340)
T COG0552         270 GQNALSQAKIF  280 (340)
T ss_pred             ChhHHHHHHHH
Confidence            77655555555

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.67  E-value=0.58  Score=49.52  Aligned_cols=25  Identities=20%  Similarity=0.207  Sum_probs=17.5

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      .+|+.||.|+|||..+. .+...+.+
T Consensus        40 a~Lf~Gp~G~GKttlA~-~lAk~L~c   64 (620)
T PRK14948         40 AYLFTGPRGTGKTSSAR-ILAKSLNC   64 (620)
T ss_pred             eEEEECCCCCChHHHHH-HHHHHhcC
Confidence            47999999999998653 23334333

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

Probab=93.63  E-value=0.29  Score=46.76  Aligned_cols=16  Identities=25%  Similarity=0.382  Sum_probs=14.0

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+|+.||+|+|||..+
T Consensus       164 SmIlWGppG~GKTtlA  179 (554)
T KOG2028|consen  164 SMILWGPPGTGKTTLA  179 (554)
T ss_pred             ceEEecCCCCchHHHH
Confidence            5999999999999743

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=93.60  E-value=0.44  Score=49.11  Aligned_cols=40  Identities=15%  Similarity=0.257  Sum_probs=27.3

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ...++++||||||+|... -...+.+.+...++...+|+.+
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            457899999999987533 3445666666666666656554

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=93.54  E-value=0.18  Score=44.56  Aligned_cols=31  Identities=32%  Similarity=0.404  Sum_probs=23.8

Q ss_pred             CcHHHHHHHHHHh-cCCCeEEEccCCCchhHH
Q 010709          144 PTSIQAQAMPVAL-SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       144 ~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~  174 (503)
                      ..+-|.+.+.... .+..++++||||+|||+.
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTl   41 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTL   41 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            4455666666654 577899999999999984

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.

>PRK13764 ATPase; Provisional

Probab=93.50  E-value=0.18  Score=52.62  Aligned_cols=27  Identities=15%  Similarity=0.258  Sum_probs=19.8

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCV  184 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~  184 (503)
                      .+++++++||||||||+.. ..++.++.
T Consensus       256 ~~~~ILIsG~TGSGKTTll-~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFA-QALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4667999999999999843 44454443

>TIGR03689 pup_AAA proteasome ATPase

Probab=93.46  E-value=0.49  Score=48.50  Aligned_cols=18  Identities=28%  Similarity=0.314  Sum_probs=15.1

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+.+++.||+|+|||+.+
T Consensus       216 p~GILLyGPPGTGKT~LA  233 (512)
T TIGR03689       216 PKGVLLYGPPGCGKTLIA  233 (512)
T ss_pred             CcceEEECCCCCcHHHHH
Confidence            356999999999999743

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.

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=93.44  E-value=0.79  Score=39.74  Aligned_cols=54  Identities=22%  Similarity=0.378  Sum_probs=38.8

Q ss_pred             CCCccEEEecchhHHhhCCC--HHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHH
Q 010709          267 LSRVSFVILDEADRMLDMGF--EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQE  320 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~  320 (503)
                      -.++++||+||.--.+..++  ...+..++...|...-+|+..-..|+.+-+.+..
T Consensus       120 ~~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~ADl  175 (198)
T COG2109         120 DGKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADL  175 (198)
T ss_pred             CCCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHH
Confidence            34799999999998877764  3556677777777776666665667777766553

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

Probab=93.42  E-value=0.19  Score=47.10  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=24.5

Q ss_pred             cHHHHHHHHHHhc--CCCeEEEccCCCchhHHhHHHHHHHH
Q 010709          145 TSIQAQAMPVALS--GRDLLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       145 ~~~Q~~~i~~i~~--~~~vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      .+.|.+.+..++.  +..++|+|+||||||+.. ..++..+
T Consensus        65 ~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i  104 (264)
T cd01129          65 KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSEL  104 (264)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhh
Confidence            3345666655543  335899999999999853 3344443

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=93.37  E-value=0.77  Score=44.25  Aligned_cols=52  Identities=10%  Similarity=0.176  Sum_probs=31.9

Q ss_pred             HHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          255 RFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       255 ~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      .+.+.+.... .....+++|||+||.|... -.+.+.+++..-+ +..+|+++..
T Consensus       111 ~i~~~l~~~p-~~~~~kVvII~~ae~m~~~-aaNaLLK~LEEPp-~~~fILi~~~  162 (314)
T PRK07399        111 EIKRFLSRPP-LEAPRKVVVIEDAETMNEA-AANALLKTLEEPG-NGTLILIAPS  162 (314)
T ss_pred             HHHHHHccCc-ccCCceEEEEEchhhcCHH-HHHHHHHHHhCCC-CCeEEEEECC
Confidence            3444444322 3467899999999987432 3555667776655 5655555543

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

Probab=93.30  E-value=0.083  Score=55.10  Aligned_cols=151  Identities=20%  Similarity=0.316  Sum_probs=0.0

Q ss_pred             CcHHHHHHHHHHh--------cCCC--eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          144 PTSIQAQAMPVAL--------SGRD--LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       144 ~~~~Q~~~i~~i~--------~~~~--vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      +...|.+++-..-        .|..  .+|-...|.||-....-.++...++-       .+++|.+.=+..|--...+.
T Consensus       265 lSALQLEav~YAcQ~He~llPsG~RaGfLiGDGAGVGKGRTvAgiIfeNyLkG-------RKrAlW~SVSsDLKfDAERD  337 (1300)
T KOG1513|consen  265 LSALQLEAVTYACQAHEVLLPSGQRAGFLIGDGAGVGKGRTVAGIIFENYLKG-------RKRALWFSVSSDLKFDAERD  337 (1300)
T ss_pred             hhHHHHHHHHHHHhhhhhcCCCCccceeeeccCcccCCCceeEEEEehhhhcc-------cceeEEEEeccccccchhhc


Q ss_pred             HHHHh------ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHH-cCCCCCCCcc------------EEE
Q 010709          214 VKALS------RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQ-QGNTSLSRVS------------FVI  274 (503)
Q Consensus       214 ~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~-~~~~~l~~~~------------~vV  274 (503)
                      ++..+      ..++.+++.-+.+..+..-.       -.|+|+|+..|.-.-+ .+.....+++            +||
T Consensus       338 L~DigA~~I~V~alnK~KYakIss~en~n~k-------rGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIv  410 (1300)
T KOG1513|consen  338 LRDIGATGIAVHALNKFKYAKISSKENTNTK-------RGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIV  410 (1300)
T ss_pred             hhhcCCCCccceehhhcccccccccccCCcc-------ceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEE


Q ss_pred             ecchhHHhhCC---------CHHHHHHHHHhCCCCCcEEEEEee
Q 010709          275 LDEADRMLDMG---------FEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       275 iDEaH~l~~~~---------~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      +||||+.-+..         .+..+..+-+.+|+.+ +|.-|||
T Consensus       411 fDECHkAKNL~p~~~~k~TKtG~tVLdLQk~LP~AR-VVYASAT  453 (1300)
T KOG1513|consen  411 FDECHKAKNLVPTAGAKSTKTGKTVLDLQKKLPNAR-VVYASAT  453 (1300)
T ss_pred             ehhhhhhcccccccCCCcCcccHhHHHHHHhCCCce-EEEeecc

>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=93.21  E-value=0.38  Score=45.04  Aligned_cols=39  Identities=23%  Similarity=0.238  Sum_probs=25.1

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      .|.=++|.|.||.|||..+ +-+...+...      .+..+++++.
T Consensus        18 ~g~L~vi~a~pg~GKT~~~-l~ia~~~a~~------~~~~vly~Sl   56 (259)
T PF03796_consen   18 PGELTVIAARPGVGKTAFA-LQIALNAALN------GGYPVLYFSL   56 (259)
T ss_dssp             TT-EEEEEESTTSSHHHHH-HHHHHHHHHT------TSSEEEEEES
T ss_pred             cCcEEEEEecccCCchHHH-HHHHHHHHHh------cCCeEEEEcC
Confidence            3445999999999999855 4344444432      1356888874

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 ....

>PRK10436 hypothetical protein; Provisional

Probab=93.20  E-value=0.18  Score=51.22  Aligned_cols=38  Identities=32%  Similarity=0.309  Sum_probs=25.8

Q ss_pred             cHHHHHHHHHHhc--CCCeEEEccCCCchhHHhHHHHHHHH
Q 010709          145 TSIQAQAMPVALS--GRDLLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       145 ~~~Q~~~i~~i~~--~~~vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      .+.|.+.+..++.  +.-++++||||||||+.. ..++.++
T Consensus       203 ~~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~  242 (462)
T PRK10436        203 TPAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTL  242 (462)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhh
Confidence            4446666666553  345999999999999864 4455553

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=93.19  E-value=0.065  Score=53.50  Aligned_cols=49  Identities=31%  Similarity=0.335  Sum_probs=37.3

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      +++++|+||+|||.++++|-+..   .       +..++|+=|.-++........+..+
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~---~-------~~s~vv~D~Kge~~~~t~~~r~~~G   49 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLT---W-------PGSVVVLDPKGENFELTSEHRRALG   49 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhc---C-------CCCEEEEccchhHHHHHHHHHHHcC
Confidence            57899999999999998887653   1       2447777799899887776665543

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.

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=93.00  E-value=1.1  Score=45.68  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=23.7

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF  306 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~  306 (503)
                      ..+.++|||||+|.+... -...+.+.+...++...+|+.
T Consensus       119 ~~~~kvvIIdead~lt~~-~~n~LLk~lEep~~~~~~Il~  157 (451)
T PRK06305        119 KSRYKIYIIDEVHMLTKE-AFNSLLKTLEEPPQHVKFFLA  157 (451)
T ss_pred             cCCCEEEEEecHHhhCHH-HHHHHHHHhhcCCCCceEEEE
Confidence            356789999999987532 133445555554444544443

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

Probab=93.00  E-value=0.11  Score=47.69  Aligned_cols=14  Identities=29%  Similarity=0.434  Sum_probs=12.3

Q ss_pred             eEEEccCCCchhHH
Q 010709          161 LLGCAETGSGKTAA  174 (503)
Q Consensus       161 vii~~~TGsGKTl~  174 (503)
                      ++|.|+.|+|||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999984

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PF12846 AAA_10: AAA-like domain

Probab=92.93  E-value=0.14  Score=49.11  Aligned_cols=43  Identities=23%  Similarity=0.485  Sum_probs=30.4

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      +++++|+|+||+|||.... .++......       +..++++=|..+...
T Consensus         1 n~h~~i~G~tGsGKT~~~~-~l~~~~~~~-------g~~~~i~D~~g~~~~   43 (304)
T PF12846_consen    1 NPHTLILGKTGSGKTTLLK-NLLEQLIRR-------GPRVVIFDPKGDYSP   43 (304)
T ss_pred             CCeEEEECCCCCcHHHHHH-HHHHHHHHc-------CCCEEEEcCCchHHH
Confidence            4679999999999998664 555555554       466777766655544

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

Probab=92.90  E-value=0.079  Score=54.51  Aligned_cols=50  Identities=30%  Similarity=0.351  Sum_probs=38.7

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++++.||||||||..+++|.+..   +       +.-+||+=|--+|........++.+
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~---~-------~~s~iV~D~KgEl~~~t~~~r~~~G   94 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLN---Y-------PGSMIVTDPKGELYEKTAGYRKKRG   94 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHh---c-------cCCEEEEECCCcHHHHHHHHHHHCC
Confidence            469999999999999999997743   2       1246777798899887777666654

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

>PRK07004 replicative DNA helicase; Provisional

Probab=92.89  E-value=0.57  Score=47.82  Aligned_cols=18  Identities=28%  Similarity=0.287  Sum_probs=14.8

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      |.-++|.|.+|.|||..+
T Consensus       213 g~liviaarpg~GKT~~a  230 (460)
T PRK07004        213 GELIIVAGRPSMGKTAFS  230 (460)
T ss_pred             CceEEEEeCCCCCccHHH
Confidence            445899999999999754

>PRK08840 replicative DNA helicase; Provisional

Probab=92.88  E-value=1  Score=45.96  Aligned_cols=19  Identities=21%  Similarity=0.169  Sum_probs=15.1

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|.=++|.|.||.|||.-+
T Consensus       216 ~g~LiviaarPg~GKTafa  234 (464)
T PRK08840        216 GSDLIIVAARPSMGKTTFA  234 (464)
T ss_pred             CCceEEEEeCCCCchHHHH
Confidence            3445899999999999754

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.87  E-value=0.78  Score=48.41  Aligned_cols=41  Identities=12%  Similarity=0.165  Sum_probs=24.4

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+.+.+++||||+|.|.... ...+.+.+...++...+|+++
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            35678999999999875332 233444455544444444444

>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=92.86  E-value=0.21  Score=45.68  Aligned_cols=55  Identities=15%  Similarity=0.381  Sum_probs=29.3

Q ss_pred             CcHHHHHHHHcCCCCCCCccEEEecchhHHh-hC----CCHHHHHHHHHhCCC-CCcEEEEEeeC
Q 010709          252 TPGRFLDHLQQGNTSLSRVSFVILDEADRML-DM----GFEPQIREVMQNLPD-KHQTLLFSATM  310 (503)
Q Consensus       252 Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~-~~----~~~~~~~~il~~~~~-~~q~i~~SAT~  310 (503)
                      +...+.+.+......    -+|||||+|.+. ..    .+...+..++..... ....++++++-
T Consensus       105 ~l~~~~~~l~~~~~~----~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~v~~~S~  165 (234)
T PF01637_consen  105 ALERLLEKLKKKGKK----VIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLSQQNVSIVITGSS  165 (234)
T ss_dssp             -HHHHHHHHHHCHCC----EEEEEETGGGGGBCTTTTHHHHHHHHHHHHH----TTEEEEEEESS
T ss_pred             HHHHHHHHHHhcCCc----EEEEEecHHHHhhcccchHHHHHHHHHHHhhccccCCceEEEECCc
Confidence            334455555542211    689999999988 21    345556666666322 22344456654

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=92.84  E-value=0.14  Score=35.72  Aligned_cols=25  Identities=32%  Similarity=0.411  Sum_probs=18.7

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCV  184 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~  184 (503)
                      |+..++.|++|+|||+.  +-++..++
T Consensus        23 g~~tli~G~nGsGKSTl--lDAi~~~L   47 (62)
T PF13555_consen   23 GDVTLITGPNGSGKSTL--LDAIQTVL   47 (62)
T ss_pred             CcEEEEECCCCCCHHHH--HHHHHHHH
Confidence            45699999999999983  55555443

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=92.83  E-value=0.17  Score=52.55  Aligned_cols=39  Identities=13%  Similarity=0.152  Sum_probs=23.5

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+.+++||||||.|... -...+.+.+...++...+|+++
T Consensus       118 ~~~KVIIIDEad~Lt~~-A~NaLLKtLEEPp~~tvfIL~T  156 (605)
T PRK05896        118 FKYKVYIIDEAHMLSTS-AWNALLKTLEEPPKHVVFIFAT  156 (605)
T ss_pred             CCcEEEEEechHhCCHH-HHHHHHHHHHhCCCcEEEEEEC
Confidence            45789999999977432 2344555555555555444433

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

Probab=92.83  E-value=0.36  Score=50.11  Aligned_cols=68  Identities=31%  Similarity=0.516  Sum_probs=56.1

Q ss_pred             EEEEEcchhhHHHHHHHHHHC-----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-----cccccC-CCCCCCCE
Q 010709          377 TIVFVERKTRCDEVSEALVAE-----GLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-----DVASRG-LDVMGVAH  445 (503)
Q Consensus       377 ~lIF~~~~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-----~~~~~G-ldip~v~~  445 (503)
                      +||.++|++.|.++++.+...     ++.+..++||.+...+...++   .| .+|||+|     +.+.+| +++..+.+
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~---~~-~~ivVaTPGRllD~i~~~~l~l~~v~~  177 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK---RG-VDIVVATPGRLLDLIKRGKLDLSGVET  177 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh---cC-CCEEEECccHHHHHHHcCCcchhhcCE
Confidence            899999999999998888653     577899999999877775554   46 9999999     467777 88999998


Q ss_pred             EEE
Q 010709          446 VVN  448 (503)
Q Consensus       446 VI~  448 (503)
                      +|.
T Consensus       178 lVl  180 (513)
T COG0513         178 LVL  180 (513)
T ss_pred             EEe
Confidence            884

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=92.77  E-value=0.095  Score=49.07  Aligned_cols=27  Identities=30%  Similarity=0.324  Sum_probs=19.0

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      ...|+++.||||||||+.+  --|..++.
T Consensus        96 ~KSNILLiGPTGsGKTlLA--qTLAk~Ln  122 (408)
T COG1219          96 SKSNILLIGPTGSGKTLLA--QTLAKILN  122 (408)
T ss_pred             eeccEEEECCCCCcHHHHH--HHHHHHhC
Confidence            4457999999999999743  23444443

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

Probab=92.76  E-value=0.3  Score=46.97  Aligned_cols=55  Identities=20%  Similarity=0.212  Sum_probs=35.2

Q ss_pred             CCcHHHHH-HHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          143 RPTSIQAQ-AMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       143 ~~~~~Q~~-~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      .+.+.|.. .+.++.++++++++|+||+|||+. +.+++..+-.        ..+++.+=-+.++
T Consensus       127 t~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~Ip~--------~~rivtIEdt~E~  182 (312)
T COG0630         127 TISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFIPP--------EERIVTIEDTPEL  182 (312)
T ss_pred             CCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhCCc--------hhcEEEEeccccc
Confidence            44555554 445556788999999999999984 3444444322        3446666566555

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.75  E-value=0.33  Score=47.58  Aligned_cols=43  Identities=21%  Similarity=0.226  Sum_probs=25.6

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      .+..++++||||||||+.. ..++.++...      .+.+++.+-...+.
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~~------~~~~i~tiEdp~E~  163 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINKN------AAGHIITIEDPIEY  163 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCcC------CCCEEEEEcCChhh
Confidence            3567999999999999853 3344433211      13455655544443

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=92.68  E-value=0.42  Score=46.59  Aligned_cols=64  Identities=19%  Similarity=0.183  Sum_probs=38.8

Q ss_pred             HHHHHHHCCCCCCcHHHHHHHHHHh-cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          132 IMKDIEFHEYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       132 l~~~l~~~~~~~~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      -+..+...|+  ..+.+.+.+..+. .+++++++|+||+|||+.  +.++.....       ...+++++-.+.||
T Consensus       153 tl~~l~~~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTl--l~al~~~i~-------~~~riv~iEd~~El  217 (340)
T TIGR03819       153 TLDELVASGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTL--LSALLALVA-------PDERIVLVEDAAEL  217 (340)
T ss_pred             CHHHHHHcCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHH--HHHHHccCC-------CCCcEEEECCccee
Confidence            3455555554  3455666666554 566899999999999983  223322221       13456666666666

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.

>PRK09087 hypothetical protein; Validated

Probab=92.66  E-value=0.32  Score=44.49  Aligned_cols=42  Identities=14%  Similarity=0.109  Sum_probs=24.7

Q ss_pred             cEEEecchhHHhhCCCHHHHHHHHHhCCC-CCcEEEEEeeCCHHH
Q 010709          271 SFVILDEADRMLDMGFEPQIREVMQNLPD-KHQTLLFSATMPVEI  314 (503)
Q Consensus       271 ~~vViDEaH~l~~~~~~~~~~~il~~~~~-~~q~i~~SAT~~~~~  314 (503)
                      ++|+||++|.+.  .....+..++..+.. ..++|+.|.+.|...
T Consensus        89 ~~l~iDDi~~~~--~~~~~lf~l~n~~~~~g~~ilits~~~p~~~  131 (226)
T PRK09087         89 GPVLIEDIDAGG--FDETGLFHLINSVRQAGTSLLMTSRLWPSSW  131 (226)
T ss_pred             CeEEEECCCCCC--CCHHHHHHHHHHHHhCCCeEEEECCCChHHh
Confidence            389999999652  234556666665544 444444444455443

>PRK08006 replicative DNA helicase; Provisional

Probab=92.61  E-value=1.5  Score=44.85  Aligned_cols=18  Identities=22%  Similarity=0.171  Sum_probs=14.6

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      |.=++|.|.+|.|||.-+
T Consensus       224 G~LiiIaarPgmGKTafa  241 (471)
T PRK08006        224 SDLIIVAARPSMGKTTFA  241 (471)
T ss_pred             CcEEEEEeCCCCCHHHHH
Confidence            344899999999999754

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=92.58  E-value=2.9  Score=40.69  Aligned_cols=41  Identities=15%  Similarity=0.246  Sum_probs=27.5

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEe
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA  308 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SA  308 (503)
                      ....+++||||+|+|... -.+.+.+.+..-++...+|+.+.
T Consensus       108 ~~~~kvviI~~a~~~~~~-a~NaLLK~LEEPp~~~~~Il~t~  148 (329)
T PRK08058        108 ESNKKVYIIEHADKMTAS-AANSLLKFLEEPSGGTTAILLTE  148 (329)
T ss_pred             ccCceEEEeehHhhhCHH-HHHHHHHHhcCCCCCceEEEEeC
Confidence            457899999999987533 34556666666566665555443

>PRK08506 replicative DNA helicase; Provisional

Probab=92.58  E-value=0.83  Score=46.84  Aligned_cols=49  Identities=18%  Similarity=0.168  Sum_probs=27.9

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      .|.-++|.|.||.|||..+ +-+.......       +..++++.. ..-..|+..++
T Consensus       191 ~G~LivIaarpg~GKT~fa-l~ia~~~~~~-------g~~V~~fSl-EMs~~ql~~Rl  239 (472)
T PRK08506        191 KGDLIIIAARPSMGKTTLC-LNMALKALNQ-------DKGVAFFSL-EMPAEQLMLRM  239 (472)
T ss_pred             CCceEEEEcCCCCChHHHH-HHHHHHHHhc-------CCcEEEEeC-cCCHHHHHHHH
Confidence            3445899999999999754 3344443332       445666643 22334444433

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=92.53  E-value=0.43  Score=47.62  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||+.+
T Consensus       166 ~gvLL~GppGtGKT~lA  182 (389)
T PRK03992        166 KGVLLYGPPGTGKTLLA  182 (389)
T ss_pred             CceEEECCCCCChHHHH
Confidence            46999999999999753

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=92.45  E-value=0.78  Score=48.95  Aligned_cols=40  Identities=15%  Similarity=0.186  Sum_probs=23.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+.+++||||||.|... -...+.+.+...++...+|+.+
T Consensus       116 ~g~~KV~IIDEa~~LT~~-A~NALLKtLEEPP~~tifILaT  155 (725)
T PRK07133        116 QSKYKIYIIDEVHMLSKS-AFNALLKTLEEPPKHVIFILAT  155 (725)
T ss_pred             cCCCEEEEEEChhhCCHH-HHHHHHHHhhcCCCceEEEEEc
Confidence            467899999999977532 2334444455544444344433

>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=92.44  E-value=0.19  Score=47.48  Aligned_cols=43  Identities=21%  Similarity=0.291  Sum_probs=28.3

Q ss_pred             hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      ..+.+++++|+||||||+.. -.++.++...       ..+++++-...|+
T Consensus       125 ~~~~~ili~G~tGSGKTT~l-~all~~i~~~-------~~~iv~iEd~~E~  167 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLL-NALLEEIPPE-------DERIVTIEDPPEL  167 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHH-HHHHHHCHTT-------TSEEEEEESSS-S
T ss_pred             ccceEEEEECCCccccchHH-HHHhhhcccc-------ccceEEeccccce
Confidence            35678999999999999854 4444443221       3567777766665

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 ....

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.42  E-value=1  Score=49.21  Aligned_cols=18  Identities=28%  Similarity=0.383  Sum_probs=15.3

Q ss_pred             cCCCeEEEccCCCchhHH
Q 010709          157 SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~  174 (503)
                      .++.+++.||+|+|||+.
T Consensus       211 ~~~giLL~GppGtGKT~l  228 (733)
T TIGR01243       211 PPKGVLLYGPPGTGKTLL  228 (733)
T ss_pred             CCceEEEECCCCCChHHH
Confidence            356799999999999974

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.41  E-value=0.92  Score=46.76  Aligned_cols=60  Identities=18%  Similarity=0.246  Sum_probs=38.6

Q ss_pred             HHHHHHhc-----CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          150 QAMPVALS-----GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       150 ~~i~~i~~-----~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..+..++.     |.-++|.||+|+|||+..+. ++.....       ++.+++|+. ..|-..|+.+.++.++
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~-f~~~~~~-------~ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSK-FLENACA-------NKERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHH-HHHHHHH-------CCCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            34555554     45699999999999985433 2222222       255688877 4466677777777765

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.

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=92.41  E-value=1.4  Score=41.99  Aligned_cols=56  Identities=16%  Similarity=0.215  Sum_probs=31.8

Q ss_pred             HHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC---CCCCcEEEEEeeC
Q 010709          255 RFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL---PDKHQTLLFSATM  310 (503)
Q Consensus       255 ~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~---~~~~q~i~~SAT~  310 (503)
                      .|+..+..+...-+.--+.|+||+|-.........+..++..-   +.++-++++|.-+
T Consensus       123 ~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrl  181 (408)
T KOG2228|consen  123 KLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRL  181 (408)
T ss_pred             HHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccc
Confidence            3455555433322222467889999766665555555555433   3455577777665

>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=92.35  E-value=1.7  Score=42.85  Aligned_cols=146  Identities=20%  Similarity=0.170  Sum_probs=60.5

Q ss_pred             EEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH-HHHHHHHH---HHHHHhccCCCceEEEEECCccHHH
Q 010709          162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR-ELAQQIEK---EVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       162 ii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr-~La~q~~~---~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      ++.++-|+|||......++.++...+.     ...++++ |+. .+...+.+   .+..+.................   
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~-----~~~vi~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---   71 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP-----GRRVIIA-STYRQARDIFGRFWKGIIELLPSWFEIKFNEWNDRKI---   71 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS-------EEEEE-ESSHHHHHHHHHHHHHHHHTS-TTTS--EEEE-SSEE---
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC-----CcEEEEe-cCHHHHHHHHHHhHHHHHHHHHHhcCcccccCCCCcE---
Confidence            578899999999877767777666421     2344444 665 44444333   2223322211111110011100   


Q ss_pred             HHHHhhCCCcEEEECcHHH--HHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC--CHH
Q 010709          238 QRSELRGGVSIVVATPGRF--LDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM--PVE  313 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l--~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~--~~~  313 (503)
                         .+.++..|.+.+.+.-  ..-+.     =..+++|++||+-.+.+..+...+........... .+..|.|+  ...
T Consensus        72 ---~~~nG~~i~~~~~~~~~~~~~~~-----G~~~~~i~iDE~~~~~~~~~~~~~~~~~~~~~~~~-~~~~s~p~~~~~~  142 (384)
T PF03237_consen   72 ---ILPNGSRIQFRGADSPDSGDNIR-----GFEYDLIIIDEAAKVPDDAFSELIRRLRATWGGSI-RMYISTPPNPGGW  142 (384)
T ss_dssp             ---EETTS-EEEEES-----SHHHHH-----TS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT---EEEEEE---SSSH
T ss_pred             ---EecCceEEEEecccccccccccc-----ccccceeeeeecccCchHHHHHHHHhhhhcccCcc-eEEeecCCCCCCc
Confidence               0134455666663321  11111     14678999999875543323333333333332222 22444433  334


Q ss_pred             HHHHHHHhcCCC
Q 010709          314 IEALAQEYLTDP  325 (503)
Q Consensus       314 ~~~~~~~~~~~~  325 (503)
                      ...+......+.
T Consensus       143 ~~~~~~~~~~~~  154 (384)
T PF03237_consen  143 FYEIFQRNLDDD  154 (384)
T ss_dssp             HHHHHHHHHCTS
T ss_pred             eeeeeehhhcCC
Confidence            445555555544

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=92.33  E-value=0.7  Score=51.93  Aligned_cols=43  Identities=12%  Similarity=0.373  Sum_probs=32.9

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      .--+||||++|.+-+......+..++...++...+|+.|-+.|
T Consensus       121 ~~~~lvlDD~h~~~~~~~~~~l~~l~~~~~~~~~lv~~sR~~~  163 (903)
T PRK04841        121 QPLYLVIDDYHLITNPEIHEAMRFFLRHQPENLTLVVLSRNLP  163 (903)
T ss_pred             CCEEEEEeCcCcCCChHHHHHHHHHHHhCCCCeEEEEEeCCCC
Confidence            3458999999987544456678888888888888888887643

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=92.32  E-value=0.4  Score=46.70  Aligned_cols=17  Identities=29%  Similarity=0.296  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||..+
T Consensus        52 ~~~ll~GppG~GKT~la   68 (328)
T PRK00080         52 DHVLLYGPPGLGKTTLA   68 (328)
T ss_pred             CcEEEECCCCccHHHHH
Confidence            46999999999999754

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=92.29  E-value=0.26  Score=47.51  Aligned_cols=17  Identities=35%  Similarity=0.339  Sum_probs=14.3

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||..+
T Consensus        31 ~~~ll~Gp~G~GKT~la   47 (305)
T TIGR00635        31 DHLLLYGPPGLGKTTLA   47 (305)
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35999999999999743

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=92.22  E-value=1.8  Score=42.59  Aligned_cols=95  Identities=17%  Similarity=0.142  Sum_probs=47.5

Q ss_pred             CCCCCCcccCCCHHHHHHHHHHcCceEEecCCCCCCC---CCcCCcccC-CCCHHHHHHHHHC-CCCCCcHHHHHHHHH-
Q 010709           81 NWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAP---APIESFTDM-CLHPSIMKDIEFH-EYTRPTSIQAQAMPV-  154 (503)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~---~~~~~~~~~-~l~~~l~~~l~~~-~~~~~~~~Q~~~i~~-  154 (503)
                      .|.+.+.-.=.++.++..+..+.+..+.+....+..-   .++...+.. +.+++-...-..+ ....++|.++..+.. 
T Consensus        71 ~y~~~~~d~yvs~~~ir~~~lr~gd~v~g~~r~~~~~e~~~~l~~v~~vng~~~~~~~~r~~f~~l~p~~p~~R~~le~~  150 (416)
T PRK09376         71 NYLPGPDDIYVSPSQIRRFNLRTGDTVEGKIRPPKEGERYFALLKVETVNGEDPEKARNRPLFENLTPLYPNERLRLETG  150 (416)
T ss_pred             CCCCCCCCeeeCHHHHHhcCCCCCCEEEEEeeCCCCCCCccceEEEeeeCCCCHHHhcCCCCcccCCCCChhhcccccCC
Confidence            3444444444667778888777777776543211000   011111111 2333333222111 223334444443332 


Q ss_pred             ------------H---hcCCCeEEEccCCCchhHHh
Q 010709          155 ------------A---LSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       155 ------------i---~~~~~vii~~~TGsGKTl~~  175 (503)
                                  +   -.|+..+|.||.|+|||+..
T Consensus       151 ~~~~~~~rvID~l~PIGkGQR~lIvgppGvGKTTLa  186 (416)
T PRK09376        151 NPEDLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVLL  186 (416)
T ss_pred             CCcccceeeeeeecccccCceEEEeCCCCCChhHHH
Confidence                        2   25788999999999999743

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=92.21  E-value=0.11  Score=54.43  Aligned_cols=50  Identities=24%  Similarity=0.159  Sum_probs=40.1

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++++.||||+|||..+++|-+...          +.-++|+=|.-|+....+...++.+
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~----------~~S~VV~DpKGEl~~~Ta~~R~~~G  208 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW----------EDSVVVHDIKLENYELTSGWREKQG  208 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC----------CCCEEEEeCcHHHHHHHHHHHHHCC
Confidence            4699999999999999999988652          2337777799999988877776654

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.20  E-value=0.52  Score=49.89  Aligned_cols=42  Identities=12%  Similarity=0.239  Sum_probs=26.3

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      .+.+.+++||||+|.|... -...+.+.+...+.... +++.+|
T Consensus       118 ~~~~~KVvIIdea~~Ls~~-a~naLLK~LEepp~~ti-fIL~tt  159 (614)
T PRK14971        118 QIGKYKIYIIDEVHMLSQA-AFNAFLKTLEEPPSYAI-FILATT  159 (614)
T ss_pred             ccCCcEEEEEECcccCCHH-HHHHHHHHHhCCCCCeE-EEEEeC
Confidence            3567899999999987532 23445566666555453 444444

>PHA00012 I assembly protein

Probab=92.05  E-value=2  Score=40.94  Aligned_cols=54  Identities=11%  Similarity=0.225  Sum_probs=29.8

Q ss_pred             CCCccEEEecchhHHhhC-CCH----HHHHHHHHhCCC-CCcEEEEEeeCCHHHHHHHHHh
Q 010709          267 LSRVSFVILDEADRMLDM-GFE----PQIREVMQNLPD-KHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~-~~~----~~~~~il~~~~~-~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                      ..+-.++|+||||..++. .+.    ..+.+.+...++ ..-++++|-.+ ..+...++..
T Consensus        79 ep~gsLlVlDEaq~~fp~R~~~sk~p~~vie~l~~hRh~G~DvilITQ~p-s~VDs~IR~l  138 (361)
T PHA00012         79 ESKNGLLVLDECGTWFNSRSWNDKERQPVIDWFLHARKLGWDIIFIIQDI-SIMDKQAREA  138 (361)
T ss_pred             CCCCcEEEEECcccccCCCCcCcCCcHHHHHHHHHhccCCceEEEEcCCH-HHHhHHHHHh
Confidence            356679999999987753 222    334554444433 34455555444 3455445433

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.01  E-value=0.89  Score=46.70  Aligned_cols=41  Identities=15%  Similarity=0.280  Sum_probs=23.4

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      ..+.+++||||||.+.... ...+.+.+...++.. ++++.+|
T Consensus       117 ~~~~KVvIIDEad~Lt~~a-~naLLk~LEepp~~~-v~Il~tt  157 (486)
T PRK14953        117 KGKYKVYIIDEAHMLTKEA-FNALLKTLEEPPPRT-IFILCTT  157 (486)
T ss_pred             cCCeeEEEEEChhhcCHHH-HHHHHHHHhcCCCCe-EEEEEEC
Confidence            4578999999999775322 233444444444444 3334333

>PRK05748 replicative DNA helicase; Provisional

Probab=91.91  E-value=1.3  Score=45.16  Aligned_cols=50  Identities=14%  Similarity=0.139  Sum_probs=27.9

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      .|.-++|.|+||.|||.-. +-++......      .+..++++.. ..-..|+..++
T Consensus       202 ~G~livIaarpg~GKT~~a-l~ia~~~a~~------~g~~v~~fSl-Ems~~~l~~R~  251 (448)
T PRK05748        202 PNDLIIVAARPSVGKTAFA-LNIAQNVATK------TDKNVAIFSL-EMGAESLVMRM  251 (448)
T ss_pred             CCceEEEEeCCCCCchHHH-HHHHHHHHHh------CCCeEEEEeC-CCCHHHHHHHH
Confidence            3445899999999999754 4444443321      1345666542 23334444444

>PRK05973 replicative DNA helicase; Provisional

Probab=91.89  E-value=0.39  Score=44.02  Aligned_cols=66  Identities=18%  Similarity=0.184  Sum_probs=38.1

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++|. .+..--+..|.-++|.|++|+|||+..+-.+. ....+       |.+++|+.-- +-..|+.+++..++
T Consensus        50 ~~~p~-~~l~GGl~~Gsl~LIaG~PG~GKT~lalqfa~-~~a~~-------Ge~vlyfSlE-es~~~i~~R~~s~g  115 (237)
T PRK05973         50 ATTPA-EELFSQLKPGDLVLLGARPGHGKTLLGLELAV-EAMKS-------GRTGVFFTLE-YTEQDVRDRLRALG  115 (237)
T ss_pred             CCCCH-HHhcCCCCCCCEEEEEeCCCCCHHHHHHHHHH-HHHhc-------CCeEEEEEEe-CCHHHHHHHHHHcC
Confidence            34552 22333444566799999999999985533333 22222       4557777532 22456666666653

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=91.87  E-value=1.6  Score=45.83  Aligned_cols=39  Identities=26%  Similarity=0.540  Sum_probs=26.5

Q ss_pred             hhCCCcEEE-ECcHHHHHHHHcCCCCCCCccEEEecchhHHhh
Q 010709          242 LRGGVSIVV-ATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD  283 (503)
Q Consensus       242 ~~~~~~Ilv-~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~  283 (503)
                      +++..+-.| +-||++.+.+.+-...   --++.|||+|.+..
T Consensus       480 IkGHRRTYVGAMPGkiIq~LK~v~t~---NPliLiDEvDKlG~  519 (906)
T KOG2004|consen  480 IKGHRRTYVGAMPGKIIQCLKKVKTE---NPLILIDEVDKLGS  519 (906)
T ss_pred             hcccceeeeccCChHHHHHHHhhCCC---CceEEeehhhhhCC
Confidence            334344444 4699999999874332   23899999998873

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=91.83  E-value=0.36  Score=44.75  Aligned_cols=18  Identities=33%  Similarity=0.252  Sum_probs=16.4

Q ss_pred             hcCCCeEEEccCCCchhH
Q 010709          156 LSGRDLLGCAETGSGKTA  173 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl  173 (503)
                      -.|+.++|.|+.|+|||+
T Consensus        14 ~~Gqr~~I~G~~G~GKTT   31 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTT   31 (249)
T ss_pred             CCCCEEEEECCCCCCHHH
Confidence            478889999999999997

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=91.83  E-value=0.29  Score=50.21  Aligned_cols=37  Identities=19%  Similarity=0.210  Sum_probs=25.3

Q ss_pred             cHHHHHHHHHHhcCC--CeEEEccCCCchhHHhHHHHHHH
Q 010709          145 TSIQAQAMPVALSGR--DLLGCAETGSGKTAAFTIPMIQH  182 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~--~vii~~~TGsGKTl~~~lp~l~~  182 (503)
                      .+-|.+.+..+....  -++++||||||||+.. ..++..
T Consensus       227 ~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~  265 (486)
T TIGR02533       227 SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSR  265 (486)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhc
Confidence            455677777666543  3789999999999853 334444

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=91.82  E-value=0.27  Score=47.39  Aligned_cols=20  Identities=35%  Similarity=0.449  Sum_probs=17.1

Q ss_pred             HhcCCCeEEEccCCCchhHH
Q 010709          155 ALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~  174 (503)
                      +..+.+++++|+||+|||+.
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            34678899999999999983

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=91.74  E-value=0.32  Score=51.02  Aligned_cols=38  Identities=24%  Similarity=0.195  Sum_probs=26.2

Q ss_pred             cHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHH
Q 010709          145 TSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      .+.|.+.+..+...  .-++++||||||||+.. ..++.++
T Consensus       301 ~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~  340 (564)
T TIGR02538       301 EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNIL  340 (564)
T ss_pred             CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhh
Confidence            45566667665543  44899999999999864 4455554

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.

>COG4185 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.71  E-value=1  Score=37.95  Aligned_cols=17  Identities=24%  Similarity=0.417  Sum_probs=14.3

Q ss_pred             eEEEccCCCchhHHhHH
Q 010709          161 LLGCAETGSGKTAAFTI  177 (503)
Q Consensus       161 vii~~~TGsGKTl~~~l  177 (503)
                      .|+.||.|+|||..|..
T Consensus         5 ~IvaG~NGsGKstv~~~   21 (187)
T COG4185           5 DIVAGPNGSGKSTVYAS   21 (187)
T ss_pred             EEEecCCCCCceeeeec
Confidence            57889999999997754

>cd01131 PilT Pilus retraction ATPase PilT

Probab=91.70  E-value=0.27  Score=43.96  Aligned_cols=22  Identities=36%  Similarity=0.504  Sum_probs=16.2

Q ss_pred             eEEEccCCCchhHHhHHHHHHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      ++++||||||||+.. ..++.++
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~   25 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYI   25 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHh
Confidence            789999999999853 3344443

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

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

Probab=91.68  E-value=0.5  Score=49.11  Aligned_cols=74  Identities=16%  Similarity=0.249  Sum_probs=62.1

Q ss_pred             CcEEEEEcchhhHHHHHH----HHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-cccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSE----ALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-DVASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~----~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-~~~~~Gldip~v~~VI~  448 (503)
                      .++..-++|.--|++.+.    .|...|+.|..+.|.+..++|.++++...+|+++++|.| -++...+++.++.+||.
T Consensus       312 ~Q~ALMAPTEILA~QH~~~~~~~l~~~~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd~V~F~~LgLVIi  390 (677)
T COG1200         312 YQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLVII  390 (677)
T ss_pred             CeeEEeccHHHHHHHHHHHHHHHhhhcCCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhcceeecceeEEEE
Confidence            358889999666655544    455569999999999999999999999999999999999 56678899988888774

>TIGR00665 DnaB replicative DNA helicase

Probab=91.66  E-value=1.4  Score=44.85  Aligned_cols=38  Identities=16%  Similarity=0.234  Sum_probs=23.3

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|.-++|.|++|+|||... +-+..+....      .+..++++.
T Consensus       194 ~G~l~vi~g~pg~GKT~~~-l~~a~~~a~~------~g~~vl~~S  231 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFA-LNIAENAAIK------EGKPVAFFS  231 (434)
T ss_pred             CCeEEEEEeCCCCChHHHH-HHHHHHHHHh------CCCeEEEEe
Confidence            3445899999999999744 3333333321      134566665

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.

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=91.61  E-value=0.41  Score=48.18  Aligned_cols=69  Identities=19%  Similarity=0.289  Sum_probs=54.9

Q ss_pred             cEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----ccccCC----CCCC
Q 010709          376 LTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VASRGL----DVMG  442 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~~Gl----dip~  442 (503)
                      -.|||.++++.+-++.++|...    ++.+..+.|||....+++++++    ...|+|||.     +++.+=    ++..
T Consensus       265 ~~LV~tPTRELa~QV~~Hl~ai~~~t~i~v~si~GGLavqKQqRlL~~----~p~IVVATPGRlweli~e~n~~l~~~k~  340 (731)
T KOG0347|consen  265 IALVVTPTRELAHQVKQHLKAIAEKTQIRVASITGGLAVQKQQRLLNQ----RPDIVVATPGRLWELIEEDNTHLGNFKK  340 (731)
T ss_pred             eeEEecChHHHHHHHHHHHHHhccccCeEEEEeechhHHHHHHHHHhc----CCCEEEecchHHHHHHHhhhhhhhhhhh
Confidence            3899999999999999999764    8899999999999999999987    678999994     222221    3556


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      ++++|.
T Consensus       341 vkcLVl  346 (731)
T KOG0347|consen  341 VKCLVL  346 (731)
T ss_pred             ceEEEE
Confidence            666553

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=91.57  E-value=0.62  Score=48.69  Aligned_cols=16  Identities=25%  Similarity=0.316  Sum_probs=14.1

Q ss_pred             eEEEccCCCchhHHhH
Q 010709          161 LLGCAETGSGKTAAFT  176 (503)
Q Consensus       161 vii~~~TGsGKTl~~~  176 (503)
                      .+++||.|+|||.++.
T Consensus        41 yLf~Gp~G~GKTt~Ar   56 (563)
T PRK06647         41 YIFSGPRGVGKTSSAR   56 (563)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7899999999998653

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

Probab=91.55  E-value=1.6  Score=39.84  Aligned_cols=22  Identities=36%  Similarity=0.342  Sum_probs=17.2

Q ss_pred             HhcCC-CeEEEccCCCchhHHhH
Q 010709          155 ALSGR-DLLGCAETGSGKTAAFT  176 (503)
Q Consensus       155 i~~~~-~vii~~~TGsGKTl~~~  176 (503)
                      +..|+ -+.++|+-|||||...-
T Consensus        47 i~d~qg~~~vtGevGsGKTv~~R   69 (269)
T COG3267          47 IADGQGILAVTGEVGSGKTVLRR   69 (269)
T ss_pred             HhcCCceEEEEecCCCchhHHHH
Confidence            34555 58999999999998654

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.53  E-value=0.16  Score=49.22  Aligned_cols=16  Identities=38%  Similarity=0.532  Sum_probs=14.4

Q ss_pred             CCeEEEccCCCchhHH
Q 010709          159 RDLLGCAETGSGKTAA  174 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~  174 (503)
                      +|++..||+|+|||+.
T Consensus       385 RNilfyGPPGTGKTm~  400 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMF  400 (630)
T ss_pred             hheeeeCCCCCCchHH
Confidence            5899999999999974

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=91.45  E-value=0.8  Score=46.13  Aligned_cols=69  Identities=16%  Similarity=0.189  Sum_probs=37.7

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHH----HHh---cC-----CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCC
Q 010709          126 MCLHPSIMKDIEFHEYTRPTSIQAQAMP----VAL---SG-----RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGD  193 (503)
Q Consensus       126 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~----~i~---~~-----~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~  193 (503)
                      ++.+++-++.....|.-.-.+.-.+.+.    .+.   +.     ..+++.||.|+|||..  .+-+...        ..
T Consensus       494 FG~see~l~~~~~~Gmi~~g~~v~~il~~G~llv~qvk~s~~s~lvSvLl~Gp~~sGKTaL--AA~iA~~--------S~  563 (744)
T KOG0741|consen  494 FGISEEDLERFVMNGMINWGPPVTRILDDGKLLVQQVKNSERSPLVSVLLEGPPGSGKTAL--AAKIALS--------SD  563 (744)
T ss_pred             cCCCHHHHHHHHhCCceeecccHHHHHhhHHHHHHHhhccccCcceEEEEecCCCCChHHH--HHHHHhh--------cC
Confidence            3666666666666654332222222221    111   11     2489999999999953  2222221        23


Q ss_pred             CCeEEEEcccH
Q 010709          194 GPLALVLAPTR  204 (503)
Q Consensus       194 ~~~~lil~Ptr  204 (503)
                      .|.+=++.|..
T Consensus       564 FPFvKiiSpe~  574 (744)
T KOG0741|consen  564 FPFVKIISPED  574 (744)
T ss_pred             CCeEEEeChHH
Confidence            57777777764

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

Probab=91.45  E-value=0.093  Score=45.87  Aligned_cols=44  Identities=25%  Similarity=0.279  Sum_probs=29.2

Q ss_pred             HHhhCCCcEEEECcHHHHHHHHcCCC--CCCCccEEEecchhHHhh
Q 010709          240 SELRGGVSIVVATPGRFLDHLQQGNT--SLSRVSFVILDEADRMLD  283 (503)
Q Consensus       240 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~--~l~~~~~vViDEaH~l~~  283 (503)
                      +.....++|+|++...|++......+  ...+-.+|||||||.+.+
T Consensus       114 r~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~  159 (174)
T PF06733_consen  114 RELAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLED  159 (174)
T ss_dssp             HHCGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGG
T ss_pred             HHhcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHH
Confidence            44456699999999988765443322  123457999999998754

RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.

>PHA00350 putative assembly protein

Probab=91.45  E-value=1.7  Score=43.10  Aligned_cols=17  Identities=18%  Similarity=0.069  Sum_probs=14.0

Q ss_pred             eEEEccCCCchhHHhHH
Q 010709          161 LLGCAETGSGKTAAFTI  177 (503)
Q Consensus       161 vii~~~TGsGKTl~~~l  177 (503)
                      .++.|..|||||+.++-
T Consensus         4 ~l~tG~pGSGKT~~aV~   20 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVV   20 (399)
T ss_pred             EEEecCCCCchhHHHHH
Confidence            47899999999986654

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

Probab=91.41  E-value=1.4  Score=44.85  Aligned_cols=145  Identities=13%  Similarity=0.091  Sum_probs=81.4

Q ss_pred             CCcHHHHHHHHHHh------cC----CCeEEEccCCCchhHHhH-HHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHH
Q 010709          143 RPTSIQAQAMPVAL------SG----RDLLGCAETGSGKTAAFT-IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIE  211 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~------~~----~~vii~~~TGsGKTl~~~-lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~  211 (503)
                      .+-|+|.-.+-.++      .|    +.++|..|=+-|||..+. +.+...+..+     ..+..+.|++|+.+-+.+.+
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~-----~~~~~~~i~A~s~~qa~~~F  135 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNW-----RSGAGIYILAPSVEQAANSF  135 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhh-----hcCCcEEEEeccHHHHHHhh
Confidence            56789999998887      12    247899999999997433 2122222222     34677899999999888888


Q ss_pred             HHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHH---HHHHHHc--CCCCCCCccEEEecchhHHhhCCC
Q 010709          212 KEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGR---FLDHLQQ--GNTSLSRVSFVILDEADRMLDMGF  286 (503)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~---l~~~l~~--~~~~l~~~~~vViDEaH~l~~~~~  286 (503)
                      ..++.......++...              .....+-...+...   ....+..  +...-.+..+.|+||.|...+.+ 
T Consensus       136 ~~ar~mv~~~~~l~~~--------------~~~q~~s~~i~~~~~~s~ik~~aa~~~~~Dg~~~~~~I~DEih~f~~~~-  200 (546)
T COG4626         136 NPARDMVKRDDDLRDL--------------CNVQTHSRTITHRKTDSTIKAVAADPNTVDGLNSVGAIIDELHLFGKQE-  200 (546)
T ss_pred             HHHHHHHHhCcchhhh--------------hccccceeEEEecccceeeeeeccCCCcccCCCcceEEEehhhhhcCHH-
Confidence            8887766443211111              11111111122211   1222222  12344567899999999765441 


Q ss_pred             HHHHHHHHHhC--CCCCcEEEEEe
Q 010709          287 EPQIREVMQNL--PDKHQTLLFSA  308 (503)
Q Consensus       287 ~~~~~~il~~~--~~~~q~i~~SA  308 (503)
                       ..+..+..-+  +++.+++..|.
T Consensus       201 -~~~~~~~~g~~ar~~~l~~~ITT  223 (546)
T COG4626         201 -DMYSEAKGGLGARPEGLVVYITT  223 (546)
T ss_pred             -HHHHHHHhhhccCcCceEEEEec
Confidence             3333333322  34555666664

>TIGR02012 tigrfam_recA protein RecA

Probab=91.38  E-value=0.42  Score=45.94  Aligned_cols=43  Identities=23%  Similarity=0.233  Sum_probs=27.7

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      .|+-+.|.||+|+|||+.+ +.++......       +..++++-.-..+-
T Consensus        54 ~G~iteI~G~~GsGKTtLa-L~~~~~~~~~-------g~~v~yId~E~~~~   96 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLA-LHAIAEAQKA-------GGTAAFIDAEHALD   96 (321)
T ss_pred             CCeEEEEECCCCCCHHHHH-HHHHHHHHHc-------CCcEEEEcccchhH
Confidence            4456899999999999865 3344443332       56677775544443

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.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=91.37  E-value=0.3  Score=53.49  Aligned_cols=61  Identities=21%  Similarity=0.289  Sum_probs=36.9

Q ss_pred             EECcHHHHHHHHcCCCCCCCccEEEecchhHHhh----------CCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          250 VATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD----------MGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       250 v~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~----------~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      |+.+++=++++... ..-.....+.+||.+-+.-          ......+..++.-++...|+++.+||..
T Consensus       345 vgEaERqlrllFee-A~k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqVvvigATnR  415 (1080)
T KOG0732|consen  345 VGEAERQLRLLFEE-AQKTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQVVVIGATNR  415 (1080)
T ss_pred             cCcHHHHHHHHHHH-HhccCceEEeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCceEEEcccCC
Confidence            55666555555431 2234577899999992211          1123344555556677889999999963

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=91.25  E-value=1.8  Score=45.45  Aligned_cols=94  Identities=23%  Similarity=0.331  Sum_probs=54.3

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ  238 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (503)
                      .=++++||+|.|||-                                |+..+++.+.+-       -+-.-.||.....+
T Consensus       351 pILcLVGPPGVGKTS--------------------------------LgkSIA~al~Rk-------fvR~sLGGvrDEAE  391 (782)
T COG0466         351 PILCLVGPPGVGKTS--------------------------------LGKSIAKALGRK-------FVRISLGGVRDEAE  391 (782)
T ss_pred             cEEEEECCCCCCchh--------------------------------HHHHHHHHhCCC-------EEEEecCccccHHH
Confidence            348899999999994                                334444444321       12334456544433


Q ss_pred             HHHhhCCCcEEE-ECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          239 RSELRGGVSIVV-ATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       239 ~~~~~~~~~Ilv-~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                         +++.-+-.| +-||++.+-+.+....   --++++||+|.|.....+.--..+|.-+
T Consensus       392 ---IRGHRRTYIGamPGrIiQ~mkka~~~---NPv~LLDEIDKm~ss~rGDPaSALLEVL  445 (782)
T COG0466         392 ---IRGHRRTYIGAMPGKIIQGMKKAGVK---NPVFLLDEIDKMGSSFRGDPASALLEVL  445 (782)
T ss_pred             ---hccccccccccCChHHHHHHHHhCCc---CCeEEeechhhccCCCCCChHHHHHhhc
Confidence               333333334 4699999888764321   2389999999987654333334444433

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=91.23  E-value=1.3  Score=43.71  Aligned_cols=16  Identities=31%  Similarity=0.351  Sum_probs=13.7

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      ..++.||.|+|||..+
T Consensus        38 ~~Ll~G~~G~GKt~~a   53 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIA   53 (355)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4789999999999754

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.

>TIGR00767 rho transcription termination factor Rho

Probab=91.13  E-value=1.1  Score=44.18  Aligned_cols=18  Identities=33%  Similarity=0.302  Sum_probs=16.3

Q ss_pred             cCCCeEEEccCCCchhHH
Q 010709          157 SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~  174 (503)
                      .|+.++|.||+|+|||+.
T Consensus       167 ~Gq~~~IvG~~g~GKTtL  184 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVL  184 (415)
T ss_pred             CCCEEEEECCCCCChhHH
Confidence            678899999999999974

Members of this family differ in the specificity of RNA binding.

>PRK14701 reverse gyrase; Provisional

Probab=91.12  E-value=0.73  Score=54.11  Aligned_cols=59  Identities=19%  Similarity=0.258  Sum_probs=52.6

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC------CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE------GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV  433 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~------~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~  433 (503)
                      .++||.+|+++-+.++++.|+..      ++.+..+||+++..++.++++.+.+|+.+|||+|.-
T Consensus       123 ~~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPg  187 (1638)
T PRK14701        123 KKCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQ  187 (1638)
T ss_pred             CeEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCc
Confidence            46999999999999999998863      467889999999999999999999999999999963

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

Probab=91.12  E-value=0.86  Score=48.18  Aligned_cols=34  Identities=32%  Similarity=0.444  Sum_probs=23.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK  300 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~  300 (503)
                      +++-.++|+|||..-+|......+.+.+..+.++
T Consensus       481 l~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~~  514 (567)
T COG1132         481 LRNPPILILDEATSALDTETEALIQDALKKLLKG  514 (567)
T ss_pred             hcCCCEEEEeccccccCHHhHHHHHHHHHHHhcC
Confidence            4555788889988777776666677666655444

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=91.11  E-value=6.4  Score=35.13  Aligned_cols=44  Identities=14%  Similarity=0.226  Sum_probs=28.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHH---HhCCCCCcEEEEEeeC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVM---QNLPDKHQTLLFSATM  310 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il---~~~~~~~q~i~~SAT~  310 (503)
                      ..+-+++|||=...+.-.+-...+...+   +.+-..-++|++|+-+
T Consensus       121 ~~~~dViIIDSls~~~~~~~~~~vl~fm~~~r~l~d~gKvIilTvhp  167 (235)
T COG2874         121 RWEKDVIIIDSLSAFATYDSEDAVLNFMTFLRKLSDLGKVIILTVHP  167 (235)
T ss_pred             hhcCCEEEEecccHHhhcccHHHHHHHHHHHHHHHhCCCEEEEEeCh
Confidence            5667899999988766554333343333   3333456799999876

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=91.10  E-value=0.76  Score=50.13  Aligned_cols=17  Identities=29%  Similarity=0.378  Sum_probs=14.3

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||+.+
T Consensus       488 ~giLL~GppGtGKT~la  504 (733)
T TIGR01243       488 KGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            45899999999999743

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.

>COG1485 Predicted ATPase [General function prediction only]

Probab=91.02  E-value=3.7  Score=39.48  Aligned_cols=110  Identities=15%  Similarity=0.198  Sum_probs=60.8

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ  238 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (503)
                      +-+-+.|+-|.|||.  ++-++-..+--.     .    -.-++.-.-...+.+++..+-            |.      
T Consensus        66 ~GlYl~GgVGrGKT~--LMD~Fy~~lp~~-----~----k~R~HFh~FM~~vH~~l~~l~------------g~------  116 (367)
T COG1485          66 RGLYLWGGVGRGKTM--LMDLFYESLPGE-----R----KRRLHFHRFMARVHQRLHTLQ------------GQ------  116 (367)
T ss_pred             ceEEEECCCCccHHH--HHHHHHhhCCcc-----c----cccccHHHHHHHHHHHHHHHc------------CC------
Confidence            458899999999995  454444322210     0    122344556666666666553            11      


Q ss_pred             HHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh-CCCCCcEEEEEeeCCHHHH
Q 010709          239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN-LPDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       239 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~-~~~~~q~i~~SAT~~~~~~  315 (503)
                             .+.+    ..+.+.+      ..+.+++.|||+| +.+-+-.-.+.+++.. +...+.+++.|-|.|+++.
T Consensus       117 -------~dpl----~~iA~~~------~~~~~vLCfDEF~-VtDI~DAMiL~rL~~~Lf~~GV~lvaTSN~~P~~LY  176 (367)
T COG1485         117 -------TDPL----PPIADEL------AAETRVLCFDEFE-VTDIADAMILGRLLEALFARGVVLVATSNTAPDNLY  176 (367)
T ss_pred             -------CCcc----HHHHHHH------HhcCCEEEeeeee-ecChHHHHHHHHHHHHHHHCCcEEEEeCCCChHHhc
Confidence                   1111    1111222      3457899999998 2222212224444443 3457888999999987754

>PRK09354 recA recombinase A; Provisional

Probab=90.92  E-value=0.59  Score=45.39  Aligned_cols=42  Identities=24%  Similarity=0.191  Sum_probs=27.6

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      |+-+.|.||+|+|||+..+. ++......       +..++|+-.-..+-
T Consensus        60 G~IteI~G~~GsGKTtLal~-~~~~~~~~-------G~~~~yId~E~s~~  101 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALH-AIAEAQKA-------GGTAAFIDAEHALD  101 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHH-HHHHHHHc-------CCcEEEECCccchH
Confidence            45688999999999986543 33333332       56678887555444

>TIGR00763 lon ATP-dependent protease La

Probab=90.91  E-value=2.8  Score=46.09  Aligned_cols=18  Identities=33%  Similarity=0.237  Sum_probs=14.9

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      +..+++.||+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            345999999999999743

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.

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

Probab=90.77  E-value=0.2  Score=50.82  Aligned_cols=45  Identities=16%  Similarity=0.188  Sum_probs=29.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHH
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~  315 (503)
                      ..+-++.|+|||-..++.+.+..+.+.++...    +-++|---.+.+.
T Consensus       586 y~kPk~AiLDE~TSAv~~dvE~~~Yr~~r~~g----iT~iSVgHRkSL~  630 (659)
T KOG0060|consen  586 YHKPKFAILDECTSAVTEDVEGALYRKCREMG----ITFISVGHRKSLW  630 (659)
T ss_pred             hcCCceEEeechhhhccHHHHHHHHHHHHHcC----CeEEEeccHHHHH
Confidence            45678899999998777766777777777654    4444444333333

>TIGR00602 rad24 checkpoint protein rad24

Probab=90.76  E-value=1.2  Score=47.00  Aligned_cols=17  Identities=35%  Similarity=0.503  Sum_probs=14.4

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +-+++.||+|+|||+.+
T Consensus       111 ~illL~GP~GsGKTTl~  127 (637)
T TIGR00602       111 RILLITGPSGCGKSTTI  127 (637)
T ss_pred             cEEEEECCCCCCHHHHH
Confidence            34999999999999854

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

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=90.69  E-value=0.2  Score=53.21  Aligned_cols=50  Identities=24%  Similarity=0.215  Sum_probs=37.6

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .+++++||||+|||..+++|-+...          +..+||+=|.-|+........++.+
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~~----------~gS~VV~DpKGE~~~~Ta~~R~~~G  189 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLTF----------KGSVIALDVKGELFELTSRARKASG  189 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhcC----------CCCEEEEeCCchHHHHHHHHHHhCC
Confidence            4799999999999999999987642          2346777788888776665555543

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

Probab=90.63  E-value=1.6  Score=43.76  Aligned_cols=69  Identities=22%  Similarity=0.385  Sum_probs=53.4

Q ss_pred             cEEEEEcchhhHHHHHHH---H-HHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc--ccc----cCCCCCCCCE
Q 010709          376 LTIVFVERKTRCDEVSEA---L-VAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD--VAS----RGLDVMGVAH  445 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~---L-~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~--~~~----~Gldip~v~~  445 (503)
                      -.+|.|++++.|.++...   | +..|++++++|||.+..++..-++    -...++|||.  ++.    .++|+..+.+
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~ygl~~v~~ygGgsk~eQ~k~Lk----~g~EivVaTPgRlid~VkmKatn~~rvS~  373 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAYGLRVVAVYGGGSKWEQSKELK----EGAEIVVATPGRLIDMVKMKATNLSRVSY  373 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhccceEEEeecCCcHHHHHHhhh----cCCeEEEechHHHHHHHHhhcccceeeeE
Confidence            368889999988877544   4 345899999999999988887776    3578999994  322    4788988888


Q ss_pred             EEE
Q 010709          446 VVN  448 (503)
Q Consensus       446 VI~  448 (503)
                      +|.
T Consensus       374 LV~  376 (731)
T KOG0339|consen  374 LVL  376 (731)
T ss_pred             EEE
Confidence            774

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=90.58  E-value=0.73  Score=43.15  Aligned_cols=37  Identities=11%  Similarity=0.046  Sum_probs=24.0

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|.-++|.|++|+|||+..+-.+. ....       .+.+++|+.
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~-~~a~-------~Ge~vlyis   71 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAV-TQAS-------RGNPVLFVT   71 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH-HHHh-------CCCcEEEEE
Confidence            455699999999999975433222 2222       245677777

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PRK04328 hypothetical protein; Provisional

Probab=90.53  E-value=0.54  Score=43.76  Aligned_cols=53  Identities=15%  Similarity=0.201  Sum_probs=31.8

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|..++|.|++|+|||+..+-.+... +..       +.+++|+. +.+-..++.+.++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~-~~~-------ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNG-LQM-------GEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH-Hhc-------CCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            45669999999999997543333332 222       45567776 3344445555555554

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=90.44  E-value=0.27  Score=46.17  Aligned_cols=27  Identities=26%  Similarity=0.251  Sum_probs=21.5

Q ss_pred             HHHHHHHhcCCCeEEEccCCCchhHHh
Q 010709          149 AQAMPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       149 ~~~i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      .+++..+..|+++++.||+|+|||..+
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA   38 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLA   38 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHH
Confidence            344555668889999999999999854

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=90.42  E-value=0.39  Score=43.98  Aligned_cols=35  Identities=17%  Similarity=0.242  Sum_probs=23.7

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      +++|.|++|||||.. ++-++..+...       ...+++++|
T Consensus        15 r~viIG~sGSGKT~l-i~~lL~~~~~~-------f~~I~l~t~   49 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTL-IKSLLYYLRHK-------FDHIFLITP   49 (241)
T ss_pred             eEEEECCCCCCHHHH-HHHHHHhhccc-------CCEEEEEec
Confidence            689999999999973 45555443332       355666667

This is thought to be an ATPase involved in viral DNA packaging [].

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=90.38  E-value=2.1  Score=39.17  Aligned_cols=17  Identities=29%  Similarity=0.425  Sum_probs=14.6

Q ss_pred             CCCeEEEccCCCchhHH
Q 010709          158 GRDLLGCAETGSGKTAA  174 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~  174 (503)
                      -+.++..||+|+|||+.
T Consensus       205 PKGvLmYGPPGTGKTlm  221 (424)
T KOG0652|consen  205 PKGVLMYGPPGTGKTLM  221 (424)
T ss_pred             CCceEeeCCCCCcHHHH
Confidence            35699999999999974

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=90.35  E-value=0.37  Score=48.03  Aligned_cols=45  Identities=31%  Similarity=0.459  Sum_probs=30.0

Q ss_pred             hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      ...+++++.|.||+|||.+ +-.++..+..+       +.+++|.=|.-+...
T Consensus        13 ~e~~~~li~G~~GsGKT~~-i~~ll~~~~~~-------g~~~iI~D~kg~~~~   57 (386)
T PF10412_consen   13 SENRHILIIGATGSGKTQA-IRHLLDQIRAR-------GDRAIIYDPKGEFTE   57 (386)
T ss_dssp             GGGG-EEEEE-TTSSHHHH-HHHHHHHHHHT-------T-EEEEEEETTHHHH
T ss_pred             hhhCcEEEECCCCCCHHHH-HHHHHHHHHHc-------CCEEEEEECCchHHH
Confidence            4678899999999999974 46777776664       445666666655544

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

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

Probab=90.25  E-value=1.2  Score=49.36  Aligned_cols=74  Identities=14%  Similarity=0.230  Sum_probs=65.9

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-cccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-DVASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-~~~~~Gldip~v~~VI~  448 (503)
                      +.+.|.++|---|++.++.|+++    +++|..+..-.+.+++.++++..++|+++|||.| .++..++-+.++..||.
T Consensus       644 KQVAvLVPTTlLA~QHy~tFkeRF~~fPV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~kdv~FkdLGLlII  722 (1139)
T COG1197         644 KQVAVLVPTTLLAQQHYETFKERFAGFPVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLSKDVKFKDLGLLII  722 (1139)
T ss_pred             CeEEEEcccHHhHHHHHHHHHHHhcCCCeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhCCCcEEecCCeEEE
Confidence            56999999998888888888765    6778888888899999999999999999999999 78999999999998884

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=90.17  E-value=3.5  Score=41.94  Aligned_cols=71  Identities=15%  Similarity=0.286  Sum_probs=53.8

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc------ccccCCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVA----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD------VASRGLDVMGV  443 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~------~~~~Gldip~v  443 (503)
                      ..++||.+++++.+.++++.+..    .++.+..++|+.....+...+    .+..+|||+|.      +....+++.++
T Consensus        73 ~~~~lil~Pt~eLa~Q~~~~~~~l~~~~~~~v~~~~gg~~~~~~~~~l----~~~~~IlV~Tp~rl~~~~~~~~~~~~~v  148 (434)
T PRK11192         73 PPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVF----SENQDIVVATPGRLLQYIKEENFDCRAV  148 (434)
T ss_pred             CceEEEECCcHHHHHHHHHHHHHHHccCCcEEEEEECCCCHHHHHHHh----cCCCCEEEEChHHHHHHHHcCCcCcccC
Confidence            35799999999999888776654    478899999999887766554    35678999995      12245677888


Q ss_pred             CEEEE
Q 010709          444 AHVVN  448 (503)
Q Consensus       444 ~~VI~  448 (503)
                      ++||.
T Consensus       149 ~~lVi  153 (434)
T PRK11192        149 ETLIL  153 (434)
T ss_pred             CEEEE
Confidence            88774

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=90.12  E-value=1.6  Score=44.80  Aligned_cols=58  Identities=21%  Similarity=0.354  Sum_probs=53.8

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      +.+||.+++++.+....+.|...|+.+..++++.+..++..++.....|..+++++|.
T Consensus        52 ~~~lVi~P~~~L~~dq~~~l~~~gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TP  109 (470)
T TIGR00614        52 GITLVISPLISLMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTP  109 (470)
T ss_pred             CcEEEEecHHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            3589999999999999999999999999999999999999999999999999999995

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

>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=90.07  E-value=1.1  Score=37.78  Aligned_cols=31  Identities=23%  Similarity=0.414  Sum_probs=22.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                      ..+-+++++||.-.-++......+.+++..+
T Consensus        86 ~~~p~illlDEP~~~LD~~~~~~l~~~l~~~  116 (144)
T cd03221          86 LENPNLLLLDEPTNHLDLESIEALEEALKEY  116 (144)
T ss_pred             hcCCCEEEEeCCccCCCHHHHHHHHHHHHHc
Confidence            4466799999998766665566677777766

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.

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=90.05  E-value=2.7  Score=43.64  Aligned_cols=56  Identities=16%  Similarity=0.223  Sum_probs=34.2

Q ss_pred             CCCcCCcccCCCCHHHHHHHHH---CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHh
Q 010709          117 PAPIESFTDMCLHPSIMKDIEF---HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       117 ~~~~~~~~~~~l~~~l~~~l~~---~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      ..+--+|++.+=-+.+.+.|+.   +....|-.+..-.+   -.-+-|++.||+|+|||+++
T Consensus       427 e~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi---~ppkGVLlyGPPGC~KT~lA  485 (693)
T KOG0730|consen  427 EMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGI---SPPKGVLLYGPPGCGKTLLA  485 (693)
T ss_pred             cCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcC---CCCceEEEECCCCcchHHHH
Confidence            4455678888755777777652   22233322222221   12356999999999999854

>PRK05416 glmZ(sRNA)-inactivating NTPase; Provisional

Probab=90.04  E-value=8.5  Score=36.56  Aligned_cols=25  Identities=16%  Similarity=0.274  Sum_probs=20.4

Q ss_pred             hhhHHHHHHHHHHCCCeEEEEcCCCC
Q 010709          384 KTRCDEVSEALVAEGLHAVALHGGRN  409 (503)
Q Consensus       384 ~~~~~~l~~~L~~~~~~v~~lh~~~~  409 (503)
                      ...++.|++.| +.++.|...|-++.
T Consensus       260 V~~~e~l~~~l-~~~~~v~~~Hrd~~  284 (288)
T PRK05416        260 VAIAERLAERL-SKGYNVQVRHRDLE  284 (288)
T ss_pred             HHHHHHHHHHH-hCCCcEEEEeCccc
Confidence            56788999999 46899999998875

>TIGR00416 sms DNA repair protein RadA

Probab=90.00  E-value=1.4  Score=44.95  Aligned_cols=53  Identities=21%  Similarity=0.197  Sum_probs=33.1

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|.-+++.|++|+|||+..+. +......       .+.+++|+..- +-..|+..+...++
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq-~a~~~a~-------~g~kvlYvs~E-Es~~qi~~ra~rlg  145 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQ-VACQLAK-------NQMKVLYVSGE-ESLQQIKMRAIRLG  145 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHH-HHHHHHh-------cCCcEEEEECc-CCHHHHHHHHHHcC
Confidence            345699999999999985432 3233222       13568888754 44566666665553

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)).

>CHL00176 ftsH cell division protein; Validated

Probab=90.00  E-value=2.2  Score=45.43  Aligned_cols=17  Identities=29%  Similarity=0.393  Sum_probs=14.6

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||+.+
T Consensus       217 ~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999743

>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=89.79  E-value=0.27  Score=43.15  Aligned_cols=41  Identities=20%  Similarity=0.388  Sum_probs=26.7

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCC-CCcEEEEEe
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPD-KHQTLLFSA  308 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~-~~q~i~~SA  308 (503)
                      .+.+++++||...-++......+.+.+..+.. ..++|+.|-
T Consensus       115 ~~p~llilDEp~~~LD~~~~~~i~~~L~~~~~~g~tiIiiSH  156 (178)
T cd03239         115 KPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITL  156 (178)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEEEC
Confidence            56789999999976666555566666655433 355555543

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.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=89.71  E-value=1.9  Score=41.76  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=32.5

Q ss_pred             CCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeCCHH
Q 010709          268 SRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATMPVE  313 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~  313 (503)
                      +..-++|+|-|+.+-+++  ..+.+.++-..++.+.-.|.+|+++.+.
T Consensus       114 d~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~~~i~iils~~~~e~  161 (438)
T KOG2543|consen  114 DQKVFLILDNADALRDMDAILLQCLFRLYELLNEPTIVIILSAPSCEK  161 (438)
T ss_pred             CceEEEEEcCHHhhhccchHHHHHHHHHHHHhCCCceEEEEeccccHH
Confidence            456689999999988775  3344555555556566678889998654

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=89.53  E-value=0.59  Score=48.92  Aligned_cols=17  Identities=29%  Similarity=0.470  Sum_probs=15.8

Q ss_pred             cCCCeEEEccCCCchhH
Q 010709          157 SGRDLLGCAETGSGKTA  173 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl  173 (503)
                      .|+-+.++||+|+|||+
T Consensus       360 ~G~~vaIvG~SGsGKST  376 (529)
T TIGR02868       360 PGERVAILGPSGSGKST  376 (529)
T ss_pred             CCCEEEEECCCCCCHHH
Confidence            67889999999999998

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.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=89.52  E-value=2.9  Score=39.23  Aligned_cols=25  Identities=20%  Similarity=0.267  Sum_probs=18.5

Q ss_pred             HHHHHHHhcC---CCeEEEccCCCchhH
Q 010709          149 AQAMPVALSG---RDLLGCAETGSGKTA  173 (503)
Q Consensus       149 ~~~i~~i~~~---~~vii~~~TGsGKTl  173 (503)
                      ...++.+...   +++++.||+|+|||+
T Consensus        99 ~~~l~~l~~~~~~~~~~i~g~~g~GKtt  126 (270)
T TIGR02858        99 DKLLPYLVRNNRVLNTLIISPPQCGKTT  126 (270)
T ss_pred             HHHHHHHHhCCCeeEEEEEcCCCCCHHH
Confidence            3345555543   578999999999998

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	503
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		1e-70
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		4e-63
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		5e-52
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		6e-52
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		4e-49
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		9e-49
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-48
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		4e-47
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		4e-47
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		4e-47
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		4e-47
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		9e-47
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		9e-47
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		1e-46
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		3e-45
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-44
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-44
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		2e-41
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		5e-41
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		6e-40
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-38
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-38
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		6e-37
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		1e-36
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		4e-36
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		7e-34
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-33
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		5e-33
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-32
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		4e-32
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		1e-31
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		1e-31
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		2e-31
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-29
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		4e-29
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		6e-28
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		1e-27
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		2e-27
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-27
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-27
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-27
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-27
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-25
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		5e-23
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		4e-22
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-20
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		8e-20
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-19
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		3e-19
2p6n_A	191	Human Dead-box Rna Helicase Ddx41, Helicase Domain		3e-17
2jgn_A	185	Ddx3 Helicase Domain Length = 185		7e-17
2yjt_D	170	Crystal Structure Of E. Coli Dead-Box Protein Srmb		8e-11
3eaq_A	212	Novel Dimerization Motif In The Dead Box Rna Helica		2e-10
3i32_A	300	Dimeric Structure Of A Hera Helicase Fragment Inclu		4e-10
2hjv_A	163	Structure Of The Second Domain (Residues 207-368) O		2e-09
1fuk_A	165	Crystal Structure Of The Carboxy Terminal Domain Of		7e-09
2kbf_A	187	Solution Structure Of Carboxyl-Terminal Domain Of D		3e-08
3gfp_A	189	Structure Of The C-Terminal Domain Of The Dead-Box		3e-08
3peu_A	188	S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To		3e-08
2wax_A	193	Structure Of The Human Ddx6 C-Terminal Domain In Co		5e-08
1t5i_A	172	Crystal Structure Of The C-Terminal Domain Of Uap56		8e-08
1oyw_A	523	Structure Of The Recq Catalytic Core Length = 523		3e-06
1oyy_A	523	Structure Of The Recq Catalytic Core Bound To Atp-G		3e-06
2rb4_A	175	Crystal Structure Of The Helicase Domain Of Human D		5e-06
1gm5_A	780	Structure Of Recg Bound To Three-Way Dna Junction L		5e-04
4db2_A	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-04
4db4_A	256	Mss116p Dead-Box Helicase Domain 2 Bound To A Chima		8e-04
4db2_C	257	Mss116p Dead-Box Helicase Domain 2 Bound To An Rna		8e-04

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  263 bits (673), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 147/353 (41%), Positives = 209/353 (59%), Gaps = 26/353 (7%)
Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           P  IESF+D+ +   IM +IE   YTRPT +Q  A+P+    RDL+ CA+TGSGKTAAF 
Sbjct: 11  PPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFL 70
Query: 177 IPMIQHCVAQTP------------VGR-GDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
           +P++    +  P             GR    P++LVLAPTRELA QI +E +  S     
Sbjct: 71  LPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYR-SR 129
Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD 283
            +  +V GG +I +Q  +L  G  ++VATPGR +D +++G   L    +++LDEADRMLD
Sbjct: 130 VRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLD 189
Query: 284 MGFEPQIREVMQN--LPDK--HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTAN 339
           MGFEPQIR +++   +P K    T++FSAT P EI+ LA+++L + + + VG+V S + N
Sbjct: 190 MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSEN 249
Query: 340 VIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGL 399
           + Q +  V E++K                 +     LT+VFVE K   D + + L  EG 
Sbjct: 250 ITQKVVWVEESDK--------RSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGY 301
Query: 400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
              ++HG R+Q DRE AL  FR+G + ILVAT VA+RGLD+  V HV+N DLP
Sbjct: 302 ACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLP 354

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  239 bits (609), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 141/355 (39%), Positives = 202/355 (56%), Gaps = 23/355 (6%)
Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLG 163
           N+ V V    VP P  I+ FT   L   I+ ++    Y  PT IQ  ++PV  SGRDL+ 
Sbjct: 41  NIPVKVTGSDVPQP--IQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMA 98
Query: 164 CAETGSGKTAAFTIPMIQHCVA---QTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS 220
           CA+TGSGKTAAF +P++   +    +  +GR   P  ++++PTRELA QI  E +  +  
Sbjct: 99  CAQTGSGKTAAFLLPILSKLLEDPHELELGR---PQVVIVSPTRELAIQIFNEARKFA-- 153
Query: 221 LDSF-KTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD 279
            +S+ K  IV GGT+   Q   +  G  +V+ATPGR LD + +   +     FV+LDEAD
Sbjct: 154 FESYLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVVLDEAD 213
Query: 280 RMLDMGFEPQIREVMQN--LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPT 337
           RMLDMGF   +R +M +  +  +HQTL+FSAT P EI+ +A E+L + V V +G V    
Sbjct: 214 RMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGAC 273
Query: 338 ANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAE 397
           ++V Q + +V++  K  +                     TIVFVE K   D ++  L  +
Sbjct: 274 SDVKQTIYEVNKYAKRSKLIEILSEQADG----------TIVFVETKRGADFLASFLSEK 323
Query: 398 GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
                ++HG R QS RE ALRDF+NGS  +L+AT VASRGLD+  + HV+N D+P
Sbjct: 324 EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDIKNIKHVINYDMP 378

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score =  202 bits (513), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 98/218 (44%), Positives = 142/218 (65%), Gaps = 1/218 (0%)
Query: 116 APAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF 175
            P P+ +F +     ++M  I    +T PT+IQAQ  PVALSG D++G A+TGSGKT ++
Sbjct: 24  CPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSY 83
Query: 176 TIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI 235
            +P I H   Q  + RGDGP+ LVLAPTRELAQQ+++      R+    K+  + GG   
Sbjct: 84  LLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPK 142
Query: 236 AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ 295
             Q  +L  GV I +ATPGR +D L+ G T+L R ++++LDEADRMLDMGFEPQIR+++ 
Sbjct: 143 GPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVD 202
Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKV 333
            +    QTL++SAT P E+  LA+++L D + + +G +
Sbjct: 203 QIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL 240

>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 =  201 bits (512), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 101/230 (43%), Positives = 148/230 (64%), Gaps = 3/230 (1%)
Query: 102 RLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDL 161
           R + ++TV   +   P P+ +F +     ++M  I    +T PT+IQAQ  PVALSG D+
Sbjct: 26  RRSKEITVRGHN--CPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDM 83
Query: 162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL 221
           +G A+TGSGKT ++ +P I H   Q  + RGDGP+ LVLAPTRELAQQ+++      R+ 
Sbjct: 84  VGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRAC 143
Query: 222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM 281
              K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L R ++++LDEADRM
Sbjct: 144 -RLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRM 202
Query: 282 LDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG 331
           LDMGFEPQIR+++  +    QTL++SAT P E+  LA+++L D + + +G
Sbjct: 203 LDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG 252

>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 =  192 bits (487), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 104/247 (42%), Positives = 152/247 (61%), Gaps = 9/247 (3%)
Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLG 163
           ++ V+V      A   IE+F ++ L P+I  +I    Y RPT IQ  A+P  L  RD++ 
Sbjct: 6   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMA 65
Query: 164 CAETGSGKTAAFTIPMIQHCVA----QTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR 219
           CA+TGSGKTAAF IP+I H V     Q    +   P  L+LAPTRELA QI  E +  S 
Sbjct: 66  CAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL 125
Query: 220 SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD 279
           +    ++ +V GG +   Q  E++ G  ++VATPGR +D +++   SL    +++LDEAD
Sbjct: 126 N-TPLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEAD 184
Query: 280 RMLDMGFEPQIREVMQ--NLPD--KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS 335
           RMLDMGFEPQIR++++  N+P     QTL+FSAT P EI+ LA ++L + + + VG+V S
Sbjct: 185 RMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGS 244
Query: 336 PTANVIQ 342
            + ++ Q
Sbjct: 245 TSDSIKQ 251

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score =  191 bits (485), Expect = 9e-49,   Method: Compositional matrix adjust.
 Identities = 115/340 (33%), Positives = 187/340 (55%), Gaps = 27/340 (7%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           ++SF DM L  S+++ I  + + +P++IQ +A+   + G D++  A++G+GKTA F I +
Sbjct: 13  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 72
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q         +     ALVLAPTRELAQQI+K V AL   + +   A  +GGTN+  + 
Sbjct: 73  LQQIELDLKATQ-----ALVLAPTRELAQQIQKVVMALGDYMGASCHA-CIGGTNVRAEV 126
Query: 240 SELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
            +L+     I+V TPGR  D L +   S   +   +LDEAD ML  GF+ QI ++ Q L 
Sbjct: 127 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 186
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXX 357
              Q +L SATMP ++  + ++++ DP+++ V K       + Q    V   E K+D   
Sbjct: 187 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTL- 245
Query: 358 XXXXXXXXXXXKSCHPFP-LTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSD 412
                        C  +  LTI    +F+  + + D ++E + A      A+HG  +Q +
Sbjct: 246 -------------CDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE 292
Query: 413 RESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           R+  +R+FR+GS+ +L+ TD+ +RG+DV  V+ V+N DLP
Sbjct: 293 RDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP 332

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score =  190 bits (483), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 115/340 (33%), Positives = 187/340 (55%), Gaps = 27/340 (7%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           ++SF DM L  S+++ I  + + +P++IQ +A+   + G D++  A++G+GKTA F I +
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q         +     ALVLAPTRELAQQI+K V AL   + +   A  +GGTN+  + 
Sbjct: 99  LQQIELDLKATQ-----ALVLAPTRELAQQIQKVVMALGDYMGASCHA-CIGGTNVRAEV 152
Query: 240 SELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
            +L+     I+V TPGR  D L +   S   +   +LDEAD ML  GF+ QI ++ Q L 
Sbjct: 153 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 212
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXX 357
              Q +L SATMP ++  + ++++ DP+++ V K       + Q    V   E K+D   
Sbjct: 213 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTL- 271
Query: 358 XXXXXXXXXXXKSCHPFP-LTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSD 412
                        C  +  LTI    +F+  + + D ++E + A      A+HG  +Q +
Sbjct: 272 -------------CDLYETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKE 318
Query: 413 RESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           R+  +R+FR+GS+ +L+ TD+ +RG+DV  V+ V+N DLP
Sbjct: 319 RDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLP 358

>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 =  186 bits (471), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 110/337 (32%), Positives = 186/337 (55%), Gaps = 26/337 (7%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F+I ++Q
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 98
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               Q    +     AL+LAPTRELA QI+K + AL   ++  +    +GGTN+ E   +
Sbjct: 99  CLDIQVRETQ-----ALILAPTRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRK 152
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP   
Sbjct: 153 LDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT 212
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXXXXX 360
           Q +L SAT+P EI  +  +++TDP+++ V +       + Q    V   E K D      
Sbjct: 213 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL---- 268
Query: 361 XXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
                     C  +  LTI    +F   K + D ++E +        ++HG   Q +RES
Sbjct: 269 ----------CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 318
Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP
Sbjct: 319 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLP 355

>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 =  186 bits (471), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 110/337 (32%), Positives = 186/337 (55%), Gaps = 26/337 (7%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F+I ++Q
Sbjct: 39  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 98
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               Q    +     AL+LAPTRELA QI+K + AL   ++  +    +GGTN+ E   +
Sbjct: 99  CLDIQVRETQ-----ALILAPTRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRK 152
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP   
Sbjct: 153 LDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT 212
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXXXXX 360
           Q +L SAT+P EI  +  +++TDP+++ V +       + Q    V   E K D      
Sbjct: 213 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL---- 268
Query: 361 XXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
                     C  +  LTI    +F   K + D ++E +        ++HG   Q +RES
Sbjct: 269 ----------CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 318
Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP
Sbjct: 319 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLP 355

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score =  186 bits (471), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 110/337 (32%), Positives = 186/337 (55%), Gaps = 26/337 (7%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F+I ++Q
Sbjct: 17  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 76
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               Q    +     AL+LAPTRELA QI+K + AL   ++  +    +GGTN+ E   +
Sbjct: 77  CLDIQVRETQ-----ALILAPTRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRK 130
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP   
Sbjct: 131 LDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT 190
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXXXXX 360
           Q +L SAT+P EI  +  +++TDP+++ V +       + Q    V   E K D      
Sbjct: 191 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL---- 246
Query: 361 XXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
                     C  +  LTI    +F   K + D ++E +        ++HG   Q +RES
Sbjct: 247 ----------CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 296
Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP
Sbjct: 297 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLP 333

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score =  186 bits (471), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 110/337 (32%), Positives = 186/337 (55%), Gaps = 26/337 (7%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F+I ++Q
Sbjct: 38  TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQ 97
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               Q    +     AL+LAPTRELA QI+K + AL   ++  +    +GGTN+ E   +
Sbjct: 98  CLDIQVRETQ-----ALILAPTRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRK 151
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP   
Sbjct: 152 LDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT 211
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXXXXX 360
           Q +L SAT+P EI  +  +++TDP+++ V +       + Q    V   E K D      
Sbjct: 212 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL---- 267
Query: 361 XXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
                     C  +  LTI    +F   K + D ++E +        ++HG   Q +RES
Sbjct: 268 ----------CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 317
Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP
Sbjct: 318 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLP 354

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  184 bits (467), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 107/337 (31%), Positives = 187/337 (55%), Gaps = 26/337 (7%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F++ ++Q
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               Q    +     AL+LAPTRELA Q++K + AL   ++  ++   +GGTN+ E   +
Sbjct: 62  CLDIQVRETQ-----ALILAPTRELAVQVQKGLLALGDYMN-VQSHACIGGTNVGEDIRK 115
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP   
Sbjct: 116 LDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT 175
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXXXXX 360
           Q +L SAT+P E+  +  +++TDP+++ V +       + Q    V   E K D      
Sbjct: 176 QVVLISATLPHEVLEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL---- 231
Query: 361 XXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
                     C  +  LTI    +F   K + D ++E +        ++HG   Q +RES
Sbjct: 232 ----------CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 281
Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP
Sbjct: 282 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLP 318

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score =  184 bits (467), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 108/337 (32%), Positives = 186/337 (55%), Gaps = 26/337 (7%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F++ ++Q
Sbjct: 2   TFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               Q    +     AL+LAPTRELA Q++K + AL   ++  +    +GGTN+ E   +
Sbjct: 62  CLDIQVRETQ-----ALILAPTRELAVQVQKGLLALGDYMN-VQCHACIGGTNVGEDIRK 115
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP   
Sbjct: 116 LDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPAT 175
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRXXXXX 360
           Q +L SAT+P EI  +  +++TDP+++ V +       + Q    V   E K D      
Sbjct: 176 QVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL---- 231
Query: 361 XXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES 415
                     C  +  LTI    +F   K + D ++E +        ++HG   Q +RES
Sbjct: 232 ----------CDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERES 281
Query: 416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP
Sbjct: 282 IMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLP 318

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

Iteration: 1
 Score =  184 bits (467), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 118/333 (35%), Positives = 180/333 (54%), Gaps = 23/333 (6%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMI 180
           +F ++ L  +I+  I    + +PT IQ + +P+ L+   +++  A TGSGKTA+F IP+I
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 181 QHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS 240
           +       V   +G  A++L PTRELA Q+  E+++L +   + K A + GG  I  Q  
Sbjct: 67  E------LVNENNGIEAIILTPTRELAIQVADEIESL-KGNKNLKIAKIYGGKAIYPQIK 119
Query: 241 ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK 300
            L+   +IVV TPGR LDH+ +G  +L  V + ILDEAD  L+ GF   + +++      
Sbjct: 120 ALKNA-NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKD 178
Query: 301 HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRXXXXX 360
            + LLFSAT P EI  LA++Y  D   +K    +   AN+ Q   +V+ENE+ +      
Sbjct: 179 KRILLFSATXPREILNLAKKYXGDYSFIK----AKINANIEQSYVEVNENERFE------ 228
Query: 361 XXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF 420
                   K+   + L  VF + K    E++  L   G  A A+HG  +QS RE  +R F
Sbjct: 229 --ALCRLLKNKEFYGL--VFCKTKRDTKELASXLRDIGFKAGAIHGDLSQSQREKVIRLF 284
Query: 421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           +     IL+ATDV SRG+DV  +  V+N  LP+
Sbjct: 285 KQKKIRILIATDVXSRGIDVNDLNCVINYHLPQ 317

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score =  179 bits (454), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 122/395 (30%), Positives = 198/395 (50%), Gaps = 35/395 (8%)
Query: 96  IEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVA 155
           IEE +++ N D  V             F DM L  ++++ +  + +  P++IQ +A+   
Sbjct: 8   IEESQIQTNYDKVVYK-----------FDDMELDENLLRGVFGYGFEEPSAIQQRAIMPI 56
Query: 156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK 215
           + G D+L  A++G+GKT  F+I  +Q     T V     P AL+LAPTRELA QI+K V 
Sbjct: 57  IEGHDVLAQAQSGTGKTGTFSIAALQRI--DTSVK---APQALMLAPTRELALQIQKVVM 111
Query: 216 ALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL 275
           AL+  +D  K    +GGT+  E    LR    IVV TPGR  D++Q+      ++   IL
Sbjct: 112 ALAFHMD-IKVHACIGGTSFVEDAEGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFIL 169
Query: 276 DEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS 335
           DEAD ML  GF+ QI ++   LP   Q +L SATMP ++  +  +++ +PV++ V K   
Sbjct: 170 DEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDEL 229
Query: 336 PTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALV 395
               + Q    V E E                          ++F   + + +E++  L 
Sbjct: 230 TLEGIKQFYVNVEEEE--------YKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLR 281
Query: 396 AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP--- 452
            +     A++    Q +R++ +++FR+GS+ IL++TD+ +RG+DV  V+ V+N DLP   
Sbjct: 282 NDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANK 341
Query: 453 -----KVLLAASESLCTTSFNITTNLD-GDMKKLE 481
                ++           + N  TN D G M++LE
Sbjct: 342 ENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELE 376

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  177 bits (449), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 97/210 (46%), Positives = 127/210 (60%), Gaps = 5/210 (2%)
Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F D  L P I++ +     T PT IQA A+P+AL G+DL+G A TG+GKT AF +P+ + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 183 CVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL 242
                   RG  P ALVL PTRELA Q+  E+ A++  L   K   V GGT   +Q+  L
Sbjct: 63  LAPSQE--RGRKPRALVLTPTRELALQVASELTAVAPHL---KVVAVYGGTGYGKQKEAL 117
Query: 243 RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ 302
             G   VVATPGR LD+L+QG   LSRV   +LDEAD ML MGFE ++  ++   P   Q
Sbjct: 118 LRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQ 177
Query: 303 TLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           TLLFSAT+P   + LA+ Y+ +PV + V K
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINVIK 207

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  176 bits (445), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 96/210 (45%), Positives = 127/210 (60%), Gaps = 5/210 (2%)
Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F D  L P I++ +     T PT I+A A+P+AL G+DL+G A TG+GKT AF +P+ + 
Sbjct: 3   FKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAER 62
Query: 183 CVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL 242
                   RG  P ALVL PTRELA Q+  E+ A++  L   K   V GGT   +Q+  L
Sbjct: 63  LAPSQE--RGRKPRALVLTPTRELALQVASELTAVAPHL---KVVAVYGGTGYGKQKEAL 117
Query: 243 RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ 302
             G   VVATPGR LD+L+QG   LSRV   +LDEAD ML MGFE ++  ++   P   Q
Sbjct: 118 LRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQ 177
Query: 303 TLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           TLLFSAT+P   + LA+ Y+ +PV + V K
Sbjct: 178 TLLFSATLPSWAKRLAERYMKNPVLINVIK 207

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score =  166 bits (421), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 111/357 (31%), Positives = 178/357 (49%), Gaps = 26/357 (7%)
Query: 96  IEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVA 155
           IEE +++ N D  V             F D  L  ++++ +  + +  P++IQ +A+   
Sbjct: 7   IEESQIQTNYDKVVYK-----------FDDXELDENLLRGVFGYGFEEPSAIQQRAIXPI 55
Query: 156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK 215
           + G D+L  A++G+GKT  F+I  +Q     T V     P AL LAPTRELA QI+K V 
Sbjct: 56  IEGHDVLAQAQSGTGKTGTFSIAALQRI--DTSVK---APQALXLAPTRELALQIQKVVX 110
Query: 216 ALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL 275
           AL+   D  K    +GGT+  E    LR    IVV TPGR  D++Q+      ++   IL
Sbjct: 111 ALAFHXD-IKVHACIGGTSFVEDAEGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKXFIL 168
Query: 276 DEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS 335
           DEAD  L  GF+ QI ++   LP   Q +L SAT P ++  +  ++  +PV++ V K   
Sbjct: 169 DEADEXLSSGFKEQIYQIFTLLPPTTQVVLLSATXPNDVLEVTTKFXRNPVRILVKKDEL 228
Query: 336 PTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALV 395
               + Q    V E E                          ++F   + + +E++  L 
Sbjct: 229 TLEGIKQFYVNVEEEE--------YKYECLTDLYDSISVTQAVIFCNTRRKVEELTTKLR 280
Query: 396 AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            +     A++    Q +R++  ++FR+GS+ IL++TD+ +RG+DV  V+ V+N DLP
Sbjct: 281 NDKFTVSAIYSDLPQQERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLP 337

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score =  165 bits (418), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 101/332 (30%), Positives = 161/332 (48%), Gaps = 16/332 (4%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F D  L   ++  I    + +P+ IQ +A+PVA++GRD+L  A+ G+GKTAAF IP ++
Sbjct: 22  TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 81
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               +      +   AL++ PTRELA Q  + V+ L +        +  GGTN+ +    
Sbjct: 82  KVKPKL-----NKIQALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILR 135
Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L   V I+V TPGR LD   +    LS  S  I+DEAD+ML   F+  I +++  LP  H
Sbjct: 136 LNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTH 195
Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRXXXXXX 361
           Q+LLFSAT P+ ++    ++L  P ++ + +       + Q    V E +K+        
Sbjct: 196 QSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYAFVEERQKLHCLNTLFS 254
Query: 362 XXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFR 421
                           I+F     R + +++ +   G      H    Q +R     +FR
Sbjct: 255 KLQINQ---------AIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFR 305
Query: 422 NGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            G    LV +D+ +RG+D+  V  V+N D PK
Sbjct: 306 QGKVRTLVCSDLLTRGIDIQAVNVVINFDFPK 337

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score =  161 bits (408), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 104/342 (30%), Positives = 179/342 (52%), Gaps = 19/342 (5%)
Query: 116 APAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF 175
           +P  +  F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA F
Sbjct: 2   SPGHMSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVF 61
Query: 176 TIPMIQHCVAQTPVGRGDGPLA-LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN 234
            +  +Q      PV    G ++ LV+  TRELA QI KE +  S+ + + K A+  GG +
Sbjct: 62  VLATLQQL---EPVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLS 115
Query: 235 IAEQRSELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIRE 292
           I +    L+     IVV TPGR L   +  + +L  +   ILDEAD+ML+ +     ++E
Sbjct: 116 IKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQE 175
Query: 293 VMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQ-ILEKVSENE 351
           + +  P + Q ++FSAT+  EI  + ++++ DP+++ V   +  T + +Q    K+ +NE
Sbjct: 176 IFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNE 235
Query: 352 KVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQS 411
           K  +                  F   ++FV+   RC  +++ LV +   A+A+H G  Q 
Sbjct: 236 KNRKLFDLLDVL---------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQE 286
Query: 412 DRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           +R S  + F++    ILVAT++  RG+D+  V    N D+P+
Sbjct: 287 ERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPE 328

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score =  157 bits (396), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/343 (30%), Positives = 179/343 (52%), Gaps = 20/343 (5%)
Query: 116 APAPIES-FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAA 174
           +P  + S F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA 
Sbjct: 2   SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 61
Query: 175 FTIPMIQHCVAQTPVGRGDGPLA-LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT 233
           F +  +Q      PV    G ++ LV+  TRELA QI KE +  S+ + + K A+  GG 
Sbjct: 62  FVLATLQQL---EPVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGL 115
Query: 234 NIAEQRSELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIR 291
           +I +    L+     IVV TPGR L   +  + +L  +   ILDE D+ML+ +     ++
Sbjct: 116 SIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQ 175
Query: 292 EVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQ-ILEKVSEN 350
           E+ +  P + Q ++FSAT+  EI  + ++++ DP+++ V   +  T + +Q    K+ +N
Sbjct: 176 EIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDN 235
Query: 351 EKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQ 410
           EK  +                  F   ++FV+   RC  +++ LV +   A+A+H G  Q
Sbjct: 236 EKNRKLFDLLDVL---------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQ 286
Query: 411 SDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            +R S  + F++    ILVAT++  RG+D+  V    N D+P+
Sbjct: 287 EERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPE 329

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score =  157 bits (396), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/343 (30%), Positives = 179/343 (52%), Gaps = 20/343 (5%)
Query: 116 APAPIES-FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAA 174
           +P  + S F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA 
Sbjct: 2   SPGHMSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV 61
Query: 175 FTIPMIQHCVAQTPVGRGDGPLA-LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT 233
           F +  +Q      PV    G ++ LV+  TRELA QI KE +  S+ + + K A+  GG 
Sbjct: 62  FVLATLQQL---EPVT---GQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGL 115
Query: 234 NIAEQRSELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIR 291
           +I +    L+     IVV TPGR L   +  + +L  +   ILDE D+ML+ +     ++
Sbjct: 116 SIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQ 175
Query: 292 EVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQ-ILEKVSEN 350
           E+ +  P + Q ++FSAT+  EI  + ++++ DP+++ V   +  T + +Q    K+ +N
Sbjct: 176 EIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDN 235
Query: 351 EKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQ 410
           EK  +                  F   ++FV+   RC  +++ LV +   A+A+H G  Q
Sbjct: 236 EKNRKLFDLLDVL---------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQ 286
Query: 411 SDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            +R S  + F++    ILVAT++  RG+D+  V    N D+P+
Sbjct: 287 EERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPE 329

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  152 bits (383), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 84/224 (37%), Positives = 140/224 (62%), Gaps = 7/224 (3%)
Query: 108 TVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAET 167
           T AS  +      ++F D+ +   + +  +   +T+PT IQ +A+P+AL GRD++G AET
Sbjct: 30  TEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAET 89
Query: 168 GSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA 227
           GSGKT AF +P++ + + +TP        ALVL PTRELA QI ++ +AL  S+   ++A
Sbjct: 90  GSGKTGAFALPIL-NALLETP----QRLFALVLTPTRELAFQISEQFEALGSSI-GVQSA 143
Query: 228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGF 286
           ++VGG +   Q   L     I++ATPGR +DHL+     +L  + ++++DEADR+L+M F
Sbjct: 144 VIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDF 203
Query: 287 EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           E ++ ++++ +P   +T LFSATM  +++ L +  L +PV+  V
Sbjct: 204 ETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score =  150 bits (380), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 86/217 (39%), Positives = 126/217 (58%), Gaps = 6/217 (2%)
Query: 117 PAPIESFTD-MCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF 175
           P P   F D    +P ++K I      +PT IQ+QA P+ L G DL+  A+TG+GKT ++
Sbjct: 15  PKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSY 74
Query: 176 TIPMIQHCVAQTPVGRG--DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT 233
            +P   H  +Q P+ R   +GP  LVL PTRELA  +E E    S      K+  + GG 
Sbjct: 75  LMPGFIHLDSQ-PISREQRNGPGMLVLTPTRELALHVEAECSKYSYK--GLKSICIYGGR 131
Query: 234 NIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREV 293
           N   Q  ++  GV I++ATPGR  D     + +L  ++++++DEAD+MLDM FEPQIR++
Sbjct: 132 NRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKI 191
Query: 294 MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           + ++    QT++ SAT P  +  LA  YL DP+ V V
Sbjct: 192 LLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score =  149 bits (376), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 105/311 (33%), Positives = 162/311 (52%), Gaps = 31/311 (9%)
Query: 145 TSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR 204
           T +Q++ +P+ L G++++  A+TGSGKTAA+ IP+++            G  +LV+ PTR
Sbjct: 18  TEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL-----------GMKSLVVTPTR 66
Query: 205 ELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN 264
           EL +Q+   ++ + R +D+ K A V GG     Q + +R    IVVATPGR LD   +G 
Sbjct: 67  ELTRQVASHIRDIGRYMDT-KVAEVYGGMPYKAQINRVRNA-DIVVATPGRLLDLWSKGV 124
Query: 265 TSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTD 324
             LS    VI+DEAD M +MGF   I+ ++    ++  T LFSAT+P EI  + ++++T+
Sbjct: 125 IDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITN 184
Query: 325 PVQVKVGKVSSPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHPFPLTIVFVERK 384
             ++   +     ANV      V ++ +                K        IVFV  +
Sbjct: 185 YEEI---EACIGLANVEHKFVHVKDDWR-----SKVQALRENKDKGV------IVFVRTR 230
Query: 385 TRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVA 444
            R  +    LV    +A+ L G   QS R   +  FR G  ++L+ TDVASRGLD+  V 
Sbjct: 231 NRVAK----LVRLFDNAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVE 286
Query: 445 HVVNLDLPKVL 455
            V+N D P+ L
Sbjct: 287 KVINFDAPQDL 297

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  141 bits (356), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 79/212 (37%), Positives = 129/212 (60%), Gaps = 4/212 (1%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           I  F+D  L    +K ++  +Y   T IQ Q + +AL G+D+LG A+TGSGKT AF +P+
Sbjct: 24  ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPV 83
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           ++  + +      DG   L+++PTRELA Q  + ++ + ++ D F   +++GG ++  + 
Sbjct: 84  LE-ALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHD-FSAGLIIGGKDLKHE- 140
Query: 240 SELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
           +E    ++I+V TPGR L H+ +  +   + +  ++LDEADR+LDMGF   +  V++NLP
Sbjct: 141 AERINNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLP 200
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
            K QTLLFSAT    ++ LA+  L +P  V V
Sbjct: 201 KKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score =  141 bits (355), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 79/214 (36%), Positives = 127/214 (59%), Gaps = 7/214 (3%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           +++F DM L  S+++ I  + + +P++IQ +A+   + G D++  A++G+GKTA F I +
Sbjct: 29  VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISI 88
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q    +    +     ALVLAPTRELAQQI+K + AL   + +   A  +GGTN+  + 
Sbjct: 89  LQQLEIEFKETQ-----ALVLAPTRELAQQIQKVILALGDYMGATCHA-CIGGTNVRNEM 142
Query: 240 SELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
            +L+     IVV TPGR  D L +   S   +   +LDEAD ML  GF+ QI E+ Q L 
Sbjct: 143 QKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLN 202
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
              Q +L SATMP ++  + ++++ DP+++ V K
Sbjct: 203 TSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKK 236

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score =  139 bits (349), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 69/206 (33%), Positives = 117/206 (56%), Gaps = 5/206 (2%)
Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F D CL   ++  I    + +P+ IQ +++P+ALSGRD+L  A+ G+GK+ A+ IP+++ 
Sbjct: 5   FEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLER 64
Query: 183 CVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL 242
                   + D   A+V+ PTRELA Q+ +    +S+ +   K     GGTN+ +    L
Sbjct: 65  LDL-----KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL 119
Query: 243 RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ 302
              V +V+ATPGR LD +++G   +  V  ++LDEAD++L   F   + +++  LP   Q
Sbjct: 120 DDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQ 179
Query: 303 TLLFSATMPVEIEALAQEYLTDPVQV 328
            LL+SAT P+ ++     +L  P ++
Sbjct: 180 ILLYSATFPLSVQKFMNSHLEKPYEI 205

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score =  137 bits (345), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 78/202 (38%), Positives = 131/202 (64%), Gaps = 7/202 (3%)
Query: 122 SFTDMC--LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           SF  +C  ++ + +K I+   +T  T IQ +++   L GRDLL  A+TGSGKT AF IP 
Sbjct: 53  SFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPA 112
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL-SRSLDSFKTAIVVGGTNIAEQ 238
           ++  V    + R +G   L+L+PTRELA Q    +K L +  + ++   +++GG+N + +
Sbjct: 113 VELIVKLRFMPR-NGTGVLILSPTRELAMQTFGVLKELMTHHVHTY--GLIMGGSNRSAE 169
Query: 239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSR-VSFVILDEADRMLDMGFEPQIREVMQNL 297
             +L  G++I+VATPGR LDH+Q     + + +  +++DEADR+LD+GFE +++++++ L
Sbjct: 170 AQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLL 229
Query: 298 PDKHQTLLFSATMPVEIEALAQ 319
           P + QT+LFSAT   ++E LA+
Sbjct: 230 PTRRQTMLFSATQTRKVEDLAR 251

>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 =  135 bits (341), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 80/213 (37%), Positives = 123/213 (57%), Gaps = 7/213 (3%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           +  F DM L  ++++ +  + +  P++IQ +A+   + G D+L  A++G+GKT  F+I  
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q     T V     P AL+LAPTRELA QI+K V AL+  +D  K    +GGT+  E  
Sbjct: 73  LQRI--DTSV---KAPQALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVEDA 126
Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD 299
             LR    IVV TPGR  D++Q+      ++   ILDEAD ML  GF+ QI ++   LP 
Sbjct: 127 EGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 185
Query: 300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
             Q +L SATMP ++  +  +++ +PV++ V K
Sbjct: 186 TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK 218

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  134 bits (337), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 99/339 (29%), Positives = 175/339 (51%), Gaps = 23/339 (6%)
Query: 118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAF 175
           A  +SF ++ L P ++K I   ++ +P+ IQ +A+P+ L    R+++  +++G+GKTAAF
Sbjct: 2   AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAF 61
Query: 176 TIPMIQHCVAQTPVGRGDG-PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN 234
           ++ M+      T V   D  P A+ LAP+RELA+Q  + V+ + +      + ++V  + 
Sbjct: 62  SLTML------TRVNPEDASPQAICLAPSRELARQTLEVVQEMGK-FTKITSQLIVPDS- 113
Query: 235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREV 293
             E+  ++     ++V TPG  LD +++    L ++   +LDEAD MLD  G   Q   V
Sbjct: 114 -FEKNKQINA--QVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRV 170
Query: 294 MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
            + LP   Q +LFSAT    +   A++ + +   +++ + +    + I+ L    +NE  
Sbjct: 171 KRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLEL-QTNEVNVDAIKQLYMDCKNE-A 228
Query: 354 DRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR 413
           D+              S      +I+FV  K   + +   L +EG     LHG     +R
Sbjct: 229 DKFDVLTELYGVMTIGS------SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQER 282
Query: 414 ESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           +  + DFR G + +L+ T+V +RG+D+  V+ VVN DLP
Sbjct: 283 DRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score =  134 bits (337), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 99/339 (29%), Positives = 175/339 (51%), Gaps = 23/339 (6%)
Query: 118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAF 175
           A  +SF ++ L P ++K I   ++ +P+ IQ +A+P+ L    R+++  +++G+GKTAAF
Sbjct: 2   AMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAF 61
Query: 176 TIPMIQHCVAQTPVGRGDG-PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN 234
           ++ M+      T V   D  P A+ LAP+RELA+Q  + V+ + +      + ++V  + 
Sbjct: 62  SLTML------TRVNPEDASPQAICLAPSRELARQTLEVVQEMGK-FTKITSQLIVPDS- 113
Query: 235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREV 293
             E+  ++     ++V TPG  LD +++    L ++   +LDEAD MLD  G   Q   V
Sbjct: 114 -FEKNKQINA--QVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRV 170
Query: 294 MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
            + LP   Q +LFSAT    +   A++ + +   +++ + +    + I+ L    +NE  
Sbjct: 171 KRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLEL-QTNEVNVDAIKQLYMDCKNE-A 228
Query: 354 DRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR 413
           D+              S      +I+FV  K   + +   L +EG     LHG     +R
Sbjct: 229 DKFDVLTELYGLMTIGS------SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQER 282
Query: 414 ESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           +  + DFR G + +L+ T+V +RG+D+  V+ VVN DLP
Sbjct: 283 DRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score =  134 bits (336), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 79/211 (37%), Positives = 121/211 (57%), Gaps = 7/211 (3%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           +  F DM L   +++ +  + +  P++IQ +A+   + G D+L  A++G+GKT  F+I  
Sbjct: 20  VYKFDDMELDEQLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 79
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q     T V     P AL+LAPTRELA QI+K V AL+  +D  K    +GGT+  E  
Sbjct: 80  LQRI--DTSV---KAPQALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVEDA 133
Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD 299
             LR    IVV TPGR  D++Q+      ++   ILDEAD ML  GF+ QI ++   LP 
Sbjct: 134 EGLRDA-QIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 192
Query: 300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
             Q +L SATMP ++  +  +++ +PV++ V
Sbjct: 193 TTQVVLLSATMPNDVLEVTTKFMRNPVRILV 223

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score =  127 bits (320), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 76/212 (35%), Positives = 118/212 (55%), Gaps = 7/212 (3%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           ++SF DM L  S+++ I  + +  P++IQ +A+   + G D++  A++G+G TA F I +
Sbjct: 14  VDSFDDMNLSESLLRGIYAYGFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISI 73
Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q         +     ALVLAPTRELAQQI+  V AL   + +   A  +GGTN+  + 
Sbjct: 74  LQQIELDLXATQ-----ALVLAPTRELAQQIQXVVMALGDYMGASCHA-CIGGTNVRAEV 127
Query: 240 SELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
             L+     I+V TPGR  D L +   S   +   +LDEAD ML  GF  QI ++ Q L 
Sbjct: 128 QXLQMEAPHIIVGTPGRVFDMLNRRYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLN 187
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
              Q +L SATMP ++  +   ++ DP+++ V
Sbjct: 188 SNTQVVLLSATMPSDVLEVTXXFMRDPIRILV 219

>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 =  122 bits (305), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 105/349 (30%), Positives = 172/349 (49%), Gaps = 25/349 (7%)
Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVA 185
           L   I K I   E+   T +Q + +   LS  D  ++  A+TG+GKT AF IP+ QH + 
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI- 86
Query: 186 QTPVGRGDGPLALVLAPTRELAQQIEKEVKA---LSRSLDSFKTAIVVGGTNI---AEQR 239
            T         A+++APTR+LA QIE EVK    ++  L  +    +VGGT+      + 
Sbjct: 87  NTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 146
Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSR-VSFVILDEADRMLDMGFEPQIREVMQNLP 298
           ++LR   +IV+ATPGR +D L++ +    R V + +LDEADR+L++GF   +  +   L 
Sbjct: 147 NKLRP--NIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILN 204
Query: 299 DKH-------QTLLFSATMPVEIEALAQEYLTDPVQVKVGKV--SSPTANVIQILEKVSE 349
           +K+       +TLLFSAT+  +++ LA   +     + +  V  + P A+  +I + V  
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE-RIDQSVVI 263
Query: 350 NEKVDRXXXXXXXXXXXXXKSCHPFPLTIVF---VERKTRCDEVSEALVAEGLHAVALHG 406
           +EK                K        I+F   V+  +    + +    + L  +  HG
Sbjct: 264 SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG 323
Query: 407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
              Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P  L
Sbjct: 324 KITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSEL 372

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  121 bits (303), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 105/349 (30%), Positives = 172/349 (49%), Gaps = 25/349 (7%)
Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVA 185
           L   I K I   E+   T +Q + +   LS  D  ++  A+TG+GKT AF IP+ QH + 
Sbjct: 79  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI- 137
Query: 186 QTPVGRGDGPLALVLAPTRELAQQIEKEVKA---LSRSLDSFKTAIVVGGTNI---AEQR 239
            T         A+++APTR+LA QIE EVK    ++  L  +    +VGGT+      + 
Sbjct: 138 NTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 197
Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSR-VSFVILDEADRMLDMGFEPQIREVMQNLP 298
           ++LR   +IV+ATPGR +D L++ +    R V + +LDEADR+L++GF   +  +   L 
Sbjct: 198 NKLRP--NIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILN 255
Query: 299 DKH-------QTLLFSATMPVEIEALAQEYLTDPVQVKVGKV--SSPTANVIQILEKVSE 349
           +K+       +TLLFSAT+  +++ LA   +     + +  V  + P A+  +I + V  
Sbjct: 256 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE-RIDQSVVI 314
Query: 350 NEKVDRXXXXXXXXXXXXXKSCHPFPLTIVF---VERKTRCDEVSEALVAEGLHAVALHG 406
           +EK                K        I+F   V+  +    + +    + L  +  HG
Sbjct: 315 SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG 374
Query: 407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
              Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P  L
Sbjct: 375 KITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSEL 423

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  120 bits (302), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 105/349 (30%), Positives = 172/349 (49%), Gaps = 25/349 (7%)
Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHCVA 185
           L   I K I   E+   T +Q + +   LS  D  ++  A+TG+GKT AF IP+ QH + 
Sbjct: 28  LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLI- 86
Query: 186 QTPVGRGDGPLALVLAPTRELAQQIEKEVKA---LSRSLDSFKTAIVVGGTNI---AEQR 239
            T         A+++APTR+LA QIE EVK    ++  L  +    +VGGT+      + 
Sbjct: 87  NTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKM 146
Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSR-VSFVILDEADRMLDMGFEPQIREVMQNLP 298
           ++LR   +IV+ATPGR +D L++ +    R V + +LDEADR+L++GF   +  +   L 
Sbjct: 147 NKLRP--NIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILN 204
Query: 299 DKH-------QTLLFSATMPVEIEALAQEYLTDPVQVKVGKV--SSPTANVIQILEKVSE 349
           +K+       +TLLFSAT+  +++ LA   +     + +  V  + P A+  +I + V  
Sbjct: 205 EKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHE-RIDQSVVI 263
Query: 350 NEKVDRXXXXXXXXXXXXXKSCHPFPLTIVF---VERKTRCDEVSEALVAEGLHAVALHG 406
           +EK                K        I+F   V+  +    + +    + L  +  HG
Sbjct: 264 SEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHG 323
Query: 407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
              Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P  L
Sbjct: 324 KITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSEL 372

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 97/343 (28%), Positives = 164/343 (47%), Gaps = 32/343 (9%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
           ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L+  +++G+GKTAAF +
Sbjct: 40  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 99
Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
            M+       P  +   P  L L+PT ELA Q  K ++ + +     K A  V G  +  
Sbjct: 100 AMLSQV---EPANKY--PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL-- 152
Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADRML-DMGFEPQIREVMQ 295
           +R + +    IV+ TPG  LD   +       ++   +LDEAD M+   G + Q   + +
Sbjct: 153 ERGQ-KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQR 211
Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDR 355
            LP   Q LLFSAT    +   AQ+ + DP             NVI++  +    + + +
Sbjct: 212 MLPRNCQMLLFSATFEDSVWKFAQKVVPDP-------------NVIKLKREEETLDTIKQ 258
Query: 356 XXXXXXXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQ 410
                          C+ +  +TI    +F   +     ++  L  EG H VAL  G   
Sbjct: 259 YYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGEMM 317
Query: 411 SDRESA-LRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            ++ +A +  FR G   +LV T+V +RG+DV  V+ V+N DLP
Sbjct: 318 VEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 360

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 98/345 (28%), Positives = 164/345 (47%), Gaps = 36/345 (10%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
           ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L+  +++G+GKTAAF +
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI-- 235
            M+       P  +   P  L L+PT ELA Q  K ++ + +     K A  V G  +  
Sbjct: 84  AMLSQV---EPANKY--PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 138
Query: 236 AEQRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADRML-DMGFEPQIREV 293
            ++ SE      IV+ TPG  LD   +       ++   +LDEAD M+   G + Q   +
Sbjct: 139 GQKISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 193
Query: 294 MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
            + LP   Q LLFSAT    +   AQ+ + DP             NVI++  +    + +
Sbjct: 194 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-------------NVIKLKREEETLDTI 240
Query: 354 DRXXXXXXXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGR 408
            +               C+ +  +TI    +F   +     ++  L  EG H VAL  G 
Sbjct: 241 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGE 299
Query: 409 NQSDRESA-LRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
              ++ +A +  FR G   +LV T+V +RG+DV  V+ V+N DLP
Sbjct: 300 MMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 344

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 97/343 (28%), Positives = 164/343 (47%), Gaps = 32/343 (9%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
           ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L+  +++G+GKTAAF +
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
            M+       P  +   P  L L+PT ELA Q  K ++ + +     K A  V G  +  
Sbjct: 151 AMLSQV---EPANKY--PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL-- 203
Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADRML-DMGFEPQIREVMQ 295
           +R + +    IV+ TPG  LD   +       ++   +LDEAD M+   G + Q   + +
Sbjct: 204 ERGQ-KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQR 262
Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDR 355
            LP   Q LLFSAT    +   AQ+ + DP             NVI++  +    + + +
Sbjct: 263 MLPRNCQMLLFSATFEDSVWKFAQKVVPDP-------------NVIKLKREEETLDTIKQ 309
Query: 356 XXXXXXXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGRNQ 410
                          C+ +  +TI    +F   +     ++  L  EG H VAL  G   
Sbjct: 310 YYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGEMM 368
Query: 411 SDRESA-LRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            ++ +A +  FR G   +LV T+V +RG+DV  V+ V+N DLP
Sbjct: 369 VEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 411

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score =  120 bits (301), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 98/345 (28%), Positives = 164/345 (47%), Gaps = 36/345 (10%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
           ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L+  +++G+GKTAAF +
Sbjct: 61  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 120
Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI-- 235
            M+       P  +   P  L L+PT ELA Q  K ++ + +     K A  V G  +  
Sbjct: 121 AMLSQV---EPANKY--PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 175
Query: 236 AEQRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADRML-DMGFEPQIREV 293
            ++ SE      IV+ TPG  LD   +       ++   +LDEAD M+   G + Q   +
Sbjct: 176 GQKISE-----QIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 230
Query: 294 MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
            + LP   Q LLFSAT    +   AQ+ + DP             NVI++  +    + +
Sbjct: 231 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP-------------NVIKLKREEETLDTI 277
Query: 354 DRXXXXXXXXXXXXXKSCHPF-PLTI----VFVERKTRCDEVSEALVAEGLHAVALHGGR 408
            +               C+ +  +TI    +F   +     ++  L  EG H VAL  G 
Sbjct: 278 KQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASWLAAELSKEG-HQVALLSGE 336
Query: 409 NQSDRESA-LRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
              ++ +A +  FR G   +LV T+V +RG+DV  V+ V+N DLP
Sbjct: 337 MMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 381

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score =  114 bits (285), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 117/212 (55%), Gaps = 9/212 (4%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA F +  +Q
Sbjct: 15  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74
Query: 182 HCVAQTPVGRGDGPLA-LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS 240
                 PV    G ++ LV+  TRELA QI KE +  S+ + + K A+  GG +I +   
Sbjct: 75  QL---EPV---TGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE 128
Query: 241 ELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIREVMQNLP 298
            L+     IVV TPGR L   +  + +L  +   ILDE D+ML+ +     ++E+ +  P
Sbjct: 129 VLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTP 188
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
            + Q ++FSAT+  EI  + ++++ DP+++ V
Sbjct: 189 HEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score =  105 bits (263), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 63/212 (29%), Positives = 111/212 (52%), Gaps = 8/212 (3%)
Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            FT     P I++ I+   + +PT IQ + +P AL G   +G ++TG+GKT A+ +P+ +
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXE 64
Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAI---VVGGTNIAEQ 238
               +    +     A++ APTRELA QI  E   +++     +  +   ++GGT+  + 
Sbjct: 65  KIKPERAEVQ-----AVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKA 119
Query: 239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
             +L     IV+ TPGR  D +++    +     +++DEAD  LD GF   + ++    P
Sbjct: 120 LEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXP 179
Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
              Q L+FSAT+P +++   ++Y  +P  V V
Sbjct: 180 KDLQXLVFSATIPEKLKPFLKKYXENPTFVHV 211

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score =  102 bits (255), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 113/214 (52%), Gaps = 17/214 (7%)
Query: 123 FTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQH 182
           F  + L   +++ +    + RP+ +Q +A+P+   G DL+  A++G+GKT  F+   +  
Sbjct: 26  FESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDS 85
Query: 183 CVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL 242
            V +    +      L+LAPTRE+A QI   + A+   ++  +  + +GGT +++ ++ L
Sbjct: 86  LVLENLSTQ-----ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL 140
Query: 243 RGGVSIVVATPGRF-----LDHLQQGNTSLSRVSFVILDEADRMLDMG-FEPQIREVMQN 296
           +    I V +PGR      LD+L  G+     +   ILDEAD++L+ G F+ QI  +  +
Sbjct: 141 K-KCHIAVGSPGRIKQLIELDYLNPGS-----IRLFILDEADKLLEEGSFQEQINWIYSS 194
Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           LP   Q L  SAT P  +     +Y+ DP  V++
Sbjct: 195 LPASKQMLAVSATYPEFLANALTKYMRDPTFVRL 228

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 122/233 (52%), Gaps = 22/233 (9%)
Query: 117 PAPIESFTDM----CLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKT 172
           P PI +F  +     ++  ++++I    +  PT IQ QA+PV L GR+LL  A TGSGKT
Sbjct: 21  PDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKT 80
Query: 173 AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIV--- 229
            AF+IP++     + P  +G    AL+++PTRELA QI +E+  +S     F+  ++   
Sbjct: 81  LAFSIPILMQL--KQPANKGFR--ALIISPTRELASQIHRELIKISEG-TGFRIHMIHKA 135
Query: 230 -VGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG--NTSLSRVSFVILDEADRMLD--- 283
            V       + S+      I+V TP R +  L+Q      L+ V ++++DE+D++ +   
Sbjct: 136 AVAAKKFGPKSSK---KFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGK 192
Query: 284 MGFEPQIREV-MQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS 335
            GF  Q+  + +     K +  +FSAT   ++E   +  L + + V +G  +S
Sbjct: 193 TGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGARNS 245

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 95.1 bits (235), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 65/204 (31%), Positives = 113/204 (55%), Gaps = 15/204 (7%)
Query: 121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIP 178
           +SF ++ L P ++K I   ++ +P+ IQ +A+P+ L    R+++  +++G+GKTAAF++ 
Sbjct: 22  KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLT 81
Query: 179 MIQHCVAQTPVGRGDG-PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
           M+      T V   D  P A+ LAP+RELA+Q  + V+ + +      + ++V  +   E
Sbjct: 82  ML------TRVNPEDASPQAICLAPSRELARQTLEVVQEMGK-FTKITSQLIVPDS--FE 132
Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIREVMQN 296
           +  ++   V  +V TPG  LD +++    L ++   +LDEAD MLD  G   Q   V + 
Sbjct: 133 KNKQINAQV--IVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRF 190
Query: 297 LPDKHQTLLFSATMPVEIEALAQE 320
           LP   Q +LFSAT    +   A++
Sbjct: 191 LPKDTQLVLFSATFADAVRQYAKK 214

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 93.6 bits (231), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 112/217 (51%), Gaps = 12/217 (5%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
           ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L+  +++G+GKTAAF +
Sbjct: 91  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150
Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
            M+       P  +   P  L L+PT ELA Q  K ++ + +     K A  V G  +  
Sbjct: 151 AMLSQV---EPANKY--PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL-- 203
Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADRML-DMGFEPQIREVMQ 295
           +R + +    IV+ TPG  LD   +       ++   +LDEAD M+   G + Q   + +
Sbjct: 204 ERGQ-KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQR 262
Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
            LP   Q LLFSAT    +   AQ+ + DP  +K+ +
Sbjct: 263 MLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR 299

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 93.2 bits (230), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 112/217 (51%), Gaps = 12/217 (5%)
Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
           ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L+  +++G+GKTAAF +
Sbjct: 24  VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83
Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
            M+       P  +   P  L L+PT ELA Q  K ++ + +     K A  V G  +  
Sbjct: 84  AMLSQV---EPANKY--PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL-- 136
Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADRML-DMGFEPQIREVMQ 295
           +R + +    IV+ TPG  LD   +       ++   +LDEAD M+   G + Q   + +
Sbjct: 137 ERGQ-KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQR 195
Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
            LP   Q LLFSAT    +   AQ+ + DP  +K+ +
Sbjct: 196 MLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR 232

>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain Length = 191

Iteration: 1
 Score = 86.3 bits (212), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/79 (45%), Positives = 55/79 (69%)
Query: 375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA 434
           P  ++F E+K   D + E L+ +G+ AVA+HGG++Q +R  A+  FR G  ++LVATDVA
Sbjct: 55  PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVA 114
Query: 435 SRGLDVMGVAHVVNLDLPK 453
           S+GLD   + HV+N D+P+
Sbjct: 115 SKGLDFPAIQHVINYDMPE 133

>pdb|2JGN|A Chain A, Ddx3 Helicase Domain Length = 185

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 52/78 (66%)
Query: 375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA 434
            LT+VFVE K   D + + L  EG    ++HG R+Q DRE AL  FR+G + ILVAT VA
Sbjct: 47  SLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVA 106
Query: 435 SRGLDVMGVAHVVNLDLP 452
           +RGLD+  V HV+N DLP
Sbjct: 107 ARGLDISNVKHVINFDLP 124

>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound To Regulator Of Ribonuclease Activity A (Rraa) Length = 170

Iteration: 1
 Score = 65.1 bits (157), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 47/77 (61%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
           +IVFV ++ R  E++  L   G++   L G   Q  R  A++    G  N+LVATDVA+R
Sbjct: 33  SIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAAR 92
Query: 437 GLDVMGVAHVVNLDLPK 453
           G+D+  V+HV N D+P+
Sbjct: 93  GIDIPDVSHVFNFDMPR 109

>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera Form 2, Complete Dimer, Symmetric Length = 212

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 46/76 (60%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
            +VF   K   +E+++ L+  G  A ALHG  +Q +RE  L  FR G   +LVATDVA+R
Sbjct: 34  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAAR 93
Query: 437 GLDVMGVAHVVNLDLP 452
           GLD+  V  VV+  LP
Sbjct: 94  GLDIPQVDLVVHYRLP 109

>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including The C-Terminal Reca Domain, The Dimerization Domain, And The Rna Binding Domain Length = 300

Iteration: 1
 Score = 62.8 bits (151), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 32/76 (42%), Positives = 46/76 (60%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
            +VF   K   +E+++ L+  G  A ALHG  +Q +RE  +  FR G   +LVATDVA+R
Sbjct: 31  AMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAAR 90
Query: 437 GLDVMGVAHVVNLDLP 452
           GLD+  V  VV+  +P
Sbjct: 91  GLDIPQVDLVVHYRMP 106

>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The Bacillus Subtilis Yxin Protein Length = 163

Iteration: 1
 Score = 60.1 bits (144), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/75 (37%), Positives = 44/75 (58%)
Query: 378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG 437
           I+F   K   +++++ L   G     +HGG  Q DR   + +F+ G    LVATDVA+RG
Sbjct: 39  IIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARG 98
Query: 438 LDVMGVAHVVNLDLP 452
           +D+  ++ V+N DLP
Sbjct: 99  IDIENISLVINYDLP 113

>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast Eif4a Length = 165

Iteration: 1
 Score = 58.9 bits (141), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 32/113 (28%), Positives = 62/113 (54%), Gaps = 9/113 (7%)
Query: 378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG 437
           ++F   + + +E++  L  +     A++    Q +R++ +++FR+GS+ IL++TD+ +RG
Sbjct: 34  VIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARG 93
Query: 438 LDVMGVAHVVNLDLP--------KVLLAASESLCTTSFNITTNLD-GDMKKLE 481
           +DV  V+ V+N DLP        ++           + N  TN D G M++LE
Sbjct: 94  IDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFVTNEDVGAMRELE 146

>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p Length = 187

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
           +I+FV  K   + +   L +EG     LHG     +R+  + DFR G + +L+ T+V +R
Sbjct: 38  SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 97
Query: 437 GLDVMGVAHVVNLDLP 452
           G+D+  V+ VVN DLP
Sbjct: 98  GIDIPTVSMVVNYDLP 113

>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein Dbp5 Length = 189

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
           +I+FV  K   + +   L +EG     LHG     +R+  + DFR G + +L+ T+V +R
Sbjct: 40  SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 99
Query: 437 GLDVMGVAHVVNLDLP 452
           G+D+  V+ VVN DLP
Sbjct: 100 GIDIPTVSXVVNYDLP 115

>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1 H337r And Ip6 Length = 188

Iteration: 1
 Score = 56.6 bits (135), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
           +I+FV  K   + +   L +EG     LHG     +R+  + DFR G + +L+ T+V +R
Sbjct: 39  SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 98
Query: 437 GLDVMGVAHVVNLDLP 452
           G+D+  V+ VVN DLP
Sbjct: 99  GIDIPTVSXVVNYDLP 114

>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex With An Edc3-Fdf Peptide Length = 193

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 39/78 (50%)
Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
           +I+F     R + +++ +   G     +H    Q  R     DFRNG    LV TD+ +R
Sbjct: 47  SIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTR 106
Query: 437 GLDVMGVAHVVNLDLPKV 454
           G+D+  V  V+N D PK+
Sbjct: 107 GIDIQAVNVVINFDFPKL 124

>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56 Length = 172

Iteration: 1
 Score = 55.1 bits (131), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 46/80 (57%)
Query: 374 FPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV 433
           F   ++FV+   RC  +++ LV +   A+A+H G  Q +R S  + F++    ILVAT++
Sbjct: 31  FNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL 90
Query: 434 ASRGLDVMGVAHVVNLDLPK 453
             RG+D+  V    N D+P+
Sbjct: 91  FGRGMDIERVNIAFNYDMPE 110

>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core Length = 523

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 73/340 (21%), Positives = 133/340 (39%), Gaps = 56/340 (16%)
Query: 131 SIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG 190
            ++++   ++  RP   Q + +   LSGRD L    TG GK+  + IP +          
Sbjct: 15  QVLQETFGYQQFRPG--QEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPALLL-------- 64
Query: 191 RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-----GG 245
                L +V++P   L +    +++A      +   A  +  T   EQ+ E+      G 
Sbjct: 65  ---NGLTVVVSPLISLXKDQVDQLQA------NGVAAACLNSTQTREQQLEVXTGCRTGQ 115
Query: 246 VSIVVATPGR-----FLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEPQIREVMQNLP 298
           + ++   P R     FL+HL   N  L     + +DEA  +   G  F P+   + Q L 
Sbjct: 116 IRLLYIAPERLXLDNFLEHLAHWNPVL-----LAVDEAHCISQWGHDFRPEYAALGQ-LR 169
Query: 299 DKHQTLLFSATMPVEIEALAQEY-----LTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
            +  TL F A      +   Q+      L DP+ +++     P      + EK    +++
Sbjct: 170 QRFPTLPFXALTATADDTTRQDIVRLLGLNDPL-IQISSFDRPNIRYX-LXEKFKPLDQL 227
Query: 354 DRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR 413
            R                      I++   + + ++ +  L ++G+ A A H G   + R
Sbjct: 228 XRYVQEQRGKS------------GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVR 275
Query: 414 ESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
                 F+     I+VAT     G++   V  VV+ D+P+
Sbjct: 276 ADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPR 315

>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S Length = 523

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 73/340 (21%), Positives = 135/340 (39%), Gaps = 56/340 (16%)
Query: 131 SIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVG 190
            ++++   ++  RP   Q + +   LSGRD L    TG GK+  + IP +          
Sbjct: 15  QVLQETFGYQQFRPG--QEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-------- 64
Query: 191 RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL-----RGG 245
                L +V++P   L +    +++A      +   A  +  T   EQ+ E+      G 
Sbjct: 65  ---NGLTVVVSPLISLMKDQVDQLQA------NGVAAACLNSTQTREQQLEVMTGCRTGQ 115
Query: 246 VSIVVATPGR-----FLDHLQQGNTSLSRVSFVILDEADRMLDMG--FEPQIREVMQNLP 298
           + ++   P R     FL+HL   N  L     + +DEA  +   G  F P+   + Q L 
Sbjct: 116 IRLLYIAPERLMLDNFLEHLAHWNPVL-----LAVDEAHCISQWGHDFRPEYAALGQ-LR 169
Query: 299 DKHQTLLFSATMPVEIEALAQEY-----LTDPVQVKVGKVSSPTANVIQILEKVSENEKV 353
            +  TL F A      +   Q+      L DP+ +++     P    + ++EK    +++
Sbjct: 170 QRFPTLPFMALTATADDTTRQDIVRLLGLNDPL-IQISSFDRPNIRYM-LMEKFKPLDQL 227
Query: 354 DRXXXXXXXXXXXXXKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR 413
            R                      I++   + + ++ +  L ++G+ A A H G   + R
Sbjct: 228 MRYVQEQRGKS------------GIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVR 275
Query: 414 ESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
                 F+     I+VAT     G++   V  VV+ D+P+
Sbjct: 276 ADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPR 315

>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna Helicase Length = 175

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 40/75 (53%)
Query: 378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG 437
           I+F + +     ++  ++ +G     L G      R S ++ FR+G   +L+ T+V +RG
Sbjct: 38  IIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNVCARG 97
Query: 438 LDVMGVAHVVNLDLP 452
           +DV  V  VVN DLP
Sbjct: 98  IDVKQVTIVVNFDLP 112

>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction Length = 780

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 75/315 (23%), Positives = 130/315 (41%), Gaps = 49/315 (15%)
Query: 139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL 198
           H+  R   I  + M   L G       + GSGKT    + ++ +  A        G    
Sbjct: 377 HQEIRNDMISEKPMNRLLQG-------DVGSGKTVVAQLAILDNYEA--------GFQTA 421
Query: 199 VLAPTRELA-QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ---RSELRGG-VSIVVATP 253
            + PT  LA Q   + V++ S+   +   A+++G T  +E+   +S LR G + +V+ T 
Sbjct: 422 FMVPTSILAIQHYRRTVESFSKF--NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTH 479
Query: 254 GRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVE 313
                 L Q +     +  VI+DE  R     F  + RE + N      TL+ SAT P+ 
Sbjct: 480 A-----LIQEDVHFKNLGLVIIDEQHR-----FGVKQREALMNKGKMVDTLVMSAT-PIP 528
Query: 314 IEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRXXXXXXXXXXXXXKSCHP 373
             ++A  +  D + V V     P    +Q +  +   ++V+              ++   
Sbjct: 529 -RSMALAFYGD-LDVTVIDEMPPGRKEVQTM--LVPMDRVNEVYEFVRQEVMRGGQAFIV 584
Query: 374 FPLTIVFVERKTRCD-----EVSEALVAEGLHAVAL---HGGRNQSDRESALRDFRNGST 425
           +PL    +E   + +     E+ E L  E      L   HG  +Q +++  + +F  G  
Sbjct: 585 YPL----IEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRY 640
Query: 426 NILVATDVASRGLDV 440
           +ILV+T V   G+DV
Sbjct: 641 DILVSTTVIEVGIDV 655

>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           L  +  HG   Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P  L
Sbjct: 61  LPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSEL 117

>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric Rna-Dna Duplex Length = 256

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           L  +  HG   Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P  L
Sbjct: 61  LPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSEL 117

>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex Length = 257

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVL 455
           L  +  HG   Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P  L
Sbjct: 61  LPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSEL 117

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	503
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	1e-178
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-174
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	1e-128
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	1e-128
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	1e-127
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-126
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-125
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-125
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-125
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-124
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	1e-123
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	1e-121
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-120
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-120
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-118
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-116
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-115
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-114
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-112
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	1e-108
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	2e-95
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	7e-95
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-91
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-88
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	1e-86
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	1e-85
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-84
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-84
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	4e-83
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-82
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	3e-73
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	4e-50
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	5e-49
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	1e-33
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	7e-33
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	1e-31
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	3e-31
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	3e-30
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	7e-27
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	8e-26
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-22
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-17
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	3e-18
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	5e-16
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	3e-15
3b6e_A	216	Interferon-induced helicase C domain-containing P;	1e-14
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	3e-14
1yks_A	440	Genome polyprotein [contains: flavivirin protease	1e-13
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	1e-13
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	8e-13
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	2e-12
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	3e-12
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	1e-06
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	3e-12
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	1e-06
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	5e-12
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	4e-07
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	3e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-11
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	4e-08
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	5e-11
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	2e-07
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	1e-10
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	8e-10
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	2e-09
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	3e-09
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-08
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	1e-07
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	2e-07
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	2e-07
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	8e-07
3h1t_A	590	Type I site-specific restriction-modification syst	8e-06
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	7e-05

>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 =  505 bits (1303), Expect = e-178
 Identities = 143/373 (38%), Positives = 209/373 (56%), Gaps = 15/373 (4%)

Query: 84  PSDRVLRFNPEQIEEVRLRLNVDVTV-ASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYT 142
            +D +  F+      +      ++ V  +GS   P PI+ FT   L   I+ ++    Y 
Sbjct: 19  SNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDV-PQPIQHFTSADLRDIIIDNVNKSGYK 77

Query: 143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP 202
            PT IQ  ++PV  SGRDL+ CA+TGSGKTAAF +P++   +          P  ++++P
Sbjct: 78  IPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGRPQVVIVSP 137

Query: 203 TRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ 262
           TRELA QI  E +  +      K  IV GGT+   Q   +  G  +V+ATPGR LD + +
Sbjct: 138 TRELAIQIFNEARKFAFESY-LKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDR 196

Query: 263 GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN--LPDKHQTLLFSATMPVEIEALAQE 320
              +     FV+LDEADRMLDMGF   +R +M +  +  +HQTL+FSAT P EI+ +A E
Sbjct: 197 TFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGE 256

Query: 321 YLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVF 380
           +L + V V +G V    ++V Q + +V++  K  +L+ +L E+A            TIVF
Sbjct: 257 FLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQA----------DGTIVF 306

Query: 381 VERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDV 440
           VE K   D ++  L  +     ++HG R QS RE ALRDF+NGS  +L+AT VASRGLD+
Sbjct: 307 VETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVASRGLDI 366

Query: 441 MGVAHVVNLDLPK 453
             + HV+N D+P 
Sbjct: 367 KNIKHVINYDMPS 379

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  495 bits (1276), Expect = e-174
 Identities = 150/354 (42%), Positives = 212/354 (59%), Gaps = 26/354 (7%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
           P  IESF+D+ +   IM +IE   YTRPT +Q  A+P+    RDL+ CA+TGSGKTAAF 
Sbjct: 11  PPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFL 70

Query: 177 IPMIQHCVAQTPV-------------GRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
           +P++    +  P               R   P++LVLAPTRELA QI +E +  S     
Sbjct: 71  LPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSR- 129

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD 283
            +  +V GG +I +Q  +L  G  ++VATPGR +D +++G   L    +++LDEADRMLD
Sbjct: 130 VRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLD 189

Query: 284 MGFEPQIREVMQ--NLPDK--HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTAN 339
           MGFEPQIR +++   +P K    T++FSAT P EI+ LA+++L + + + VG+V S + N
Sbjct: 190 MGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSEN 249

Query: 340 VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL 399
           + Q +  V E++K   LL LL         +     LT+VFVE K   D + + L  EG 
Sbjct: 250 ITQKVVWVEESDKRSFLLDLL--------NATGKDSLTLVFVETKKGADSLEDFLYHEGY 301

Query: 400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
              ++HG R+Q DRE AL  FR+G + ILVAT VA+RGLD+  V HV+N DLP 
Sbjct: 302 ACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPS 355

>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 =  376 bits (967), Expect = e-128
 Identities = 104/327 (31%), Positives = 166/327 (50%), Gaps = 31/327 (9%)

Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQT 187
           ++  I + I    +   T +Q++ +P+ L G++++  A+TGSGKTAA+ IP+++      
Sbjct: 1   MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----- 55

Query: 188 PVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVS 247
                 G  +LV+ PTREL +Q+   ++ + R +D  K A V GG     Q + +R    
Sbjct: 56  ------GMKSLVVTPTRELTRQVASHIRDIGRYMD-TKVAEVYGGMPYKAQINRVRN-AD 107

Query: 248 IVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS 307
           IVVATPGR LD   +G   LS    VI+DEAD M +MGF   I+ ++    ++  T LFS
Sbjct: 108 IVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFS 167

Query: 308 ATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLA 367
           AT+P EI  + ++++T+  ++   +     ANV      V ++ +        + E    
Sbjct: 168 ATIPEEIRKVVKDFITNYEEI---EACIGLANVEHKFVHVKDDWR---SKVQALRE---- 217

Query: 368 EKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNI 427
               +     IVFV  + R  ++          A+ L G   QS R   +  FR G  ++
Sbjct: 218 ----NKDKGVIVFVRTRNRVAKLVRLFDN----AIELRGDLPQSVRNRNIDAFREGEYDM 269

Query: 428 LVATDVASRGLDVMGVAHVVNLDLPKV 454
           L+ TDVASRGLD+  V  V+N D P+ 
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQD 296

>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 =  378 bits (972), Expect = e-128
 Identities = 106/348 (30%), Positives = 166/348 (47%), Gaps = 17/348 (4%)

Query: 106 DVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCA 165
           D    +  V       +F D  L   ++  I    + +P+ IQ +A+PVA++GRD+L  A
Sbjct: 7   DTRPQTDDVLNTKGN-TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARA 65

Query: 166 ETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFK 225
           + G+GKTAAF IP ++    +          AL++ PTRELA Q  + V+ L +      
Sbjct: 66  KNGTGKTAAFVIPTLEKVKPKLNK-----IQALIMVPTRELALQTSQVVRTLGKHCG-IS 119

Query: 226 TAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG 285
             +  GGTN+ +    L   V I+V TPGR LD   +    LS  S  I+DEAD+ML   
Sbjct: 120 CMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRD 179

Query: 286 FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILE 345
           F+  I +++  LP  HQ+LLFSAT P+ ++    ++L  P ++ + +       + Q   
Sbjct: 180 FKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYA 238

Query: 346 KVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALH 405
            V E +K+  L  L          S       I+F     R + +++ +   G      H
Sbjct: 239 FVEERQKLHCLNTLF---------SKLQINQAIIFCNSTNRVELLAKKITDLGYSCYYSH 289

Query: 406 GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
               Q +R     +FR G    LV +D+ +RG+D+  V  V+N D PK
Sbjct: 290 ARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPK 337

>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 =  376 bits (967), Expect = e-127
 Identities = 114/372 (30%), Positives = 193/372 (51%), Gaps = 26/372 (6%)

Query: 83  KPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYT 142
             S R      E + +V    + +V V            +F  M L   +++ I  + + 
Sbjct: 9   SGSARKRLLKEEDMTKVEFETSEEVDV----------TPTFDTMGLREDLLRGIYAYGFE 58

Query: 143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP 202
           +P++IQ +A+   + GRD++  +++G+GKTA F+I ++Q    Q          AL+LAP
Sbjct: 59  KPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVR-----ETQALILAP 113

Query: 203 TRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ 262
           TRELA QI+K + AL   ++  +    +GGTN+ E   +L  G  +V  TPGR  D +++
Sbjct: 114 TRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR 172

Query: 263 GNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYL 322
            +     +  ++LDEAD ML+ GF+ QI +V + LP   Q +L SAT+P EI  +  +++
Sbjct: 173 RSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFM 232

Query: 323 TDPVQVKVGKVSSPTANVIQILEKVS-ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFV 381
           TDP+++ V +       + Q    V  E  K D L  L                  ++F 
Sbjct: 233 TDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLY---------DTLTITQAVIFC 283

Query: 382 ERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM 441
             K + D ++E +        ++HG   Q +RES +++FR+G++ +L++TDV +RGLDV 
Sbjct: 284 NTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVP 343

Query: 442 GVAHVVNLDLPK 453
            V+ ++N DLP 
Sbjct: 344 QVSLIINYDLPN 355

>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 =  372 bits (958), Expect = e-126
 Identities = 122/332 (36%), Positives = 184/332 (55%), Gaps = 23/332 (6%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMI 180
           +F ++ L  +I+  I    + +PT IQ + +P+ L+   +++  A TGSGKTA+F IP+I
Sbjct: 7   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 181 QHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS 240
           +       V   +G  A++L PTRELA Q+  E+++L  + +  K A + GG  I  Q  
Sbjct: 67  EL------VNENNGIEAIILTPTRELAIQVADEIESLKGNKN-LKIAKIYGGKAIYPQIK 119

Query: 241 ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK 300
            L+   +IVV TPGR LDH+ +G  +L  V + ILDEAD ML+MGF   + +++      
Sbjct: 120 ALKNA-NIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKD 178

Query: 301 HQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALL 360
            + LLFSATMP EI  LA++Y+ D   +K    +    N+ Q   +V+ENE+ + L  LL
Sbjct: 179 KRILLFSATMPREILNLAKKYMGDYSFIKAKINA----NIEQSYVEVNENERFEALCRLL 234

Query: 361 VEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF 420
             + F            +VF + K    E++  L   G  A A+HG  +QS RE  +R F
Sbjct: 235 KNKEFYG----------LVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLF 284

Query: 421 RNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           +     IL+ATDV SRG+DV  +  V+N  LP
Sbjct: 285 KQKKIRILIATDVMSRGIDVNDLNCVINYHLP 316

>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 =  371 bits (954), Expect = e-125
 Identities = 109/336 (32%), Positives = 179/336 (53%), Gaps = 17/336 (5%)

Query: 119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIP 178
            +  F DM L  ++++ +  + +  P++IQ +A+   + G D+L  A++G+GKT  F+I 
Sbjct: 19  VVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIA 78

Query: 179 MIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ 238
            +Q             P AL+LAPTRELA QI+K V AL+  +D  K    +GGT+  E 
Sbjct: 79  ALQRIDTSVK-----APQALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVED 132

Query: 239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
              LR    IVV TPGR  D++Q+      ++   ILDEAD ML  GF+ QI ++   LP
Sbjct: 133 AEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLP 191

Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRLL 357
              Q +L SATMP ++  +  +++ +PV++ V K       + Q    V E E K + L 
Sbjct: 192 PTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLT 251

Query: 358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL 417
            L                  ++F   + + +E++  L  +     A++    Q +R++ +
Sbjct: 252 DLY---------DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIM 302

Query: 418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           ++FR+GS+ IL++TD+ +RG+DV  V+ V+N DLP 
Sbjct: 303 KEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPA 338

>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 =  364 bits (938), Expect = e-125
 Identities = 102/242 (42%), Positives = 150/242 (61%), Gaps = 5/242 (2%)

Query: 93  PEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAM 152
            +++E  R    + V    G    P P+ +F +     ++M  I    +T PT+IQAQ  
Sbjct: 5   AQEVETYRRSKEITV---RGH-NCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGW 60

Query: 153 PVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEK 212
           PVALSG D++G A+TGSGKT ++ +P I H   Q  + RGDGP+ LVLAPTRELAQQ+++
Sbjct: 61  PVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQ 120

Query: 213 EVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSF 272
                 R+    K+  + GG     Q  +L  GV I +ATPGR +D L+ G T+L R ++
Sbjct: 121 VAAEYCRACR-LKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTY 179

Query: 273 VILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           ++LDEADRMLDMGFEPQIR+++  +    QTL++SAT P E+  LA+++L D + + +G 
Sbjct: 180 LVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGA 239

Query: 333 VS 334
           + 
Sbjct: 240 LE 241

>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 =  371 bits (954), Expect = e-125
 Identities = 112/336 (33%), Positives = 182/336 (54%), Gaps = 17/336 (5%)

Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           ++SF DM L  S+++ I  + + +P++IQ +A+   + G D++  A++G+GKTA F I +
Sbjct: 39  VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISI 98

Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q               ALVLAPTRELAQQI+K V AL   +        +GGTN+  + 
Sbjct: 99  LQQIELDLK-----ATQALVLAPTRELAQQIQKVVMALGDYMG-ASCHACIGGTNVRAEV 152

Query: 240 SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
            +L+     I+V TPGR  D L +   S   +   +LDEAD ML  GF+ QI ++ Q L 
Sbjct: 153 QKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLN 212

Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS-ENEKVDRLL 357
              Q +L SATMP ++  + ++++ DP+++ V K       + Q    V  E  K+D L 
Sbjct: 213 SNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLDTLC 272

Query: 358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL 417
            L                  ++F+  + + D ++E + A      A+HG  +Q +R+  +
Sbjct: 273 DLY---------ETLTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIM 323

Query: 418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           R+FR+GS+ +L+ TD+ +RG+DV  V+ V+N DLP 
Sbjct: 324 REFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPT 359

>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 =  362 bits (932), Expect = e-124
 Identities = 101/249 (40%), Positives = 150/249 (60%), Gaps = 9/249 (3%)

Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLG 163
           ++ V+V      A   IE+F ++ L P+I  +I    Y RPT IQ  A+P  L  RD++ 
Sbjct: 6   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMA 65

Query: 164 CAETGSGKTAAFTIPMIQHC----VAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR 219
           CA+TGSGKTAAF IP+I H     + Q    +   P  L+LAPTRELA QI  E +  S 
Sbjct: 66  CAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL 125

Query: 220 SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD 279
           +    ++ +V GG +   Q  E++ G  ++VATPGR +D +++   SL    +++LDEAD
Sbjct: 126 NTP-LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEAD 184

Query: 280 RMLDMGFEPQIREVMQNL----PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSS 335
           RMLDMGFEPQIR++++          QTL+FSAT P EI+ LA ++L + + + VG+V S
Sbjct: 185 RMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGS 244

Query: 336 PTANVIQIL 344
            + ++ Q +
Sbjct: 245 TSDSIKQEI 253

>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 =  364 bits (937), Expect = e-123
 Identities = 103/335 (30%), Positives = 174/335 (51%), Gaps = 17/335 (5%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA F +  +Q
Sbjct: 9   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
                T          LV+  TRELA QI KE +  S+ + + K A+  GG +I +    
Sbjct: 69  QLEPVTG-----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV 123

Query: 242 LRGGVS-IVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIREVMQNLPD 299
           L+     IVV TPGR L   +  + +L  +   ILDE D+ML+ +     ++E+ +  P 
Sbjct: 124 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 183

Query: 300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKVSENEKVDRLLA 358
           + Q ++FSAT+  EI  + ++++ DP+++ V   +  T + + Q   K+ +NEK  +L  
Sbjct: 184 EKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFD 243

Query: 359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALR 418
           LL             F   ++FV+   RC  +++ LV +   A+A+H G  Q +R S  +
Sbjct: 244 LL---------DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQ 294

Query: 419 DFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            F++    ILVAT++  RG+D+  V    N D+P+
Sbjct: 295 QFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPE 329

>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 =  365 bits (938), Expect = e-121
 Identities = 106/429 (24%), Positives = 181/429 (42%), Gaps = 32/429 (7%)

Query: 45  KLSFSSKSLPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRFNPEQIEEVRLRLN 104
             +  ++   NF  +  N    R   S    +P   + +  D V        + + +   
Sbjct: 3   LYNDGNRDQRNFGRNQRNNNSNRYRNSRFNSRPRTRSREDDDEVHFDKTTFSKLIHVP-- 60

Query: 105 VDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLL 162
                   +           +  L   I K I   E+   T +Q + +   LS    D++
Sbjct: 61  -----KEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVI 115

Query: 163 GCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR--- 219
             A+TG+GKT AF IP+ QH +  T         A+++APTR+LA QIE EVK +     
Sbjct: 116 ARAKTGTGKTFAFLIPIFQH-LINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNY 174

Query: 220 SLDSFKTAIVVGGTNIAEQRSEL-RGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDE 277
            L  +    +VGGT+     +++ +   +IV+ATPGR +D L++ +      V + +LDE
Sbjct: 175 GLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDE 234

Query: 278 ADRMLDMGFEPQIREVMQNLPDKH-------QTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           ADR+L++GF   +  +   L +K+       +TLLFSAT+  +++ LA   +     + +
Sbjct: 235 ADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFL 294

Query: 331 GKVSSPT----ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR 386
             V          + Q +    +       +   VE      K        I+F      
Sbjct: 295 DTVDKNEPEAHERIDQSVVISEKFAN---SIFAAVEHIKKQIKERDSNYKAIIFAPTVKF 351

Query: 387 CDEVSEAL---VAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGV 443
              +   L     + L  +  HG   Q+ R S ++ F+   + ILV TDV +RG+D   V
Sbjct: 352 TSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNV 411

Query: 444 AHVVNLDLP 452
             V+ + +P
Sbjct: 412 HEVLQIGVP 420

>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 =  351 bits (902), Expect = e-120
 Identities = 85/227 (37%), Positives = 126/227 (55%), Gaps = 5/227 (2%)

Query: 106 DVTVASGSVPAPAPIESFTD-MCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGC 164
           D+         P P   F D    +P ++K I      +PT IQ+QA P+ L G DL+  
Sbjct: 5   DLKSGEKR-LIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVV 63

Query: 165 AETGSGKTAAFTIPMIQHCVAQ-TPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
           A+TG+GKT ++ +P   H  +Q     + +GP  LVL PTRELA  +E E    S     
Sbjct: 64  AQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYK--G 121

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD 283
            K+  + GG N   Q  ++  GV I++ATPGR  D     + +L  ++++++DEAD+MLD
Sbjct: 122 LKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVIDEADKMLD 181

Query: 284 MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           M FEPQIR+++ ++    QT++ SAT P  +  LA  YL DP+ V V
Sbjct: 182 MEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV 228

>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 =  363 bits (934), Expect = e-120
 Identities = 99/353 (28%), Positives = 163/353 (46%), Gaps = 25/353 (7%)

Query: 121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIP 178
               +  L   I K I   E+   T +Q + +   LS    D++  A+TG+GKT AF IP
Sbjct: 21  SLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIP 80

Query: 179 MIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR---SLDSFKTAIVVGGTNI 235
           + QH +  T         A+++APTR+LA QIE EVK +      L  +    +VGGT+ 
Sbjct: 81  IFQH-LINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDF 139

Query: 236 AEQRSEL-RGGVSIVVATPGRFLDHLQQGNTSLSR-VSFVILDEADRMLDMGFEPQIREV 293
               +++ +   +IV+ATPGR +D L++ +    R V + +LDEADR+L++GF   +  +
Sbjct: 140 RAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETI 199

Query: 294 MQNLPDKH-------QTLLFSATMPVEIEALAQEYLTDPVQVKVGKV---SSPTA-NVIQ 342
              L +K+       +TLLFSAT+  +++ LA   +     + +  V          + Q
Sbjct: 200 SGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQ 259

Query: 343 ILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL---VAEGL 399
            +    +       +   VE      K        I+F         +   L     + L
Sbjct: 260 SVVISEKFAN---SIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDL 316

Query: 400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             +  HG   Q+ R S ++ F+   + ILV TDV +RG+D   V  V+ + +P
Sbjct: 317 PILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVP 369

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  346 bits (890), Expect = e-116
 Identities = 56/358 (15%), Positives = 109/358 (30%), Gaps = 60/358 (16%)

Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQT 187
            +       +       T  Q       + G+     A TG GKT    +  +       
Sbjct: 6   EYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWL----- 60

Query: 188 PVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR---- 243
                 G  + ++ PT  L +Q  + ++ L+   +  K           E+    +    
Sbjct: 61  ---ARKGKKSALVFPTVTLVKQTLERLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEE 115

Query: 244 GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQT 303
               I+V +      +  +   S  R  FV +D+ D +L          +M  +P++   
Sbjct: 116 DDYHILVFSTQFVSKN--REKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIR 173

Query: 304 LLFSATMPVEIEALAQE---------------------YLTDPVQVKVGKVSSPTANVIQ 342
             FS     +I    +                         D +   VG++ S   N+  
Sbjct: 174 KAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITH 233

Query: 343 ILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV 402
           +       EK+  LL +  +               ++F + +    E+ E L     +  
Sbjct: 234 VRISSRSKEKLVELLEIFRD-------------GILIFAQTEEEGKELYEYLKRFKFNVG 280

Query: 403 ALHGGRNQSDRESALRDFRNGSTNILVATDV----ASRGLDVM-GVAHVVNLDLPKVL 455
                    + E    DF+ G  NIL+         +RG+D+   + +V+    P   
Sbjct: 281 ETWS-----EFEKNFEDFKVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGP 333

>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 =  344 bits (886), Expect = e-115
 Identities = 97/338 (28%), Positives = 168/338 (49%), Gaps = 25/338 (7%)

Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTI 177
            +SF ++ L P ++K I   ++ +P+ IQ +A+P+ L    R+++  +++G+GKTAAF++
Sbjct: 4   AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL 63

Query: 178 PMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE 237
            M+     +        P A+ LAP+RELA+Q  + V+ + +        IV       +
Sbjct: 64  TMLTRVNPEDA-----SPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNK 118

Query: 238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQN 296
           Q         ++V TPG  LD +++    L ++   +LDEAD MLD  G   Q   V + 
Sbjct: 119 QI-----NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRF 173

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI-QILEKV-SENEKVD 354
           LP   Q +LFSAT    +   A++ + +   +++ + +    + I Q+     +E +K D
Sbjct: 174 LPKDTQLVLFSATFADAVRQYAKKIVPNANTLEL-QTNEVNVDAIKQLYMDCKNEADKFD 232

Query: 355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRE 414
            L  L                 +I+FV  K   + +   L +EG     LHG     +R+
Sbjct: 233 VLTELY---------GLMTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERD 283

Query: 415 SALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             + DFR G + +L+ T+V +RG+D+  V+ VVN DLP
Sbjct: 284 RLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLP 321

>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 =  343 bits (882), Expect = e-114
 Identities = 96/354 (27%), Positives = 157/354 (44%), Gaps = 23/354 (6%)

Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDL 161
            V+V     + P  + ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L
Sbjct: 9   QVEVLQRDPNSPLYS-VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 67

Query: 162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL 221
           +  +++G+GKTAAF + M+              P  L L+PT ELA Q  K ++ + +  
Sbjct: 68  IAQSQSGTGKTAAFVLAMLSQVEPANK-----YPQCLCLSPTYELALQTGKVIEQMGKFY 122

Query: 222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQ-QGNTSLSRVSFVILDEADR 280
              K A  V G  +       +    IV+ TPG  LD           ++   +LDEAD 
Sbjct: 123 PELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV 179

Query: 281 MLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTAN 339
           M+   G + Q   + + LP   Q LLFSAT    +   AQ+ + DP  +K+ +       
Sbjct: 180 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDT 239

Query: 340 VIQILEKV-SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG 398
           + Q      S +EK   L  L                  ++F   +     ++  L  EG
Sbjct: 240 IKQYYVLCSSRDEKFQALCNLY---------GAITIAQAMIFCHTRKTASWLAAELSKEG 290

Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
                L G      R + +  FR G   +LV T+V +RG+DV  V+ V+N DLP
Sbjct: 291 HQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLP 344

>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 =  338 bits (870), Expect = e-112
 Identities = 106/428 (24%), Positives = 174/428 (40%), Gaps = 25/428 (5%)

Query: 32  SSSVVTLDSDLTTKLSFSSKSLPNFSNSNSNTTCRRSYASHPVPQPVFNNWKPSDRVLRF 91
           ++    L  D     + S  +L          T      ++   +      K        
Sbjct: 2   ATDSWALAVDEQEAAAESLSNLHLKEEKIKPDTNGAVVKTNANAEKTDEEEKEDRAAQSL 61

Query: 92  NPEQIEEVRLRLNVDVTVASGSVPAPAP-IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQ 150
             + I    +     V V      +P   ++SF ++ L P +++ +    + RP+ IQ  
Sbjct: 62  LNKLIRSNLVDNTNQVEVLQRDPNSPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQEN 121

Query: 151 AMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ 208
           A+P+ L+   ++L+  +++G+GKTAAF + M+              P  L L+PT ELA 
Sbjct: 122 ALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKY-----PQCLCLSPTYELAL 176

Query: 209 QIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SL 267
           Q  K ++ + +     K A  V G  +       +    IV+ TPG  LD   +      
Sbjct: 177 QTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDP 233

Query: 268 SRVSFVILDEADRMLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPV 326
            ++   +LDEAD M+   G + Q   + + LP   Q LLFSAT    +   AQ+ + DP 
Sbjct: 234 KKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPN 293

Query: 327 QVKVGKVSSPTANVI-QILEKV-SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERK 384
            +K+ K    T + I Q      S +EK   L  L                  ++F   +
Sbjct: 294 VIKL-KREEETLDTIKQYYVLCSSRDEKFQALCNLY---------GAITIAQAMIFCHTR 343

Query: 385 TRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVA 444
                ++  L  EG     L G      R + +  FR G   +LV T+V +RG+DV  V+
Sbjct: 344 KTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVS 403

Query: 445 HVVNLDLP 452
            V+N DLP
Sbjct: 404 VVINFDLP 411

>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 =  320 bits (823), Expect = e-108
 Identities = 73/253 (28%), Positives = 127/253 (50%), Gaps = 20/253 (7%)

Query: 94  EQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMC----LHPSIMKDIEFHEYTRPTSIQA 149
            +I  +R +  + V    G+   P PI +F  +     ++  ++++I    +  PT IQ 
Sbjct: 2   MKINFLRNKHKIHV---QGTDL-PDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQM 57

Query: 150 QAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ 209
           QA+PV L GR+LL  A TGSGKT AF+IP++             G  AL+++PTRELA Q
Sbjct: 58  QAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQP----ANKGFRALIISPTRELASQ 113

Query: 210 IEKEVKALSRSLDSFKTAIVVGGTNIAEQ-RSELRGGVSIVVATPGRFLDHLQQGNT--S 266
           I +E+  +S     F+  ++      A++   +      I+V TP R +  L+Q      
Sbjct: 114 IHRELIKISEGTG-FRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGID 172

Query: 267 LSRVSFVILDEADRMLD---MGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYL 322
           L+ V ++++DE+D++ +    GF  Q+  +       K +  +FSAT   ++E   +  L
Sbjct: 173 LASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNL 232

Query: 323 TDPVQVKVGKVSS 335
            + + V +G  +S
Sbjct: 233 DNVISVSIGARNS 245

>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 =  288 bits (739), Expect = 2e-95
 Identities = 84/224 (37%), Positives = 139/224 (62%), Gaps = 7/224 (3%)

Query: 108 TVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAET 167
           T AS  +      ++F D+ +   + +  +   +T+PT IQ +A+P+AL GRD++G AET
Sbjct: 30  TEASQPIVEEEETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAET 89

Query: 168 GSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTA 227
           GSGKT AF +P++   + +TP        ALVL PTRELA QI ++ +AL  S+   ++A
Sbjct: 90  GSGKTGAFALPILNA-LLETP----QRLFALVLTPTRELAFQISEQFEALGSSIG-VQSA 143

Query: 228 IVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGF 286
           ++VGG +   Q   L     I++ATPGR +DHL+     +L  + ++++DEADR+L+M F
Sbjct: 144 VIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDF 203

Query: 287 EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           E ++ ++++ +P   +T LFSATM  +++ L +  L +PV+  V
Sbjct: 204 ETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAV 247

>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 =  285 bits (732), Expect = 7e-95
 Identities = 97/211 (45%), Positives = 127/211 (60%), Gaps = 5/211 (2%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D  L P I++ +     T PT IQA A+P+AL G+DL+G A TG+GKT AF +P+ +
Sbjct: 2   EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
                   GR   P ALVL PTRELA Q+  E+ A++  L   K   V GGT   +Q+  
Sbjct: 62  RLAPSQERGRK--PRALVLTPTRELALQVASELTAVAPHL---KVVAVYGGTGYGKQKEA 116

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L  G   VVATPGR LD+L+QG   LSRV   +LDEAD ML MGFE ++  ++   P   
Sbjct: 117 LLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSR 176

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           QTLLFSAT+P   + LA+ Y+ +PV + V K
Sbjct: 177 QTLLFSATLPSWAKRLAERYMKNPVLINVIK 207

>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 =  277 bits (710), Expect = 3e-91
 Identities = 78/215 (36%), Positives = 126/215 (58%), Gaps = 4/215 (1%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
              I  F+D  L    +K ++  +Y   T IQ Q + +AL G+D+LG A+TGSGKT AF 
Sbjct: 21  VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFL 80

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           +P+++           DG   L+++PTRELA Q  + ++ + ++ D F   +++GG ++ 
Sbjct: 81  VPVLEALYRLQWTST-DGLGVLIISPTRELAYQTFEVLRKVGKNHD-FSAGLIIGGKDLK 138

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGFEPQIREVMQ 295
            +   +   ++I+V TPGR L H+ +  +   + +  ++LDEADR+LDMGF   +  V++
Sbjct: 139 HEAERINN-INILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIE 197

Query: 296 NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           NLP K QTLLFSAT    ++ LA+  L +P  V V
Sbjct: 198 NLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWV 232

>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 =  269 bits (689), Expect = 2e-88
 Identities = 68/207 (32%), Positives = 116/207 (56%), Gaps = 5/207 (2%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D CL   ++  I    + +P+ IQ +++P+ALSGRD+L  A+ G+GK+ A+ IP+++
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               +          A+V+ PTRELA Q+ +    +S+ +   K     GGTN+ +    
Sbjct: 64  RLDLKKD-----NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR 118

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L   V +V+ATPGR LD +++G   +  V  ++LDEAD++L   F   + +++  LP   
Sbjct: 119 LDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNR 178

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQV 328
           Q LL+SAT P+ ++     +L  P ++
Sbjct: 179 QILLYSATFPLSVQKFMNSHLEKPYEI 205

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  264 bits (678), Expect = 1e-86
 Identities = 65/214 (30%), Positives = 115/214 (53%), Gaps = 8/214 (3%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            FT     P I++ I+   + +PT IQ + +P AL G  ++G ++TG+GKT A+ +P+++
Sbjct: 5   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVV---GGTNIAEQ 238
               +          A++ APTRELA QI  E   +++     +  +     GGT+  + 
Sbjct: 65  KIKPERA-----EVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKA 119

Query: 239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
             +L     IV+ TPGR  D +++    +     +++DEAD MLDMGF   + ++   +P
Sbjct: 120 LEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMP 179

Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
              Q L+FSAT+P +++   ++Y+ +P  V V +
Sbjct: 180 KDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE 213

>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 =  263 bits (675), Expect = 1e-85
 Identities = 81/227 (35%), Positives = 132/227 (58%), Gaps = 6/227 (2%)

Query: 106 DVTVASGSVPAPAPIESFTDM--CLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLG 163
           +V      +       SF  +   ++ + +K I+   +T  T IQ +++   L GRDLL 
Sbjct: 37  EVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLA 96

Query: 164 CAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
            A+TGSGKT AF IP ++  V    + R +G   L+L+PTRELA Q    +K L      
Sbjct: 97  AAKTGSGKTLAFLIPAVELIVKLRFMPR-NGTGVLILSPTRELAMQTFGVLKELMTHH-V 154

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRML 282
               +++GG+N + +  +L  G++I+VATPGR LDH+Q         +  +++DEADR+L
Sbjct: 155 HTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRIL 214

Query: 283 DMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLT-DPVQV 328
           D+GFE +++++++ LP + QT+LFSAT   ++E LA+  L  +P+ V
Sbjct: 215 DVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 261

>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 =  260 bits (667), Expect = 1e-84
 Identities = 77/212 (36%), Positives = 123/212 (58%), Gaps = 7/212 (3%)

Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           +++F DM L  S+++ I  + + +P++IQ +A+   + G D++  A++G+GKTA F I +
Sbjct: 29  VDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISI 88

Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q    +          ALVLAPTRELAQQI+K + AL   +        +GGTN+  + 
Sbjct: 89  LQQLEIEFK-----ETQALVLAPTRELAQQIQKVILALGDYMG-ATCHACIGGTNVRNEM 142

Query: 240 SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
            +L+     IVV TPGR  D L +   S   +   +LDEAD ML  GF+ QI E+ Q L 
Sbjct: 143 QKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLN 202

Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
              Q +L SATMP ++  + ++++ DP+++ V
Sbjct: 203 TSIQVVLLSATMPTDVLEVTKKFMRDPIRILV 234

>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 =  259 bits (665), Expect = 1e-84
 Identities = 77/211 (36%), Positives = 120/211 (56%), Gaps = 7/211 (3%)

Query: 120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPM 179
           +  F DM L  ++++ +  + +  P++IQ +A+   + G D+L  A++G+GKT  F+I  
Sbjct: 13  VYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72

Query: 180 IQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR 239
           +Q             P AL+LAPTRELA QI+K V AL+  +D  K    +GGT+  E  
Sbjct: 73  LQRIDTSVK-----APQALMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVEDA 126

Query: 240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPD 299
             LR    IVV TPGR  D++Q+      ++   ILDEAD ML  GF+ QI ++   LP 
Sbjct: 127 EGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPP 185

Query: 300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
             Q +L SATMP ++  +  +++ +PV++ V
Sbjct: 186 TTQVVLLSATMPNDVLEVTTKFMRNPVRILV 216

>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 =  256 bits (655), Expect = 4e-83
 Identities = 60/210 (28%), Positives = 109/210 (51%), Gaps = 7/210 (3%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F  + L   +++ +    + RP+ +Q +A+P+   G DL+  A++G+GKT  F+   + 
Sbjct: 25  DFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALD 84

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
             V +           L+LAPTRE+A QI   + A+   ++  +  + +GGT +++ ++ 
Sbjct: 85  SLVLENL-----STQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTR 139

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG-FEPQIREVMQNLPDK 300
           L+    I V +PGR    ++    +   +   ILDEAD++L+ G F+ QI  +  +LP  
Sbjct: 140 LK-KCHIAVGSPGRIKQLIELDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPAS 198

Query: 301 HQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
            Q L  SAT P  +     +Y+ DP  V++
Sbjct: 199 KQMLAVSATYPEFLANALTKYMRDPTFVRL 228

>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 =  254 bits (652), Expect = 1e-82
 Identities = 67/211 (31%), Positives = 113/211 (53%), Gaps = 7/211 (3%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA F +  +Q
Sbjct: 15  GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
                T          LV+  TRELA QI KE +  S+ + + K A+  GG +I +    
Sbjct: 75  QLEPVTG-----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV 129

Query: 242 LRGGVS-IVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIREVMQNLPD 299
           L+     IVV TPGR L   +  + +L  +   ILDE D+ML+ +     ++E+ +  P 
Sbjct: 130 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 189

Query: 300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           + Q ++FSAT+  EI  + ++++ DP+++ V
Sbjct: 190 EKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 220

>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 =  233 bits (595), Expect = 3e-73
 Identities = 66/233 (28%), Positives = 112/233 (48%), Gaps = 13/233 (5%)

Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDL 161
            V+V     + P    ++SF ++ L P +++ +    + RP+ IQ  A+P+ L+   ++L
Sbjct: 76  QVEVLQRDPNSPLY-SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNL 134

Query: 162 LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL 221
           +  +++G+GKTAAF + M+              P  L L+PT ELA Q  K ++ + +  
Sbjct: 135 IAQSQSGTGKTAAFVLAMLSQVEPANKY-----PQCLCLSPTYELALQTGKVIEQMGKFY 189

Query: 222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADR 280
              K A  V G  +       +    IV+ TPG  LD   +       ++   +LDEAD 
Sbjct: 190 PELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADV 246

Query: 281 MLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           M+   G + Q   + + LP   Q LLFSAT    +   AQ+ + DP  +K+ +
Sbjct: 247 MIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR 299

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens} Length = 191

 Score =  168 bits (429), Expect = 4e-50
 Identities = 48/141 (34%), Positives = 76/141 (53%), Gaps = 17/141 (12%)

Query: 320 EYLTDPVQVKVG-------KVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCH 372
            +      V +G        + + + +VIQ +E V E  K+  LL  L +          
Sbjct: 3   HHHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTP-------- 54

Query: 373 PFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD 432
             P  ++F E+K   D + E L+ +G+ AVA+HGG++Q +R  A+  FR G  ++LVATD
Sbjct: 55  --PPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD 112

Query: 433 VASRGLDVMGVAHVVNLDLPK 453
           VAS+GLD   + HV+N D+P+
Sbjct: 113 VASKGLDFPAIQHVINYDMPE 133

>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} Length = 185

 Score =  165 bits (421), Expect = 5e-49
 Identities = 51/130 (39%), Positives = 69/130 (53%), Gaps = 8/130 (6%)

Query: 324 DPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVER 383
                 +    S + N+ Q +  V E++K   LL LL         +     LT+VFVE 
Sbjct: 4   HHHHENLYFQGSTSENITQKVVWVEESDKRSFLLDLL--------NATGKDSLTLVFVET 55

Query: 384 KTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGV 443
           K   D + + L  EG    ++HG R+Q DRE AL  FR+G + ILVAT VA+RGLD+  V
Sbjct: 56  KKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNV 115

Query: 444 AHVVNLDLPK 453
            HV+N DLP 
Sbjct: 116 KHVINFDLPS 125

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli} Length = 170

 Score =  124 bits (313), Expect = 1e-33
 Identities = 36/116 (31%), Positives = 58/116 (50%), Gaps = 8/116 (6%)

Query: 339 NVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG 398
            + Q   +  + E    LL  L+++             +IVFV ++ R  E++  L   G
Sbjct: 3   KIHQWYYRADDLEHKTALLVHLLKQ--------PEATRSIVFVRKRERVHELANWLREAG 54

Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKV 454
           ++   L G   Q  R  A++    G  N+LVATDVA+RG+D+  V+HV N D+P+ 
Sbjct: 55  INNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRS 110

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis} Length = 163

 Score =  121 bits (307), Expect = 7e-33
 Identities = 36/117 (30%), Positives = 56/117 (47%), Gaps = 10/117 (8%)

Query: 337 TANVI-QILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV 395
           T   I   + +V E  K   L  +L+ E              I+F   K   +++++ L 
Sbjct: 6   TTRNIEHAVIQVREENKFSLLKDVLMTE---------NPDSCIIFCRTKEHVNQLTDELD 56

Query: 396 AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
             G     +HGG  Q DR   + +F+ G    LVATDVA+RG+D+  ++ V+N DLP
Sbjct: 57  DLGYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLP 113

>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 Length = 212

 Score =  120 bits (302), Expect = 1e-31
 Identities = 37/116 (31%), Positives = 53/116 (45%), Gaps = 9/116 (7%)

Query: 337 TANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA 396
                +         +++ L  LL                 +VF   K   +E+++ L+ 
Sbjct: 3   PVTYEEEAVPAPVRGRLEVLSDLL---------YVASPDRAMVFTRTKAETEEIAQGLLR 53

Query: 397 EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP 452
            G  A ALHG  +Q +RE  L  FR G   +LVATDVA+RGLD+  V  VV+  LP
Sbjct: 54  LGHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLP 109

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus} Length = 300

 Score =  121 bits (305), Expect = 3e-31
 Identities = 35/115 (30%), Positives = 53/115 (46%), Gaps = 9/115 (7%)

Query: 339 NVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG 398
              +         +++ L  LL                 +VF   K   +E+++ L+  G
Sbjct: 2   TYEEEAVPAPVRGRLEVLSDLL---------YVASPDRAMVFTRTKAETEEIAQGLLRLG 52

Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
             A ALHG  +Q +RE  +  FR G   +LVATDVA+RGLD+  V  VV+  +P 
Sbjct: 53  HPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPD 107

>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 Length = 172

 Score =  114 bits (289), Expect = 3e-30
 Identities = 34/108 (31%), Positives = 56/108 (51%), Gaps = 9/108 (8%)

Query: 346 KVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALH 405
           K+ +NEK  +L  LL             F   ++FV+   RC  +++ LV +   A+A+H
Sbjct: 12  KLKDNEKNRKLFDLL---------DVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIH 62

Query: 406 GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            G  Q +R S  + F++    ILVAT++  RG+D+  V    N D+P+
Sbjct: 63  RGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPE 110

>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural genomics, structural consortium, SGC, alternative initiation, ATP-binding, devel protein; 2.80A {Homo sapiens} Length = 175

 Score =  105 bits (265), Expect = 7e-27
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 9/106 (8%)

Query: 348 SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGG 407
              +K   L  +                  I+F + +     ++  ++ +G     L G 
Sbjct: 17  HRKDKYQALCNIY---------GSITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGE 67

Query: 408 RNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
                R S ++ FR+G   +L+ T+V +RG+DV  V  VVN DLP 
Sbjct: 68  LTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPV 113

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19 Length = 165

 Score =  102 bits (256), Expect = 8e-26
 Identities = 28/106 (26%), Positives = 54/106 (50%), Gaps = 9/106 (8%)

Query: 348 SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGG 407
            E  K + L  L                  ++F   + + +E++  L  +     A++  
Sbjct: 13  EEEYKYECLTDLY---------DSISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSD 63

Query: 408 RNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
             Q +R++ +++FR+GS+ IL++TD+ +RG+DV  V+ V+N DLP 
Sbjct: 64  LPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPA 109

>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 = 99.5 bits (247), Expect = 2e-22
 Identities = 42/194 (21%), Positives = 69/194 (35%), Gaps = 19/194 (9%)

Query: 126 MCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVA 185
           M L   +++         P   Q           + L    TG GKT    +        
Sbjct: 1   MVLRRDLIQ---------PRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRL-- 48

Query: 186 QTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGG 245
               G+      L+LAPT+ L  Q  +  + L  +L   K   + G  +  E+RS+    
Sbjct: 49  TKYGGK-----VLMLAPTKPLVLQHAESFRRLF-NLPPEKIVALTGEKS-PEERSKAWAR 101

Query: 246 VSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLL 305
             ++VATP    + L  G  SL  VS ++ DEA R +       I    +        + 
Sbjct: 102 AKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIG 161

Query: 306 FSATMPVEIEALAQ 319
            +A+     E + +
Sbjct: 162 LTASPGSTPEKIME 175

>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 = 84.1 bits (207), Expect = 2e-17
 Identities = 46/260 (17%), Positives = 93/260 (35%), Gaps = 30/260 (11%)

Query: 202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQ 261
                 +  +   + L  +L       ++  ++    + E+     I+     +    L+
Sbjct: 211 LPEIYKEVRKLLREMLRDALKPLAETGLLESSSPDIPKKEVLRAGQIINEEMAKGNHDLR 270

Query: 262 QGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY 321
                L     + L  A  +L+      +R  ++ L ++ +     A+  +  +   ++ 
Sbjct: 271 G--LLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKEIFSDKRMKKA 328

Query: 322 LTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFV 381
           ++  VQ K   +  P               K+D+L  ++ E+              IVF 
Sbjct: 329 ISLLVQAKEIGLDHP---------------KMDKLKEIIREQ-----LQRKQNSKIIVFT 368

Query: 382 ERKTRCDEVSEALVAEGLHAVALHG--------GRNQSDRESALRDFRNGSTNILVATDV 433
             +    ++   LV +G+ A    G        G +Q +++  L +F  G  N+LVAT V
Sbjct: 369 NYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSV 428

Query: 434 ASRGLDVMGVAHVVNLDLPK 453
              GLDV  V  VV  +   
Sbjct: 429 GEEGLDVPEVDLVVFYEPVP 448

>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 = 87.0 bits (215), Expect = 3e-18
 Identities = 60/315 (19%), Positives = 95/315 (30%), Gaps = 65/315 (20%)

Query: 133 MKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRG 192
           ++ +E    +   +  +    V  S +     A TGSGK+    +P      AQ      
Sbjct: 207 VESMETTMRSPVFTDNSSPPAVPQSFQVAHLHAPTGSGKSTK--VP--AAYAAQ------ 256

Query: 193 DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVAT 252
            G   LVL P+          +                   NI      +  G  +  +T
Sbjct: 257 -GYKVLVLNPSVAATLGFGAYMSKAHG-----------IDPNIRTGVRTITTGAPVTYST 304

Query: 253 PGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF--SATM 310
            G+FL        S      +I DE     D      I  V+         L+   +AT 
Sbjct: 305 YGKFLADGG---CSGGAYDIIICDECHST-DSTTILGIGTVLDQAETAGARLVVLATATP 360

Query: 311 PVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKS 370
           P  +        T P         S            +  E      A+ +E      + 
Sbjct: 361 PGSV--------TVPHPNIEEVALS------------NTGEIPFYGKAIPIEA----IRG 396

Query: 371 CHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVA 430
                  ++F   K +CDE++  L   G++AVA + G + S   +            +VA
Sbjct: 397 GR----HLIFCHSKKKCDELAAKLSGLGINAVAYYRGLDVSVIPTIGDVV-------VVA 445

Query: 431 TDVASRGL--DVMGV 443
           TD    G   D   V
Sbjct: 446 TDALMTGYTGDFDSV 460

>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 = 79.1 bits (195), Expect = 5e-16
 Identities = 41/312 (13%), Positives = 94/312 (30%), Gaps = 63/312 (20%)

Query: 142 TRPTSIQAQAMPVALS-GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL 200
           +       +         R  +     G+GKT      +++  + +    R      L+L
Sbjct: 2   SAMGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRR--LRT-----LIL 54

Query: 201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHL 260
           APTR +A ++E+ ++ L                     +S+  G   + +     F   L
Sbjct: 55  APTRVVAAEMEEALRGL------------PIRYQTPAVKSDHTGREIVDLMCHATFTTRL 102

Query: 261 QQGNTSLSRVSFVILDEA-----DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIE 315
                 +   + +++DEA       +   G+     E       +   +  +AT P   +
Sbjct: 103 LSST-RVPNYNLIVMDEAHFTDPCSVAARGYISTRVE-----MGEAAAIFMTATPPGSTD 156

Query: 316 ALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFP 375
              Q     P++    ++   + N                          + +       
Sbjct: 157 PFPQSNS--PIEDIEREIPERSWNTGFDW---------------------ITDYQGK--- 190

Query: 376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS 435
            T+ FV      ++++  L   G   + L      ++        +    + +V TD++ 
Sbjct: 191 -TVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKT----KLTDWDFVVTTDISE 245

Query: 436 RGLDVMGVAHVV 447
            G +      V+
Sbjct: 246 MGANF-RAGRVI 256

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A Length = 431

 Score = 76.8 bits (189), Expect = 3e-15
 Identities = 41/290 (14%), Positives = 82/290 (28%), Gaps = 66/290 (22%)

Query: 165 AETGSGKTAAFT-IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
              G+GKT     +      V +           ++LAPTR +A ++ + +         
Sbjct: 9   LHPGAGKT---RRVL--PQLVRE---AVKKRLRTVILAPTRVVASEMYEAL--------- 51

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA----- 278
                          +SE  G   +       F   L QG   +   +  I+DEA     
Sbjct: 52  ---RGEPIRYMTPAVQSERTGNEIVDFMCHSTFTMKLLQGV-RVPNYNLYIMDEAHFLDP 107

Query: 279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP-VEIEALAQEYLTDPVQVKVGKVSSPT 337
             +   G+                 +  +AT P                + ++     P 
Sbjct: 108 ASVAARGYIETRVS-----MGDAGAIFMTATPPGTTEAFPPSNSPIIDEETRI-----PD 157

Query: 338 ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE 397
                  E ++E +                         T+ FV    +  E+   L   
Sbjct: 158 KAWNSGYEWITEFDGR-----------------------TVWFVHSIKQGAEIGTCLQKA 194

Query: 398 GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
           G   + L+    +S+        ++   + ++ TD++  G +      V+
Sbjct: 195 GKKVLYLNRKTFESEYPKC----KSEKWDFVITTDISEMGANF-KADRVI 239

>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 = 72.2 bits (177), Expect = 1e-14
 Identities = 32/139 (23%), Positives = 55/139 (39%), Gaps = 13/139 (9%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTA-AFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL 206
           Q +    AL G++++ C  TGSGKT  A  I   +  + +       G   +VL     L
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYI--AKDHLDKKKKASEPGK-VIVLVNKVLL 94

Query: 207 A-QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHL----- 260
             Q   KE +   +    ++   + G T +     E+     I+++T     + L     
Sbjct: 95  VEQLFRKEFQPFLK--KWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLEN 152

Query: 261 -QQGNTSLSRVSFVILDEA 278
            +     LS  S +I+DE 
Sbjct: 153 GEDAGVQLSDFSLIIIDEC 171

>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 = 73.7 bits (181), Expect = 3e-14
 Identities = 63/424 (14%), Positives = 118/424 (27%), Gaps = 112/424 (26%)

Query: 74  VPQPVFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIM 133
           VP   F++   + R L F    I E      ++                F D    P   
Sbjct: 42  VPHAKFDSRSGTYRALAFRYRDIIEYFESNGIE----------------FVDNAADPIPT 85

Query: 134 KDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGD 193
              +          Q +A+   L  +       TGSGKT      +    + +       
Sbjct: 86  PYFDAE--ISLRDYQEKALERWLVDKRGCIVLPTGSGKTH-----VAMAAINELSTP--- 135

Query: 194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATP 253
               L++ PT  LA+Q ++ +                G   + E    ++    + V+T 
Sbjct: 136 ---TLIVVPTLALAEQWKERLGIF-------------GEEYVGEFSGRIKELKPLTVSTY 179

Query: 254 GRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP--------------D 299
                + ++     +R   +I DE   +          ++ Q                 D
Sbjct: 180 DSAYVNAEK---LGNRFMLLIFDEVHHLPA----ESYVQIAQMSIAPFRLGLTATFERED 232

Query: 300 KHQTLLFSATMPV----EIEALAQEYLTDPVQVKVGKVSSPTA----------------- 338
               +L             ++LA ++L     +K   V                      
Sbjct: 233 GRHEILKEVVGGKVFELFPDSLAGKHLA-KYTIKRIFVPLAEDERVEYEKREKVYKQFLR 291

Query: 339 ----------NVIQILEKVSENEKVDRLLALLVEEAFLAEKSC------------HPFPL 376
                     +  +I+     +E+    L    E   +A  S             H    
Sbjct: 292 ARGITLRRAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILERHRKDK 351

Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
            I+F         +S+  +   +         ++ +RE  L  FR G    +V++ V   
Sbjct: 352 IIIFTRHNELVYRISKVFLIPAIT-----HRTSREEREEILEGFRTGRFRAIVSSQVLDE 406

Query: 437 GLDV 440
           G+DV
Sbjct: 407 GIDV 410

>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 = 72.2 bits (177), Expect = 1e-13
 Identities = 42/288 (14%), Positives = 85/288 (29%), Gaps = 62/288 (21%)

Query: 165 AETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSF 224
              G+GKT       +   +A+    R      LVLAPTR +  ++++    L       
Sbjct: 15  FHPGAGKTRR----FLPQILAECARRRLR---TLVLAPTRVVLSEMKEAFHGLD------ 61

Query: 225 KTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE-----AD 279
                    +     +   G   I          +     T +     +I+DE       
Sbjct: 62  ------VKFHTQAFSAHGSGREVIDAMCHATLT-YRMLEPTRVVNWEVIIMDEAHFLDPA 114

Query: 280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTAN 339
            +   G+        +   ++  T+L +AT P   +              V     P+  
Sbjct: 115 SIAARGWAAH-----RARANESATILMTATPPGTSDEFPHSN---GEIEDVQT-DIPSEP 165

Query: 340 VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL 399
                + +  +++                        T  F+      + ++ +L   G 
Sbjct: 166 WNTGHDWILADKRP-----------------------TAWFLPSIRAANVMAASLRKAGK 202

Query: 400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
             V L+        E      +    + ++ATD+A  G ++  V  V+
Sbjct: 203 SVVVLNRK----TFEREYPTIKQKKPDFILATDIAEMGANL-CVERVL 245

>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* Length = 720

 Score = 72.2 bits (177), Expect = 1e-13
 Identities = 65/361 (18%), Positives = 129/361 (35%), Gaps = 68/361 (18%)

Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQ 186
           +   I   ++          QA+A+   +  G++ L    T SGKT    I M+      
Sbjct: 8   VDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRI--- 64

Query: 187 TPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGV 246
                  G  A+ + P + LA++  +E +   +     + A+  G  +  ++     G  
Sbjct: 65  ----LTQGGKAVYIVPLKALAEEKFQEFQDWEKI--GLRVAMATGDYDSKDEW---LGKY 115

Query: 247 SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLF 306
            I++AT  +F   L+ G++ +  V  ++ DE   +        +  ++ ++  K Q +  
Sbjct: 116 DIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGL 175

Query: 307 SATMPVEIEALAQ-----EYLTD--PVQVKVGKVSSPTANVIQILEKVSENEKVDRLLAL 359
           SAT+    E LA+       ++D  PV+++ G         +     V+  +      + 
Sbjct: 176 SATIG-NPEELAEWLNAELIVSDWRPVKLRRG---------VFYQGFVTWEDGSIDRFSS 225

Query: 360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL-------------------- 399
             E  + A +        ++FV  + + + V+  L  +                      
Sbjct: 226 WEELVYDAIRKKKG---ALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEE 282

Query: 400 ------------HAVALH-GGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHV 446
                         VA H  G  + +R     +FR G    +VAT   S G++    A  
Sbjct: 283 NPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINT--PAFR 340

Query: 447 V 447
           V
Sbjct: 341 V 341

>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 Length = 618

 Score = 70.0 bits (171), Expect = 8e-13
 Identities = 47/312 (15%), Positives = 92/312 (29%), Gaps = 63/312 (20%)

Query: 142 TRPTSIQAQAMPVALS-GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL 200
            R      +         R  +     G+GKT    I      V +    R      L+L
Sbjct: 169 ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKR--IL--PSIVREALKRRL---RTLIL 221

Query: 201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHL 260
           APTR +A ++E+ ++ L                     +S+  G   + +     F   L
Sbjct: 222 APTRVVAAEMEEALRGL------------PIRYQTPAVKSDHTGREIVDLMCHATFTTRL 269

Query: 261 QQGNTSLSRVSFVILDE-----ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIE 315
              +T +   + +++DE        +   G+     E       +   +  +AT P    
Sbjct: 270 LS-STRVPNYNLIVMDEAHFTDPCSVAARGYISTRVE-----MGEAAAIFMTATPPGS-- 321

Query: 316 ALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFP 375
                  TDP       +               E E  +R      +     +       
Sbjct: 322 -------TDPFPQSNSPIED------------IEREIPERSWNTGFDWITDYQGK----- 357

Query: 376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS 435
            T+ FV      ++++  L   G   + L      ++        +    + +V TD++ 
Sbjct: 358 -TVWFVPSIKAGNDIANCLRKSGKRVIQLSRKTFDTEYPKT----KLTDWDFVVTTDISE 412

Query: 436 RGLDVMGVAHVV 447
            G +      V+
Sbjct: 413 MGANF-RAGRVI 423

>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 = 68.7 bits (168), Expect = 2e-12
 Identities = 66/373 (17%), Positives = 120/373 (32%), Gaps = 92/373 (24%)

Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQT 187
           +    +  ++          QA+A+    SG++LL    T +GKT    + M++  +   
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAI--- 66

Query: 188 PVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVS 247
                 G  +L + P R LA +  +  K   +     +  I  G       R E  G   
Sbjct: 67  -----KGGKSLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYES---RDEHLGDCD 116

Query: 248 IVVATPGRFLDHLQQGNTSLSRVSFVILDE----AD------------RMLDMGFEPQIR 291
           I+V T  +    ++   + +  VS +++DE                  +M  M    ++ 
Sbjct: 117 IIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRV- 175

Query: 292 EVMQNLPDKHQTLLFSATMPVEIEALAQ-----EYLTD--PVQVKVGKVSSPTANVIQIL 344
                       +  SAT P  +  +A+      Y++D  PV +  G +   T  +    
Sbjct: 176 ------------IGLSATAP-NVTEIAEWLDADYYVSDWRPVPLVEGVLCEGTLELFDGA 222

Query: 345 EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL----- 399
              S   K + L+   V E              +VF   +   ++ +  L A        
Sbjct: 223 FSTSRRVKFEELVEECVAE----NGGV------LVFESTRRGAEKTAVKLSAITAKYVEN 272

Query: 400 ------------------------HAVALH-GGRNQSDRESALRDFRNGSTNILVATDVA 434
                                      A H  G     R      FR G+  ++VAT   
Sbjct: 273 EGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTL 332

Query: 435 SRGLDVMGVAHVV 447
           + G+++   A  V
Sbjct: 333 AAGVNL--PARRV 343

>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 = 68.0 bits (165), Expect = 3e-12
 Identities = 36/153 (23%), Positives = 58/153 (37%), Gaps = 13/153 (8%)

Query: 133 MKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRG 192
           M+  +   Y      Q +    A++G++ L CA TGSGKT   +I + +H     P GR 
Sbjct: 3   METKKARSY------QIELAQPAINGKNALICAPTGSGKTFV-SILICEHHFQNMPAGR- 54

Query: 193 DGPLALVLAPTREL-AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVA 251
                + LA    +  QQ              +    + G         ++     I+V 
Sbjct: 55  -KAKVVFLATKVPVYEQQKNVFKHHF--ERQGYSVQGISGENFSNVSVEKVIEDSDIIVV 111

Query: 252 TPGRFLDHLQQGN-TSLSRVSFVILDEADRMLD 283
           TP   ++  + G  TSLS  + +I DE      
Sbjct: 112 TPQILVNSFEDGTLTSLSIFTLMIFDECHNTTG 144

>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 = 49.9 bits (118), Expect = 1e-06
 Identities = 22/122 (18%), Positives = 49/122 (40%), Gaps = 18/122 (14%)

Query: 345 EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA----EGLH 400
           ++ +EN K++ L+ +L +      ++      T++F + +     + + +        + 
Sbjct: 366 DETNENPKLEELVCILDDAYRYNPQTR-----TLLFAKTRALVSALKKCMEENPILNYIK 420

Query: 401 AVALHG--------GRNQSDRESALRDFRNGSTN-ILVATDVASRGLDVMGVAHVVNLDL 451
              L G        G     ++  L  F+    N +L+AT VA  G+D++    VV  + 
Sbjct: 421 PGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEY 480

Query: 452 PK 453
             
Sbjct: 481 SG 482

>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 = 68.1 bits (165), Expect = 3e-12
 Identities = 40/206 (19%), Positives = 70/206 (33%), Gaps = 9/206 (4%)

Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLG 163
            ++ ++       P    S         I K    +E  +  S Q +    A++G++ L 
Sbjct: 209 CLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAINGKNALI 268

Query: 164 CAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD- 222
           CA TGSGKT   +I + +H     P GR      + LA    + +Q            + 
Sbjct: 269 CAPTGSGKTFV-SILICEHHFQNMPAGR--KAKVVFLATKVPVYEQQ---KNVFKHHFER 322

Query: 223 -SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN-TSLSRVSFVILDEADR 280
             +    + G         ++     I+V TP   ++  + G  TSLS  + +I DE   
Sbjct: 323 QGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHN 382

Query: 281 MLDMGFEPQIREVMQNLPDKHQTLLF 306
                    +            + L 
Sbjct: 383 TTGNHPYNVLMTRYLEQKFNSASQLP 408

>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 = 50.0 bits (118), Expect = 1e-06
 Identities = 32/206 (15%), Positives = 75/206 (36%), Gaps = 27/206 (13%)

Query: 261 QQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQE 320
           ++  + + R  F+  +   +  D      I E  + +        F   +        ++
Sbjct: 532 KEEESRICRALFICTEHLRKYNDALI---ISEDARIIDALSYLTEFFTNVKNGPYTELEQ 588

Query: 321 YLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVF 380
           +LT   Q K  ++ + + +        +EN K++ L+ +L +      ++      T++F
Sbjct: 589 HLTAKFQEKEPELIALSKDET------NENPKLEELVCILDDAYRYNPQTR-----TLLF 637

Query: 381 VERKTRCDEVSEALVA----EGLHAVALHG--------GRNQSDRESALRDFRNGSTN-I 427
            + +     + + +        +    L G        G     ++  L  F+    N +
Sbjct: 638 AKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRL 697

Query: 428 LVATDVASRGLDVMGVAHVVNLDLPK 453
           L+AT VA  G+D++    VV  +   
Sbjct: 698 LIATSVADEGIDIVQCNLVVLYEYSG 723

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 67.2 bits (163), Expect = 5e-12
 Identities = 30/136 (22%), Positives = 55/136 (40%), Gaps = 7/136 (5%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL- 206
           Q +    A  G++ + CA TG GKT   ++ + +H + + P   G     +  A    + 
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFV-SLLICEHHLKKFP--CGQKGKVVFFANQIPVY 65

Query: 207 AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN-T 265
            QQ     +        +  A + G T+ +     +     I++ TP   +++L  G   
Sbjct: 66  EQQATVFSRYF--ERLGYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIP 123

Query: 266 SLSRVSFVILDEADRM 281
           SLS  + +I DE    
Sbjct: 124 SLSVFTLMIFDECHNT 139

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 51.4 bits (122), Expect = 4e-07
 Identities = 31/118 (26%), Positives = 47/118 (39%), Gaps = 18/118 (15%)

Query: 349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA----EGLHAVAL 404
           EN K+  L  +L EE         P   TI+FV+ +   D + + +        L    L
Sbjct: 369 ENPKLRDLYLVLQEE-----YHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGIL 423

Query: 405 HG--------GRNQSDRESALRDFR-NGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            G        G     ++  L  FR +G  NIL+AT VA  G+D+     V+  +   
Sbjct: 424 TGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVG 481

>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane, nucleotide-binding, RNA replication, transmembrane, viral protein; 1.80A {Japanese encephalitis virus} PDB: 2v8o_A 2qeq_A Length = 459

 Score = 64.1 bits (156), Expect = 3e-11
 Identities = 45/284 (15%), Positives = 83/284 (29%), Gaps = 59/284 (20%)

Query: 165 AETGSGKTAAFT-IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
              GSGKT     I      +              VLAPTR +A ++ + ++ L      
Sbjct: 28  LHPGSGKT---RKIL--PQIIKD---AIQQRLRTAVLAPTRVVAAEMAEALRGLP----- 74

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM-- 281
                 V     A QR   +G   + V        H       +   +  ++DEA     
Sbjct: 75  ------VRYQTSAVQREH-QGNEIVDVMCHATLT-HRLMSPNRVPNYNLFVMDEAHFTDP 126

Query: 282 LDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVI 341
             +     I   ++        +  +AT P   +         P+     ++  P     
Sbjct: 127 ASIAARGYIATKVELGEAA--AIFMTATPPGTTDPFPDSNA--PIHDLQDEI--PDRAWS 180

Query: 342 QILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHA 401
              E ++E                           T+ FV      +E++  L   G   
Sbjct: 181 SGYEWITEYAGK-----------------------TVWFVASVKMGNEIAMCLQRAGKKV 217

Query: 402 VALHGGRNQSDRESALRDFRNGSTNILVATDVASRGL--DVMGV 443
           + L+     ++        +NG  + ++ TD++  G       V
Sbjct: 218 IQLNRKSYDTEYPKC----KNGDWDFVITTDISEMGANFGASRV 257

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 64.6 bits (156), Expect = 4e-11
 Identities = 31/152 (20%), Positives = 60/152 (39%), Gaps = 7/152 (4%)

Query: 143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP 202
           +P + Q +    A+ G++ + CA TG GKT    + + +H + + P  +G     +  A 
Sbjct: 13  KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLL-ICEHHLKKFP--QGQKGKVVFFAN 69

Query: 203 TREL-AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQ 261
              +  Q      K        ++   + G T       ++     I++ TP   +++L+
Sbjct: 70  QIPVYEQNKSVFSKYF--ERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLK 127

Query: 262 QGN-TSLSRVSFVILDEADRMLDMGFEPQIRE 292
           +G   SLS  + +I DE            I  
Sbjct: 128 KGTIPSLSIFTLMIFDECHNTSKQHPYNMIMF 159

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 54.6 bits (130), Expect = 4e-08
 Identities = 30/118 (25%), Positives = 49/118 (41%), Gaps = 18/118 (15%)

Query: 349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA----EGLHAVAL 404
           EN K++ L  +L EE  L  ++      TI+FV+ +   D +   +        L    L
Sbjct: 378 ENPKLEDLCFILQEEYHLNPETI-----TILFVKTRALVDALKNWIEGNPKLSFLKPGIL 432

Query: 405 HG--------GRNQSDRESALRDFR-NGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            G        G     ++  L  F+ +G  NIL+AT VA  G+D+     V+  +   
Sbjct: 433 TGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVG 490

>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 = 64.2 bits (155), Expect = 5e-11
 Identities = 43/197 (21%), Positives = 73/197 (37%), Gaps = 12/197 (6%)

Query: 92  NPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHP---SIMKDIEFHEYTRPTSIQ 148
           N + ++      + D   AS +    A  +      L      I K    +E  +  S Q
Sbjct: 194 NAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQ 253

Query: 149 AQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ 208
            +    A++G++ L CA TGSGKT   +I + +H     P GR      + LA    + +
Sbjct: 254 IELAQPAINGKNALICAPTGSGKTFV-SILICEHHFQNMPAGR--KAKVVFLATKVPVYE 310

Query: 209 QIEKEVKALSRSLD--SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN-T 265
           Q            +   +    + G         ++     I+V TP   ++  + G  T
Sbjct: 311 QQ---KNVFKHHFERQGYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 367

Query: 266 SLSRVSFVILDEADRML 282
           SLS  + +I DE     
Sbjct: 368 SLSIFTLMIFDECHNTT 384

>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 = 52.6 bits (125), Expect = 2e-07
 Identities = 22/122 (18%), Positives = 50/122 (40%), Gaps = 18/122 (14%)

Query: 345 EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL----VAEGLH 400
           ++ +EN K++ L+ +L +      ++      T++F + +     + + +    +   + 
Sbjct: 607 DETNENPKLEELVCILDDAYRYNPQTR-----TLLFAKTRALVSALKKCMEENPILNYIK 661

Query: 401 AVALHG--------GRNQSDRESALRDFRNGSTN-ILVATDVASRGLDVMGVAHVVNLDL 451
              L G        G     ++  L  F+    N +L+AT VA  G+D++    VV  + 
Sbjct: 662 PGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNLVVLYEY 721

Query: 452 PK 453
             
Sbjct: 722 SG 723

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 62.8 bits (153), Expect = 1e-10
 Identities = 58/372 (15%), Positives = 115/372 (30%), Gaps = 90/372 (24%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAF 175
             PI    D+ L  ++++ I+     +    Q +A+   L  G  LL  + TGSGKT   
Sbjct: 7   WMPI---EDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIA 63

Query: 176 TIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI 235
            + +I        + +  G  A+ + P R L  +     K        FK A+  G  + 
Sbjct: 64  EMGIISF------LLKNGGK-AIYVTPLRALTNEKYLTFKDWELI--GFKVAMTSGDYDT 114

Query: 236 AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE------ADRMLDMGFEPQ 289
            +          I++ T  +     +     L+ V++ +LDE       +R    G    
Sbjct: 115 DDAW---LKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPER----G---P 164

Query: 290 IREVMQNLPDKHQTLLFSATMPVEIEALAQ-----EYLTD--PVQVK---VGKVSSPTAN 339
           + E +     +   L  SAT+    + +A+        T+  PV +    +         
Sbjct: 165 VVESVTIRAKRRNLLALSATIS-NYKQIAKWLGAEPVATNWRPVPLIEGVIYPERKKKEY 223

Query: 340 VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-- 397
            +   +  ++    D  +     ++             +VF   +   +  +  +     
Sbjct: 224 NVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQV------LVFRNSRKMAESTALKIANYMN 277

Query: 398 --------------------------------------GLHAVALHGGRNQSDRESALRD 419
                                                   H    H G +++ R+     
Sbjct: 278 FVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYH----HAGLSKALRDLIEEG 333

Query: 420 FRNGSTNILVAT 431
           FR     ++VAT
Sbjct: 334 FRQRKIKVIVAT 345

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus} Length = 673

 Score = 60.3 bits (146), Expect = 8e-10
 Identities = 44/289 (15%), Positives = 85/289 (29%), Gaps = 64/289 (22%)

Query: 165 AETGSGKTAAFT-IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
              G+GKT     I      +      R       VLAPTR +A ++ + +         
Sbjct: 248 LHPGAGKT---RRIL--PQIIKDAIQKRL---RTAVLAPTRVVAAEMAEAL--------- 290

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE-----A 278
                +         + E  G   + V        H       +   +  ++DE      
Sbjct: 291 ---RGLPVRYLTPAVQREHSGNEIVDVMCHATLT-HRLMSPLRVPNYNLFVMDEAHFTDP 346

Query: 279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTA 338
             +   G+        +    +   +  +AT P           +DP       V     
Sbjct: 347 ASIAARGYIAT-----RVEAGEAAAIFMTATPPG---------TSDPFPDTNSPVHD--- 389

Query: 339 NVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG 398
                      +E  DR  +   E              T+ FV      +E+++ L   G
Sbjct: 390 ---------VSSEIPDRAWSSGFEWITDYAGK------TVWFVASVKMSNEIAQCLQRAG 434

Query: 399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
              + L+     ++        +NG  + ++ TD++  G +  G + V+
Sbjct: 435 KRVIQLNRKSYDTEYPKC----KNGDWDFVITTDISEMGANF-GASRVI 478

>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* Length = 1054

 Score = 59.3 bits (144), Expect = 2e-09
 Identities = 50/308 (16%), Positives = 96/308 (31%), Gaps = 59/308 (19%)

Query: 165 AETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSF 224
           A TG GKT+ F + M      +       G    V+ PT  L  Q  + ++  +      
Sbjct: 78  APTGVGKTS-FGLAMSLFLALK-------GKRCYVIFPTSLLVIQAAETIRKYAEKAGVG 129

Query: 225 KTAIVVG--GTNIAEQRSELRGGV---SIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD 279
              ++    G     ++      +    IV+ T      H ++    L    F+ +D+ D
Sbjct: 130 TENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE----LGHFDFIFVDDVD 185

Query: 280 RMLD-----------MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQV 328
            +L            +GF   ++        +   ++ +AT     +A     L +    
Sbjct: 186 AILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQLLN---F 242

Query: 329 KVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCD 388
            +G       NV  +         +  +L  L                 I++       +
Sbjct: 243 DIGSSRITVRNVEDVAVNDESISTLSSILEKL-------------GTGGIIYARTGEEAE 289

Query: 389 EVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVAS-RGLDVMGVAHVV 447
           E+ E+L         +      + ++     F  G  + L+    A   G  V G     
Sbjct: 290 EIYESL-KNKFRIGIVT-----ATKKGDYEKFVEGEIDHLIG--TAHYYGTLVRG----- 336

Query: 448 NLDLPKVL 455
            LDLP+ +
Sbjct: 337 -LDLPERI 343

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4} Length = 510

 Score = 58.4 bits (140), Expect = 3e-09
 Identities = 45/387 (11%), Positives = 108/387 (27%), Gaps = 56/387 (14%)

Query: 86  DRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPT 145
            ++ +F      +  +   ++         +    + +       S  K IE H Y    
Sbjct: 66  GQIKKFCDNFGYKAWIDPQINE----KEELSRKDFDEWLSKLEIYSGNKRIEPHWY---- 117

Query: 146 SIQAQAMPVALS-GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR 204
             Q  A+   L   R +L    +         +        +  +        L++ PT 
Sbjct: 118 --QKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENYEGKI--------LIIVPTT 167

Query: 205 ELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN 264
            L  Q+  +         +    I  G +   + +++    V        +  +   Q  
Sbjct: 168 ALTTQMADDFVDYRLFSHAMIKKIGGGASKDDKYKNDAPVVVGTWQTVVKQPKEWFSQ-- 225

Query: 265 TSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP-----------DKHQTLLFSATMPV- 312
                   ++ DE            I  +   +              +          + 
Sbjct: 226 -----FGMMMNDECHLATGKSISSIISGLNNCMFKFGLSGSLRDGKANIMQYVGMFGEIF 280

Query: 313 ---EIEALAQEYLTDPVQVKVGKVSSPTANVI--------QILEKVSENEKVDRLLALLV 361
                  L ++     +++    +  P             + ++ ++   K ++ +A L 
Sbjct: 281 KPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRNKWIAKLA 340

Query: 362 EEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFR 421
            +    +++        V  +  +    + + +  E      + G  +   R        
Sbjct: 341 IKLAQKDEN------AFVMFKHVSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAE 394

Query: 422 NGSTNILVAT-DVASRGLDVMGVAHVV 447
           NG   I+VA+  V S G+ V  + HVV
Sbjct: 395 NGKGIIIVASYGVFSTGISVKNLHHVV 421

>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription factor, RNA polymerase recycling, activator, ATP-binding, DNA-binding; 3.20A {Escherichia coli K12} Length = 968

 Score = 55.9 bits (134), Expect = 2e-08
 Identities = 22/106 (20%), Positives = 45/106 (42%), Gaps = 12/106 (11%)

Query: 350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL-VAEGLHAVALHGGR 408
           + +V+ L+  L      ++K        +V   +     ++ + L   EG+ A   H G 
Sbjct: 488 DPRVEWLMGYLTSH--RSQK-------VLVICAKAATALQLEQVLREREGIRAAVFHEGM 538

Query: 409 NQSDRESALRDFRN--GSTNILVATDVASRGLDVMGVAHVVNLDLP 452
           +  +R+ A   F        +L+ +++ S G +    +H+V  DLP
Sbjct: 539 SIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLP 584

>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 = 54.9 bits (131), Expect = 5e-08
 Identities = 60/404 (14%), Positives = 117/404 (28%), Gaps = 116/404 (28%)

Query: 78  VFNNWKPSDRVLRFNPEQIEEVRLRLNVDVTV-ASGSVPAPAPIESFTDMCLHPSIMKDI 136
           + +  K   R          E R RL  D  V A  +V    P        L  ++++  
Sbjct: 94  LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK-----LRQALLEL- 147

Query: 137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKT--AAFTI--PMIQHC----VAQTP 188
                 RP         V + G  +LG      GKT  A        +Q      +    
Sbjct: 148 ------RPAKN------VLIDG--VLGS-----GKTWVALDVCLSYKVQCKMDFKIFWLN 188

Query: 189 VGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSI 248
           +   + P   VL   ++L  QI+    + S    + K         I   ++ELR     
Sbjct: 189 LKNCNSP-ETVLEMLQKLLYQIDPNWTSRSDHSSNIK-------LRIHSIQAELR----- 235

Query: 249 VVATPGRFLDHLQQGNTSLSRVSFVILD--------EA-D---RML----------DMGF 286
                 R L   +     L     ++L          A +   ++L           +  
Sbjct: 236 ------RLLKS-KPYENCL-----LVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSA 283

Query: 287 EPQIREVMQNLPD---KHQTL-LFSATMPVEIEALAQEYL-TDPVQVK-VGKVSSPTANV 340
                  + +        +   L    +    + L +E L T+P ++  + +        
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT 343

Query: 341 IQILEKVSENEKVDRLLALLVEEAFLAE-----KSCHPFP---------LTIVFVERKTR 386
               + V   +K+  ++   +     AE          FP         L++++ +    
Sbjct: 344 WDNWKHV-NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402

Query: 387 CDE------VSEALVAE-------GLHAVALHGGRNQSDRESAL 417
                       +LV +        + ++ L   + + + E AL
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLE-LKVKLENEYAL 445

>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 = 53.3 bits (127), Expect = 1e-07
 Identities = 38/166 (22%), Positives = 62/166 (37%), Gaps = 24/166 (14%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKT--AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE 205
           Q  A+     G  +L  A T +GKT  A + I               +    +  +P + 
Sbjct: 91  QDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK----------NKQRVIYTSPIKA 140

Query: 206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT 265
           L+ Q  +E+ A    +      ++ G   I             +V T       L +G+ 
Sbjct: 141 LSNQKYRELLAEFGDV-----GLMTGDITINPDAG-------CLVMTTEILRSMLYRGSE 188

Query: 266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP 311
            +  V++VI DE   M D        E +  LPDK + +  SAT+P
Sbjct: 189 VMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 234

>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 = 53.3 bits (127), Expect = 2e-07
 Identities = 38/166 (22%), Positives = 62/166 (37%), Gaps = 24/166 (14%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKT--AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE 205
           Q  A+     G  +L  A T +GKT  A + I               +    +  +P + 
Sbjct: 189 QDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLK----------NKQRVIYTSPIKA 238

Query: 206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT 265
           L+ Q  +E+ A    +      ++ G   I             +V T       L +G+ 
Sbjct: 239 LSNQKYRELLAEFGDV-----GLMTGDITINPDAG-------CLVMTTEILRSMLYRGSE 286

Query: 266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP 311
            +  V++VI DE   M D        E +  LPDK + +  SAT+P
Sbjct: 287 VMREVAWVIFDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIP 332

>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* Length = 591

 Score = 52.7 bits (127), Expect = 2e-07
 Identities = 59/344 (17%), Positives = 118/344 (34%), Gaps = 84/344 (24%)

Query: 148 QAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA 207
           Q + + V ++G+++     TG GK+  + +P +           G     LV+ P   L 
Sbjct: 49  QLETINVTMAGKEVFLVMPTGGGKSLCYQLPAL--------CSDG---FTLVICPLISLM 97

Query: 208 Q-QIEK------EVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIV------VATPG 254
           + Q+            L+ S              +  +       + ++      +A   
Sbjct: 98  EDQLMVLKQLGISATMLNASSSKEHVK------WVHAEMVNKNSELKLIYVTPEKIAKSK 151

Query: 255 RFLDHLQQGNTSLSRVSFVILDEA--------DRMLDMGFEP---QIREVMQNLPDKHQT 303
            F+  L++   +  R + + +DE         D      F P    +  + +  P+    
Sbjct: 152 MFMSRLEKAYEA-RRFTRIAVDEVHCCSQWGHD------FRPDYKALGILKRQFPNA-SL 203

Query: 304 LLFSAT--MPVEIEALAQEYLTDPVQVKVGKVSS---PTANVI-QILEKVSENEKVDRLL 357
           +  +AT    V  +A     +           +S   P  N+  ++ +K S  E     +
Sbjct: 204 IGLTATATNHVLTDAQKILCIEKCFTFT----ASFNRP--NLYYEVRQKPSNTEDFIEDI 257

Query: 358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL 417
             L+   +   +S       I++   +   ++V+ +L   G+HA A H      D+ +  
Sbjct: 258 VKLINGRY-KGQSG------IIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVH 310

Query: 418 RDFRNGSTNILVATDVASRGLDVMG--------VAHVVNLDLPK 453
           R +      ++VAT VA  G   MG        V H     + K
Sbjct: 311 RKWSANEIQVVVAT-VAF-G---MGIDKPDVRFVIH---HSMSK 346

>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* Length = 523

 Score = 50.6 bits (122), Expect = 8e-07
 Identities = 46/232 (19%), Positives = 74/232 (31%), Gaps = 79/232 (34%)

Query: 255 RFLDHLQQGNTSLSRVSFVILDEA--------DRMLDMGFEP---QIREVMQNLPDKHQT 303
            FL+HL   N        + +DEA        D      F P    + ++ Q  P     
Sbjct: 130 NFLEHLAHWN-----PVLLAVDEAHCISQWGHD------FRPEYAALGQLRQRFPTL-PF 177

Query: 304 LLFSAT--MPVEIEALAQEYLTDPVQVKVG--------KVSSPTANVIQILEKVSENEKV 353
           +  +AT       + +    L DP+              +      + Q++  V E    
Sbjct: 178 MALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQR-- 235

Query: 354 DRLLALLVEEAFLAEKS----CHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRN 409
                          KS    C     +     R  + ++ +  L ++G+ A A H G  
Sbjct: 236 --------------GKSGIIYC----NS-----RA-KVEDTAARLQSKGISAAAYHAGLE 271

Query: 410 QSDRESALRDFRNGSTNILVATDVASRGLDVMG--------VAHVVNLDLPK 453
            + R      F+     I+VAT VA  G   MG        V H    D+P+
Sbjct: 272 NNVRADVQEKFQRDDLQIVVAT-VAF-G---MGINKPNVRFVVH---FDIPR 315

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus} Length = 590

 Score = 47.5 bits (113), Expect = 8e-06
 Identities = 53/339 (15%), Positives = 94/339 (27%), Gaps = 66/339 (19%)

Query: 159 RDLLGCAETGSGKT--AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA 216
           R L+  A TG+GKT  A      +               + L LA    L          
Sbjct: 200 RSLITMA-TGTGKTVVAFQISWKLWSARWNRTGDYRKPRI-LFLADRNVLVDD------- 250

Query: 217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFL--DHLQQGNTSLSRVSF-- 272
                D   T    G      +  ++     I  A        +          +  F  
Sbjct: 251 ---PKDKTFT--PFGDARHKIEGGKVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDL 305

Query: 273 VILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM--------------PV-EI--- 314
           +I+DE  R          RE+++      Q +  +AT               P+      
Sbjct: 306 IIIDECHRGSARD-NSNWREILEYFEPAFQ-IGMTATPLREDNRDTYRYFGNPIYTYSLR 363

Query: 315 EALAQEYLTDPVQVKV-----GKVSSPTANVIQILEKVSENEKVDR--LLALLVEEAF-- 365
           + +   +L      +V          P+   +    +   + +        ++  +A   
Sbjct: 364 QGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGREIPDGEYQTKDFERVIALKARTD 423

Query: 366 -----LAE--KSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG----------GR 408
                L +  K    F  TIVF   +   DE+  AL          H           G+
Sbjct: 424 AFAKHLTDFMKRTDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGK 483

Query: 409 NQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV 447
                 S  ++    +  IL  + + + G+D     +VV
Sbjct: 484 IGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVV 522

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A Length = 997

 Score = 44.4 bits (104), Expect = 7e-05
 Identities = 42/200 (21%), Positives = 73/200 (36%), Gaps = 28/200 (14%)

Query: 114 VPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKT- 172
           V     IE+F ++  +P+     E   +      Q +A+     G  +   A T +GKT 
Sbjct: 16  VDLNHKIENFDELIPNPARSWPFELDTF------QKEAVYHLEQGDSVFVAAHTSAGKTV 69

Query: 173 -AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVG 231
            A + I M             +    +  +P + L+ Q  ++      + D     ++ G
Sbjct: 70  VAEYAIAMAHR----------NMTKTIYTSPIKALSNQKFRD---FKETFDDVNIGLITG 116

Query: 232 GTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIR 291
              I           + ++ T       L +G   +  V FVI DE   + D        
Sbjct: 117 DVQI-------NPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWE 169

Query: 292 EVMQNLPDKHQTLLFSATMP 311
           EV+  LP   + +L SAT+P
Sbjct: 170 EVIIMLPQHVKFILLSATVP 189

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	503
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	100.0
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	100.0
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	100.0
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	100.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	100.0
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	100.0
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	100.0
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	100.0
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	100.0
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	100.0
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	100.0
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	100.0
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	100.0
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	100.0
4gl2_A	699	Interferon-induced helicase C domain-containing P;	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	100.0
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	100.0
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	100.0
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	100.0
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	100.0
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	100.0
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	100.0
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	100.0
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	100.0
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	100.0
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
3h1t_A	590	Type I site-specific restriction-modification syst	100.0
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	100.0
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	100.0
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	100.0
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	100.0
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	100.0
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.98
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.97
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.95
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	99.95
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	99.94
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	99.92
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.91
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	99.91
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	99.9
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	99.9
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.9
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	99.9
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	99.9
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	99.89
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.89
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	99.88
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.88
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.85
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	99.75
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.81
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.77
1z5z_A	271	Helicase of the SNF2/RAD54 family; hydrolase, reco	99.7
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	98.89
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.43
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.4
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.37
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	98.24
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.23
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.22
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.17
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.43
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	97.33
3hgt_A	328	HDA1 complex subunit 3; RECA-like domain, SWI2/SNF	97.19
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.11
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.1
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	97.04
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.01
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.01
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.0
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	96.97
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.78
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.68
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.65
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.59
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.52
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.47
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	96.37
3bos_A	242	Putative DNA replication factor; P-loop containing	96.32
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.3
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.25
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	96.23
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.22
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	96.16
2chg_A	226	Replication factor C small subunit; DNA-binding pr	96.11
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.96
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.91
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.88
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	95.84
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.83
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	95.79
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.71
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.69
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	95.65
2qgz_A	308	Helicase loader, putative primosome component; str	95.62
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.51
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	95.5
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	95.31
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	95.26
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.22
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	95.19
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	94.9
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	94.78
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	94.72
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.66
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	94.65
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	94.54
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	94.4
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	94.27
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.23
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	93.97
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	93.88
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.85
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	93.84
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	93.84
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	93.64
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	93.64
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	93.59
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	93.53
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	93.47
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.39
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	93.37
3pvs_A	447	Replication-associated recombination protein A; ma	93.28
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	93.13
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	93.11
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	92.5
2fna_A	357	Conserved hypothetical protein; structural genomic	91.87
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	91.84
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	91.73
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	91.72
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	91.62
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	91.61
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	91.48
3co5_A	143	Putative two-component system transcriptional RES	91.26
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	91.19
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	90.97
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	90.71
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	90.7
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	90.59
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	90.56
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	90.55
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	90.29
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	89.75
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	89.39
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.86
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	88.78
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	88.16
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	87.87
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	87.59
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	87.56
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	87.53
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	87.46
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	87.45
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	87.33
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	87.3
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	87.28
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	87.05
3io5_A	333	Recombination and repair protein; storage dimer, i	87.04
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	86.9
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	86.84
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	86.57
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	86.46
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	86.37
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	86.36
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	86.35
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	86.06
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	85.91
2l82_A	162	Designed protein OR32; structural genomics, northe	85.79
2eyu_A	261	Twitching motility protein PILT; pilus retraction	85.75
3bor_A	237	Human initiation factor 4A-II; translation initiat	85.49
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	85.31
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	84.7
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	84.36
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	84.28
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	84.01
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	83.88
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	83.84
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	83.81
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	83.81
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	83.24
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	83.21
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	83.21
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	83.13
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	83.02
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	82.95
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	82.79
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	82.74
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	82.36
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	82.33
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	82.02
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	81.82
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	81.77
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	81.38
2r44_A	331	Uncharacterized protein; putative ATPase, structur	81.37
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	81.36
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	81.34
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	81.17
2ewv_A	372	Twitching motility protein PILT; pilus retraction	81.16
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	81.08
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	81.06
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	80.97
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	80.81
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	80.75
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	80.72
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	80.45
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	80.33
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	80.31
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	80.31
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	80.27

>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=5.2e-61  Score=485.30  Aligned_cols=343  Identities=40%  Similarity=0.626  Sum_probs=317.4

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      ..|.++.+|+++++++.+++.+..+||..|+++|.++|+.+++|+|+++++|||+|||++|++|++.++...+......+
T Consensus        50 ~~p~~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~~~~~~  129 (434)
T 2db3_A           50 DVPQPIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHELELGR  129 (434)
T ss_dssp             SCCCCCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCCCCTTC
T ss_pred             CCCCCcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccccccCC
Confidence            66788999999999999999999999999999999999999999999999999999999999999999887654334457


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      +++||++|||+|+.|+++++++++... ++++.+++||.....+...+..+++|+|+||++|.+++.+....+.++++||
T Consensus       130 ~~~lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~~~lV  208 (434)
T 2db3_A          130 PQVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDRTFITFEDTRFVV  208 (434)
T ss_dssp             CSEEEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHTTSCCCTTCCEEE
T ss_pred             ccEEEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHhCCcccccCCeEE
Confidence            899999999999999999999998654 5788899999998888888888999999999999999998888899999999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhC--CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhH
Q 010709          275 LDEADRMLDMGFEPQIREVMQNL--PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEK  352 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~--~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k  352 (503)
                      +||||++++++|...+..++..+  ++..|+++||||+++.+..++..++.++..+.+.........+.+.+..+....|
T Consensus       209 lDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~~~~~~~~~~~k  288 (434)
T 2db3_A          209 LDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAK  288 (434)
T ss_dssp             EETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTEEEEEEECCGGGH
T ss_pred             EccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccccccccccceEEEEeCcHHH
Confidence            99999999999999999999885  6789999999999999999999999999999888877777889999999998889


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      ...+..++...          ..++||||++++.|+.+++.|.+.++.+..+||++++.+|.++++.|++|+.+|||||+
T Consensus       289 ~~~l~~~l~~~----------~~~~lVF~~t~~~a~~l~~~L~~~~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~  358 (434)
T 2db3_A          289 RSKLIEILSEQ----------ADGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS  358 (434)
T ss_dssp             HHHHHHHHHHC----------CTTEEEECSSHHHHHHHHHHHHHTTCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG
T ss_pred             HHHHHHHHHhC----------CCCEEEEEeCcHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch
Confidence            88888777652          12499999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          433 VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++++|+|+|++++||+||+|.+..+|+||+||+||.
T Consensus       359 v~~rGlDi~~v~~VI~~d~p~~~~~y~qriGR~gR~  394 (434)
T 2db3_A          359 VASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRV  394 (434)
T ss_dssp             GGTSSCCCTTCCEEEESSCCSSHHHHHHHHTTSSCT
T ss_pred             hhhCCCCcccCCEEEEECCCCCHHHHHHHhcccccC
Confidence            999999999999999999999999999999999994

>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=1.5e-56  Score=452.22  Aligned_cols=345  Identities=43%  Similarity=0.696  Sum_probs=307.6

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCC-----
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPV-----  189 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~-----  189 (503)
                      ..|.++.+|+++++++.+.+.|...||..|+++|.++++.++.++++++++|||+|||++|++|++..+......     
T Consensus         9 ~~p~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~   88 (417)
T 2i4i_A            9 NCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRA   88 (417)
T ss_dssp             TCCCCCSSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHH
T ss_pred             cCCcccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhc
Confidence            668888999999999999999999999999999999999999999999999999999999999999887654321     


Q ss_pred             --------CCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHH
Q 010709          190 --------GRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQ  261 (503)
Q Consensus       190 --------~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~  261 (503)
                              ....++++||++||++|+.|+++.+++++... ++.+..++|+.....+...+..+++|+|+||++|.+.+.
T Consensus        89 ~~~~~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~  167 (417)
T 2i4i_A           89 MKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMME  167 (417)
T ss_dssp             HHHCBTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHH
T ss_pred             cccccccccccCCccEEEECCcHHHHHHHHHHHHHHhCcC-CceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHH
Confidence                    12234789999999999999999999998654 588899999999888888888889999999999999999


Q ss_pred             cCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC--CC--CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCC
Q 010709          262 QGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL--PD--KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPT  337 (503)
Q Consensus       262 ~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~--~~--~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~  337 (503)
                      ...+.+.++++|||||||++.+++|...+..++...  ++  ..|++++|||+++.+..+...++.++..+.........
T Consensus       168 ~~~~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (417)
T 2i4i_A          168 RGKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTS  247 (417)
T ss_dssp             TTSBCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC----CC
T ss_pred             cCCcChhhCcEEEEEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCCCCCc
Confidence            888888999999999999999999999999998853  32  67899999999999999999999999888887776777


Q ss_pred             CceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHH
Q 010709          338 ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL  417 (503)
Q Consensus       338 ~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~  417 (503)
                      ..+.+.+..+....+...+..++...        ...+++||||++++.++.+++.|...++.+..+||++++.+|.+++
T Consensus       248 ~~i~~~~~~~~~~~~~~~l~~~l~~~--------~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~  319 (417)
T 2i4i_A          248 ENITQKVVWVEESDKRSFLLDLLNAT--------GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEAL  319 (417)
T ss_dssp             SSEEEEEEECCGGGHHHHHHHHHHTC--------CTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             cCceEEEEEeccHhHHHHHHHHHHhc--------CCCCeEEEEECCHHHHHHHHHHHHHCCCCeeEecCCCCHHHHHHHH
Confidence            78888888888888887777766542        2456799999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       418 ~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|++|+.+|||||+++++|+|+|++++||++|+|.+...|+||+||+||.
T Consensus       320 ~~f~~g~~~vlvaT~~~~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  370 (417)
T 2i4i_A          320 HQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV  370 (417)
T ss_dssp             HHHHHTSSCEEEECHHHHTTSCCCCEEEEEESSCCSSHHHHHHHHTTBCC-
T ss_pred             HHHHcCCCCEEEECChhhcCCCcccCCEEEEEcCCCCHHHHHHhcCccccC
Confidence            999999999999999999999999999999999999999999999999995

>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=6.4e-56  Score=446.56  Aligned_cols=336  Identities=32%  Similarity=0.529  Sum_probs=302.7

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeE
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLA  197 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~  197 (503)
                      .+..+|+++++++.+.+.+..+||..|+++|.++++.+++|+++++++|||+|||++|++|++..+...     ..++++
T Consensus        34 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~~~~  108 (410)
T 2j0s_A           34 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRETQA  108 (410)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCSCCE
T ss_pred             cCCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc-----cCCceE
Confidence            345679999999999999999999999999999999999999999999999999999999998765321     236789


Q ss_pred             EEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecc
Q 010709          198 LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE  277 (503)
Q Consensus       198 lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDE  277 (503)
                      ||++|+++|+.|+++.+++++... ++.+..+.|+.........+..+++|+|+||++|.+.+.+....+.++++||+||
T Consensus       109 lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~~~~~~~~~~~vViDE  187 (410)
T 2j0s_A          109 LILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE  187 (410)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEET
T ss_pred             EEEcCcHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHhCCccHhheeEEEEcc
Confidence            999999999999999999998665 5888899999998888777878899999999999999998878889999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh-HHHHH
Q 010709          278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVDRL  356 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~~~l  356 (503)
                      ||++.+++|...+..++..+++..|++++|||+++.+..+...++.+|..+...........+.+.+..+.... +...+
T Consensus       188 ah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l  267 (410)
T 2j0s_A          188 ADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTL  267 (410)
T ss_dssp             HHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSCTTEEEEEEEESSTTHHHHHH
T ss_pred             HHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccCCCceEEEEEeCcHHhHHHHH
Confidence            99999999999999999999999999999999999998888999999988877666666677788777776554 66666


Q ss_pred             HHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccccc
Q 010709          357 LALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR  436 (503)
Q Consensus       357 ~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~  436 (503)
                      ..++...         ..+++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||+++++
T Consensus       268 ~~~~~~~---------~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~~~  338 (410)
T 2j0s_A          268 CDLYDTL---------TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWAR  338 (410)
T ss_dssp             HHHHHHH---------TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGGSS
T ss_pred             HHHHHhc---------CCCcEEEEEcCHHHHHHHHHHHHhCCCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECChhhC
Confidence            6655442         2347999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          437 GLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       437 Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|+|++++||++|+|.+...|+||+||+||.
T Consensus       339 Gidi~~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  370 (410)
T 2j0s_A          339 GLDVPQVSLIINYDLPNNRELYIHRIGRSGRY  370 (410)
T ss_dssp             SCCCTTEEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             cCCcccCCEEEEECCCCCHHHHHHhcccccCC
Confidence            99999999999999999999999999999995

>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=100.00  E-value=2e-54  Score=436.20  Aligned_cols=337  Identities=33%  Similarity=0.538  Sum_probs=290.8

Q ss_pred             CCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCe
Q 010709          117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPL  196 (503)
Q Consensus       117 ~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~  196 (503)
                      +....+|+++++++.+.+.+..+|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+...     ..+++
T Consensus        36 ~~~~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~  110 (414)
T 3eiq_A           36 NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LKATQ  110 (414)
T ss_dssp             CCCCCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT-----SCSCC
T ss_pred             cchhcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc-----CCcee
Confidence            3456679999999999999999999999999999999999999999999999999999999999876442     23678


Q ss_pred             EEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEe
Q 010709          197 ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL  275 (503)
Q Consensus       197 ~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vVi  275 (503)
                      +||++|+++|+.|+++.+++++... +..+....|+.........+. .+++|+|+||++|.+.+.+..+.+.++++||+
T Consensus       111 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~~~~vVi  189 (414)
T 3eiq_A          111 ALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVL  189 (414)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHHTSSCSTTCCEEEE
T ss_pred             EEEEeChHHHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHcCCcccccCcEEEE
Confidence            9999999999999999999998665 578888888888777666655 67899999999999999988888899999999


Q ss_pred             cchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh-HHH
Q 010709          276 DEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVD  354 (503)
Q Consensus       276 DEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~~  354 (503)
                      ||||++.++++...+..++..++++.|+++||||++..+..+...++.++..+...........+.+.+....... +..
T Consensus       190 DEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (414)
T 3eiq_A          190 DEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIRQFYINVEREEWKLD  269 (414)
T ss_dssp             CSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCCEEEEECSSSTTHHH
T ss_pred             ECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCceEEEEEeChHHhHHH
Confidence            9999999999999999999999999999999999999999999999999988877766666677777777665544 665


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccc
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA  434 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~  434 (503)
                      .+..++..         .+.+++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++
T Consensus       270 ~l~~~~~~---------~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~~  340 (414)
T 3eiq_A          270 TLCDLYET---------LTITQAVIFINTRRKVDWLTEKMHARDFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLL  340 (414)
T ss_dssp             HHHHHHHS---------SCCSSCEEECSCHHHHHHHHHHHHTTTCCCEEC---CHHHHHHHHHHHHSCC---CEEECSSC
T ss_pred             HHHHHHHh---------CCCCcEEEEeCCHHHHHHHHHHHHhcCCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCcc
Confidence            55555433         245679999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          435 SRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       435 ~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++|+|+|++++||++|+|.+..+|+||+||+||.
T Consensus       341 ~~Gidip~v~~Vi~~~~p~s~~~~~Qr~GR~gR~  374 (414)
T 3eiq_A          341 ARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRF  374 (414)
T ss_dssp             C--CCGGGCSCEEESSCCSSTHHHHHHSCCC---
T ss_pred             ccCCCccCCCEEEEeCCCCCHHHhhhhcCcccCC
Confidence            9999999999999999999999999999999995

>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=100.00  E-value=1.9e-53  Score=427.21  Aligned_cols=334  Identities=31%  Similarity=0.511  Sum_probs=297.1

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ...+|+++++++.+.+.|..+||..|+++|.++++.+++++++++++|||+|||++|++|++..+...     ..++++|
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~~l   93 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQAL   93 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEE
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc-----cCCccEE
Confidence            45679999999999999999999999999999999999999999999999999999999998875432     2356899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      |++|+++|+.|+++.+++++... ++.+....|+............+++|+|+||++|.+.+.+....+.++++||+|||
T Consensus        94 il~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEa  172 (400)
T 1s2m_A           94 IMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEA  172 (400)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESH
T ss_pred             EEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHhCCcccccCCEEEEeCc
Confidence            99999999999999999998665 57888899998887777777788999999999999999887778899999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      |++.+.+|...+..++..+++..|++++|||++..+...+..++.+|..+.... ......+.+.+..+....+...+..
T Consensus       173 H~~~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~k~~~l~~  251 (400)
T 1s2m_A          173 DKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLME-ELTLKGITQYYAFVEERQKLHCLNT  251 (400)
T ss_dssp             HHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCS-SCBCTTEEEEEEECCGGGHHHHHHH
T ss_pred             hHhhhhchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEecc-ccccCCceeEEEEechhhHHHHHHH
Confidence            999888888889999999988999999999999999999999999887664433 2344567777777777777777666


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCC
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGL  438 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl  438 (503)
                      ++..         ...+++||||++++.++.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+++++|+
T Consensus       252 ~~~~---------~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~~~~~Gi  322 (400)
T 1s2m_A          252 LFSK---------LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLLTRGI  322 (400)
T ss_dssp             HHHH---------SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCSSSSC
T ss_pred             HHhh---------cCCCcEEEEEecHHHHHHHHHHHHhcCCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcCccccCC
Confidence            6543         2456899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          439 DVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       439 dip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|++++||++|+|.+...|+||+||+||.
T Consensus       323 dip~~~~Vi~~~~p~s~~~~~Qr~GR~gR~  352 (400)
T 1s2m_A          323 DIQAVNVVINFDFPKTAETYLHRIGRSGRF  352 (400)
T ss_dssp             CCTTEEEEEESSCCSSHHHHHHHHCBSSCT
T ss_pred             CccCCCEEEEeCCCCCHHHHHHhcchhcCC
Confidence            999999999999999999999999999995

>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=100.00  E-value=3.2e-53  Score=424.16  Aligned_cols=334  Identities=30%  Similarity=0.492  Sum_probs=297.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      ..|+++++++.+.+.|..+|+..|+++|.++++.++.++++++++|||+|||++|++|++..+...     ..++++||+
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~-----~~~~~~lil   82 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVM   82 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC-----TTCCCEEEE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc-----CCCeeEEEE
Confidence            469999999999999999999999999999999999999999999999999999999998775432     235689999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      +|+++|+.|+++.++++.....++.+..+.|+.........+. ..++|+|+||++|...+.+....+.++++||+||||
T Consensus        83 ~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~vViDEaH  162 (391)
T 1xti_A           83 CHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECD  162 (391)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCSEEEECSHH
T ss_pred             CCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHcCCccccccCEEEEeCHH
Confidence            9999999999999999987766788999999988776655554 447999999999999998877788999999999999


Q ss_pred             HHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCC-CCCCceEEEEEEcChhhHHHHHH
Q 010709          280 RMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS-SPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       280 ~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      ++.++ ++...+..++...++..|++++|||+++.+...+..++.+|..+...... .....+.+.+..+....+...+.
T Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  242 (391)
T 1xti_A          163 KMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLF  242 (391)
T ss_dssp             HHTSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCCCCCCTTCEEEEEECCGGGHHHHHH
T ss_pred             HHhhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCccccCcccceEEEEEcCchhHHHHHH
Confidence            99874 67888899999988899999999999999999999999999888765543 33455777778888888887777


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccC
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRG  437 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~G  437 (503)
                      .++..         ...+++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||+++++|
T Consensus       243 ~~l~~---------~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~G  313 (391)
T 1xti_A          243 DLLDV---------LEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRG  313 (391)
T ss_dssp             HHHHH---------SCCSEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCCCSSC
T ss_pred             HHHHh---------cCCCcEEEEeCcHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECChhhcC
Confidence            76654         245689999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|+|++++||++++|.+...|+||+||+||.
T Consensus       314 idi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  344 (391)
T 1xti_A          314 MDIERVNIAFNYDMPEDSDTYLHRVARAGRF  344 (391)
T ss_dssp             BCCTTEEEEEESSCCSSHHHHHHHHCBCSSS
T ss_pred             CCcccCCEEEEeCCCCCHHHHHHhcccccCC
Confidence            9999999999999999999999999999995

>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=100.00  E-value=7.4e-53  Score=424.50  Aligned_cols=337  Identities=28%  Similarity=0.430  Sum_probs=293.5

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRG  192 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~  192 (503)
                      .......+|+++++++.+.+.+..+|+..|+++|.++++.++.+  +++++++|||+|||++|++|++..+...     .
T Consensus        19 ~~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~   93 (412)
T 3fht_A           19 SPLYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----N   93 (412)
T ss_dssp             STTCCSSCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----S
T ss_pred             CCccccCCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc-----C
Confidence            33456778999999999999999999999999999999999987  8999999999999999999999876442     2


Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-CCCCCCCcc
Q 010709          193 DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-GNTSLSRVS  271 (503)
Q Consensus       193 ~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~~~  271 (503)
                      .++++||++|+++|+.|+++.++++.....++.+....++......   ....++|+|+||++|.+.+.+ ..+.+.+++
T Consensus        94 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~  170 (412)
T 3fht_A           94 KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIK  170 (412)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCSSCGGGCC
T ss_pred             CCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhh---hcCCCCEEEECchHHHHHHHhcCCcChhhCc
Confidence            3568999999999999999999999877667888888877654332   234579999999999999865 455678999


Q ss_pred             EEEecchhHHhh-CCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcCh-
Q 010709          272 FVILDEADRMLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE-  349 (503)
Q Consensus       272 ~vViDEaH~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  349 (503)
                      +||+||||++.+ .++...+..++..+++..|++++|||+++.+..+...++.++..+...........+.+.+..... 
T Consensus       171 ~iViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (412)
T 3fht_A          171 VFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSR  250 (412)
T ss_dssp             EEEEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGGGSSCTTEEEEEEECSSH
T ss_pred             EEEEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccccccccCceEEEEEcCCh
Confidence            999999999987 578889999999999999999999999999999999999999988777766667777777776655 


Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEE
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILV  429 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLv  429 (503)
                      ..+...+..++...         ..+++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||
T Consensus       251 ~~~~~~l~~~~~~~---------~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv  321 (412)
T 3fht_A          251 DEKFQALCNLYGAI---------TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLV  321 (412)
T ss_dssp             HHHHHHHHHHHHHH---------SSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCSEEE
T ss_pred             HHHHHHHHHHHhhc---------CCCCEEEEeCCHHHHHHHHHHHHhCCCeEEEecCCCCHHHHHHHHHHHHCCCCcEEE
Confidence            45555555555432         345799999999999999999999999999999999999999999999999999999


Q ss_pred             EccccccCCCCCCCCEEEEccCC------CChhHHHHhhCcceee
Q 010709          430 ATDVASRGLDVMGVAHVVNLDLP------KVLLAASESLCTTSFN  468 (503)
Q Consensus       430 aT~~~~~Gldip~v~~VI~~~~p------~s~~~~~Qr~GR~gR~  468 (503)
                      ||+++++|+|+|++++||++|+|      .+..+|+||+||+||.
T Consensus       322 ~T~~~~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~  366 (412)
T 3fht_A          322 TTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRF  366 (412)
T ss_dssp             ECGGGTSSCCCTTEEEEEESSCCBCSSSSBCHHHHHHHHTTSSCT
T ss_pred             EcCccccCCCccCCCEEEEECCCCCCCCCcchheeecccCcccCC
Confidence            99999999999999999999999      5678999999999993

>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=100.00  E-value=1.6e-52  Score=419.59  Aligned_cols=331  Identities=28%  Similarity=0.468  Sum_probs=287.8

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCe
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPL  196 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~  196 (503)
                      ...+|+++++++.+.+.+...|+..|+++|.++++.++++  +++++++|||+|||++|++|++..+...     ..+++
T Consensus         3 ~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~-----~~~~~   77 (395)
T 3pey_A            3 MAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE-----DASPQ   77 (395)
T ss_dssp             -CCSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT-----CCSCC
T ss_pred             cccCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC-----CCCcc
Confidence            3467999999999999999999999999999999999988  8999999999999999999998875432     24678


Q ss_pred             EEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEec
Q 010709          197 ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD  276 (503)
Q Consensus       197 ~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViD  276 (503)
                      +||++|+++|+.|+++.+++++... ++.+....++.....    ...+++|+|+||++|.+.+.+....+.++++||+|
T Consensus        78 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~----~~~~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiD  152 (395)
T 3pey_A           78 AICLAPSRELARQTLEVVQEMGKFT-KITSQLIVPDSFEKN----KQINAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLD  152 (395)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSCTT----SCBCCSEEEECHHHHHHHHHTTCBCCTTCCEEEEE
T ss_pred             EEEECCCHHHHHHHHHHHHHHhccc-CeeEEEEecCchhhh----ccCCCCEEEEcHHHHHHHHHcCCcccccCCEEEEE
Confidence            9999999999999999999998654 467777776654322    23468999999999999998877889999999999


Q ss_pred             chhHHhh-CCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChh-hHHH
Q 010709          277 EADRMLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSEN-EKVD  354 (503)
Q Consensus       277 EaH~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~k~~  354 (503)
                      |||++.+ .++...+..+...++++.|++++|||+++.+..+...++.++..+...........+.+.+...... .+..
T Consensus       153 Eah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (395)
T 3pey_A          153 EADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFD  232 (395)
T ss_dssp             THHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTTEEEEEEECSSHHHHHH
T ss_pred             ChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEccccccccccccEEEEEcCchHHHHH
Confidence            9999988 5788889999999999999999999999999999999999998887776666667777777776544 3443


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccc
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA  434 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~  434 (503)
                      .+..++..         ...+++||||++++.++.+++.|+..++.+..+||++++.+|.++++.|++|+.+|||||+++
T Consensus       233 ~l~~~~~~---------~~~~~~lvf~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~~  303 (395)
T 3pey_A          233 VLTELYGL---------MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL  303 (395)
T ss_dssp             HHHHHHTT---------TTSSEEEEECSCHHHHHHHHHHHHHTTCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGGG
T ss_pred             HHHHHHHh---------ccCCCEEEEeCCHHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECChh
Confidence            33333221         245689999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCEEEEccCCC------ChhHHHHhhCcceee
Q 010709          435 SRGLDVMGVAHVVNLDLPK------VLLAASESLCTTSFN  468 (503)
Q Consensus       435 ~~Gldip~v~~VI~~~~p~------s~~~~~Qr~GR~gR~  468 (503)
                      ++|+|+|++++||++|+|+      +..+|+||+||+||.
T Consensus       304 ~~Gidip~~~~Vi~~~~p~~~~~~~s~~~~~Qr~GR~gR~  343 (395)
T 3pey_A          304 ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRF  343 (395)
T ss_dssp             SSSCCCTTEEEEEESSCCBCTTSSBCHHHHHHHHTTSSCT
T ss_pred             hcCCCcccCCEEEEcCCCCCCcCCCCHHHhhHhccccccC
Confidence            9999999999999999999      999999999999994

>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=100.00  E-value=1.2e-51  Score=409.00  Aligned_cols=327  Identities=37%  Similarity=0.570  Sum_probs=291.3

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ..+|+++++++.+.+.|...|+..|+++|.++++.++++ +++++++|||+|||++|++|++..+...      .++++|
T Consensus         5 ~~~f~~~~l~~~~~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~~------~~~~~l   78 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN------NGIEAI   78 (367)
T ss_dssp             CCCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCSS------SSCCEE
T ss_pred             cCchhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhccc------CCCcEE
Confidence            346999999999999999999999999999999999988 6899999999999999999988765432      367899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      |++|+++|+.|+++.++++.... ++.+....|+.........+. +++|+|+||++|.+.+......+.++++||+|||
T Consensus        79 il~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~~~~~~~~~~~iIiDEa  156 (367)
T 1hv8_A           79 ILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEA  156 (367)
T ss_dssp             EECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETH
T ss_pred             EEcCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHcCCcccccCCEEEEeCc
Confidence            99999999999999999998654 578888899888776655554 6899999999999999887788899999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      |++.++++...+..++..+++..+++++|||+++........++.++..+....    ...+.+.+..+....+...+..
T Consensus       157 h~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l~~  232 (367)
T 1hv8_A          157 DEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKI----NANIEQSYVEVNENERFEALCR  232 (367)
T ss_dssp             HHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCS----SSSSEEEEEECCGGGHHHHHHH
T ss_pred             hHhhhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecC----CCCceEEEEEeChHHHHHHHHH
Confidence            999999999999999999999999999999999999999999998876665432    2356677777777888777766


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCC
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGL  438 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl  438 (503)
                      .+.          ....++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||+++++|+
T Consensus       233 ~l~----------~~~~~~lvf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gi  302 (367)
T 1hv8_A          233 LLK----------NKEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGI  302 (367)
T ss_dssp             HHC----------STTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTTHHHHC
T ss_pred             HHh----------cCCCcEEEEECCHHHHHHHHHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECChhhcCC
Confidence            653          2445799999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          439 DVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       439 dip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|++++||++++|.+..+|+||+||+||.
T Consensus       303 d~~~~~~Vi~~~~~~s~~~~~Q~~GR~~R~  332 (367)
T 1hv8_A          303 DVNDLNCVINYHLPQNPESYMHRIGRTGRA  332 (367)
T ss_dssp             CCSCCSEEEESSCCSCHHHHHHHSTTTCCS
T ss_pred             CcccCCEEEEecCCCCHHHhhhcccccccC
Confidence            999999999999999999999999999995

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=100.00  E-value=3.4e-52  Score=436.37  Aligned_cols=336  Identities=29%  Similarity=0.414  Sum_probs=280.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHh--cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVAL--SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~--~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      +++++++.+..+||..|+++|.++++.++  .++++++++|||+|||++|++|++..+..... ....++++|||+||++
T Consensus        28 l~~~l~~~l~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~-~~~~~~~~lvl~Ptr~  106 (579)
T 3sqw_A           28 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-DSQYMVKAVIVAPTRD  106 (579)
T ss_dssp             SCHHHHHHHHTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-SSTTSCCEEEECSSHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhccc-cccCCCeEEEEcchHH
Confidence            99999999999999999999999999999  67899999999999999999999988776432 2234578999999999


Q ss_pred             HHHHHHHHHHHHhc---cCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecchhH
Q 010709          206 LAQQIEKEVKALSR---SLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDEADR  280 (503)
Q Consensus       206 La~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDEaH~  280 (503)
                      |+.|+++.++++..   ....+.+..++|+.........+. .+++|+|+||++|.+++.+. ...+..+++|||||||+
T Consensus       107 La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  186 (579)
T 3sqw_A          107 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  186 (579)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccCCEEEEEChHH
Confidence            99999999999864   233567888899988777666654 47999999999999888764 34578899999999999


Q ss_pred             HhhCCCHHHHHHHHHhCC-------CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCC----CCCCceEEEEEEcCh
Q 010709          281 MLDMGFEPQIREVMQNLP-------DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS----SPTANVIQILEKVSE  349 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~-------~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  349 (503)
                      +.+++|...+..++..++       +.+|+++||||+++.+..++..++.++..+......    .....+.+.+.....
T Consensus       187 l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~  266 (579)
T 3sqw_A          187 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  266 (579)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             hhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCccccccccccceEEEEecc
Confidence            999999999988877653       367999999999999999999999988777654322    233345555554443


Q ss_pred             -hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC---CCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q 010709          350 -NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE---GLHAVALHGGRNQSDRESALRDFRNGST  425 (503)
Q Consensus       350 -~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~---~~~v~~lh~~~~~~~r~~~~~~f~~g~~  425 (503)
                       ..+...++..+......    ..+..++||||+++..|+.+++.|...   ++.+..+||++++.+|.++++.|++|+.
T Consensus       267 ~~~~~~~~~~~l~~~~~~----~~~~~~~iVF~~t~~~~~~l~~~L~~~~~~~~~v~~~hg~~~~~~R~~~~~~F~~g~~  342 (579)
T 3sqw_A          267 FANSIFAAVEHIKKQIKE----RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDES  342 (579)
T ss_dssp             TTHHHHHHHHHHHHHHHH----TTTCCEEEEECSSHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSS
T ss_pred             hhhhHHHHHHHHHHHHhh----cCCCCcEEEECCcHHHHHHHHHHHHHhhcCCCcEEEecCCCCHHHHHHHHHHhhcCCC
Confidence             33333444433332221    134568999999999999999999887   8999999999999999999999999999


Q ss_pred             cEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          426 NILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       426 ~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|||||+++++|||+|++++||++|+|.+...|+||+||+||.
T Consensus       343 ~vLVaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~  385 (579)
T 3sqw_A          343 GILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARS  385 (579)
T ss_dssp             EEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCT
T ss_pred             eEEEEcchhhcCCCcccCCEEEEcCCCCCHHHhhhhccccccC
Confidence            9999999999999999999999999999999999999999994

>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=100.00  E-value=2.3e-53  Score=425.57  Aligned_cols=337  Identities=32%  Similarity=0.511  Sum_probs=187.8

Q ss_pred             CCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCC
Q 010709          116 APAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGP  195 (503)
Q Consensus       116 ~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~  195 (503)
                      ...+...|+++++++.+.+.+..+|+..|+++|.++++.+++++++++++|||+|||++|++|++..+...     ..++
T Consensus        16 ~~~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~-----~~~~   90 (394)
T 1fuu_A           16 YDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKAP   90 (394)
T ss_dssp             SCCCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----CCSC
T ss_pred             cccccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc-----CCCC
Confidence            44556789999999999999999999999999999999999999999999999999999999999875442     2367


Q ss_pred             eEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEe
Q 010709          196 LALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL  275 (503)
Q Consensus       196 ~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vVi  275 (503)
                      ++||++|+++|+.|+++.++++.... ++.+..+.|+....+....+. +++|+|+||++|.+.+.+....+.++++||+
T Consensus        91 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~vIi  168 (394)
T 1fuu_A           91 QALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQRRRFRTDKIKMFIL  168 (394)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHTTSSCCTTCCEEEE
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHhCCcchhhCcEEEE
Confidence            89999999999999999999988665 588888999888766555444 5899999999999999887778889999999


Q ss_pred             cchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhh-HHH
Q 010709          276 DEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENE-KVD  354 (503)
Q Consensus       276 DEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~~  354 (503)
                      ||||++.+.++...+..++..+++..|++++|||+++.+......++.+|..+...........+.+.+..+.... +..
T Consensus       169 DEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  248 (394)
T 1fuu_A          169 DEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYE  248 (394)
T ss_dssp             ETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC-----------------------
T ss_pred             EChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCCceEEEEEcCchhhHHH
Confidence            9999999999999999999999999999999999999999999999999988877665555555555555444333 433


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcccc
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVA  434 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~  434 (503)
                      .+..++..         ...+++||||++++.++.+++.|...++.+..+||++++.+|.++++.|++|+.+|||||+++
T Consensus       249 ~l~~~~~~---------~~~~~~lVf~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~  319 (394)
T 1fuu_A          249 CLTDLYDS---------ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL  319 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHhc---------CCCCcEEEEECCHHHHHHHHHHHHHcCCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECChh
Confidence            33333322         134579999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          435 SRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       435 ~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++|+|+|++++||++|+|.+...|+||+||+||.
T Consensus       320 ~~Gldi~~~~~Vi~~~~p~s~~~~~Qr~GR~~R~  353 (394)
T 1fuu_A          320 ARGIDVQQVSLVINYDLPANKENYIHRIGRGGRF  353 (394)
T ss_dssp             ----------------------------------
T ss_pred             hcCCCcccCCEEEEeCCCCCHHHHHHHcCcccCC
Confidence            9999999999999999999999999999999995

>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=100.00  E-value=1.5e-51  Score=431.27  Aligned_cols=336  Identities=29%  Similarity=0.416  Sum_probs=279.0

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHh--cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVAL--SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~--~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      +++.+++.+..+||..|+++|.++++.++  .++++++++|||+|||++|++|++..+..... ....++++|||+||++
T Consensus        79 l~~~l~~~l~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~-~~~~~~~~lil~Ptr~  157 (563)
T 3i5x_A           79 LDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKF-DSQYMVKAVIVAPTRD  157 (563)
T ss_dssp             SCHHHHHHHHTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTT-SSTTSCCEEEECSSHH
T ss_pred             CCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhccc-cccCCeeEEEEcCcHH
Confidence            99999999999999999999999999999  67899999999999999999999998876532 1233568999999999


Q ss_pred             HHHHHHHHHHHHhcc---CCCceEEEEECCccHHHHHHHh-hCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecchhH
Q 010709          206 LAQQIEKEVKALSRS---LDSFKTAIVVGGTNIAEQRSEL-RGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDEADR  280 (503)
Q Consensus       206 La~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDEaH~  280 (503)
                      |+.|+++.++++...   .....+..++|+.........+ ..+++|+|+||++|.+++.+. ...+..+++|||||||+
T Consensus       158 La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~~lViDEah~  237 (563)
T 3i5x_A          158 LALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADR  237 (563)
T ss_dssp             HHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTCCEEEEETHHH
T ss_pred             HHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccceEEEEeCHHH
Confidence            999999999997542   2346688888988877666555 457999999999999888764 23578899999999999


Q ss_pred             HhhCCCHHHHHHHHHhC-------CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCC----CCCCceEEEEEEcCh
Q 010709          281 MLDMGFEPQIREVMQNL-------PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS----SPTANVIQILEKVSE  349 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~-------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  349 (503)
                      +.+++|...+..++..+       .+..|+++||||+++.+..++..++.++..+......    .....+.+.+.....
T Consensus       238 l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  317 (563)
T 3i5x_A          238 LLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEK  317 (563)
T ss_dssp             HTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSSSCSSCTTEEEEEEEESS
T ss_pred             HhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCCCccccccCceEEEECch
Confidence            99999999998887665       3378999999999999999999999988777654322    233345555544443


Q ss_pred             -hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC---CCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q 010709          350 -NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE---GLHAVALHGGRNQSDRESALRDFRNGST  425 (503)
Q Consensus       350 -~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~---~~~v~~lh~~~~~~~r~~~~~~f~~g~~  425 (503)
                       ..+...+...+......    ..+..++||||+++..|+.+++.|...   ++.+..+||++++.+|..+++.|++|+.
T Consensus       318 ~~~~~~~~~~~l~~~~~~----~~~~~~~iVF~~s~~~~~~l~~~L~~~~~~~~~v~~~h~~~~~~~R~~~~~~f~~g~~  393 (563)
T 3i5x_A          318 FANSIFAAVEHIKKQIKE----RDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDES  393 (563)
T ss_dssp             TTHHHHHHHHHHHHHHHH----TTTCCEEEEECSCHHHHHHHHHHHHHHHTTTSCEEEESTTSCHHHHHHHHHHHHHCSS
T ss_pred             hHhhHHHHHHHHHHHHhh----cCCCCcEEEEcCcHHHHHHHHHHHHHhccCCceEEEecCCCCHHHHHHHHHHHhcCCC
Confidence             33333444433332221    134568999999999999999999886   8999999999999999999999999999


Q ss_pred             cEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          426 NILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       426 ~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|||||+++++|||+|++++||++|+|.+...|+||+||+||.
T Consensus       394 ~vLvaT~~~~~GiDip~v~~VI~~~~p~s~~~y~Qr~GRagR~  436 (563)
T 3i5x_A          394 GILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARS  436 (563)
T ss_dssp             EEEEECGGGTSSCCCTTCCEEEEESCCSSTTHHHHHHTTSSCT
T ss_pred             CEEEEcchhhcCCCcccCCEEEEECCCCchhhhhhhcCccccC
Confidence            9999999999999999999999999999999999999999994

>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=1.5e-53  Score=437.46  Aligned_cols=334  Identities=28%  Similarity=0.436  Sum_probs=179.4

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCC
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGP  195 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~  195 (503)
                      .+..+|+++++++.+++.|..+||..|+++|.++++.++.+  ++++++||||+|||++|++|++..+...     ..++
T Consensus        89 ~~~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~-----~~~~  163 (479)
T 3fmp_B           89 YSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKYP  163 (479)
T ss_dssp             CCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT-----SCSC
T ss_pred             cCcCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc-----CCCC
Confidence            45678999999999999999999999999999999999987  8899999999999999999998765432     2356


Q ss_pred             eEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-CCCCCCCccEEE
Q 010709          196 LALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-GNTSLSRVSFVI  274 (503)
Q Consensus       196 ~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~~~~vV  274 (503)
                      ++||++|+++|+.|+++.++++......+.+....++......   ....++|+|+||++|.+++.+ ..+.+.++++||
T Consensus       164 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iV  240 (479)
T 3fmp_B          164 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFV  240 (479)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTSCCCCGGGCCEEE
T ss_pred             cEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCcccccc---ccCCCCEEEECchHHHHHHHhcCCcCcccCCEEE
Confidence            8999999999999999999999877666778877777654321   234579999999999999866 345678999999


Q ss_pred             ecchhHHhh-CCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcCh-hhH
Q 010709          275 LDEADRMLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSE-NEK  352 (503)
Q Consensus       275 iDEaH~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~k  352 (503)
                      |||||++.+ .++...+..++..+++.+|++++|||++..+..++..++.+|..+...........+.+.+..+.. ..+
T Consensus       241 iDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  320 (479)
T 3fmp_B          241 LDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSRDEK  320 (479)
T ss_dssp             ECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC----------------------
T ss_pred             EECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEeccccccCcCCceEEEEEeCCHHHH
Confidence            999999987 578888999999999999999999999999999999999999988887766666666666655544 344


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       353 ~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      ...+..++...         ..+++||||+++..|+.+++.|...++.+..+||++++.+|..+++.|++|+.+|||||+
T Consensus       321 ~~~l~~~~~~~---------~~~~~lvF~~s~~~~~~l~~~L~~~~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~  391 (479)
T 3fmp_B          321 FQALCNLYGAI---------TIAQAMIFCHTRKTASWLAAELSKEGHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN  391 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHhhc---------cCCceEEEeCcHHHHHHHHHHHHhCCccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEcc
Confidence            44444444332         334799999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCCCCEEEEccCC------CChhHHHHhhCcceee
Q 010709          433 VASRGLDVMGVAHVVNLDLP------KVLLAASESLCTTSFN  468 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p------~s~~~~~Qr~GR~gR~  468 (503)
                      ++++|+|+|++++||+||+|      .+...|+||+||+||.
T Consensus       392 ~~~~GlDip~v~~VI~~d~p~~~~~~~s~~~~~Qr~GRagR~  433 (479)
T 3fmp_B          392 VCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRF  433 (479)
T ss_dssp             ------------------------------------------
T ss_pred             ccccCCccccCCEEEEecCCCCCccCCCHHHHHHHhcccccC
Confidence            99999999999999999999      4678999999999994

>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=100.00  E-value=1e-49  Score=390.39  Aligned_cols=310  Identities=34%  Similarity=0.513  Sum_probs=269.2

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      +++.+.+.+..+|+..|+++|.++++.+++++++++++|||+|||++|++|++..           ++++||++|+++|+
T Consensus         1 l~~~i~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~-----------~~~~liv~P~~~L~   69 (337)
T 2z0m_A            1 MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL-----------GMKSLVVTPTRELT   69 (337)
T ss_dssp             CCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH-----------TCCEEEECSSHHHH
T ss_pred             CCHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh-----------cCCEEEEeCCHHHH
Confidence            4688999999999999999999999999999999999999999999999988764           46799999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCH
Q 010709          208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFE  287 (503)
Q Consensus       208 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~  287 (503)
                      .|+++.+++++... +..+..++|+.........+. .++|+|+||++|.+.+.+....+.++++||+||||++.++++.
T Consensus        70 ~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~~~~~~~  147 (337)
T 2z0m_A           70 RQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSKGVIDLSSFEIVIIDEADLMFEMGFI  147 (337)
T ss_dssp             HHHHHHHHHHTTTS-CCCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHTTSCCGGGCSEEEEESHHHHHHTTCH
T ss_pred             HHHHHHHHHHhhhc-CCcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHcCCcchhhCcEEEEEChHHhhccccH
Confidence            99999999998655 478888999888776655554 4899999999999998887777889999999999999999999


Q ss_pred             HHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhh
Q 010709          288 PQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLA  367 (503)
Q Consensus       288 ~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~  367 (503)
                      ..+..++..++...+++++|||+++.+......++.++..+...   .....+.+.+..+....+.  ....+.      
T Consensus       148 ~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~--~~~~~~------  216 (337)
T 2z0m_A          148 DDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEAC---IGLANVEHKFVHVKDDWRS--KVQALR------  216 (337)
T ss_dssp             HHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECS---GGGGGEEEEEEECSSSSHH--HHHHHH------
T ss_pred             HHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeecc---cccCCceEEEEEeChHHHH--HHHHHH------
Confidence            99999999999999999999999999999999999988776432   2334455555555543322  112221      


Q ss_pred             hccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEE
Q 010709          368 EKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV  447 (503)
Q Consensus       368 ~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI  447 (503)
                         ....+++||||++++.++.+++.|.    .+..+||++++.+|.++++.|++|+.+|||||+++++|+|+|++++||
T Consensus       217 ---~~~~~~~lvf~~~~~~~~~l~~~l~----~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~~~~Gid~~~~~~Vi  289 (337)
T 2z0m_A          217 ---ENKDKGVIVFVRTRNRVAKLVRLFD----NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVI  289 (337)
T ss_dssp             ---TCCCSSEEEECSCHHHHHHHHTTCT----TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECHHHHTTCCCCCBSEEE
T ss_pred             ---hCCCCcEEEEEcCHHHHHHHHHHhh----hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcCccccCCCccCCCEEE
Confidence               1355689999999999999999886    678999999999999999999999999999999999999999999999


Q ss_pred             EccCCCChhHHHHhhCcceee
Q 010709          448 NLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       448 ~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++++|.+...|+||+||+||.
T Consensus       290 ~~~~~~s~~~~~Q~~GR~gR~  310 (337)
T 2z0m_A          290 NFDAPQDLRTYIHRIGRTGRM  310 (337)
T ss_dssp             ESSCCSSHHHHHHHHTTBCGG
T ss_pred             EecCCCCHHHhhHhcCccccC
Confidence            999999999999999999995

>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=100.00  E-value=1.1e-49  Score=413.84  Aligned_cols=320  Identities=16%  Similarity=0.237  Sum_probs=258.5

Q ss_pred             cccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          123 FTDMCLHPSIMKDIEF-HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       123 ~~~~~l~~~l~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      +.++++++.+.+.|+. +||..|+|+|.++++.+++|+|+++++|||+|||++|++|++..           ++++|||+
T Consensus        23 ~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~-----------~g~~lVis   91 (591)
T 2v1x_A           23 KEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS-----------DGFTLVIC   91 (591)
T ss_dssp             CSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS-----------SSEEEEEC
T ss_pred             cccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc-----------CCcEEEEe
Confidence            3457899999999998 69999999999999999999999999999999999999999852           46899999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHH------hhCCCcEEEECcHHHH------HHHHcCCCCCCC
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE------LRGGVSIVVATPGRFL------DHLQQGNTSLSR  269 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~Ilv~Tp~~l~------~~l~~~~~~l~~  269 (503)
                      |+++|+.|+.+.++++     ++.+..+.++....+....      .....+|+|+||++|.      +.+.+ ...+.+
T Consensus        92 P~~~L~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~-~~~~~~  165 (591)
T 2v1x_A           92 PLISLMEDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEK-AYEARR  165 (591)
T ss_dssp             SCHHHHHHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHH-HHHTTC
T ss_pred             CHHHHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHh-hhhccC
Confidence            9999999999999987     3677888888776544322      2457899999999874      22322 334678


Q ss_pred             ccEEEecchhHHhhCC--CHHHHHH--HHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEE
Q 010709          270 VSFVILDEADRMLDMG--FEPQIRE--VMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILE  345 (503)
Q Consensus       270 ~~~vViDEaH~l~~~~--~~~~~~~--il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (503)
                      +++|||||||++.+++  |.+.+..  .+....++.+++++|||+++.+...+..++..+....+.. .....++...+.
T Consensus       166 i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~-~~~r~nl~~~v~  244 (591)
T 2v1x_A          166 FTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTA-SFNRPNLYYEVR  244 (591)
T ss_dssp             EEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEEC-CCCCTTEEEEEE
T ss_pred             CcEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEec-CCCCcccEEEEE
Confidence            9999999999999887  7776654  3444456789999999999998888888876543332222 222334443333


Q ss_pred             EcC--hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q 010709          346 KVS--ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNG  423 (503)
Q Consensus       346 ~~~--~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g  423 (503)
                      ...  ...+...+..++...        .+..++||||++++.++.+++.|...|+.+..+||+|++.+|.++++.|++|
T Consensus       245 ~~~~~~~~~~~~l~~~l~~~--------~~~~~~IVf~~sr~~~e~la~~L~~~g~~~~~~h~~l~~~~R~~~~~~F~~g  316 (591)
T 2v1x_A          245 QKPSNTEDFIEDIVKLINGR--------YKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSAN  316 (591)
T ss_dssp             ECCSSHHHHHHHHHHHHTTT--------TTTCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTT
T ss_pred             eCCCcHHHHHHHHHHHHHHh--------ccCCCeEEEeCcHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcC
Confidence            322  223344444443221        2456799999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          424 STNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       424 ~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.+|||||+++++|||+|+|++||+|++|++++.|+||+||+||.
T Consensus       317 ~~~VlVAT~a~~~GID~p~V~~VI~~~~p~s~~~y~Qr~GRaGR~  361 (591)
T 2v1x_A          317 EIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRD  361 (591)
T ss_dssp             SSSEEEECTTSCTTCCCSCEEEEEESSCCSSHHHHHHHHTTSCTT
T ss_pred             CCeEEEEechhhcCCCcccccEEEEeCCCCCHHHHHHHhccCCcC
Confidence            999999999999999999999999999999999999999999994

>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=100.00  E-value=6.6e-49  Score=404.13  Aligned_cols=317  Identities=19%  Similarity=0.283  Sum_probs=256.1

Q ss_pred             CCcccCCCCHHHHHHHHH-CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          121 ESFTDMCLHPSIMKDIEF-HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      .+|+++++++.+.+.|+. +|+..|+++|.++++.+++|+|+++++|||+|||++|++|++..           ++.+||
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~-----------~g~~lv   70 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVV   70 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEE
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh-----------CCCEEE
Confidence            468999999999999998 89999999999999999999999999999999999999998853           367999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHH----HhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEe
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS----ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL  275 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vVi  275 (503)
                      ++|+++|+.|+.+.++.++     +.+..+.++....+...    ...+..+|+|+||++|........+...++++|||
T Consensus        71 i~P~~aL~~q~~~~l~~~g-----i~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~~~l~~~~~~~vVi  145 (523)
T 1oyw_A           71 VSPLISLMKDQVDQLQANG-----VAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAV  145 (523)
T ss_dssp             ECSCHHHHHHHHHHHHHTT-----CCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEE
T ss_pred             ECChHHHHHHHHHHHHHcC-----CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHHHHHhhCCCCEEEE
Confidence            9999999999999998863     66777777776544322    22456899999999995322222234578999999


Q ss_pred             cchhHHhhCC--CHHHHHHH---HHhCCCCCcEEEEEeeCCHHHHHHHHHhc--CCCeEEEeCCCCCCCCceEEEEEEcC
Q 010709          276 DEADRMLDMG--FEPQIREV---MQNLPDKHQTLLFSATMPVEIEALAQEYL--TDPVQVKVGKVSSPTANVIQILEKVS  348 (503)
Q Consensus       276 DEaH~l~~~~--~~~~~~~i---l~~~~~~~q~i~~SAT~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  348 (503)
                      ||||++.++|  |...+..+   ...+ ++.+++++|||+++.....+...+  .++..+ ....  ...++...+  ..
T Consensus       146 DEaH~i~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~-~~~~--~r~~l~~~v--~~  219 (523)
T 1oyw_A          146 DEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQ-ISSF--DRPNIRYML--ME  219 (523)
T ss_dssp             SSGGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEE-ECCC--CCTTEEEEE--EE
T ss_pred             eCccccCcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEE-eCCC--CCCceEEEE--Ee
Confidence            9999998876  76665543   4444 468899999999988765444443  345433 3222  223333332  23


Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      ...+...+...+..         .+.+++||||++++.++.+++.|+..|+.+..+||++++++|.++++.|++|+.+||
T Consensus       220 ~~~~~~~l~~~l~~---------~~~~~~IVf~~sr~~~e~l~~~L~~~g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vl  290 (523)
T 1oyw_A          220 KFKPLDQLMRYVQE---------QRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIV  290 (523)
T ss_dssp             CSSHHHHHHHHHHH---------TTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCSEE
T ss_pred             CCCHHHHHHHHHHh---------cCCCcEEEEeCCHHHHHHHHHHHHHCCCCEEEecCCCCHHHHHHHHHHHHcCCCeEE
Confidence            34556666666544         244579999999999999999999999999999999999999999999999999999


Q ss_pred             EEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          429 VATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |||+++++|||+|++++||++++|+++++|+||+||+||.
T Consensus       291 VaT~a~~~GiD~p~v~~VI~~~~p~s~~~y~Qr~GRaGR~  330 (523)
T 1oyw_A          291 VATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRD  330 (523)
T ss_dssp             EECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTT
T ss_pred             EEechhhCCCCccCccEEEEECCCCCHHHHHHHhccccCC
Confidence            9999999999999999999999999999999999999994

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=100.00  E-value=2.2e-47  Score=384.55  Aligned_cols=302  Identities=19%  Similarity=0.227  Sum_probs=241.6

Q ss_pred             HHHHHHH-CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q 010709          132 IMKDIEF-HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI  210 (503)
Q Consensus       132 l~~~l~~-~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~  210 (503)
                      +.+.++. +++ .|+++|.++++.+++|+++++++|||+|||++|++|++... .       .++++||++||++|+.|+
T Consensus        10 ~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~-~-------~~~~~lil~Pt~~L~~q~   80 (414)
T 3oiy_A           10 FRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-R-------KGKKSALVFPTVTLVKQT   80 (414)
T ss_dssp             HHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHH-T-------TTCCEEEEESSHHHHHHH
T ss_pred             HHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHh-c-------CCCEEEEEECCHHHHHHH
Confidence            3344444 355 89999999999999999999999999999999988877654 1       267899999999999999


Q ss_pred             HHHHHHHhccCCCceEEEEECCccH---HHHHHHhhCC-CcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhh---
Q 010709          211 EKEVKALSRSLDSFKTAIVVGGTNI---AEQRSELRGG-VSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD---  283 (503)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~---  283 (503)
                      ++.+++++.  .++.+..++|+...   ..+...+..+ ++|+|+||++|.+++..  +.+.++++||+||||++.+   
T Consensus        81 ~~~~~~~~~--~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~--~~~~~~~~iViDEaH~~~~~~~  156 (414)
T 3oiy_A           81 LERLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASR  156 (414)
T ss_dssp             HHHHHHHCC--SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH--HTTCCCSEEEESCHHHHHHCHH
T ss_pred             HHHHHHHcc--CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH--hccccccEEEEeChHhhhhccc
Confidence            999999876  36889999999987   4445555544 99999999999888764  5677899999999987654   


Q ss_pred             --------CCCHHH-HHHHHHhCC-----------CCCcEEEEEee-CCHHHH-HHHHHhcCCCeEEEeCCCCCCCCceE
Q 010709          284 --------MGFEPQ-IREVMQNLP-----------DKHQTLLFSAT-MPVEIE-ALAQEYLTDPVQVKVGKVSSPTANVI  341 (503)
Q Consensus       284 --------~~~~~~-~~~il~~~~-----------~~~q~i~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  341 (503)
                              .+|... +..++..++           +..|++++||| .|..+. .+...++.    +...........+.
T Consensus       157 ~~d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~----~~~~~~~~~~~~i~  232 (414)
T 3oiy_A          157 NIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNIT  232 (414)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS----CCSSCCCCCCCSEE
T ss_pred             hhhhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc----cCcCccccccccch
Confidence                    667777 778887765           78999999999 555543 23333332    12223334445566


Q ss_pred             EEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEE-EEcCCCCHHHHHHHHHHH
Q 010709          342 QILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV-ALHGGRNQSDRESALRDF  420 (503)
Q Consensus       342 ~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~-~lh~~~~~~~r~~~~~~f  420 (503)
                      +.+....   +...+..++...          .+++||||+++..|+.+++.|...|+.+. .+||.    +|.  ++.|
T Consensus       233 ~~~~~~~---~~~~l~~~l~~~----------~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~h~~----~r~--~~~f  293 (414)
T 3oiy_A          233 HVRISSR---SKEKLVELLEIF----------RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEF----EKN--FEDF  293 (414)
T ss_dssp             EEEESSC---CHHHHHHHHHHH----------CSSEEEEESSHHHHHHHHHHHHHTTCCEEESSSCH----HHH--HHHH
T ss_pred             heeeccC---HHHHHHHHHHHc----------CCCEEEEECCHHHHHHHHHHHHHcCCceehhhcCc----chH--HHHH
Confidence            6666553   344445554441          14699999999999999999999999998 89984    343  9999


Q ss_pred             hcCCCcEEEE----ccccccCCCCCC-CCEEEEccCC--CChhHHHHhhCcceeee
Q 010709          421 RNGSTNILVA----TDVASRGLDVMG-VAHVVNLDLP--KVLLAASESLCTTSFNI  469 (503)
Q Consensus       421 ~~g~~~vLva----T~~~~~Gldip~-v~~VI~~~~p--~s~~~~~Qr~GR~gR~~  469 (503)
                      ++|+.+||||    |+++++|+|+|+ |++||+||+|  .+...|+||+||+||..
T Consensus       294 ~~g~~~vLvat~s~T~~~~~GiDip~~v~~VI~~~~p~~~~~~~y~qr~GR~gR~g  349 (414)
T 3oiy_A          294 KVGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRIL  349 (414)
T ss_dssp             HTTSCSEEEEECCTTCCCCCCCCCTTTCCEEEEESCCTTTCHHHHHHHHGGGCCEE
T ss_pred             hCCCCeEEEEecCcCchhhccCccccccCEEEEECCCCCCCHHHHHHHhCccccCC
Confidence            9999999999    999999999999 9999999999  99999999999999964

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=100.00  E-value=1.4e-45  Score=395.84  Aligned_cols=322  Identities=18%  Similarity=0.228  Sum_probs=250.0

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH-HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~-i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      .+|+++++++.+.+.+...||..|+++|.++++. +.++++++++||||+|||++|.++++..+...       +++++|
T Consensus         8 ~~~~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~il~   80 (715)
T 2va8_A            8 MPIEDLKLPSNVIEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN-------GGKAIY   80 (715)
T ss_dssp             CBGGGSSSCHHHHHHHHTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS-------CSEEEE
T ss_pred             CcHHHcCCCHHHHHHHHhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC-------CCeEEE
Confidence            4699999999999999999999999999999999 77899999999999999999999999876643       578999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++|+++|+.|+++.++.+...  ++.+...+|+....+.  .. .+++|+|+||++|..++.+....+.++++|||||||
T Consensus        81 i~P~r~La~q~~~~~~~~~~~--g~~v~~~~G~~~~~~~--~~-~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H  155 (715)
T 2va8_A           81 VTPLRALTNEKYLTFKDWELI--GFKVAMTSGDYDTDDA--WL-KNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDELH  155 (715)
T ss_dssp             ECSCHHHHHHHHHHHGGGGGG--TCCEEECCSCSSSCCG--GG-GGCSEEEECHHHHHHHHHHCCGGGGGEEEEEECSGG
T ss_pred             EeCcHHHHHHHHHHHHHhhcC--CCEEEEEeCCCCCchh--hc-CCCCEEEEcHHHHHHHHhCChhHhhccCEEEEechh
Confidence            999999999999999655432  5788888887655432  12 368999999999999988866668899999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEE------------EEEc
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQI------------LEKV  347 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~~  347 (503)
                      ++.+.+++..+..++.+++ +.|+|+||||+++ ...+.. ++..+. +.......+   +...            ....
T Consensus       156 ~l~~~~~~~~l~~i~~~~~-~~~ii~lSATl~n-~~~~~~-~l~~~~-~~~~~r~~~---l~~~~~~~~~~~~~~~~~~~  228 (715)
T 2va8_A          156 YLNDPERGPVVESVTIRAK-RRNLLALSATISN-YKQIAK-WLGAEP-VATNWRPVP---LIEGVIYPERKKKEYNVIFK  228 (715)
T ss_dssp             GGGCTTTHHHHHHHHHHHH-TSEEEEEESCCTT-HHHHHH-HHTCEE-EECCCCSSC---EEEEEEEECSSTTEEEEEET
T ss_pred             hcCCcccchHHHHHHHhcc-cCcEEEEcCCCCC-HHHHHH-HhCCCc-cCCCCCCCC---ceEEEEecCCcccceeeecC
Confidence            9887788988988888776 7899999999975 344444 444321 111111111   1111            1111


Q ss_pred             Chh----hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC-------------------------
Q 010709          348 SEN----EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG-------------------------  398 (503)
Q Consensus       348 ~~~----~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~-------------------------  398 (503)
                      ...    .........+.+..       .+.+++||||+++++++.+++.|....                         
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~-------~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  301 (715)
T 2va8_A          229 DNTTKKVHGDDAIIAYTLDSL-------SKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGS  301 (715)
T ss_dssp             TSCEEEEESSSHHHHHHHHHH-------TTTCCEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCH
T ss_pred             cchhhhcccchHHHHHHHHHH-------hcCCCEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccc
Confidence            100    00011222222221       234679999999999999999998642                         


Q ss_pred             -----------CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE----cc-------CCCChh
Q 010709          399 -----------LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN----LD-------LPKVLL  456 (503)
Q Consensus       399 -----------~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~----~~-------~p~s~~  456 (503)
                                 ..+..+||++++.+|..+++.|++|.++|||||+++++|||+|++++||+    ||       .|.+..
T Consensus       302 ~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~~d~~~~~~~~~~s~~  381 (715)
T 2va8_A          302 DEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIM  381 (715)
T ss_dssp             HHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHTTCSCEEEECGGGGGSSCCCBSEEEECCC--------------CHH
T ss_pred             cccHHHHHHHhcCEEEECCCCCHHHHHHHHHHHHcCCCeEEEEChHHhcccCCCceEEEEeCCeeccccCCCCCCcCCHH
Confidence                       24899999999999999999999999999999999999999999999999    99       899999


Q ss_pred             HHHHhhCcceee
Q 010709          457 AASESLCTTSFN  468 (503)
Q Consensus       457 ~~~Qr~GR~gR~  468 (503)
                      +|.||+|||||.
T Consensus       382 ~~~Qr~GRaGR~  393 (715)
T 2va8_A          382 EYKQMSGRAGRP  393 (715)
T ss_dssp             HHHHHHTTBCCT
T ss_pred             HHHHHhhhcCCC
Confidence            999999999994

>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=100.00  E-value=6.4e-46  Score=408.85  Aligned_cols=321  Identities=18%  Similarity=0.156  Sum_probs=252.5

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      ..|..+++++.+...+...++..|+++|.++++.+..|++++++||||+|||++|++|++..+..        ++++||+
T Consensus       162 ~~~~~~~l~~~~~~~~~~~~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~--------g~rvlvl  233 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN--------KQRVIYT  233 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSCCSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT--------TCEEEEE
T ss_pred             CCcccCCCChhhhHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc--------CCeEEEE
Confidence            35667777777777776677778999999999999999999999999999999999999987643        6789999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++|+.|+++.+++++.     .+++++|+..       ...+++|+|+||++|.+++.+....+.++++|||||||+
T Consensus       234 ~PtraLa~Q~~~~l~~~~~-----~VglltGd~~-------~~~~~~IlV~Tpe~L~~~L~~~~~~l~~l~lVVIDEaH~  301 (1108)
T 3l9o_A          234 SPIKALSNQKYRELLAEFG-----DVGLMTGDIT-------INPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHY  301 (1108)
T ss_dssp             ESSHHHHHHHHHHHHHHTS-----SEEEECSSCB-------CCCSCSEEEEEHHHHHHHHHHCSSHHHHEEEEEEETGGG
T ss_pred             cCcHHHHHHHHHHHHHHhC-----CccEEeCccc-------cCCCCCEEEeChHHHHHHHHcCccccccCCEEEEhhhhh
Confidence            9999999999999999873     4677888765       345689999999999999998777788999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHH--HHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC---------h
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVE--IEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS---------E  349 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~  349 (503)
                      +.+++|+..+..++..+++..|+|+||||+++.  +..++..+...+..+.......  ..+..++....         .
T Consensus       302 l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~rp--~pl~~~~~~~~~~~~~~~vd~  379 (1108)
T 3l9o_A          302 MRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRP--TPLQHYLFPAHGDGIYLVVDE  379 (1108)
T ss_dssp             TTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCCS--SCEEEEEEETTSSCCEEEEET
T ss_pred             ccccchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCc--ccceEEEeecCCcceeeeecc
Confidence            999889999999999999999999999999764  4466677777766654432221  11122211100         0


Q ss_pred             hh----------------------------------------H---HHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhh
Q 010709          350 NE----------------------------------------K---VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR  386 (503)
Q Consensus       350 ~~----------------------------------------k---~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~  386 (503)
                      ..                                        +   ...+..++.....      ...+++||||+++..
T Consensus       380 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~li~~l~~------~~~~~vIVF~~sr~~  453 (1108)
T 3l9o_A          380 KSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWK------KKYNPVIVFSFSKRD  453 (1108)
T ss_dssp             TTEECHHHHHHHHTTC-----------------------------CHHHHHHHHHHHHH------TTCCCEEEEESCHHH
T ss_pred             ccchhhhhHHHHHHHHHhhhcccccccccccccccccccccccccchhHHHHHHHHHHh------cCCCCEEEEeCcHHH
Confidence            00                                        0   1112222211111      234579999999999


Q ss_pred             HHHHHHHHHHCCCe---------------------------------------EEEEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          387 CDEVSEALVAEGLH---------------------------------------AVALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       387 ~~~l~~~L~~~~~~---------------------------------------v~~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                      |+.++..|...++.                                       +..+||+|++.+|..+++.|++|.++|
T Consensus       454 ~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gV~~~Hg~l~~~~R~~v~~~F~~G~ikV  533 (1108)
T 3l9o_A          454 CEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKV  533 (1108)
T ss_dssp             HHHHHHHTCSHHHHCC----CHHHHGGGSCTHHHHHTTCCHHHHHHTHHHHHTEEEECSCSCHHHHHHHHHHHHHTCCCE
T ss_pred             HHHHHHHHHhccCCCHHHHHHHHHHHHHHHhhcchhhhhhhhHHHHHHhhhcCeeeecCCCCHHHHHHHHHHHhCCCCeE
Confidence            99999988543222                                       789999999999999999999999999


Q ss_pred             EEEccccccCCCCCCCCEEEEccCC--------CChhHHHHhhCcceeee
Q 010709          428 LVATDVASRGLDVMGVAHVVNLDLP--------KVLLAASESLCTTSFNI  469 (503)
Q Consensus       428 LvaT~~~~~Gldip~v~~VI~~~~p--------~s~~~~~Qr~GR~gR~~  469 (503)
                      ||||+++++|||+|++++||+++.|        -+..+|+||+|||||.-
T Consensus       534 LVAT~vla~GIDiP~v~~VI~~~~~~d~~~~r~iS~~eyiQr~GRAGR~G  583 (1108)
T 3l9o_A          534 LFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRRG  583 (1108)
T ss_dssp             EEEESCCCSCCCC--CEEEESCSEEESSSCEEECCHHHHHHHHHHSCCSS
T ss_pred             EEECcHHhcCCCCCCceEEEecCcccCccccccCCHHHHHHhhcccCCCC
Confidence            9999999999999999999987764        36778999999999953

>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=100.00  E-value=8e-46  Score=397.57  Aligned_cols=318  Identities=18%  Similarity=0.241  Sum_probs=254.1

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHH-HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~-i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      +|+++++++.+.+.+...|+..|+++|.++++. +.+++++++++|||+|||++|.+|++..+...       +++++|+
T Consensus         2 ~f~~l~l~~~~~~~l~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~-------~~~~l~i   74 (720)
T 2zj8_A            2 RVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ-------GGKAVYI   74 (720)
T ss_dssp             BGGGCCSCHHHHHHHHHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH-------CSEEEEE
T ss_pred             cHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC-------CCEEEEE
Confidence            488999999999999999999999999999998 78999999999999999999999999887643       5789999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++|+.|+++.++.+...  ++.+..++|+......   ...+++|+|+||+++..++.+....+.++++|||||||+
T Consensus        75 ~P~raLa~q~~~~~~~l~~~--g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~~~~~l~~~~~vIiDE~H~  149 (720)
T 2zj8_A           75 VPLKALAEEKFQEFQDWEKI--GLRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHL  149 (720)
T ss_dssp             CSSGGGHHHHHHHTGGGGGG--TCCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHHTCTTGGGEEEEEEETGGG
T ss_pred             cCcHHHHHHHHHHHHHHHhc--CCEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHcChhhhhcCCEEEEECCcc
Confidence            99999999999999766543  5788888887654332   124689999999999998888666688999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEE------EcC-----h
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILE------KVS-----E  349 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~-----~  349 (503)
                      +.+.++...+..++..++++.|+|+||||+++ ...+ ..++..+. +......   ..+...+.      ...     .
T Consensus       150 l~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n-~~~~-~~~l~~~~-~~~~~rp---~~l~~~~~~~~~~~~~~~~~~~~  223 (720)
T 2zj8_A          150 IGSRDRGATLEVILAHMLGKAQIIGLSATIGN-PEEL-AEWLNAEL-IVSDWRP---VKLRRGVFYQGFVTWEDGSIDRF  223 (720)
T ss_dssp             GGCTTTHHHHHHHHHHHBTTBEEEEEECCCSC-HHHH-HHHTTEEE-EECCCCS---SEEEEEEEETTEEEETTSCEEEC
T ss_pred             cCCCcccHHHHHHHHHhhcCCeEEEEcCCcCC-HHHH-HHHhCCcc-cCCCCCC---CcceEEEEeCCeeeccccchhhh
Confidence            98888999999999888778999999999975 3333 34554221 1111111   11111111      111     1


Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC------------------C-------------
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE------------------G-------------  398 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~------------------~-------------  398 (503)
                      ..+...+...+           .+.+++||||++++.|+.+++.|.+.                  +             
T Consensus       224 ~~~~~~~~~~~-----------~~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~  292 (720)
T 2zj8_A          224 SSWEELVYDAI-----------RKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKA  292 (720)
T ss_dssp             SSTTHHHHHHH-----------HTTCCEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHH
T ss_pred             hHHHHHHHHHH-----------hCCCCEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHH
Confidence            12222222222           12357999999999999999998753                  1             


Q ss_pred             --CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE----cc----CCCChhHHHHhhCcceee
Q 010709          399 --LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN----LD----LPKVLLAASESLCTTSFN  468 (503)
Q Consensus       399 --~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~----~~----~p~s~~~~~Qr~GR~gR~  468 (503)
                        ..+..+||++++.+|..+++.|++|.++|||||+++++|||+|++++||+    ||    .|.+..+|.||+|||||.
T Consensus       293 ~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gvdip~~~~VI~~~~~yd~~g~~~~s~~~~~Qr~GRaGR~  372 (720)
T 2zj8_A          293 IRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRP  372 (720)
T ss_dssp             HTTTEEEECTTSCHHHHHHHHHHHHTTSSCEEEECSTTGGGCCCCBSEEEECCSEECCSSSCEECCHHHHHHHHTTBCCT
T ss_pred             HhcCeeeecCCCCHHHHHHHHHHHHCCCCeEEEECcHhhccCCCCceEEEEcCCeeecCCCCccCCHHHHHHHHhhcCCC
Confidence              24899999999999999999999999999999999999999999999999    66    589999999999999993

>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=100.00  E-value=4.4e-45  Score=382.20  Aligned_cols=319  Identities=19%  Similarity=0.232  Sum_probs=189.4

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      +...|+++|.++++.++.|+++++++|||+|||++|++|++..+...+   ...++++||++|+++|+.|+.+.+++++.
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~---~~~~~~~lil~P~~~L~~q~~~~~~~~~~   80 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHHFE   80 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC---SSCCCCEEEECSSHHHHHHHHHHHHHHHG
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCc---ccCCCeEEEEeCCHHHHHHHHHHHHHHhc
Confidence            446899999999999999999999999999999999999998876642   12367899999999999999999999987


Q ss_pred             cCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC-CCCCccEEEecchhHHhhCCCHHHH-HHHHHh-
Q 010709          220 SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGFEPQI-REVMQN-  296 (503)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~l~~~~~vViDEaH~l~~~~~~~~~-~~il~~-  296 (503)
                      .. ++.+..++|+.........+..+++|+|+||++|.+.+....+ .+.++++|||||||++.+++....+ ...+.. 
T Consensus        81 ~~-~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~  159 (556)
T 4a2p_A           81 RQ-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQK  159 (556)
T ss_dssp             GG-TCCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHHH
T ss_pred             cc-CceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHhh
Confidence            65 5888999998877666666666799999999999999988766 7899999999999999877643333 222222 


Q ss_pred             ---CCCCCcEEEEEeeCCH-----------HHHHHHHH------------------hcCCCeEEEeCCCCCCCCceE---
Q 010709          297 ---LPDKHQTLLFSATMPV-----------EIEALAQE------------------YLTDPVQVKVGKVSSPTANVI---  341 (503)
Q Consensus       297 ---~~~~~q~i~~SAT~~~-----------~~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~---  341 (503)
                         ..+..++++||||++.           .+..+...                  +...|................   
T Consensus       160 ~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~i~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (556)
T 4a2p_A          160 FNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAAII  239 (556)
T ss_dssp             HCC---CCEEEEEESCCCCTTCSSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHTCCCCEEEEECCCCSCCHHHHHH
T ss_pred             hcccCCCCeEEEEeCCcccCchhhHHHHHHHHHHHHHhcCCeEecchhcchHHHHhcCCCCceEEEEcCCCcCChHHHHH
Confidence               1456889999999943           12112121                  112222111100000000000   


Q ss_pred             ---------------------EEEE----------Ec-------------------------------------------
Q 010709          342 ---------------------QILE----------KV-------------------------------------------  347 (503)
Q Consensus       342 ---------------------~~~~----------~~-------------------------------------------  347 (503)
                                           ....          .+                                           
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  319 (556)
T 4a2p_A          240 SNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALIISE  319 (556)
T ss_dssp             HHHHHHHHHHHHHHCC---------CCCSSHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhhhhcccccccchhhHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence                                 0000          00                                           


Q ss_pred             -------------------------------------------------ChhhHHHHHHHHHHHHHHhhhccCCCCCcEE
Q 010709          348 -------------------------------------------------SENEKVDRLLALLVEEAFLAEKSCHPFPLTI  378 (503)
Q Consensus       348 -------------------------------------------------~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~l  378 (503)
                                                                       ....|...+..++.+....     .+..++|
T Consensus       320 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~~l~~~~~~-----~~~~k~l  394 (556)
T 4a2p_A          320 DARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRY-----NPQTRTL  394 (556)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTHHHHHHHHHCSSSCCHHHHHHHHHHHHHHHH-----CTTCCEE
T ss_pred             hhhHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhhHHHHhhhhccCCCCCChHHHHHHHHHHHHhcC-----CCCceEE
Confidence                                                             0011222233333222111     3457899


Q ss_pred             EEEcchhhHHHHHHHHHHC------------CCeEEEEcCCCCHHHHHHHHHHHhc-CCCcEEEEccccccCCCCCCCCE
Q 010709          379 VFVERKTRCDEVSEALVAE------------GLHAVALHGGRNQSDRESALRDFRN-GSTNILVATDVASRGLDVMGVAH  445 (503)
Q Consensus       379 IF~~~~~~~~~l~~~L~~~------------~~~v~~lh~~~~~~~r~~~~~~f~~-g~~~vLvaT~~~~~Gldip~v~~  445 (503)
                      |||+++..++.+++.|...            |.....+||++++.+|.++++.|++ |+.+|||||+++++|||+|+|++
T Consensus       395 VF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GiDip~v~~  474 (556)
T 4a2p_A          395 LFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQCNL  474 (556)
T ss_dssp             EEESSHHHHHHHHHHHTTCSGGGSCCEEC------------------------------CCEEEEEC-----------CE
T ss_pred             EEEccHHHHHHHHHHHHhCCCcceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcCchhcCCCchhCCE
Confidence            9999999999999999875            5556677889999999999999999 99999999999999999999999


Q ss_pred             EEEccCCCChhHHHHhhCcceee
Q 010709          446 VVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       446 VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ||+||+|+++..|+||+|| ||.
T Consensus       475 VI~~d~p~s~~~~~Qr~GR-gR~  496 (556)
T 4a2p_A          475 VVLYEYSGNVTKMIQVRGR-GRA  496 (556)
T ss_dssp             EEEETCCSCHHHHHHC-------
T ss_pred             EEEeCCCCCHHHHHHhcCC-CCC
Confidence            9999999999999999999 995

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=100.00  E-value=9.9e-46  Score=396.95  Aligned_cols=325  Identities=20%  Similarity=0.276  Sum_probs=206.2

Q ss_pred             HHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          134 KDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       134 ~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      ..+..+|+..|+++|.++++.++.|+++|+++|||+|||++|++|++..+...+.   ..++++||++||++|+.|+.+.
T Consensus         4 ~~l~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~---~~~~~~lvl~Pt~~L~~Q~~~~   80 (696)
T 2ykg_A            4 SDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQ---GQKGKVVFFANQIPVYEQNKSV   80 (696)
T ss_dssp             ---CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCT---TCCCCEEEECSSHHHHHHHHHH
T ss_pred             CcccccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCcc---CCCCeEEEEECCHHHHHHHHHH
Confidence            4567789999999999999999999999999999999999999999987765421   2246899999999999999999


Q ss_pred             HHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC-CCCCccEEEecchhHHhhCC-CHHHHH
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMG-FEPQIR  291 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~l~~~~~vViDEaH~l~~~~-~~~~~~  291 (503)
                      +++++... ++.+..++|+.........+..+++|+|+||++|.+.+....+ .+.++++|||||||++.+.. +...+.
T Consensus        81 ~~~~~~~~-~~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i~~  159 (696)
T 2ykg_A           81 FSKYFERH-GYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMF  159 (696)
T ss_dssp             HHHHTTTT-TCCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHHHH
T ss_pred             HHHHhccC-CceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHHHH
Confidence            99998654 5888999998865555555556799999999999999988766 68899999999999987654 222222


Q ss_pred             HHHHh-----CCCCCcEEEEEeeCC-------HH-HHHHH---------------------HHhcCCCeEEEeCCCCCCC
Q 010709          292 EVMQN-----LPDKHQTLLFSATMP-------VE-IEALA---------------------QEYLTDPVQVKVGKVSSPT  337 (503)
Q Consensus       292 ~il~~-----~~~~~q~i~~SAT~~-------~~-~~~~~---------------------~~~~~~~~~~~~~~~~~~~  337 (503)
                      ..+..     .++..++++||||+.       .+ +..+.                     ..+...|............
T Consensus       160 ~~l~~~~~~~~~~~~~il~LTATp~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~l~~~~~~p~~~~~~~~~~~~  239 (696)
T 2ykg_A          160 NYLDQKLGGSSGPLPQVIGLTASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRIS  239 (696)
T ss_dssp             HHHHHHHTTCCSCCCEEEEEESCCCCSSCCSHHHHHHHHHHHHHHTTCCEEECCCTTHHHHHHHSCCCEEEEEECCCCSC
T ss_pred             HHHHHhhcccCCCCCeEEEEeCccccCccccHHHHHHHHHHHHHhcCCceEeecccchHHHHhhcCCCceeEEecCcccC
Confidence            22222     246789999999996       11 12111                     1122223221110000000


Q ss_pred             Cc---------------------------------------------------eEEEEEEc-------------------
Q 010709          338 AN---------------------------------------------------VIQILEKV-------------------  347 (503)
Q Consensus       338 ~~---------------------------------------------------~~~~~~~~-------------------  347 (503)
                      ..                                                   ..+.....                   
T Consensus       240 ~~fs~~~~~l~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~  319 (696)
T 2ykg_A          240 DKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKY  319 (696)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHSTTGGGSSSCCSCCSSSHHHHHHHHHHHHTSCC------CCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccchhHHHHHHHHHHHHHHhhcccchhhhHHHHHHHHHHHHHHHH
Confidence            00                                                   00000000                   


Q ss_pred             ---------------------------------------------------------ChhhHHHHHHHHHHHHHHhhhcc
Q 010709          348 ---------------------------------------------------------SENEKVDRLLALLVEEAFLAEKS  370 (503)
Q Consensus       348 ---------------------------------------------------------~~~~k~~~l~~~l~~~~~~~~~~  370 (503)
                                                                               ....|...+..++....     .
T Consensus       320 ~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~ll~~~~-----~  394 (696)
T 2ykg_A          320 NDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEY-----H  394 (696)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHH-----T
T ss_pred             hHHHhccchhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHh-----c
Confidence                                                                     01223333333333221     1


Q ss_pred             CCCCCcEEEEEcchhhHHHHHHHHHHCC----CeEEEE--------cCCCCHHHHHHHHHHHhc-CCCcEEEEccccccC
Q 010709          371 CHPFPLTIVFVERKTRCDEVSEALVAEG----LHAVAL--------HGGRNQSDRESALRDFRN-GSTNILVATDVASRG  437 (503)
Q Consensus       371 ~~~~~~~lIF~~~~~~~~~l~~~L~~~~----~~v~~l--------h~~~~~~~r~~~~~~f~~-g~~~vLvaT~~~~~G  437 (503)
                      ..+.+++||||+++..++.+++.|...+    +.+..+        ||+|++.+|.++++.|++ |+.+|||||+++++|
T Consensus       395 ~~~~~~~IIF~~~~~~~~~l~~~L~~~~~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v~~~G  474 (696)
T 2ykg_A          395 LNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEG  474 (696)
T ss_dssp             TCTTCCEEEECSCHHHHHHHHHHHHHCTTCCSCCEEC-----------------------------CCSCSEEEESSCCC
T ss_pred             cCCCCcEEEEeCcHHHHHHHHHHHHhCCCccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEechhhcC
Confidence            1345689999999999999999999988    888888        559999999999999998 999999999999999


Q ss_pred             CCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          438 LDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       438 ldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ||+|++++||+||+|.+..+|+||+|| ||.
T Consensus       475 iDip~v~~VI~~d~p~s~~~~~Qr~GR-GR~  504 (696)
T 2ykg_A          475 IDIAQCNLVILYEYVGNVIKMIQTRGR-GRA  504 (696)
T ss_dssp             ---CCCSEEEEESCC--CCCC----------
T ss_pred             CcCccCCEEEEeCCCCCHHHHHHhhcc-CcC
Confidence            999999999999999999999999999 994

>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=100.00  E-value=7.8e-46  Score=396.57  Aligned_cols=317  Identities=17%  Similarity=0.202  Sum_probs=247.6

Q ss_pred             CcccCC--CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          122 SFTDMC--LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       122 ~~~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      +|++++  +++.+.+.++..||..|+++|.++++.+.+++++++++|||+|||++|.+|++..+..        +++++|
T Consensus         2 ~f~~l~~~l~~~~~~~l~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~--------~~~~l~   73 (702)
T 2p6r_A            2 KVEELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLY   73 (702)
T ss_dssp             CSHHHHHHHHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEE
T ss_pred             chhhhhhccCHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh--------CCcEEE
Confidence            477888  9999999999999999999999999999999999999999999999999999987653        467999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++|+++|+.|+++.++.+.. . ++++..++|+....+.   ...+++|+|+||+++..++.+....+.++++|||||||
T Consensus        74 i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~~~~l~~~~~vIiDE~H  148 (702)
T 2p6r_A           74 VVPLRALAGEKYESFKKWEK-I-GLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIH  148 (702)
T ss_dssp             EESSHHHHHHHHHHHTTTTT-T-TCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGG
T ss_pred             EeCcHHHHHHHHHHHHHHHh-c-CCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcChhHHhhcCEEEEeeee
Confidence            99999999999999965543 2 5788888887754332   12468999999999999988866668899999999999


Q ss_pred             HHhhCCCHHHHHHHHHhC---CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEE------EcChh
Q 010709          280 RMLDMGFEPQIREVMQNL---PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILE------KVSEN  350 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~---~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~  350 (503)
                      ++.++++...+..++..+   +++.|+|+||||+++ ...+. .++..+. +.......   .+...+.      .....
T Consensus       149 ~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~-~~l~~~~-~~~~~r~~---~l~~~~~~~~~~~~~~~~  222 (702)
T 2p6r_A          149 LLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIA-EWLDADY-YVSDWRPV---PLVEGVLCEGTLELFDGA  222 (702)
T ss_dssp             GGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHH-HHTTCEE-EECCCCSS---CEEEEEECSSEEEEEETT
T ss_pred             ecCCCCcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHH-HHhCCCc-ccCCCCCc---cceEEEeeCCeeeccCcc
Confidence            998888888888776655   578999999999975 44444 4554332 22111111   1111110      00100


Q ss_pred             -------hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--------------------------
Q 010709          351 -------EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--------------------------  397 (503)
Q Consensus       351 -------~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--------------------------  397 (503)
                             .+...+...+           .+.+++||||+++++++.+++.|...                          
T Consensus       223 ~~~~~~~~~~~~~~~~~-----------~~~~~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~i~~~~~~~~~~~l  291 (702)
T 2p6r_A          223 FSTSRRVKFEELVEECV-----------AENGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKL  291 (702)
T ss_dssp             EEEEEECCHHHHHHHHH-----------HTTCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHH-----------hcCCCEEEEcCCHHHHHHHHHHHHHHHHhhcChHHHHHHHHhhccccccHHH
Confidence                   0222222222           13467999999999999999988753                          


Q ss_pred             ----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE----cc---CCCChhHHHHhhCcce
Q 010709          398 ----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN----LD---LPKVLLAASESLCTTS  466 (503)
Q Consensus       398 ----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~----~~---~p~s~~~~~Qr~GR~g  466 (503)
                          +..+..+||++++++|..+++.|++|+++|||||+++++|||+|++++||+    ||   .|.+..+|.||+||||
T Consensus       292 ~~~~~~~v~~~h~~l~~~~R~~v~~~f~~g~~~vlvaT~~l~~Gidip~~~~VI~~~~~yd~~~~~~s~~~~~Qr~GRaG  371 (702)
T 2p6r_A          292 AECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAG  371 (702)
T ss_dssp             HHHHHTTCCEECTTSCHHHHHHHHHHHHTTSCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBS
T ss_pred             HHHHhcCeEEecCCCCHHHHHHHHHHHHCCCCeEEEECcHHhccCCCCceEEEEcCceeeCCCCCcCCHHHHHHHhhhcC
Confidence                135788999999999999999999999999999999999999999999999    66   7899999999999999


Q ss_pred             ee
Q 010709          467 FN  468 (503)
Q Consensus       467 R~  468 (503)
                      |.
T Consensus       372 R~  373 (702)
T 2p6r_A          372 RP  373 (702)
T ss_dssp             CT
T ss_pred             CC
Confidence            94

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=100.00  E-value=4.1e-44  Score=374.75  Aligned_cols=316  Identities=22%  Similarity=0.244  Sum_probs=213.1

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      -.|+++|.++++.++.|+++++++|||+|||++|++|++..+...+.   ..++++||++|+++|+.|+.+.+++++...
T Consensus         3 ~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   79 (555)
T 3tbk_A            3 LKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC---GQKGKVVFFANQIPVYEQQATVFSRYFERL   79 (555)
T ss_dssp             CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS---SCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc---CCCCEEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            37999999999999999999999999999999999999988776431   236789999999999999999999998765


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC-CCCCccEEEecchhHHhhCCC-HHHHHHHHHhC--
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGF-EPQIREVMQNL--  297 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~l~~~~~vViDEaH~l~~~~~-~~~~~~il~~~--  297 (503)
                       ++.+..++|+.........+..+++|+|+||++|.+.+..... .+.++++|||||||++.+.+. ...+...+...  
T Consensus        80 -~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~  158 (555)
T 3tbk_A           80 -GYNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLG  158 (555)
T ss_dssp             -TCCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTS
T ss_pred             -CcEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhc
Confidence             5889999999876665555666799999999999999988766 788999999999999987652 22232333321  


Q ss_pred             ---CCCCcEEEEEeeCCHH-----------HHHHHHHhcCCCeEEEeCCC------CCCCCceEEEEEEc----------
Q 010709          298 ---PDKHQTLLFSATMPVE-----------IEALAQEYLTDPVQVKVGKV------SSPTANVIQILEKV----------  347 (503)
Q Consensus       298 ---~~~~q~i~~SAT~~~~-----------~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~----------  347 (503)
                         .+..|++++|||++..           +..+. ..+...........      ..............          
T Consensus       159 ~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~~~~l~-~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (555)
T 3tbk_A          159 ESRDPLPQVVGLTASVGVGDAKTAEEAMQHICKLC-AALDASVIATVRDNVAELEQVVYKPQKISRKVASRTSNTFKCII  237 (555)
T ss_dssp             SCCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHH-HHTTCSEEECCCSCHHHHHTTCCCCCEEEEECCCCSCCHHHHHH
T ss_pred             cccCCCCeEEEEecCcccCccccHHHHHHHHHHHH-HhcCCeeeeccccCHHHHHhhcCCCceEEEEecCcccChHHHHH
Confidence               2567899999999542           11111 12221111111000      00000000000000          


Q ss_pred             --------------------------------------------------------------------------------
Q 010709          348 --------------------------------------------------------------------------------  347 (503)
Q Consensus       348 --------------------------------------------------------------------------------  347 (503)
                                                                                                      
T Consensus       238 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  317 (555)
T 3tbk_A          238 SQLMKETEKLAKDVSEELGKLFQIQNREFGTQKYEQWIVGVHKACSVFQMADKEEESRVCKALFLYTSHLRKYNDALIIS  317 (555)
T ss_dssp             HHHHHHHHHHHHTSCHHHHGGGGCCSCCSSSHHHHHHHHHHHHHHHTCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhhhhhhcccccccchhhhHHHHHHHHHhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence                                                                                            


Q ss_pred             --------------------------------------------------ChhhHHHHHHHHHHHHHHhhhccCCCCCcE
Q 010709          348 --------------------------------------------------SENEKVDRLLALLVEEAFLAEKSCHPFPLT  377 (503)
Q Consensus       348 --------------------------------------------------~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~  377 (503)
                                                                        ....|...+..++......     .+.+++
T Consensus       318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~-----~~~~k~  392 (555)
T 3tbk_A          318 EDAQMTDALNYLKAFFHDVREAAFDETERELTRRFEEKLEELEKVSRDPSNENPKLRDLYLVLQEEYHL-----KPETKT  392 (555)
T ss_dssp             HHSCHHHHHHHHHHHHHHHCC-----HHHHHHHHHHTTHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHH-----CTTCCE
T ss_pred             hhhhHHHHHHHHHHHHHHHhhcccchHHHHHHHHHhhhhhhhhhhccCCCcCCHHHHHHHHHHHHHhcc-----CCCceE
Confidence                                                              0012233333333322111     345789


Q ss_pred             EEEEcchhhHHHHHHHHHHCC------------CeEEEEcCCCCHHHHHHHHHHHhc-CCCcEEEEccccccCCCCCCCC
Q 010709          378 IVFVERKTRCDEVSEALVAEG------------LHAVALHGGRNQSDRESALRDFRN-GSTNILVATDVASRGLDVMGVA  444 (503)
Q Consensus       378 lIF~~~~~~~~~l~~~L~~~~------------~~v~~lh~~~~~~~r~~~~~~f~~-g~~~vLvaT~~~~~Gldip~v~  444 (503)
                      ||||+++..++.+++.|...+            .....+||+|++.+|.++++.|++ |+.+|||||+++++|||+|+++
T Consensus       393 lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~~~~GlDlp~v~  472 (555)
T 3tbk_A          393 ILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECN  472 (555)
T ss_dssp             EEECSSHHHHHHHHHHHHHCGGGTTCCEEECCC--------------------------CCSEEEECCCTTCCEETTSCS
T ss_pred             EEEeCcHHHHHHHHHHHhhCcCcCceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcchhhcCCccccCC
Confidence            999999999999999999864            344556679999999999999999 9999999999999999999999


Q ss_pred             EEEEccCCCChhHHHHhhCcceee
Q 010709          445 HVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       445 ~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +||+||+|+++..|+||+|| ||.
T Consensus       473 ~VI~~d~p~s~~~~~Qr~GR-gR~  495 (555)
T 3tbk_A          473 LVILYEYVGNVIKMIQTRGR-GRA  495 (555)
T ss_dssp             EEEEESCCSSCCCEECSSCC-CTT
T ss_pred             EEEEeCCCCCHHHHHHhcCc-CcC
Confidence            99999999999999999999 884

>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=100.00  E-value=5.8e-44  Score=386.78  Aligned_cols=321  Identities=19%  Similarity=0.238  Sum_probs=196.3

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .+|+..|+++|.++++.++.|+++++++|||+|||++|++|++..+...+   ...++++||++|+++|+.|+.+.++++
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~---~~~~~~~Lvl~Pt~~L~~Q~~~~~~~~  319 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKHH  319 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCC---SSCCCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhcc---ccCCCeEEEEeCCHHHHHHHHHHHHHh
Confidence            45788999999999999999999999999999999999999998877642   123678999999999999999999999


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC-CCCCccEEEecchhHHhhCCCHHHH-HHHHH
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGFEPQI-REVMQ  295 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~l~~~~~vViDEaH~l~~~~~~~~~-~~il~  295 (503)
                      +... ++.+..++|+.........+..+++|+|+||++|.+.+....+ .+.++++|||||||++.+.+....+ ...+.
T Consensus       320 ~~~~-~~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~~  398 (797)
T 4a2q_A          320 FERQ-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLE  398 (797)
T ss_dssp             HGGG-TCCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHHH
T ss_pred             cccC-CceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHHH
Confidence            8765 5889999999877766666777899999999999999988766 7889999999999998876433222 23322


Q ss_pred             h----CCCCCcEEEEEeeCCH-----------HHHHHHH------------------HhcCCCeEEEeCCCCCCCCc---
Q 010709          296 N----LPDKHQTLLFSATMPV-----------EIEALAQ------------------EYLTDPVQVKVGKVSSPTAN---  339 (503)
Q Consensus       296 ~----~~~~~q~i~~SAT~~~-----------~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~---  339 (503)
                      .    ..+..++++||||+..           .+..+..                  .++..|..............   
T Consensus       399 ~~~~~~~~~~~~l~lSATp~~~~~~~~~~~~~~i~~l~~~L~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  478 (797)
T 4a2q_A          399 QKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFAA  478 (797)
T ss_dssp             HHHTTCCCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCTTHHHHHHHSCCCCCEEEECCCCSCCHHHH
T ss_pred             HhhccCCCCCeEEEEcCCccccccccHHHHHHHHHHHHHhcCCcEEecccccHHHHHHhcCCCceEEEecCCCCCcHHHH
Confidence            2    2556889999999952           2222221                  12222221111000000000   


Q ss_pred             ---------------------eEEEEEE----------c------------C----------------------------
Q 010709          340 ---------------------VIQILEK----------V------------S----------------------------  348 (503)
Q Consensus       340 ---------------------~~~~~~~----------~------------~----------------------------  348 (503)
                                           +......          +            .                            
T Consensus       479 ~~~~l~~~i~~~~~~~~~l~~l~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~  558 (797)
T 4a2q_A          479 IISNLMSETEALMRTIYSVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALII  558 (797)
T ss_dssp             HHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhhHHhhhhccccccchhHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHhh
Confidence                                 0000000          0            0                            


Q ss_pred             ----------------------------------------------------hhhHHHHHHHHHHHHHHhhhccCCCCCc
Q 010709          349 ----------------------------------------------------ENEKVDRLLALLVEEAFLAEKSCHPFPL  376 (503)
Q Consensus       349 ----------------------------------------------------~~~k~~~l~~~l~~~~~~~~~~~~~~~~  376 (503)
                                                                          ...|...+..++.....     ..+..+
T Consensus       559 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~~~~-----~~~~~k  633 (797)
T 4a2q_A          559 SEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYR-----YNPQTR  633 (797)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTHHHHHHHHHCTTCCCHHHHHHHHHHHHHHH-----HCSSCC
T ss_pred             hccccHHHHHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHHHHHHhc-----cCCCCe
Confidence                                                                01122222222222111     134578


Q ss_pred             EEEEEcchhhHHHHHHHHHHC------------CCeEEEEcCCCCHHHHHHHHHHHhc-CCCcEEEEccccccCCCCCCC
Q 010709          377 TIVFVERKTRCDEVSEALVAE------------GLHAVALHGGRNQSDRESALRDFRN-GSTNILVATDVASRGLDVMGV  443 (503)
Q Consensus       377 ~lIF~~~~~~~~~l~~~L~~~------------~~~v~~lh~~~~~~~r~~~~~~f~~-g~~~vLvaT~~~~~Gldip~v  443 (503)
                      +||||+++..++.+++.|...            |..+..+||++++.+|.++++.|++ |+.+|||||+++++|||+|+|
T Consensus       634 vLIF~~~~~~~~~L~~~L~~~~~~~~~~~~~l~G~~~~~~hg~~~~~eR~~~l~~F~~~g~~~vLVaT~~~~~GIDlp~v  713 (797)
T 4a2q_A          634 TLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQC  713 (797)
T ss_dssp             EEEEESSHHHHHHHHHHHHTCSTTCSCCCEEC----------------------------CCSEEEEECC-------CCC
T ss_pred             EEEEECcHHHHHHHHHHHHhCcccccccceEEEecCCcccCCCCCHHHHHHHHHHhhccCCceEEEEcCchhcCCCchhC
Confidence            999999999999999999873            5566778999999999999999999 999999999999999999999


Q ss_pred             CEEEEccCCCChhHHHHhhCcceee
Q 010709          444 AHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       444 ~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++||+||+|+++..|+||+|| ||.
T Consensus       714 ~~VI~yd~p~s~~~~iQr~GR-GR~  737 (797)
T 4a2q_A          714 NLVVLYEYSGNVTKMIQVRGR-GRA  737 (797)
T ss_dssp             SEEEEESCCSCHHHHHTC-------
T ss_pred             CEEEEeCCCCCHHHHHHhcCC-CCC
Confidence            999999999999999999999 995

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=100.00  E-value=6.1e-43  Score=381.99  Aligned_cols=299  Identities=20%  Similarity=0.219  Sum_probs=239.0

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .++|. |+++|.++++.+..|+++++++|||+|||++|.++++..+..        ++++||++|+++|+.|+++.++++
T Consensus        82 ~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~--------g~rvL~l~PtkaLa~Q~~~~l~~~  152 (1010)
T 2xgj_A           82 TYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN--------KQRVIYTSPIKALSNQKYRELLAE  152 (1010)
T ss_dssp             CCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT--------TCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             hCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc--------CCeEEEECChHHHHHHHHHHHHHH
Confidence            34564 999999999999999999999999999999999888876532        578999999999999999999998


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                      +.     .+++++|+...       ...++|+|+||++|.+++.+....+.++++|||||||++.+++++..+..++..+
T Consensus       153 ~~-----~vglltGd~~~-------~~~~~IvV~Tpe~L~~~L~~~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il~~l  220 (1010)
T 2xgj_A          153 FG-----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFDEVHYMRDKERGVVWEETIILL  220 (1010)
T ss_dssp             HS-----CEEEECSSCEE-------CTTCSEEEEEHHHHHHHHHHTCTTGGGEEEEEEETGGGGGCTTTHHHHHHHHHHS
T ss_pred             hC-----CEEEEeCCCcc-------CCCCCEEEEcHHHHHHHHHcCcchhhcCCEEEEechhhhcccchhHHHHHHHHhc
Confidence            73     56778887653       2358999999999999998877788999999999999999999999999999999


Q ss_pred             CCCCcEEEEEeeCCHHHH--HHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC---------h-----------------
Q 010709          298 PDKHQTLLFSATMPVEIE--ALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS---------E-----------------  349 (503)
Q Consensus       298 ~~~~q~i~~SAT~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~-----------------  349 (503)
                      ++..|+|+||||+++..+  ..+......+..+.......  ..+.+++....         .                 
T Consensus       221 ~~~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~rp--~pl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  298 (1010)
T 2xgj_A          221 PDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFRP--TPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASIS  298 (1010)
T ss_dssp             CTTCEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECCCS--SCEEEEEEETTSSCCEEEECTTCCBCHHHHHHHHHTCC
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCCc--ccceEEEEecCCcceeeeeccccccchHHHHHHHHHHh
Confidence            999999999999986532  33444445565554332111  12222222110         0                 


Q ss_pred             -----------------------------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC-
Q 010709          350 -----------------------------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL-  399 (503)
Q Consensus       350 -----------------------------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~-  399 (503)
                                                   ......++..+..         ....++||||+++..|+.+++.|...++ 
T Consensus       299 ~~~~~~~~~~~~~g~~~~~~k~~~~~~~~~~~l~~l~~~l~~---------~~~~~~IVF~~sr~~~e~la~~L~~~~~~  369 (1010)
T 2xgj_A          299 NQIGDDPNSTDSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWK---------KKYNPVIVFSFSKRDCEELALKMSKLDFN  369 (1010)
T ss_dssp             ------------------------------CHHHHHHHHHHH---------HTCCSEEEEESSHHHHHHHHHTTTTSCCC
T ss_pred             hhhcccccccccccccccccccccccccchHHHHHHHHHHHh---------cCCCCEEEEECCHHHHHHHHHHHHhCCCC
Confidence                                         0011112221111         1234799999999999999999876443 


Q ss_pred             --------------------------------------eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCC
Q 010709          400 --------------------------------------HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM  441 (503)
Q Consensus       400 --------------------------------------~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip  441 (503)
                                                            .+..+||++++.+|..+++.|++|.++|||||+++++|||+|
T Consensus       370 ~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gI~~~Hggl~~~eR~~ve~~F~~G~ikVLVAT~~la~GIDiP  449 (1010)
T 2xgj_A          370 SDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMP  449 (1010)
T ss_dssp             CHHHHHHHHHHHHHHHTTSCGGGTTCHHHHHHHHHHHHTEEEESTTSCHHHHHHHHHHHHTTCCSEEEEEGGGGGSTTCC
T ss_pred             ChHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHHhCCeeEECCCCCHHHHHHHHHHHhcCCCcEEEEehHhhccCCCC
Confidence                                                  278999999999999999999999999999999999999999


Q ss_pred             CCCEEEE----ccC----CCChhHHHHhhCcceee
Q 010709          442 GVAHVVN----LDL----PKVLLAASESLCTTSFN  468 (503)
Q Consensus       442 ~v~~VI~----~~~----p~s~~~~~Qr~GR~gR~  468 (503)
                      ++++||+    ||.    |.+..+|+||+|||||.
T Consensus       450 ~~~vVI~~~~kfd~~~~rp~s~~~y~Qr~GRAGR~  484 (1010)
T 2xgj_A          450 AKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGRR  484 (1010)
T ss_dssp             BSEEEESCSEEECSSCEEECCHHHHHHHHTTBCCT
T ss_pred             CceEEEeCCcccCCcCCccCCHHHHhHhhhhcccC
Confidence            9999999    998    88999999999999995

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=9.3e-44  Score=391.53  Aligned_cols=280  Identities=20%  Similarity=0.249  Sum_probs=227.8

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..|| .|+++|.++++.+++|+|++++||||+|||++|+++++..+ .       .++++||++||++||.|+++.++++
T Consensus        74 ~~gf-~pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~-~-------~~~~~Lil~PtreLa~Q~~~~l~~l  144 (1104)
T 4ddu_A           74 KFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLA-R-------KGKKSALVFPTVTLVKQTLERLQKL  144 (1104)
T ss_dssp             HSSS-CCCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHH-T-------TTCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             hcCC-CCCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHH-h-------cCCeEEEEechHHHHHHHHHHHHHh
Confidence            3677 69999999999999999999999999999998877766654 2       2678999999999999999999997


Q ss_pred             hccCCCceEEEEECCccH---HHHHHHhhCC-CcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHh----------h
Q 010709          218 SRSLDSFKTAIVVGGTNI---AEQRSELRGG-VSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRML----------D  283 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~----------~  283 (503)
                      + . .++.+..++|+...   ..+...+..+ ++|+|+||++|.+++..  +.+.++++|||||||++.          +
T Consensus       145 ~-~-~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~--l~~~~l~~lViDEaH~l~~~~r~~Dr~L~  220 (1104)
T 4ddu_A          145 A-D-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK--LSQKRFDFVFVDDVDAVLKASRNIDTLLM  220 (1104)
T ss_dssp             S-C-TTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH--HHTSCCSEEEESCHHHHTTSSHHHHHHHH
T ss_pred             h-C-CCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh--hcccCcCEEEEeCCCccccccccchhhhH
Confidence            6 3 36899999999987   5566666665 99999999999888774  667889999999997654          4


Q ss_pred             -CCCHHH-HHHHHHhCC-----------CCCcEEEEEee-CCHHHH-HHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcC
Q 010709          284 -MGFEPQ-IREVMQNLP-----------DKHQTLLFSAT-MPVEIE-ALAQEYLTDPVQVKVGKVSSPTANVIQILEKVS  348 (503)
Q Consensus       284 -~~~~~~-~~~il~~~~-----------~~~q~i~~SAT-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  348 (503)
                       ++|... +..++..++           ++.|+++|||| .|..+. .+...++.    +.+........++.+.+..+.
T Consensus       221 ~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~----i~v~~~~~~~~~i~~~~~~~~  296 (1104)
T 4ddu_A          221 MVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN----FTVGRLVSVARNITHVRISSR  296 (1104)
T ss_dssp             TSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC----CCCCBCCCCCCCEEEEEESCC
T ss_pred             hcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee----EEeccCCCCcCCceeEEEecC
Confidence             788877 888888776           78999999999 555544 23333333    233334445566777776663


Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEE-EEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV-ALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~-~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                         +...+..++...          .+++||||++++.++.+++.|...|+.+. .+||     +|.+ ++.|++|+.+|
T Consensus       297 ---k~~~L~~ll~~~----------~~~~LVF~~s~~~a~~l~~~L~~~g~~~~~~lhg-----~rr~-l~~F~~G~~~V  357 (1104)
T 4ddu_A          297 ---SKEKLVELLEIF----------RDGILIFAQTEEEGKELYEYLKRFKFNVGETWSE-----FEKN-FEDFKVGKINI  357 (1104)
T ss_dssp             ---CHHHHHHHHHHH----------CSSEEEEESSSHHHHHHHHHHHHTTCCEEESSSS-----HHHH-HHHHHHTSCSE
T ss_pred             ---HHHHHHHHHHhc----------CCCEEEEECcHHHHHHHHHHHHhCCCCeeeEecC-----cHHH-HHHHHCCCCCE
Confidence               444455555441          14699999999999999999999999998 9999     2555 99999999999


Q ss_pred             EEE----ccccccCCCCCC-CCEEEEccCCC
Q 010709          428 LVA----TDVASRGLDVMG-VAHVVNLDLPK  453 (503)
Q Consensus       428 Lva----T~~~~~Gldip~-v~~VI~~~~p~  453 (503)
                      |||    |+++++|||+|+ |++||+||+|+
T Consensus       358 LVatas~TdvlarGIDip~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          358 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPS  388 (1104)
T ss_dssp             EEEETTTHHHHCCSCCCTTTCCEEEEESCCE
T ss_pred             EEEecCCCCeeEecCcCCCCCCEEEEECCCC
Confidence            999    999999999999 99999999999

>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=100.00  E-value=4.8e-42  Score=353.06  Aligned_cols=311  Identities=22%  Similarity=0.251  Sum_probs=233.8

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+++|.++++.++.+ ++++++|||+|||++++++++..+..       .++++||++|+++|+.||.++++++... .
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~-------~~~~~liv~P~~~L~~q~~~~~~~~~~~-~   79 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK-------YGGKVLMLAPTKPLVLQHAESFRRLFNL-P   79 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH-------SCSCEEEECSSHHHHHHHHHHHHHHBCS-C
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc-------CCCeEEEEECCHHHHHHHHHHHHHHhCc-c
Confidence            6999999999999998 99999999999999999988877652       2577999999999999999999998732 2


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCc
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ  302 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q  302 (503)
                      ...+..+.|+....+.. ....+++|+|+||+.|...+....+.+.++++||+||||++.+......+...+....+..+
T Consensus        80 ~~~v~~~~g~~~~~~~~-~~~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~~~~  158 (494)
T 1wp9_A           80 PEKIVALTGEKSPEERS-KAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPL  158 (494)
T ss_dssp             GGGEEEECSCSCHHHHH-HHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSCC
T ss_pred             hhheEEeeCCcchhhhh-hhccCCCEEEecHHHHHHHHhcCCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCCCCe
Confidence            35788888887765433 33346899999999999999887778899999999999998766555555556655567788


Q ss_pred             EEEEEeeCCHH---HHHHHHHhcCCCeEEEeCCCCC-----CCCceEEEEEEcC--------------------------
Q 010709          303 TLLFSATMPVE---IEALAQEYLTDPVQVKVGKVSS-----PTANVIQILEKVS--------------------------  348 (503)
Q Consensus       303 ~i~~SAT~~~~---~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~--------------------------  348 (503)
                      +++||||+..+   +..+...+..............     ............+                          
T Consensus       159 ~l~lTaTp~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (494)
T 1wp9_A          159 VIGLTASPGSTPEKIMEVINNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAETGL  238 (494)
T ss_dssp             EEEEESCSCSSHHHHHHHHHHTTCCEEEECCTTSTTTGGGCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             EEEEecCCCCCcHHHHHHHHhcChheeeccCCCcHHHHHhcCCCceeEEecCCcHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999743   3333333322221111110000     0000111111111                          


Q ss_pred             --------------------------------------------------------------------------------
Q 010709          349 --------------------------------------------------------------------------------  348 (503)
Q Consensus       349 --------------------------------------------------------------------------------  348 (503)
                                                                                                      
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  318 (494)
T 1wp9_A          239 LESSSPDIPKKEVLRAGQIINEEMAKGNHDLRGLLLYHAMALKLHHAIELLETQGLSALRAYIKKLYEEAKAGSTKASKE  318 (494)
T ss_dssp             SSCCCTTSCHHHHHHHHHHHHHHHTTTCCSTTTHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             ccccCCCcchhHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHHHhhccccchhhhh
Confidence                                                                                            


Q ss_pred             ----------------------hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcC
Q 010709          349 ----------------------ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG  406 (503)
Q Consensus       349 ----------------------~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~  406 (503)
                                            ...|...+..++......     .+..++||||+++..++.+++.|...|+.+..+||
T Consensus       319 ~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~-----~~~~k~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g  393 (494)
T 1wp9_A          319 IFSDKRMKKAISLLVQAKEIGLDHPKMDKLKEIIREQLQR-----KQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVG  393 (494)
T ss_dssp             HHTSHHHHHHHHHHHHHHHHTCSCHHHHHHHHHHHHHHHH-----CTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECC
T ss_pred             hhhhHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhcc-----CCCCeEEEEEccHHHHHHHHHHHHHcCCCcEEEec
Confidence                                  111222222222221110     35678999999999999999999999999999999


Q ss_pred             --------CCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          407 --------GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       407 --------~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                              +++..+|.++++.|++|+.+|||||+++++|+|+|++++||++|+|+++..|.||+||+||.
T Consensus       394 ~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~~~~~Gldl~~~~~Vi~~d~~~~~~~~~Qr~GR~~R~  463 (494)
T 1wp9_A          394 QASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH  463 (494)
T ss_dssp             SSCC-------CCHHHHHHHHHHHTSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSC
T ss_pred             cccccccccCCHHHHHHHHHHHhcCCceEEEECCccccCCCchhCCEEEEeCCCCCHHHHHHHHhhccCC
Confidence                    99999999999999999999999999999999999999999999999999999999999995

>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=100.00  E-value=1.6e-41  Score=352.54  Aligned_cols=315  Identities=17%  Similarity=0.183  Sum_probs=243.4

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..|+ .|+++|..+++.+++|+  |+.++||+|||++|.+|++...+.        ++.++||+||++||.|.++.+..+
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~--------g~~vlVltptreLA~qd~e~~~~l  147 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT--------GKGVHVVTVNEYLASRDAEQMGKI  147 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc--------CCCEEEEeCCHHHHHHHHHHHHHH
Confidence            4799 99999999999999998  999999999999999999865432        567999999999999999999999


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hCC----
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DMG----  285 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~~----  285 (503)
                      ...+ ++++.+++||.......  ...+++|+|+||++| .+++..+      .+.++.+.++||||||+|+ +.+    
T Consensus       148 ~~~l-gl~v~~i~gg~~~~~r~--~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tpl  224 (844)
T 1tf5_A          148 FEFL-GLTVGLNLNSMSKDEKR--EAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPL  224 (844)
T ss_dssp             HHHT-TCCEEECCTTSCHHHHH--HHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEE
T ss_pred             Hhhc-CCeEEEEeCCCCHHHHH--HhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccch
Confidence            9877 69999999998765433  334699999999999 5665542      3567889999999999987 654    


Q ss_pred             -----------CHHHHHHHHHhCC---------CCCcEE-----------------EEEeeCCHH---HHHH--HHHhcC
Q 010709          286 -----------FEPQIREVMQNLP---------DKHQTL-----------------LFSATMPVE---IEAL--AQEYLT  323 (503)
Q Consensus       286 -----------~~~~~~~il~~~~---------~~~q~i-----------------~~SAT~~~~---~~~~--~~~~~~  323 (503)
                                 |...+..++..++         +..|++                 ++|||.+.-   +...  +..++.
T Consensus       225 Iisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~~~~i~~al~A~~l~~  304 (844)
T 1tf5_A          225 IISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQ  304 (844)
T ss_dssp             EEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHHHHHHHHHHHHHHTCC
T ss_pred             hhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCccccCCCccchhHHHHHHHHHHHHHhh
Confidence                       6688899999987         367777                 889997642   2222  222221


Q ss_pred             -CCeEE-------EeCC---------------------------------------------------------------
Q 010709          324 -DPVQV-------KVGK---------------------------------------------------------------  332 (503)
Q Consensus       324 -~~~~~-------~~~~---------------------------------------------------------------  332 (503)
                       +...+       .++.                                                               
T Consensus       305 ~d~dYiv~dg~v~ivDe~tgr~m~grr~sdGLhqaieake~v~I~~e~~t~a~It~q~~fr~y~kl~GmTGTa~te~~e~  384 (844)
T 1tf5_A          305 KDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEF  384 (844)
T ss_dssp             BTTTEEEETTEEEEBCTTTCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEEEHHHHHTTSSEEEEEESCCGGGHHHH
T ss_pred             cCCceEEecCeeEEeecccccccCCCccchhhHHHHhhcccceecccccccceeeHHHHHHHHhhhccCCcccchhHHHH
Confidence             11111       0000                                                               


Q ss_pred             ------------CCCCCCce-EEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC
Q 010709          333 ------------VSSPTANV-IQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL  399 (503)
Q Consensus       333 ------------~~~~~~~~-~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~  399 (503)
                                  ...+.... ...+.......|...+...+......       ..++||||++++.++.|++.|...|+
T Consensus       385 ~~iY~l~vv~IPtn~p~~r~d~~d~v~~~~~~K~~al~~~i~~~~~~-------~~pvLVft~s~~~se~Ls~~L~~~gi  457 (844)
T 1tf5_A          385 RNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMT-------GQPVLVGTVAVETSELISKLLKNKGI  457 (844)
T ss_dssp             HHHHCCCEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHHHH-------TCCEEEEESCHHHHHHHHHHHHTTTC
T ss_pred             HHHhCCceEEecCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHhc-------CCcEEEEECCHHHHHHHHHHHHHCCC
Confidence                        00000000 01134556778888888777653221       23699999999999999999999999


Q ss_pred             eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCC--------CCCEEEEccCCCChhHHHHhhCcceee---
Q 010709          400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVM--------GVAHVVNLDLPKVLLAASESLCTTSFN---  468 (503)
Q Consensus       400 ~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip--------~v~~VI~~~~p~s~~~~~Qr~GR~gR~---  468 (503)
                      .+..+||++.+.+|..+.+.|+.|  .|+|||++++||+||+        ++.+||+|++|.+...|+||+||+||.   
T Consensus       458 ~~~vLhg~~~~rEr~ii~~ag~~g--~VlIATdmAgRG~DI~l~~~V~~~ggl~VIn~d~p~s~r~y~hr~GRTGRqG~~  535 (844)
T 1tf5_A          458 PHQVLNAKNHEREAQIIEEAGQKG--AVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDP  535 (844)
T ss_dssp             CCEEECSSCHHHHHHHHTTTTSTT--CEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGGGCC
T ss_pred             CEEEeeCCccHHHHHHHHHcCCCC--eEEEeCCccccCcCccccchhhhcCCcEEEEecCCCCHHHHHhhcCccccCCCC
Confidence            999999999988887776666555  7999999999999999        788999999999999999999999993   


Q ss_pred             -----eeeccCc
Q 010709          469 -----ITTNLDG  475 (503)
Q Consensus       469 -----~~~~~~~  475 (503)
                           +++..|.
T Consensus       536 G~s~~~vs~eD~  547 (844)
T 1tf5_A          536 GITQFYLSMEDE  547 (844)
T ss_dssp             EEEEEEEETTSS
T ss_pred             CeEEEEecHHHH
Confidence                 6666663

>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=100.00  E-value=5.7e-43  Score=382.75  Aligned_cols=322  Identities=19%  Similarity=0.235  Sum_probs=193.7

Q ss_pred             HHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       137 ~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      ...++..|+++|.++++.+++|+++++++|||+|||++|++|++..+...+   ...++++|||+|+++|+.|+.+.+++
T Consensus       242 ~l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~---~~~~~~vLvl~Pt~~L~~Q~~~~~~~  318 (936)
T 4a2w_A          242 PVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP---AGRKAKVVFLATKVPVYEQQKNVFKH  318 (936)
T ss_dssp             ------CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC---SSCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             cccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc---ccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            345678999999999999999999999999999999999999887655432   12367899999999999999999999


Q ss_pred             HhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC-CCCCccEEEecchhHHhhCCCH-HHHHHHH
Q 010709          217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLSRVSFVILDEADRMLDMGFE-PQIREVM  294 (503)
Q Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~l~~~~~vViDEaH~l~~~~~~-~~~~~il  294 (503)
                      ++... ++.+..++|+.........+..+++|+|+||++|.+.+.+..+ .+.++++|||||||++.+.+.. ..+..++
T Consensus       319 ~~~~~-~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~  397 (936)
T 4a2w_A          319 HFERQ-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYL  397 (936)
T ss_dssp             HHHTT-TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHH
T ss_pred             Hhccc-CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHH
Confidence            98655 5889999999876665555556789999999999999988766 6889999999999998876432 2222333


Q ss_pred             Hh----CCCCCcEEEEEeeCCH-----------HHHHHHH------------------HhcCCCeEEEeCCCCCCCCc--
Q 010709          295 QN----LPDKHQTLLFSATMPV-----------EIEALAQ------------------EYLTDPVQVKVGKVSSPTAN--  339 (503)
Q Consensus       295 ~~----~~~~~q~i~~SAT~~~-----------~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~--  339 (503)
                      ..    ..+..++++||||+..           .+..+..                  .+...|..............  
T Consensus       398 ~~~~~~~~~~~~~l~LSATp~~~~~~~l~~~~~~i~~L~~~L~~~~i~~~~~~~~~l~~~~~~p~~~~~~~~~~~~~~~~  477 (936)
T 4a2w_A          398 EQKFNSASQLPQILGLTASVGVGNAKNIEETIEHICSLCSYLDIQAISTVRENIQELQRFMNKPEIDVRLVKRRIHNPFA  477 (936)
T ss_dssp             HHHHTTCSCCCEEEEEESCCCCTTCCSHHHHHHHHHHHHHHHTCSEEECCCSSHHHHHHHSCCCCEEEEECCCCSCCHHH
T ss_pred             HHhhccCCCcCeEEEecCCcccccchhHHHHHHHHHHHHHhcCCceeecccccHHHHHHhccCCcceEEecccccCcHHH
Confidence            22    2456889999999952           2222111                  12222222111100000000  


Q ss_pred             ----------------------eEEEEEE-c---------------------C---------------------------
Q 010709          340 ----------------------VIQILEK-V---------------------S---------------------------  348 (503)
Q Consensus       340 ----------------------~~~~~~~-~---------------------~---------------------------  348 (503)
                                            +...... .                     +                           
T Consensus       478 ~~l~~l~~~i~~~~~~~l~~~~l~~~~~~~~g~~~y~~~l~~l~k~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~~~al~  557 (936)
T 4a2w_A          478 AIISNLMSETEALMRTIAYVDTLSQNSKKDFGTQNYEHWIVVTQRKCRLLQLEDKEEESRICRALFICTEHLRKYNDALI  557 (936)
T ss_dssp             HHHHHHHHHHHHHHHHC------------CCSSHHHHHHHHHHHHHHHHCCCSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHhhhhhhhccccccchHHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHh
Confidence                                  0000000 0                     0                           


Q ss_pred             -----------------------------------------------------hhhHHHHHHHHHHHHHHhhhccCCCCC
Q 010709          349 -----------------------------------------------------ENEKVDRLLALLVEEAFLAEKSCHPFP  375 (503)
Q Consensus       349 -----------------------------------------------------~~~k~~~l~~~l~~~~~~~~~~~~~~~  375 (503)
                                                                           ...|...+..++.+     .....+..
T Consensus       558 i~~~~~~~~~~~~l~~~~~~~~~~~~~~~e~~l~~~~~~~~~~l~~~~~~~~~~~~K~~~L~~lL~~-----~~~~~~~~  632 (936)
T 4a2w_A          558 ISEDARIIDALSYLTEFFTNVKNGPYTELEQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDD-----AYRYNPQT  632 (936)
T ss_dssp             HHHHSCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHTSTTCCCHHHHHHHHHHHH-----TTTSCTTC
T ss_pred             hhcchhHHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHH-----HhccCCCC
Confidence                                                                 00011111111111     01124567


Q ss_pred             cEEEEEcchhhHHHHHHHHHHC------------CCeEEEEcCCCCHHHHHHHHHHHhc-CCCcEEEEccccccCCCCCC
Q 010709          376 LTIVFVERKTRCDEVSEALVAE------------GLHAVALHGGRNQSDRESALRDFRN-GSTNILVATDVASRGLDVMG  442 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~~------------~~~v~~lh~~~~~~~r~~~~~~f~~-g~~~vLvaT~~~~~Gldip~  442 (503)
                      ++||||+++..++.+++.|...            |..+..+||+|++.+|.++++.|++ |+.+|||||+++++|||+|+
T Consensus       633 rvLIF~~t~~~ae~L~~~L~~~~~l~~ik~~~l~G~~~~~~hg~m~~~eR~~il~~Fr~~g~~~VLVaT~~~~eGIDlp~  712 (936)
T 4a2w_A          633 RTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATSVADEGIDIVQ  712 (936)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHCSTTSSCCCEEC----------------------------CCSEEEEECC------CCC
T ss_pred             eEEEEeCCHHHHHHHHHHHhhCccccccceeEEecCCCcccCCCCCHHHHHHHHHHhhccCCeeEEEEeCchhcCCcchh
Confidence            8999999999999999999986            5566677999999999999999999 99999999999999999999


Q ss_pred             CCEEEEccCCCChhHHHHhhCcceee
Q 010709          443 VAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       443 v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |++||+||+|+++..|+||+|| ||.
T Consensus       713 v~~VI~yD~p~s~~~~iQr~GR-GR~  737 (936)
T 4a2w_A          713 CNLVVLYEYSGNVTKMIQVRGR-GRA  737 (936)
T ss_dssp             CSEEEEESCCSCSHHHHCC-------
T ss_pred             CCEEEEeCCCCCHHHHHHhcCC-CCC
Confidence            9999999999999999999999 995

>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=100.00  E-value=8.8e-44  Score=381.99  Aligned_cols=317  Identities=21%  Similarity=0.284  Sum_probs=218.4

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH-HHHHHHHhcc
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI-EKEVKALSRS  220 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~-~~~~~~~~~~  220 (503)
                      ..|+++|.++++.+++|+++++++|||+|||++|++|++..+.....  ...++++|||+|+++|+.|+ .+++++++..
T Consensus         6 ~~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~--~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~   83 (699)
T 4gl2_A            6 LQLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK   83 (699)
T ss_dssp             -CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH--HTCCCCBCCEESCSHHHHHHHHHTHHHHHTT
T ss_pred             CCccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc--cCCCCeEEEEECCHHHHHHHHHHHHHHHcCc
Confidence            37999999999999999999999999999999999999887665321  12236799999999999999 9999999854


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHH------HcCCCCCCCccEEEecchhHHhhCC-CHHHHHHH
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHL------QQGNTSLSRVSFVILDEADRMLDMG-FEPQIREV  293 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l------~~~~~~l~~~~~vViDEaH~l~~~~-~~~~~~~i  293 (503)
                        .+.+..++|+.........+...++|+|+||++|.+.+      ....+.+.++++|||||||++...+ +...+...
T Consensus        84 --~~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~  161 (699)
T 4gl2_A           84 --WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHY  161 (699)
T ss_dssp             --TSCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHH
T ss_pred             --CceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHH
Confidence              37888899887665555555677999999999999888      3445678899999999999875543 22222222


Q ss_pred             HHh----C---------CCCCcEEEEEeeCCHH-----------HHHHHHHh------------------cCCCeEEEeC
Q 010709          294 MQN----L---------PDKHQTLLFSATMPVE-----------IEALAQEY------------------LTDPVQVKVG  331 (503)
Q Consensus       294 l~~----~---------~~~~q~i~~SAT~~~~-----------~~~~~~~~------------------~~~~~~~~~~  331 (503)
                      +..    .         .+..++++||||+...           +..+...+                  ...|......
T Consensus       162 l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~~~~~~~~~~~~~i~~l~~~l~~~~i~~~~~~~~~l~~~~~~p~~~~~~  241 (699)
T 4gl2_A          162 LMQKLKNNRLKKENKPVIPLPQILGLTASPGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAI  241 (699)
T ss_dssp             HHHHHHHHHHHC----CCCCCEEEEECSCCCCCSCCSHHHHHHHHHHHHHHHTCSCCCCCCTTHHHHHHHSCCCEEEEEE
T ss_pred             HHhhhcccccccccccCCCCCEEEEecccccccccccHHHHHHHHHHHHhhcCCCEEEeecCchHHHhhhcCCCceEEEE
Confidence            221    1         1567899999999852           22222221                  1111111000


Q ss_pred             CCCCCC-----------------------CceE-----------------------------------------------
Q 010709          332 KVSSPT-----------------------ANVI-----------------------------------------------  341 (503)
Q Consensus       332 ~~~~~~-----------------------~~~~-----------------------------------------------  341 (503)
                      ......                       ....                                               
T Consensus       242 ~~~~~~~~~~~~l~~l~~~i~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  321 (699)
T 4gl2_A          242 ADATREDPFKEKLLEIMTRIQTYCQMSPMSDFGTQPYEQWAIQMEKKAAKEGNRKERVCAEHLRKYNEALQINDTIRMID  321 (699)
T ss_dssp             EC-----CHHHHHHHHHHHHHHHHTCCCCSCSSSHHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHHHHHHSCHHH
T ss_pred             cccccCChHHHHHHHHHHHHHHHhccCcchhccchHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            000000                       0000                                               


Q ss_pred             ------------------------EEEEEcC--------------------------hhhHHHHHHHHHHHHHHhhhccC
Q 010709          342 ------------------------QILEKVS--------------------------ENEKVDRLLALLVEEAFLAEKSC  371 (503)
Q Consensus       342 ------------------------~~~~~~~--------------------------~~~k~~~l~~~l~~~~~~~~~~~  371 (503)
                                              .......                          ...|...+..++.....     .
T Consensus       322 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~k~~~L~~~L~~~~~-----~  396 (699)
T 4gl2_A          322 AYTHLETFYNEEKDKKFAVIEDDLKKPLKLDETDRFLMTLFFENNKMLKRLAENPEYENEKLTKLRNTIMEQYT-----R  396 (699)
T ss_dssp             HHHHHHHHHHHHHHHHC------------CCHHHHHHHHHHHHHHHHHHHHHTCCC----CSSCSHHHHHHHHH-----H
T ss_pred             HHHHHHHHHHHHHhhhccccccccccccccchhHHHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHh-----c
Confidence                                    0000000                          00000011111111110     0


Q ss_pred             CC-CCcEEEEEcchhhHHHHHHHHHHC------CCeEEEEcCC--------CCHHHHHHHHHHHhcCCCcEEEEcccccc
Q 010709          372 HP-FPLTIVFVERKTRCDEVSEALVAE------GLHAVALHGG--------RNQSDRESALRDFRNGSTNILVATDVASR  436 (503)
Q Consensus       372 ~~-~~~~lIF~~~~~~~~~l~~~L~~~------~~~v~~lh~~--------~~~~~r~~~~~~f~~g~~~vLvaT~~~~~  436 (503)
                      .+ .+++||||+++..++.+++.|...      |+.+..+||+        |++.+|.++++.|++|+.+|||||+++++
T Consensus       397 ~~~~~~~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~~~~~  476 (699)
T 4gl2_A          397 TEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATTVAEE  476 (699)
T ss_dssp             SSSCCCEEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEECSCCT
T ss_pred             CCCCCcEEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEcccccc
Confidence            12 578999999999999999999987      8999999999        99999999999999999999999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          437 GLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       437 Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |||+|++++||+||+|+++..|+||+|||||
T Consensus       477 GIDip~v~~VI~~d~p~s~~~~~Qr~GRArr  507 (699)
T 4gl2_A          477 GLDIKECNIVIRYGLVTNEIAMVQARGRARA  507 (699)
T ss_dssp             TSCCCSCCCCEEESCCCCHHHHHHHHTTSCS
T ss_pred             CCccccCCEEEEeCCCCCHHHHHHHcCCCCC
Confidence            9999999999999999999999999999888

>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=100.00  E-value=3.9e-43  Score=387.02  Aligned_cols=278  Identities=19%  Similarity=0.279  Sum_probs=218.0

Q ss_pred             HHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          137 EFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       137 ~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      ..+||. | ++|.++++.++.|+|++++||||+|||+ |.+|++..+...       ++++||++||++||.|+++.+++
T Consensus        52 ~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~~-------~~~~lil~PtreLa~Q~~~~l~~  121 (1054)
T 1gku_B           52 KCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLALK-------GKRCYVIFPTSLLVIQAAETIRK  121 (1054)
T ss_dssp             TTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHTT-------SCCEEEEESCHHHHHHHHHHHHH
T ss_pred             HhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhhc-------CCeEEEEeccHHHHHHHHHHHHH
Confidence            347999 9 9999999999999999999999999998 889998887653       57899999999999999999999


Q ss_pred             HhccCCCc----eEEEEECCccHHHH---HHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHH
Q 010709          217 LSRSLDSF----KTAIVVGGTNIAEQ---RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQ  289 (503)
Q Consensus       217 ~~~~~~~~----~~~~~~~~~~~~~~---~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~  289 (503)
                      ++... ++    .+..++|+.....+   ...+.. ++|+|+||++|.+++.+    +.++++|||||||++++  +...
T Consensus       122 l~~~~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~----L~~l~~lViDEah~~l~--~~~~  193 (1054)
T 1gku_B          122 YAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE----LGHFDFIFVDDVDAILK--ASKN  193 (1054)
T ss_dssp             HHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT----SCCCSEEEESCHHHHHT--STHH
T ss_pred             HHhhc-CCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH----hccCCEEEEeChhhhhh--cccc
Confidence            98765 46    78899999877653   344445 99999999999987765    66899999999999998  4677


Q ss_pred             HHHHHHhC-----------CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          290 IREVMQNL-----------PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       290 ~~~il~~~-----------~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      +..++..+           +...|++++|||++.. ..+...++.++..+.+.........+.+.+..   ..+...+..
T Consensus       194 ~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~~~~~~~i~~~~~~---~~k~~~L~~  269 (1054)
T 1gku_B          194 VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSSRITVRNVEDVAVN---DESISTLSS  269 (1054)
T ss_dssp             HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCCEECCCCEEEEEES---CCCTTTTHH
T ss_pred             HHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCcccCcCCceEEEec---hhHHHHHHH
Confidence            88887776           3467899999999876 43333333333333333333344455555552   333334444


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEE----cccc
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVA----TDVA  434 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLva----T~~~  434 (503)
                      ++...          .+++||||++++.|+.+++.|... +.+..+||++.     ++++.|++|+.+||||    |+++
T Consensus       270 ll~~~----------~~~~LVF~~t~~~a~~l~~~L~~~-~~v~~lhg~~~-----~~l~~F~~G~~~VLVaTas~Tdv~  333 (1054)
T 1gku_B          270 ILEKL----------GTGGIIYARTGEEAEEIYESLKNK-FRIGIVTATKK-----GDYEKFVEGEIDHLIGTAHYYGTL  333 (1054)
T ss_dssp             HHTTS----------CSCEEEEESSHHHHHHHHHTTTTS-SCEEECTTSSS-----HHHHHHHHTSCSEEEEECC-----
T ss_pred             HHhhc----------CCCEEEEEcCHHHHHHHHHHHhhc-cCeeEEeccHH-----HHHHHHHcCCCcEEEEecCCCCee
Confidence            43221          356999999999999999999988 99999999984     7889999999999999    9999


Q ss_pred             ccCCCCCCC-CEEEEccCC
Q 010709          435 SRGLDVMGV-AHVVNLDLP  452 (503)
Q Consensus       435 ~~Gldip~v-~~VI~~~~p  452 (503)
                      ++|||+|+| ++||++|+|
T Consensus       334 ~rGIDip~VI~~VI~~~~P  352 (1054)
T 1gku_B          334 VRGLDLPERIRFAVFVGCP  352 (1054)
T ss_dssp             -CCSCCTTTCCEEEEESCC
T ss_pred             EeccccCCcccEEEEeCCC
Confidence            999999996 999999999

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=100.00  E-value=1.1e-41  Score=372.23  Aligned_cols=297  Identities=19%  Similarity=0.213  Sum_probs=232.7

Q ss_pred             CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ++| .|+++|.++++.+++|+++++++|||+|||++|++++......        ++++||++|+++|+.|+++.+++++
T Consensus        36 ~~f-~l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~--------g~~vlvl~PtraLa~Q~~~~l~~~~  106 (997)
T 4a4z_A           36 WPF-ELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN--------MTKTIYTSPIKALSNQKFRDFKETF  106 (997)
T ss_dssp             CSS-CCCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT--------TCEEEEEESCGGGHHHHHHHHHTTC
T ss_pred             CCC-CCCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc--------CCeEEEEeCCHHHHHHHHHHHHHHc
Confidence            344 4899999999999999999999999999999998888765432        5789999999999999999998865


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP  298 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~  298 (503)
                      .   ++.+..++|+...       ...++|+|+||++|.+++.+....+.++++|||||||++.+++++..+..++..++
T Consensus       107 ~---~~~v~~l~G~~~~-------~~~~~IlV~Tpe~L~~~l~~~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii~~l~  176 (997)
T 4a4z_A          107 D---DVNIGLITGDVQI-------NPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLP  176 (997)
T ss_dssp             -----CCEEEECSSCEE-------CTTSSEEEEEHHHHHHHHHHTCSGGGGEEEEEECCTTCCCTTCTTCCHHHHHHHSC
T ss_pred             C---CCeEEEEeCCCcc-------CCCCCEEEECHHHHHHHHHhCchhhcCCCEEEEECcccccccchHHHHHHHHHhcc
Confidence            3   4678888887643       34589999999999999988777789999999999999999999999999999999


Q ss_pred             CCCcEEEEEeeCCHHHHHHHHHh---cCCCeEEEeCCCCCCCCceEEEEEE-------c---------------------
Q 010709          299 DKHQTLLFSATMPVEIEALAQEY---LTDPVQVKVGKVSSPTANVIQILEK-------V---------------------  347 (503)
Q Consensus       299 ~~~q~i~~SAT~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~-------~---------------------  347 (503)
                      +..|+|++|||+++.. .+...+   ...+..+......  ...+.+.+..       +                     
T Consensus       177 ~~v~iIlLSAT~~n~~-ef~~~l~~~~~~~~~vi~~~~r--~~pl~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  253 (997)
T 4a4z_A          177 QHVKFILLSATVPNTY-EFANWIGRTKQKNIYVISTPKR--PVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGE  253 (997)
T ss_dssp             TTCEEEEEECCCTTHH-HHHHHHHHHHTCCEEEEECSSC--SSCEEEEEEETTEEEEEECTTCCBCHHHHHHHHHHHC--
T ss_pred             cCCCEEEEcCCCCChH-HHHHHHhcccCCceEEEecCCC--CccceEEEecCCcchhcccchhhhhHHHHHHHHHHhhcc
Confidence            9999999999997543 233322   2223322221111  1111111110       0                     


Q ss_pred             -----------------------------------------------------------------ChhhHHHHHHHHHHH
Q 010709          348 -----------------------------------------------------------------SENEKVDRLLALLVE  362 (503)
Q Consensus       348 -----------------------------------------------------------------~~~~k~~~l~~~l~~  362 (503)
                                                                                       ....+...++..+..
T Consensus       254 ~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~l~~  333 (997)
T 4a4z_A          254 SAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRK  333 (997)
T ss_dssp             ---------------------------------------------------------------CCCCTTHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhHHHHHHHHHHh
Confidence                                                                             011112222222222


Q ss_pred             HHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC---------------------------------------eEEE
Q 010709          363 EAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL---------------------------------------HAVA  403 (503)
Q Consensus       363 ~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~---------------------------------------~v~~  403 (503)
                               ....++||||++++.|+.+++.|...++                                       .+..
T Consensus       334 ---------~~~~~~IVF~~sr~~~e~la~~L~~~~~~~~~e~~~i~~~~~~~~~~l~~~d~~l~~~~~l~~~l~~gi~~  404 (997)
T 4a4z_A          334 ---------RELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAV  404 (997)
T ss_dssp             ---------TTCCSEEEECSCHHHHHHHHHTTTTCCCCCHHHHHHHHHHHHHHHTTSCHHHHTCHHHHHHHHHHTTTEEE
T ss_pred             ---------CCCCCEEEEECCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhcchhhhcchhHHHHHHHhhcCeee
Confidence                     2345799999999999999999976555                                       5789


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC---------ChhHHHHhhCccee
Q 010709          404 LHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK---------VLLAASESLCTTSF  467 (503)
Q Consensus       404 lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~---------s~~~~~Qr~GR~gR  467 (503)
                      +||+|++.+|..+++.|++|.++|||||+++++|||+|+ ..||+++.|+         +..+|+||+|||||
T Consensus       405 ~H~gl~~~~R~~v~~~F~~G~~kVLvAT~~~a~GIDiP~-~~VVi~~~~k~dg~~~~~~s~~~y~Qr~GRAGR  476 (997)
T 4a4z_A          405 HHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPT-RTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGR  476 (997)
T ss_dssp             ECTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCC-SEEEESCSEEEETTEEEECCHHHHHHHHGGGCC
T ss_pred             ecCCCCHHHHHHHHHHHHCCCCcEEEEchHhhCCCCCCC-ceEEEeccccccCccCCCCCHHHHhHHhccccc
Confidence            999999999999999999999999999999999999999 7778777776         99999999999999

>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=100.00  E-value=5.2e-41  Score=358.26  Aligned_cols=326  Identities=17%  Similarity=0.206  Sum_probs=242.1

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCe
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPL  196 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~  196 (503)
                      .++..|+++++++.+.+.+...+ ..|++.|+++++.++.+ ++++++||||+|||+  ++|++.......   .+.+++
T Consensus        69 ~~~~~f~~~~l~~~~~~~l~~r~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~~---~~~g~~  142 (773)
T 2xau_A           69 GKINPFTGREFTPKYVDILKIRR-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEMP---HLENTQ  142 (773)
T ss_dssp             SSBCTTTCSBCCHHHHHHHHHHT-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHCG---GGGTCE
T ss_pred             CCCCCccccCCCHHHHHHHHHhh-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhccc---cCCCce
Confidence            35667999999999999999888 78999999999988754 579999999999999  466664332211   112567


Q ss_pred             EEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEec
Q 010709          197 ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD  276 (503)
Q Consensus       197 ~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViD  276 (503)
                      +++++|+++|+.|+++.+.+.........++.......      ....+++|+++|||++.+.+.. ...+.++++||||
T Consensus       143 ilvl~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~-~~~l~~~~~lIlD  215 (773)
T 2xau_A          143 VACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAME-DHDLSRYSCIILD  215 (773)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHH-STTCTTEEEEEEC
T ss_pred             EEecCchHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhh-CccccCCCEEEec
Confidence            99999999999999988766542111122221111110      1124689999999999988876 3568899999999


Q ss_pred             chhH-HhhCCC-HHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHH
Q 010709          277 EADR-MLDMGF-EPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVD  354 (503)
Q Consensus       277 EaH~-l~~~~~-~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~  354 (503)
                      |+|. .++.++ ...+..++.. .++.|+|+||||++.  .. +..++.++..+.+....   ..+.+.+.......+..
T Consensus       216 Eah~R~ld~d~~~~~l~~l~~~-~~~~~iIl~SAT~~~--~~-l~~~~~~~~vi~v~gr~---~pv~~~~~~~~~~~~~~  288 (773)
T 2xau_A          216 EAHERTLATDILMGLLKQVVKR-RPDLKIIIMSATLDA--EK-FQRYFNDAPLLAVPGRT---YPVELYYTPEFQRDYLD  288 (773)
T ss_dssp             SGGGCCHHHHHHHHHHHHHHHH-CTTCEEEEEESCSCC--HH-HHHHTTSCCEEECCCCC---CCEEEECCSSCCSCHHH
T ss_pred             CccccccchHHHHHHHHHHHHh-CCCceEEEEeccccH--HH-HHHHhcCCCcccccCcc---cceEEEEecCCchhHHH
Confidence            9995 554332 2334444444 457899999999964  33 34566655455444332   23555554444444444


Q ss_pred             HHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHH-----------CCCeEEEEcCCCCHHHHHHHHHHHh--
Q 010709          355 RLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA-----------EGLHAVALHGGRNQSDRESALRDFR--  421 (503)
Q Consensus       355 ~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~-----------~~~~v~~lh~~~~~~~r~~~~~~f~--  421 (503)
                      ..+..+......     .+.+++||||+++++++.+++.|.+           .++.+..+||++++.+|.++++.|+  
T Consensus       289 ~~l~~l~~~~~~-----~~~g~iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~  363 (773)
T 2xau_A          289 SAIRTVLQIHAT-----EEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPES  363 (773)
T ss_dssp             HHHHHHHHHHHH-----SCSCEEEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCC
T ss_pred             HHHHHHHHHHHh-----cCCCCEEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccc
Confidence            444444333221     2457899999999999999999985           5788999999999999999999999  


Q ss_pred             ---cCCCcEEEEccccccCCCCCCCCEEEEccC------------------CCChhHHHHhhCcceee
Q 010709          422 ---NGSTNILVATDVASRGLDVMGVAHVVNLDL------------------PKVLLAASESLCTTSFN  468 (503)
Q Consensus       422 ---~g~~~vLvaT~~~~~Gldip~v~~VI~~~~------------------p~s~~~~~Qr~GR~gR~  468 (503)
                         +|..+|||||+++++|||||+|++||++|+                  |.+.++|+||+|||||.
T Consensus       364 ~~~~g~~kVlVAT~iae~GidIp~v~~VId~g~~k~~~yd~~~g~~~L~~~p~S~~s~~QR~GRaGR~  431 (773)
T 2xau_A          364 HNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT  431 (773)
T ss_dssp             SSSSCCEEEEEECTHHHHTCCCTTEEEEEECSEEEEEEEETTTTEEEEEEEECCHHHHHHHHHGGGSS
T ss_pred             cCCCCceEEEEeCcHHHhCcCcCCeEEEEeCCCccceeeccccCccccccccCCHHHHHhhccccCCC
Confidence               999999999999999999999999999888                  88999999999999995

>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=100.00  E-value=1.4e-40  Score=344.35  Aligned_cols=313  Identities=18%  Similarity=0.205  Sum_probs=218.4

Q ss_pred             CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|. +|+++|..+++.++.|+  |+.++||+|||++|.+|++...+.        ++.++|++||++||.|.++.+..++
T Consensus        71 lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~--------g~~vlVltPTreLA~Q~~e~~~~l~  139 (853)
T 2fsf_A           71 FGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT--------GKGVHVVTVNDYLAQRDAENNRPLF  139 (853)
T ss_dssp             HSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT--------SSCCEEEESSHHHHHHHHHHHHHHH
T ss_pred             cCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc--------CCcEEEEcCCHHHHHHHHHHHHHHH
Confidence            454 89999999999999998  999999999999999999865432        5679999999999999999999999


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcCC------CCCCCccEEEecchhHHh-hCC-----
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQGN------TSLSRVSFVILDEADRML-DMG-----  285 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~l~~~~~vViDEaH~l~-~~~-----  285 (503)
                      ..+ ++++.+++||.....  +....+++|+|+||++| .+++..+.      ..++++.++|+||||+|+ +.+     
T Consensus       140 ~~l-gl~v~~i~GG~~~~~--r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~tpLI  216 (853)
T 2fsf_A          140 EFL-GLTVGINLPGMPAPA--KREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEARTPLI  216 (853)
T ss_dssp             HHT-TCCEEECCTTCCHHH--HHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTCEEE
T ss_pred             Hhc-CCeEEEEeCCCCHHH--HHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCccccc
Confidence            877 699999999987643  33445699999999999 77776542      567899999999999998 443     


Q ss_pred             ----------CHHHHHHHHHhCCC--------------------CCcEE------------------------EEEeeCC
Q 010709          286 ----------FEPQIREVMQNLPD--------------------KHQTL------------------------LFSATMP  311 (503)
Q Consensus       286 ----------~~~~~~~il~~~~~--------------------~~q~i------------------------~~SAT~~  311 (503)
                                |...+..++..+++                    ..|++                        ++|||.+
T Consensus       217 iSg~~~~~~~~y~~i~~iv~~L~~~~~~~~~~~~~~~dy~vdek~rqv~lte~g~~~~e~~l~~~~l~~~~~~Lfsat~~  296 (853)
T 2fsf_A          217 ISGPAEDSSEMYKRVNKIIPHLIRQEKEDSETFQGEGHFSVDEKSRQVNLTERGLVLIEELLVKEGIMDEGESLYSPANI  296 (853)
T ss_dssp             EEEC----------------------------------------------------------------------------
T ss_pred             ccCCCccchhHHHHHHHHHHhchhhhccccccccccccceeccccceEEEcHHHHHHHHHHHHhCCcccccccccCcccc
Confidence                      56677788877764                    44543                        7899975


Q ss_pred             HHHHHH-----HHHhcC--------CC-----------------------------eEEEeCCCCCCCCceE--------
Q 010709          312 VEIEAL-----AQEYLT--------DP-----------------------------VQVKVGKVSSPTANVI--------  341 (503)
Q Consensus       312 ~~~~~~-----~~~~~~--------~~-----------------------------~~~~~~~~~~~~~~~~--------  341 (503)
                      .-...+     +..++.        ++                             ..+.+.........+.        
T Consensus       297 ~~~~~i~~al~A~~l~~~d~dYiV~d~~vviVde~tgR~m~grr~sdGLhQaieake~v~I~~e~~tla~It~qnyfr~Y  376 (853)
T 2fsf_A          297 MLMHHVTAALRAHALFTRDVDYIVKDGEVIIVDEHTGRTMQGRRWSDGLHQAVEAKEGVQIQNENQTLASITFQNYFRLY  376 (853)
T ss_dssp             ------------------------------------------------------------CCCCCEEEEEEEHHHHHTTS
T ss_pred             hHHHHHHHHHHHHHHhhcCccceeecCcEEEEecccCcccCCCccchhhhHHHHhcccceecccccccceeehHHHHhhh
Confidence            321111     111110        00                             0111111100000011        


Q ss_pred             ---------------------------------------EEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEc
Q 010709          342 ---------------------------------------QILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVE  382 (503)
Q Consensus       342 ---------------------------------------~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~  382 (503)
                                                             ..+.......|...+...+....       ..+.++||||+
T Consensus       377 ~kl~GmTGTa~te~~ef~~iY~l~vv~IPtn~p~~R~d~~d~v~~~~~~K~~al~~~i~~~~-------~~gqpvLVft~  449 (853)
T 2fsf_A          377 EKLAGMTGTADTEAFEFSSIYKLDTVVVPTNRPMIRKDLPDLVYMTEAEKIQAIIEDIKERT-------AKGQPVLVGTI  449 (853)
T ss_dssp             SEEEEEECTTCCCHHHHHHHHCCEEEECCCSSCCCCEECCCEEESSHHHHHHHHHHHHHHHH-------TTTCCEEEEES
T ss_pred             hhhhcCCCCchhHHHHHHHHhCCcEEEcCCCCCceeecCCcEEEeCHHHHHHHHHHHHHHHh-------cCCCCEEEEEC
Confidence                                                   11244566778878777775532       13346999999


Q ss_pred             chhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCC-------------------
Q 010709          383 RKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGV-------------------  443 (503)
Q Consensus       383 ~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v-------------------  443 (503)
                      +++.++.|++.|.+.|+.+..+||++.+.++..+.+.|+.|  .|+|||++++||+||+..                   
T Consensus       450 sie~se~Ls~~L~~~gi~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~gn~~~~~~~~~~~~~~~~~  527 (853)
T 2fsf_A          450 SIEKSELVSNELTKAGIKHNVLNAKFHANEAAIVAQAGYPA--AVTIATNMAGRGTDIVLGGSWQAEVAALENPTAEQIE  527 (853)
T ss_dssp             SHHHHHHHHHHHHHTTCCCEECCTTCHHHHHHHHHTTTSTT--CEEEEESCCSSCSCCCTTCCHHHHHHHCSSCCSSHHH
T ss_pred             cHHHHHHHHHHHHHCCCCEEEecCChhHHHHHHHHhcCCCC--eEEEecccccCCcCccCCCchHhhhhhcccchhHHHH
Confidence            99999999999999999999999999999998888888887  699999999999999973                   


Q ss_pred             ------------------CEEEEccCCCChhHHHHhhCcceee--------eeeccC
Q 010709          444 ------------------AHVVNLDLPKVLLAASESLCTTSFN--------ITTNLD  474 (503)
Q Consensus       444 ------------------~~VI~~~~p~s~~~~~Qr~GR~gR~--------~~~~~~  474 (503)
                                        .+||++++|.+...|.||+||+||.        +++..|
T Consensus       528 ~~~~~~~~~~~~V~~~GGl~VI~te~pes~riy~qr~GRTGRqGd~G~s~~fls~eD  584 (853)
T 2fsf_A          528 KIKADWQVRHDAVLEAGGLHIIGTERHESRRIDNQLRGRSGRQGDAGSSRFYLSMED  584 (853)
T ss_dssp             HHHHHHHHHHHHHHHTTSEEEEESSCCSSHHHHHHHHTTSSGGGCCEEEEEEEETTS
T ss_pred             HHHHHhhhhhhHHHhcCCcEEEEccCCCCHHHHHhhccccccCCCCeeEEEEecccH
Confidence                              5999999999999999999999993        566665

>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=100.00  E-value=3.6e-40  Score=375.15  Aligned_cols=329  Identities=15%  Similarity=0.172  Sum_probs=239.9

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSG-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      +.+...+.+...+|..++|+|.++++.++++ +|++++||||||||++|.+|++..+...      .+.++||++|+++|
T Consensus       911 L~~~~~e~l~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~------~~~kavyi~P~raL  984 (1724)
T 4f92_B          911 LRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS------SEGRCVYITPMEAL  984 (1724)
T ss_dssp             SCCHHHHTTTTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC------TTCCEEEECSCHHH
T ss_pred             ccCHHHHHHHHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC------CCCEEEEEcChHHH
Confidence            5566778888889999999999999999865 5799999999999999999999988764      25679999999999


Q ss_pred             HHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC--CCCCCccEEEecchhHHhhC
Q 010709          207 AQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN--TSLSRVSFVILDEADRMLDM  284 (503)
Q Consensus       207 a~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~--~~l~~~~~vViDEaH~l~~~  284 (503)
                      |.|.++.+++.+...-++++..++|+......   ...+++|+|||||++..++.+..  ..++++++||+||+|.+.+ 
T Consensus       985 a~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~---~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d- 1060 (1724)
T 4f92_B          985 AEQVYMDWYEKFQDRLNKKVVLLTGETSTDLK---LLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGG- 1060 (1724)
T ss_dssp             HHHHHHHHHHHHTTTSCCCEEECCSCHHHHHH---HHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGS-
T ss_pred             HHHHHHHHHHHhchhcCCEEEEEECCCCcchh---hcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhcCC-
Confidence            99999999865433336888888887654332   22458999999999977776532  3467899999999997765 


Q ss_pred             CCHHHHHHHHH-------hCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHH
Q 010709          285 GFEPQIREVMQ-------NLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLL  357 (503)
Q Consensus       285 ~~~~~~~~il~-------~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~  357 (503)
                      ..+..++.++.       ..+++.|+|+||||+++ ..++++..-.++..+...........+..++...........+.
T Consensus      1061 ~rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~~~~~~~~~~RPvpL~~~i~~~~~~~~~~~~~ 1139 (1724)
T 4f92_B         1061 ENGPVLEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLL 1139 (1724)
T ss_dssp             TTHHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCCSTTEEECCGGGCSSCEEEEEEEECCCSHHHHHH
T ss_pred             CCCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCCCeEEeCCCCCCCCeEEEEEeccCCCchhhhh
Confidence            46666655543       34678999999999974 44455544333322222222222223444443333222222221


Q ss_pred             HHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC----------------------------------CCeEEE
Q 010709          358 ALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE----------------------------------GLHAVA  403 (503)
Q Consensus       358 ~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~----------------------------------~~~v~~  403 (503)
                      .... ..........+.+++||||++++.|+.++..|...                                  ...+..
T Consensus      1140 ~~~~-~~~~~i~~~~~~~~~lVF~~sR~~~~~~A~~L~~~~~~~~~~~~~~~~~~~~l~~~l~~~~d~~L~~~l~~GIa~ 1218 (1724)
T 4f92_B         1140 SMAK-PVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGY 1218 (1724)
T ss_dssp             TTHH-HHHHHHHHHCSSSCEEEEESSHHHHHHHHHHHHHHHHHTTCTTTTBCSCHHHHHHHHTTCCCHHHHHHHHTTEEE
T ss_pred             hhcc-hHHHHHHHhcCCCCeeeeCCCHHHHHHHHHHHHHHHhhccchhhhhcccHHHHHHHHhhcccHHHHHHHhCCEEE
Confidence            1111 11111111245668999999999999888776431                                  135889


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE----c------cCCCChhHHHHhhCcceee
Q 010709          404 LHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN----L------DLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       404 lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~----~------~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|++|++.+|..+++.|++|.++|||||+.+++|||+|+..+||.    |      ..|.+..+|.||+|||||.
T Consensus      1219 hHagL~~~~R~~VE~lF~~G~i~VLvaT~tlA~GVnlPa~~VVI~~~~~~dg~~~~~~~~s~~~~~Qm~GRAGR~ 1293 (1724)
T 4f92_B         1219 LHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRP 1293 (1724)
T ss_dssp             ECTTSCHHHHHHHHHHHHHTSBCEEEEEGGGSSSCCCCBSEEEEECSEEEETTTTEEEECCHHHHHHHHTTBCCT
T ss_pred             ECCCCCHHHHHHHHHHHHCCCCeEEEEChHHHcCCCCCccEEEEecCccccCcccccCCCCHHHHHHhhccccCC
Confidence            999999999999999999999999999999999999999888883    2      2367899999999999994

>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=1.3e-39  Score=302.81  Aligned_cols=236  Identities=43%  Similarity=0.729  Sum_probs=216.2

Q ss_pred             CHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCch
Q 010709           92 NPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGK  171 (503)
Q Consensus        92 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGK  171 (503)
                      ++++++.++...++.+...    ..|.++.+|+++++++.+.+.+..+||..|+++|.++++.+++|+++++++|||+||
T Consensus         4 ~~~~~~~~~~~~~i~~~~~----~~p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGK   79 (242)
T 3fe2_A            4 TAQEVETYRRSKEITVRGH----NCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGK   79 (242)
T ss_dssp             --CHHHHHHHHHTEEEESS----CCCCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCH
T ss_pred             CHHHHHHHHhcCceEEeCC----CCCCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHH
Confidence            4567888999998888765    678899999999999999999999999999999999999999999999999999999


Q ss_pred             hHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEE
Q 010709          172 TAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVA  251 (503)
Q Consensus       172 Tl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~  251 (503)
                      |++|++|++..+...+......++++||++||++|+.|+++.+++++... ++.+..++|+.........+..+++|+|+
T Consensus        80 T~~~~l~~l~~l~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~  158 (242)
T 3fe2_A           80 TLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLERGVEICIA  158 (242)
T ss_dssp             HHHHHHHHHHHHHTSCCCCTTCCCSEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHHHHCCSEEEE
T ss_pred             HHHHHHHHHHHHHhccccccCCCCEEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHhcCCCCEEEE
Confidence            99999999999887655555568899999999999999999999998765 58899999999988888888888999999


Q ss_pred             CcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          252 TPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       252 Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      ||++|.+.+.+....+.++++||+||||++.+++|...+..++..++++.|+++||||+++.+..+++.++.+|..+.++
T Consensus       159 Tp~~l~~~l~~~~~~~~~~~~lViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~  238 (242)
T 3fe2_A          159 TPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIG  238 (242)
T ss_dssp             CHHHHHHHHHHTSCCCTTCCEEEETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             CHHHHHHHHHcCCCCcccccEEEEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEec
Confidence            99999999988888899999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             C
Q 010709          332 K  332 (503)
Q Consensus       332 ~  332 (503)
                      .
T Consensus       239 ~  239 (242)
T 3fe2_A          239 A  239 (242)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=100.00  E-value=4.5e-39  Score=356.65  Aligned_cols=309  Identities=17%  Similarity=0.171  Sum_probs=238.4

Q ss_pred             CCCHHHHHHH-HHCCCCCCcHHHHHHHHHHhc----CC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          127 CLHPSIMKDI-EFHEYTRPTSIQAQAMPVALS----GR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       127 ~l~~~l~~~l-~~~~~~~~~~~Q~~~i~~i~~----~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      +.++.+.+.+ ..++|. |+++|.++++.++.    ++  +++++++||+|||++|+++++.....        +++++|
T Consensus       587 ~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~--------g~~vlv  657 (1151)
T 2eyq_A          587 KHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN--------HKQVAV  657 (1151)
T ss_dssp             CCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT--------TCEEEE
T ss_pred             CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh--------CCeEEE
Confidence            4455566665 445664 79999999999886    65  89999999999999998888775432        578999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH---HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEe
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR---SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVIL  275 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vVi  275 (503)
                      ++||++|+.|+++.+++++... ++.+..+.+.....+..   ..+. +.++|+|+||+.+.     ....+.++++|||
T Consensus       658 lvPt~~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~-----~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          658 LVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIV  731 (1151)
T ss_dssp             ECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEE
T ss_pred             EechHHHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh-----CCccccccceEEE
Confidence            9999999999999999887654 47788887766554432   2233 35999999997663     3567889999999


Q ss_pred             cchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHH
Q 010709          276 DEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDR  355 (503)
Q Consensus       276 DEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~  355 (503)
                      ||||++     .......+..++.+.++++||||+.+.........+.++..+  .........+...+........   
T Consensus       732 DEaH~~-----g~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i--~~~~~~r~~i~~~~~~~~~~~i---  801 (1151)
T 2eyq_A          732 DEEHRF-----GVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSII--ATPPARRLAVKTFVREYDSMVV---  801 (1151)
T ss_dssp             ESGGGS-----CHHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEEC--CCCCCBCBCEEEEEEECCHHHH---
T ss_pred             echHhc-----ChHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEE--ecCCCCccccEEEEecCCHHHH---
Confidence            999984     344566677777788999999999777666665555544332  2222223334444444333222   


Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV  433 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~  433 (503)
                       ...+....       ..+++++|||++++.++.+++.|.+.  +..+..+||+|++.+|.++++.|++|+.+|||||++
T Consensus       802 -~~~il~~l-------~~g~qvlvf~~~v~~~~~l~~~L~~~~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~v  873 (1151)
T 2eyq_A          802 -REAILREI-------LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI  873 (1151)
T ss_dssp             -HHHHHHHH-------TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST
T ss_pred             -HHHHHHHH-------hcCCeEEEEECCHHHHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECCc
Confidence             22222221       23467999999999999999999987  889999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCEEEEccC-CCChhHHHHhhCcceee
Q 010709          434 ASRGLDVMGVAHVVNLDL-PKVLLAASESLCTTSFN  468 (503)
Q Consensus       434 ~~~Gldip~v~~VI~~~~-p~s~~~~~Qr~GR~gR~  468 (503)
                      +++|+|+|++++||+++. +.++.+|.||+||+||.
T Consensus       874 ~e~GiDip~v~~VIi~~~~~~~l~~l~Qr~GRvgR~  909 (1151)
T 2eyq_A          874 IETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRS  909 (1151)
T ss_dssp             TGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBT
T ss_pred             ceeeecccCCcEEEEeCCCCCCHHHHHHHHhccCcC
Confidence            999999999999999998 46899999999999993

>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=100.00  E-value=1.7e-40  Score=351.78  Aligned_cols=307  Identities=21%  Similarity=0.243  Sum_probs=228.6

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHHHHhcC------CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          130 PSIMKDIEFHEYTRPTSIQAQAMPVALSG------RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       130 ~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~------~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      +.+.+.+..++| .|+++|.++++.++++      .+++++||||+|||++|++|++..+..        +.+++|++||
T Consensus       356 ~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~--------g~qvlvlaPt  426 (780)
T 1gm5_A          356 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA--------GFQTAFMVPT  426 (780)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH--------TSCEEEECSC
T ss_pred             HHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc--------CCeEEEEeCc
Confidence            344455678899 9999999999998865      589999999999999999999987654        5789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH---HHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          204 RELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR---SELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       204 r~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++||.|+++.+++++... ++++..++|+....+..   ..+. +.++|+|+||+.+.+     ...+.++++|||||+|
T Consensus       427 r~La~Q~~~~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~-----~~~~~~l~lVVIDEaH  500 (780)
T 1gm5_A          427 SILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQH  500 (780)
T ss_dssp             HHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCC
T ss_pred             HHHHHHHHHHHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh-----hhhccCCceEEecccc
Confidence            999999999999998655 58899999998766533   2333 359999999998754     4568899999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLAL  359 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~  359 (503)
                      ++...     .+..+.......++++||||+.+.....  .++.+.....+.........+...+   ....+...++..
T Consensus       501 r~g~~-----qr~~l~~~~~~~~vL~mSATp~p~tl~~--~~~g~~~~s~i~~~p~~r~~i~~~~---~~~~~~~~l~~~  570 (780)
T 1gm5_A          501 RFGVK-----QREALMNKGKMVDTLVMSATPIPRSMAL--AFYGDLDVTVIDEMPPGRKEVQTML---VPMDRVNEVYEF  570 (780)
T ss_dssp             CC----------CCCCSSSSCCCEEEEESSCCCHHHHH--HHTCCSSCEEECCCCSSCCCCEECC---CCSSTHHHHHHH
T ss_pred             hhhHH-----HHHHHHHhCCCCCEEEEeCCCCHHHHHH--HHhCCcceeeeeccCCCCcceEEEE---eccchHHHHHHH
Confidence            85321     1222333345688999999986654433  2333322222222221122222221   122334445555


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcch--------hhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERK--------TRCDEVSEALVA---EGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~--------~~~~~l~~~L~~---~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      +....       ...++++|||+..        ..++.+++.|..   .++.+..+||+|++.+|..+++.|++|+.+||
T Consensus       571 i~~~l-------~~g~qvlVf~~~ie~se~l~~~~a~~l~~~L~~~~~~~~~v~~lHG~m~~~eR~~v~~~F~~G~~~IL  643 (780)
T 1gm5_A          571 VRQEV-------MRGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDIL  643 (780)
T ss_dssp             HHHHT-------TTSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBC
T ss_pred             HHHHH-------hcCCcEEEEecchhhhhhhhHHHHHHHHHHHHhhhcCCCcEEEEeCCCCHHHHHHHHHHHHCCCCeEE
Confidence            54432       2345699999965        457888888887   47889999999999999999999999999999


Q ss_pred             EEccccccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee
Q 010709          429 VATDVASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN  468 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~  468 (503)
                      |||+++++|+|+|++++||+++.|+ +...|.||+||+||.
T Consensus       644 VaT~vie~GIDiP~v~~VIi~d~~r~~l~~l~Qr~GRaGR~  684 (780)
T 1gm5_A          644 VSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRG  684 (780)
T ss_dssp             CCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCS
T ss_pred             EECCCCCccccCCCCCEEEEeCCCCCCHHHHHHHhcccCcC
Confidence            9999999999999999999999997 688999999999994

>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=100.00  E-value=4.6e-40  Score=374.24  Aligned_cols=320  Identities=20%  Similarity=0.254  Sum_probs=234.5

Q ss_pred             CCCCCcHHHHHHHHHHh-cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCC---CCCCCCeEEEEcccHHHHHHHHHHHH
Q 010709          140 EYTRPTSIQAQAMPVAL-SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPV---GRGDGPLALVLAPTRELAQQIEKEVK  215 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~-~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~---~~~~~~~~lil~Ptr~La~q~~~~~~  215 (503)
                      ||+.++++|.++++.++ .++|++++||||+|||++|.++++..+......   ....+.++||++|+++||+|+++.++
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            79999999999999987 467899999999999999999999988765432   22357899999999999999999999


Q ss_pred             HHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC--CCCCCccEEEecchhHHhhCCCHHHHHHH
Q 010709          216 ALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN--TSLSRVSFVILDEADRMLDMGFEPQIREV  293 (503)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~--~~l~~~~~vViDEaH~l~~~~~~~~~~~i  293 (503)
                      +.+... ++++..++|+......   ...+++|+|||||++..++.+..  ..++++++|||||+|.+.+ .++..++.+
T Consensus       156 ~~~~~~-gi~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~l~d-~RG~~lE~~  230 (1724)
T 4f92_B          156 KRLATY-GITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRGPVLEAL  230 (1724)
T ss_dssp             HHHTTT-TCCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGGGGS-TTHHHHHHH
T ss_pred             HHHhhC-CCEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchhcCC-ccHHHHHHH
Confidence            887665 5889999998764332   12458999999999865554432  2367899999999996644 677777655


Q ss_pred             HH-------hCCCCCcEEEEEeeCCHHHHHHHHHhcC-CCe--EEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHH
Q 010709          294 MQ-------NLPDKHQTLLFSATMPVEIEALAQEYLT-DPV--QVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEE  363 (503)
Q Consensus       294 l~-------~~~~~~q~i~~SAT~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~  363 (503)
                      +.       ..+++.|+|+||||+|+ .+++++ |++ ++.  ...+..... ...+.+.+........... ...+...
T Consensus       231 l~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~-wL~~~~~~~~~~~~~~~R-PvpL~~~~~~~~~~~~~~~-~~~~~~~  306 (1724)
T 4f92_B          231 VARAIRNIEMTQEDVRLIGLSATLPN-YEDVAT-FLRVDPAKGLFYFDNSFR-PVPLEQTYVGITEKKAIKR-FQIMNEI  306 (1724)
T ss_dssp             HHHHHHHHHHHTCCCEEEEEECSCTT-HHHHHH-HTTCCHHHHEEECCGGGC-SSCEEEECCEECCCCHHHH-HHHHHHH
T ss_pred             HHHHHHHHHhCCCCCcEEEEecccCC-HHHHHH-HhCCCCCCCeEEECCCCc-cCccEEEEeccCCcchhhh-hHHHHHH
Confidence            54       34678999999999974 444544 443 211  112222222 2234444333332221111 1111111


Q ss_pred             HHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-------------------------------------CCeEEEEcC
Q 010709          364 AFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-------------------------------------GLHAVALHG  406 (503)
Q Consensus       364 ~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-------------------------------------~~~v~~lh~  406 (503)
                      ...........+++||||++++.|+.+++.|.+.                                     ...+..+||
T Consensus       307 ~~~~v~~~~~~~~~LVF~~sR~~~~~~A~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Gva~HHa  386 (1724)
T 4f92_B          307 VYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHA  386 (1724)
T ss_dssp             HHHHHTTCCSSCCEEEECSSTTTTHHHHHHHHHHHHHTTSTTCCSSCCTTCSSHHHHTTSCCSTHHHHHHTTTTEEEECS
T ss_pred             HHHHHHHHhcCCcEEEECCCHHHHHHHHHHHHHHHhhccchhhhcccchhHHHHHHhhhcccccHHHHHHhhcCEEEEcC
Confidence            1122222234567999999999999998888541                                     134889999


Q ss_pred             CCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE----ccC------CCChhHHHHhhCcceee
Q 010709          407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN----LDL------PKVLLAASESLCTTSFN  468 (503)
Q Consensus       407 ~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~----~~~------p~s~~~~~Qr~GR~gR~  468 (503)
                      +|++.+|..+++.|++|.++|||||+.+++|||+|++++||.    |+.      |-+..+|.||+|||||.
T Consensus       387 gL~~~~R~~vE~~F~~G~i~vlvaTsTLa~GVNlPa~~vVI~~~~~~~~~~~~~~~ls~~~~~Qm~GRAGR~  458 (1724)
T 4f92_B          387 GMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRP  458 (1724)
T ss_dssp             SSCTHHHHHHHHHHHTTCCCEEEECHHHHHHSCCCBSEEEEECCEEEETTTTEEEECCHHHHHHHHTTBSCT
T ss_pred             CCCHHHHHHHHHHHHCCCCeEEEEcchhHhhCCCCCceEEEeCCEEecCcCCCcccCCHHHHHHhhhhccCC
Confidence            999999999999999999999999999999999999998885    443      45889999999999994

>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=100.00  E-value=9.5e-39  Score=330.94  Aligned_cols=308  Identities=17%  Similarity=0.196  Sum_probs=241.4

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..|+ +|+++|..+++.+++|+  |+.++||+|||++|.+|++...+.        ++.++||+||++||.|.++.+..+
T Consensus       107 ~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~--------g~~v~VvTpTreLA~Qdae~m~~l  175 (922)
T 1nkt_A          107 VLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA--------GNGVHIVTVNDYLAKRDSEWMGRV  175 (922)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT--------TSCEEEEESSHHHHHHHHHHHHHH
T ss_pred             HcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh--------CCCeEEEeCCHHHHHHHHHHHHHH
Confidence            4688 99999999999999998  999999999999999999865443        467999999999999999999999


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hC-----
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DM-----  284 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~-----  284 (503)
                      ...+ ++++++++||......  ....+++|+|+||++| .+++..+      ...++.+.++||||||+|+ +.     
T Consensus       176 ~~~l-GLsv~~i~gg~~~~~r--~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDeartPL  252 (922)
T 1nkt_A          176 HRFL-GLQVGVILATMTPDER--RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDEARTPL  252 (922)
T ss_dssp             HHHT-TCCEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTGGGSCE
T ss_pred             Hhhc-CCeEEEEeCCCCHHHH--HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhcCccce
Confidence            9877 6999999999875443  3344699999999999 6777654      3567889999999999998 42     


Q ss_pred             ----------CCHHHHHHHHHhCC---------CCCcEE-----------------EEEeeCCHH---HHHH--HHHhcC
Q 010709          285 ----------GFEPQIREVMQNLP---------DKHQTL-----------------LFSATMPVE---IEAL--AQEYLT  323 (503)
Q Consensus       285 ----------~~~~~~~~il~~~~---------~~~q~i-----------------~~SAT~~~~---~~~~--~~~~~~  323 (503)
                                +|...+..++..++         +..|++                 ++|||.+.-   +...  +..++.
T Consensus       253 iiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l~~~i~~aL~A~~l~~  332 (922)
T 1nkt_A          253 IISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPLVSYLNNALKAKELFS  332 (922)
T ss_dssp             EEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCHHHHHHHHHHHHHHCC
T ss_pred             eecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccccCCcchhHHHHHHHHHHHHHHhh
Confidence                      47788999999997         678888                 889998642   2221  122221


Q ss_pred             -C-------CeEEEeCCC--------------------------------------------------------------
Q 010709          324 -D-------PVQVKVGKV--------------------------------------------------------------  333 (503)
Q Consensus       324 -~-------~~~~~~~~~--------------------------------------------------------------  333 (503)
                       +       ...+.++..                                                              
T Consensus       333 ~d~dYiV~dg~vviVDe~TGR~m~grr~sdGLHQaieaKe~V~I~~e~~TlatIt~Qnyfr~Y~kL~GMTGTa~te~~Ef  412 (922)
T 1nkt_A          333 RDKDYIVRDGEVLIVDEFTGRVLIGRRYNEGMHQAIEAKEHVEIKAENQTLATITLQNYFRLYDKLAGMTGTAQTEAAEL  412 (922)
T ss_dssp             BTTTEEECSSCEEEBCSSSCCBCTTCCCSTTHHHHHHHHTTCCCCCCEEEEEEECHHHHHTTSSEEEEEESCCGGGHHHH
T ss_pred             cccceeeecCceEEEecccCcccCCccccchhhHHHhccccccccccccccceeehHHHHHhhhhhhccccCchhHHHHH
Confidence             1       111111100                                                              


Q ss_pred             -------------CCCCCce-EEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC
Q 010709          334 -------------SSPTANV-IQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL  399 (503)
Q Consensus       334 -------------~~~~~~~-~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~  399 (503)
                                   ..+.... ...+.......|...+...+.....       ...++||||++++.++.|++.|.+.|+
T Consensus       413 ~~iY~l~vv~IPtn~p~~R~d~~d~v~~t~~~K~~al~~~i~~~~~-------~gqpvLVft~Sie~sE~Ls~~L~~~Gi  485 (922)
T 1nkt_A          413 HEIYKLGVVSIPTNMPMIREDQSDLIYKTEEAKYIAVVDDVAERYA-------KGQPVLIGTTSVERSEYLSRQFTKRRI  485 (922)
T ss_dssp             HHHHCCEEEECCCSSCCCCEECCCEEESCHHHHHHHHHHHHHHHHH-------TTCCEEEEESCHHHHHHHHHHHHHTTC
T ss_pred             HHHhCCCeEEeCCCCCcccccCCcEEEeCHHHHHHHHHHHHHHHHh-------cCCcEEEEECCHHHHHHHHHHHHHCCC
Confidence                         0000000 0123455667788888877765432       223699999999999999999999999


Q ss_pred             eEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCC------------------------------------
Q 010709          400 HAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGV------------------------------------  443 (503)
Q Consensus       400 ~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v------------------------------------  443 (503)
                      .+..+||++.+.++..+.+.|+.|  .|+|||++++||+||+.+                                    
T Consensus       486 ~~~vLnak~~~rEa~iia~agr~G--~VtIATnmAgRGtDI~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  563 (922)
T 1nkt_A          486 PHNVLNAKYHEQEATIIAVAGRRG--GVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIV  563 (922)
T ss_dssp             CCEEECSSCHHHHHHHHHTTTSTT--CEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHH
T ss_pred             CEEEecCChhHHHHHHHHhcCCCC--eEEEecchhhcCccccCCCCHHHHHHHHHhhccccccccchhhHHHHHHHHHHH
Confidence            999999999888888888888877  799999999999999975                                    


Q ss_pred             ----------------CEEEEccCCCChhHHHHhhCcceee
Q 010709          444 ----------------AHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       444 ----------------~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                                      .+||++++|.+...|.||+||+||.
T Consensus       564 ~~~~~~~~~~V~~~GGlhVI~te~pes~riy~qr~GRTGRq  604 (922)
T 1nkt_A          564 KEEASKEAKEVIEAGGLYVLGTERHESRRIDNQLRGRSGRQ  604 (922)
T ss_dssp             HHHTTHHHHHHHHTTSEEEEECSCCSSHHHHHHHHHTSSGG
T ss_pred             HHHHHHhhhHHHhcCCcEEEeccCCCCHHHHHHHhcccccC
Confidence                            4999999999999999999999994

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=100.00  E-value=8.6e-41  Score=345.50  Aligned_cols=302  Identities=15%  Similarity=0.132  Sum_probs=225.4

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|+++|.++++.++.++++++++|||+|||++|+.+++..+...       ++++|||+|+++|+.|+.+.+++++.. 
T Consensus       112 ~~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~-------~~~vlvl~P~~~L~~Q~~~~~~~~~~~-  183 (510)
T 2oca_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-------EGKILIIVPTTALTTQMADDFVDYRLF-  183 (510)
T ss_dssp             ECCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC-------SSEEEEEESSHHHHHHHHHHHHHTTSS-
T ss_pred             CCCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC-------CCeEEEEECcHHHHHHHHHHHHHhhcC-
Confidence            489999999999999999999999999999999988887765432       358999999999999999999988543 


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                      .+..+..+.++....++   .....+|+|+||+.|...   ....+.++++|||||||++..    ..+..++..+++..
T Consensus       184 ~~~~v~~~~~~~~~~~~---~~~~~~I~i~T~~~l~~~---~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~~~  253 (510)
T 2oca_A          184 SHAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLATG----KSISSIISGLNNCM  253 (510)
T ss_dssp             CGGGEEECGGGCCTTGG---GCTTCSEEEEEHHHHTTS---CGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTTCC
T ss_pred             CccceEEEecCCccccc---cccCCcEEEEeHHHHhhc---hhhhhhcCCEEEEECCcCCCc----ccHHHHHHhcccCc
Confidence            24677888887665443   456789999999987542   234577899999999998764    56788888888888


Q ss_pred             cEEEEEeeCCHHHHHHHH-HhcCCCeEEEeCCC------CCCCCceEEEEEEcChh---------------------hHH
Q 010709          302 QTLLFSATMPVEIEALAQ-EYLTDPVQVKVGKV------SSPTANVIQILEKVSEN---------------------EKV  353 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~~~-~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~---------------------~k~  353 (503)
                      ++++||||+++....... ..+..+........      ......+.......+..                     .+.
T Consensus       254 ~~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  333 (510)
T 2oca_A          254 FKFGLSGSLRDGKANIMQYVGMFGEIFKPVTTSKLMEDGQVTELKINSIFLRYPDEFTTKLKGKTYQEEIKIITGLSKRN  333 (510)
T ss_dssp             EEEEEESCGGGCSSCHHHHHHHHCSEECCCCCC---------CCEEEEEEEECCHHHHHHHTTCCHHHHHHHHHTCHHHH
T ss_pred             EEEEEEeCCCCCcccHHHhHHhhCCeEEeeCHHHHhhCCcCCCceEEEEeecCChHHhccccccchHHHHHHHhccHHHH
Confidence            999999999765432211 11112222211111      11111122222222211                     111


Q ss_pred             HHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-c
Q 010709          354 DRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-D  432 (503)
Q Consensus       354 ~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-~  432 (503)
                      ..+...+.....      ....++||||+ .+.++.+++.|.+.+..+..+||++++.+|.++++.|++|+.+||||| +
T Consensus       334 ~~l~~~l~~~~~------~~~~~~ivf~~-~~~~~~l~~~L~~~~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~  406 (510)
T 2oca_A          334 KWIAKLAIKLAQ------KDENAFVMFKH-VSHGKAIFDLIKNEYDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYG  406 (510)
T ss_dssp             HHHHHHHHHHHT------TTCEEEEEESS-HHHHHHHHHHHHTTCSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHH
T ss_pred             HHHHHHHHHHHh------cCCCeEEEEec-HHHHHHHHHHHHHcCCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcC
Confidence            122222222111      12334666666 889999999999998899999999999999999999999999999999 9


Q ss_pred             ccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          433 VASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       433 ~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++++|+|+|++++||++++|.+...|.||+||+||.
T Consensus       407 ~~~~GiDip~v~~vi~~~~~~s~~~~~Q~~GR~gR~  442 (510)
T 2oca_A          407 VFSTGISVKNLHHVVLAHGVKSKIIVLQTIGRVLRK  442 (510)
T ss_dssp             HHHHSCCCCSEEEEEESSCCCSCCHHHHHHHHHHTT
T ss_pred             hhhcccccccCcEEEEeCCCCCHHHHHHHHhccccc
Confidence            999999999999999999999999999999999994

>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=100.00  E-value=1.7e-40  Score=336.07  Aligned_cols=275  Identities=14%  Similarity=0.171  Sum_probs=203.9

Q ss_pred             CCCCCcHHHHHHHHHHhcCCCe-EEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          140 EYTRPTSIQAQAMPVALSGRDL-LGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       140 ~~~~~~~~Q~~~i~~i~~~~~v-ii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      |+.+|+|+|. +++.+++++++ ++++|||||||++|++|++......       ++++||++||++|+.|+++.+..  
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~-------~~~~lvl~Ptr~La~Q~~~~l~g--   70 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLR-------RLRTLILAPTRVVAAEMEEALRG--   70 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTT--
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHhc-------CCcEEEECCCHHHHHHHHHHhcC--
Confidence            6778999985 79999999886 9999999999999999999876653       57899999999999999988742  


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH-hC
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ-NL  297 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~-~~  297 (503)
                           ..+.........     ....+..|.++|++.+.+.+.+. ..+.++++|||||||++ +..+...+..+.. ..
T Consensus        71 -----~~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~~~  138 (451)
T 2jlq_A           71 -----LPIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPCSVAARGYISTRVE  138 (451)
T ss_dssp             -----SCEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC-SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHHHH
T ss_pred             -----ceeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc-ccccCCCEEEEeCCccC-CcchHHHHHHHHHhhc
Confidence                 222211111100     12345679999999998888763 56889999999999976 3322222222222 23


Q ss_pred             CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcE
Q 010709          298 PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLT  377 (503)
Q Consensus       298 ~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~  377 (503)
                      +++.|+++||||++.....   .+..++..+..... .+....             ..+...+.+          ..+++
T Consensus       139 ~~~~~~i~~SAT~~~~~~~---~~~~~~~~~~~~~~-~p~~~~-------------~~~~~~l~~----------~~~~~  191 (451)
T 2jlq_A          139 MGEAAAIFMTATPPGSTDP---FPQSNSPIEDIERE-IPERSW-------------NTGFDWITD----------YQGKT  191 (451)
T ss_dssp             TTSCEEEEECSSCTTCCCS---SCCCSSCEEEEECC-CCSSCC-------------SSSCHHHHH----------CCSCE
T ss_pred             CCCceEEEEccCCCccchh---hhcCCCceEecCcc-CCchhh-------------HHHHHHHHh----------CCCCE
Confidence            4578999999999875332   22233333332211 000000             001111211          23479


Q ss_pred             EEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEcc-------
Q 010709          378 IVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLD-------  450 (503)
Q Consensus       378 lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~-------  450 (503)
                      ||||++++.|+.+++.|.+.++.+..+|+++.    .++++.|++|+.+|||||+++++|+|+|+ ++||++|       
T Consensus       192 lVF~~s~~~a~~l~~~L~~~g~~~~~lh~~~~----~~~~~~f~~g~~~vLVaT~v~~~GiDip~-~~VI~~~~~~~~~~  266 (451)
T 2jlq_A          192 VWFVPSIKAGNDIANCLRKSGKRVIQLSRKTF----DTEYPKTKLTDWDFVVTTDISEMGANFRA-GRVIDPRRCLKPVI  266 (451)
T ss_dssp             EEECSSHHHHHHHHHHHHTTTCCEEEECTTTH----HHHGGGGGSSCCSEEEECGGGGSSCCCCC-SEEEECCEEEEEEE
T ss_pred             EEEcCCHHHHHHHHHHHHHcCCeEEECCHHHH----HHHHHhhccCCceEEEECCHHHhCcCCCC-CEEEECCCcccccc
Confidence            99999999999999999999999999999764    57899999999999999999999999999 9999999       


Q ss_pred             -------------CCCChhHHHHhhCcceee
Q 010709          451 -------------LPKVLLAASESLCTTSFN  468 (503)
Q Consensus       451 -------------~p~s~~~~~Qr~GR~gR~  468 (503)
                                   .|.+..+|+||+||+||.
T Consensus       267 d~~~~~~l~~~~~~p~s~~~y~Qr~GRaGR~  297 (451)
T 2jlq_A          267 LTDGPERVILAGPIPVTPASAAQRRGRIGRN  297 (451)
T ss_dssp             ECSSSCEEEEEEEEECCHHHHHHHHTTSSCC
T ss_pred             cccccceeeecccccCCHHHHHHhccccCCC
Confidence                         999999999999999995

>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=100.00  E-value=3.6e-41  Score=350.90  Aligned_cols=289  Identities=15%  Similarity=0.166  Sum_probs=213.3

Q ss_pred             CCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          126 MCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       126 ~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      +++++.+++.+... ...++|+|+.+++.+++|+++++++|||||||++|++|++..+...       ++++||++|||+
T Consensus       155 l~~~~~~~~~l~~~-~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~~-------~~~vLvl~Ptre  226 (618)
T 2whx_A          155 VTKSGDYVSAITQA-ERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALKR-------RLRTLILAPTRV  226 (618)
T ss_dssp             -------CEECBCC-CCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHH
T ss_pred             ccchHHHHHHHhhc-cccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHhC-------CCeEEEEcChHH
Confidence            34555555444432 4778889888899999999999999999999999999999887663       578999999999


Q ss_pred             HHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          206 LAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       206 La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      ||.|+++.++.       ..+. +.+... .   .....+..+.++|.+.+.+.+... ..+.++++|||||||++ +.+
T Consensus       227 La~Qi~~~l~~-------~~v~-~~~~~l-~---~~~tp~~~i~~~t~~~l~~~l~~~-~~l~~~~~iViDEah~~-~~~  292 (618)
T 2whx_A          227 VAAEMEEALRG-------LPIR-YQTPAV-K---SDHTGREIVDLMCHATFTTRLLSS-TRVPNYNLIVMDEAHFT-DPC  292 (618)
T ss_dssp             HHHHHHHHTTT-------SCEE-ECCTTS-S---CCCCSSSCEEEEEHHHHHHHHHHC-SSCCCCSEEEEESTTCC-SHH
T ss_pred             HHHHHHHHhcC-------Ccee-Eecccc-e---eccCCCceEEEEChHHHHHHHhcc-ccccCCeEEEEECCCCC-Ccc
Confidence            99999987762       2222 111110 0   011234567888999888777653 56889999999999987 556


Q ss_pred             CHHHHHHHHHhCC-CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHH
Q 010709          286 FEPQIREVMQNLP-DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEA  364 (503)
Q Consensus       286 ~~~~~~~il~~~~-~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~  364 (503)
                      |...+..++..++ ++.|+++||||++..+..+..   .++..+.+....             +. .+...++..+.+  
T Consensus       293 ~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~~~-------------~~-~~~~~ll~~l~~--  353 (618)
T 2whx_A          293 SVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIEREI-------------PE-RSWNTGFDWITD--  353 (618)
T ss_dssp             HHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEECCC-------------CS-SCCSSSCHHHHH--
T ss_pred             HHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecccC-------------CH-HHHHHHHHHHHh--
Confidence            7777777777664 678999999999876443222   233333322110             00 011112222221  


Q ss_pred             HhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCC
Q 010709          365 FLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVA  444 (503)
Q Consensus       365 ~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~  444 (503)
                              ..+++||||++++.|+.+++.|.+.++.+..+||+    +|.++++.|++|+.+|||||+++++|||+| ++
T Consensus       354 --------~~~~~LVF~~s~~~a~~l~~~L~~~g~~v~~lhg~----~R~~~l~~F~~g~~~VLVaTdv~~rGiDi~-v~  420 (618)
T 2whx_A          354 --------YQGKTVWFVPSIKAGNDIANCLRKSGKRVIQLSRK----TFDTEYPKTKLTDWDFVVTTDISEMGANFR-AG  420 (618)
T ss_dssp             --------CCSCEEEECSSHHHHHHHHHHHHHTTCCEEEECTT----THHHHTTHHHHSCCSEEEECGGGGTTCCCC-CS
T ss_pred             --------CCCCEEEEECChhHHHHHHHHHHHcCCcEEEEChH----HHHHHHHhhcCCCcEEEEECcHHHcCcccC-ce
Confidence                    13479999999999999999999999999999984    688899999999999999999999999998 99


Q ss_pred             EE--------------------EEccCCCChhHHHHhhCcceee
Q 010709          445 HV--------------------VNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       445 ~V--------------------I~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|                    |+++.|.+.++|+||+||+||.
T Consensus       421 ~VId~g~~~~P~~~~~~~~~~~i~~d~P~s~~~yiQR~GRaGR~  464 (618)
T 2whx_A          421 RVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGRN  464 (618)
T ss_dssp             EEEECCEEEEEEEECSSSCEEEEEEEEECCHHHHHHHHTTSSCC
T ss_pred             EEEECcceecceecccCCCceEEcccccCCHHHHHHhccccCCC
Confidence            98                    6777799999999999999996

>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=100.00  E-value=8.1e-40  Score=337.26  Aligned_cols=263  Identities=21%  Similarity=0.236  Sum_probs=199.1

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .++.+|.++++.+..+++++++||||+|||++|.+|++..           +.++||++|||+||.|+++.+.+..    
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            3445566666666678899999999999999998887752           4579999999999999999887765    


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCc
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ  302 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q  302 (503)
                      +..+...+|+..       ...+++|+|+||++|+   ....+.+.++++||||||| +++.+|...+..++..++...+
T Consensus       282 g~~vg~~vG~~~-------~~~~~~IlV~TPGrLl---~~~~l~l~~l~~lVlDEAH-~l~~~~~~~l~~Il~~l~~~~~  350 (666)
T 3o8b_A          282 GIDPNIRTGVRT-------ITTGAPVTYSTYGKFL---ADGGCSGGAYDIIICDECH-STDSTTILGIGTVLDQAETAGA  350 (666)
T ss_dssp             SCCCEEECSSCE-------ECCCCSEEEEEHHHHH---HTTSCCTTSCSEEEETTTT-CCSHHHHHHHHHHHHHTTTTTC
T ss_pred             CCCeeEEECcEe-------ccCCCCEEEECcHHHH---hCCCcccCcccEEEEccch-hcCccHHHHHHHHHHhhhhcCC
Confidence            344566677653       3567999999999984   5556778899999999997 4566788888889998887666


Q ss_pred             --EEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEE
Q 010709          303 --TLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVF  380 (503)
Q Consensus       303 --~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF  380 (503)
                        +++||||++..+.      ...+....+.....  ..+ ..   .......                .....+++|||
T Consensus       351 ~llil~SAT~~~~i~------~~~p~i~~v~~~~~--~~i-~~---~~~~~~l----------------~~~~~~~vLVF  402 (666)
T 3o8b_A          351 RLVVLATATPPGSVT------VPHPNIEEVALSNT--GEI-PF---YGKAIPI----------------EAIRGGRHLIF  402 (666)
T ss_dssp             SEEEEEESSCTTCCC------CCCTTEEEEECBSC--SSE-EE---TTEEECG----------------GGSSSSEEEEE
T ss_pred             ceEEEECCCCCcccc------cCCcceEEEeeccc--chh-HH---HHhhhhh----------------hhccCCcEEEE
Confidence              7888999987321      11111111110000  000 00   0000000                01245679999


Q ss_pred             EcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEE----------Ecc
Q 010709          381 VERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVV----------NLD  450 (503)
Q Consensus       381 ~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI----------~~~  450 (503)
                      |++++.++.+++.|++.++.+..+||++++++       |.++..+|||||+++++|||+| +++||          |||
T Consensus       403 v~Tr~~ae~la~~L~~~g~~v~~lHG~l~q~e-------r~~~~~~VLVATdVaerGIDId-V~~VI~~Gl~~~~ViNyD  474 (666)
T 3o8b_A          403 CHSKKKCDELAAKLSGLGINAVAYYRGLDVSV-------IPTIGDVVVVATDALMTGYTGD-FDSVIDCNTCVTQTVDFS  474 (666)
T ss_dssp             CSCHHHHHHHHHHHHTTTCCEEEECTTSCGGG-------SCSSSCEEEEECTTHHHHCCCC-BSEEEECCEEEEEEEECC
T ss_pred             eCCHHHHHHHHHHHHhCCCcEEEecCCCCHHH-------HHhCCCcEEEECChHHccCCCC-CcEEEecCcccccccccc
Confidence            99999999999999999999999999999875       4567779999999999999997 99999          667


Q ss_pred             -----------CCCChhHHHHhhCccee
Q 010709          451 -----------LPKVLLAASESLCTTSF  467 (503)
Q Consensus       451 -----------~p~s~~~~~Qr~GR~gR  467 (503)
                                 .|.+.++|+||+||+||
T Consensus       475 ydP~~gl~~~~~P~s~~syiQRiGRtGR  502 (666)
T 3o8b_A          475 LDPTFTIETTTVPQDAVSRSQRRGRTGR  502 (666)
T ss_dssp             CSSSCEEEEEEEECBHHHHHHHHTTBCS
T ss_pred             cccccccccccCcCCHHHHHHHhccCCC
Confidence                       89999999999999999

>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=100.00  E-value=1.2e-38  Score=326.21  Aligned_cols=281  Identities=19%  Similarity=0.177  Sum_probs=209.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|+++|.++++.+++++++++++|||+|||++|+.++...           ++++||++|+++|+.||.++++++    
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            47999999999999999999999999999999998877654           467999999999999999999884    


Q ss_pred             CCce-EEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCC
Q 010709          222 DSFK-TAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK  300 (503)
Q Consensus       222 ~~~~-~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~  300 (503)
                       ++. +..+.|+..         ...+|+|+|++.+...+..   ...++++|||||||++.+..+..    ++..++ .
T Consensus       157 -~~~~v~~~~g~~~---------~~~~Ivv~T~~~l~~~~~~---~~~~~~liIvDEaH~~~~~~~~~----~~~~~~-~  218 (472)
T 2fwr_A          157 -GEEYVGEFSGRIK---------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAESYVQ----IAQMSI-A  218 (472)
T ss_dssp             -CGGGEEEBSSSCB---------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEETGGGTTSTTTHH----HHHTCC-C
T ss_pred             -CCcceEEECCCcC---------CcCCEEEEEcHHHHHHHHH---hcCCCCEEEEECCcCCCChHHHH----HHHhcC-C
Confidence             366 777777653         3479999999999876642   12468999999999998776653    555554 5


Q ss_pred             CcEEEEEeeCCHH-------------------HHHHHHHhcCCCeEE--EeCCCCC------------------------
Q 010709          301 HQTLLFSATMPVE-------------------IEALAQEYLTDPVQV--KVGKVSS------------------------  335 (503)
Q Consensus       301 ~q~i~~SAT~~~~-------------------~~~~~~~~~~~~~~~--~~~~~~~------------------------  335 (503)
                      .+++++|||+...                   ...+...++..+...  .+.....                        
T Consensus       219 ~~~l~lSATp~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  298 (472)
T 2fwr_A          219 PFRLGLTATFEREDGRHEILKEVVGGKVFELFPDSLAGKHLAKYTIKRIFVPLAEDERVEYEKREKVYKQFLRARGITLR  298 (472)
T ss_dssp             SEEEEEESCCCCTTSGGGSHHHHTCCEEEECCHHHHTSCCCCSEEECCEEECCCHHHHHHTTTTTHHHHSCSSSCCCTTT
T ss_pred             CeEEEEecCccCCCCHHHHHHHHhCCeEeecCHHHHhcCcCCCeEEEEEEcCCCHHHHHHHHHHHHHHHHHHHhcCcccc
Confidence            6799999999631                   222222222222111  0000000                        


Q ss_pred             CCCceEEEE---------------------EEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHH
Q 010709          336 PTANVIQIL---------------------EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL  394 (503)
Q Consensus       336 ~~~~~~~~~---------------------~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L  394 (503)
                      ....+...+                     ..+....|...+..++..         ....++||||++++.++.+++.|
T Consensus       299 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~---------~~~~k~lvF~~~~~~~~~l~~~l  369 (472)
T 2fwr_A          299 RAEDFNKIVMASGYDERAYEALRAWEEARRIAFNSKNKIRKLREILER---------HRKDKIIIFTRHNELVYRISKVF  369 (472)
T ss_dssp             CCSSSTTTTTTTCCSSSSSTTTHHHHHHHHHHHSCSHHHHHHHHHHHH---------TSSSCBCCBCSCHHHHHHHHHHT
T ss_pred             chhhHHHHHHHhccCHHHHHHHHHHHHHHHHhhcChHHHHHHHHHHHh---------CCCCcEEEEECCHHHHHHHHHHh
Confidence            000000000                     001122344444444433         24567999999999999999987


Q ss_pred             HHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          395 VAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       395 ~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      .     +..+||++++.+|.++++.|++|+.+|||||+++++|+|+|++++||++++|++...|.||+||+||.-
T Consensus       370 ~-----~~~~~g~~~~~~R~~~~~~F~~g~~~vLv~T~~~~~Gldlp~~~~Vi~~~~~~s~~~~~Q~~GR~~R~g  439 (472)
T 2fwr_A          370 L-----IPAITHRTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS  439 (472)
T ss_dssp             T-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBCSSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCC
T ss_pred             C-----cceeeCCCCHHHHHHHHHHHhCCCCCEEEEcCchhcCcccccCcEEEEECCCCCHHHHHHHHhhccCCC
Confidence            4     557899999999999999999999999999999999999999999999999999999999999999964

>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=7.6e-37  Score=281.72  Aligned_cols=215  Identities=39%  Similarity=0.603  Sum_probs=186.7

Q ss_pred             CCCCCCCcCCccc-CCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCC-CC
Q 010709          113 SVPAPAPIESFTD-MCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP-VG  190 (503)
Q Consensus       113 ~~~~~~~~~~~~~-~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~-~~  190 (503)
                      ....|.+..+|++ +++++.+.+.+...||..|+++|.++++.+++|+++++++|||+|||++|++|++..+..... ..
T Consensus        11 ~~~~p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~   90 (228)
T 3iuy_A           11 KRLIPKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISRE   90 (228)
T ss_dssp             CCCCCCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC-------
T ss_pred             cCcCCCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhh
Confidence            3477889999999 799999999999999999999999999999999999999999999999999999987654321 11


Q ss_pred             CCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCc
Q 010709          191 RGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRV  270 (503)
Q Consensus       191 ~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~  270 (503)
                      ...++++||++|+++|+.|+++.++++..  .++.+..++|+.........+..+++|+|+||+++.+.+.+....+.++
T Consensus        91 ~~~~~~~lil~Pt~~L~~q~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           91 QRNGPGMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             --CCCSEEEECSSHHHHHHHHHHHHHHCC--TTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             ccCCCcEEEEeCCHHHHHHHHHHHHHhcc--cCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            23578899999999999999999999863  3578889999988887777788889999999999999998888889999


Q ss_pred             cEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEE
Q 010709          271 SFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVK  329 (503)
Q Consensus       271 ~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~  329 (503)
                      ++||+||||++.+++|...+..++..++++.|+++||||+++.+..++..++.+|..+.
T Consensus       169 ~~lViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~  227 (228)
T 3iuy_A          169 TYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVY  227 (228)
T ss_dssp             CEEEECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEE
T ss_pred             eEEEEECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            99999999999999999999999999999999999999999999999999999998775

>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=1.4e-36  Score=284.43  Aligned_cols=224  Identities=45%  Similarity=0.743  Sum_probs=190.8

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCC----CCCC
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPV----GRGD  193 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~----~~~~  193 (503)
                      .++.+|+++++++.+.+.|...|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+......    ....
T Consensus        20 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~   99 (253)
T 1wrb_A           20 NVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTA   99 (253)
T ss_dssp             SCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCB
T ss_pred             CccCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccC
Confidence            378889999999999999999999999999999999999999999999999999999999999887654311    1234


Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEE
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFV  273 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~v  273 (503)
                      ++++||++|+++|+.|+++.+++++... ++.+..++|+.........+..+++|+|+||++|.+.+.+....+.++++|
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~l  178 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYI  178 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCTTCCEE
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHcCCCChhhCCEE
Confidence            5789999999999999999999998654 578888999998888777788889999999999999999887888999999


Q ss_pred             EecchhHHhhCCCHHHHHHHHHhC--CC--CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEE
Q 010709          274 ILDEADRMLDMGFEPQIREVMQNL--PD--KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQ  342 (503)
Q Consensus       274 ViDEaH~l~~~~~~~~~~~il~~~--~~--~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  342 (503)
                      |+||||++.+++|...+..++..+  +.  +.|+++||||+++++..+++.++.+|..+.++.......++.|
T Consensus       179 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i~q  251 (253)
T 1wrb_A          179 VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVGSTSDSIKQ  251 (253)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC-----------
T ss_pred             EEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCCCCcCCcee
Confidence            999999999999999999999853  43  6799999999999999999999999999988766554444444

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=100.00  E-value=5.7e-37  Score=322.09  Aligned_cols=308  Identities=18%  Similarity=0.165  Sum_probs=191.9

Q ss_pred             CCCcHHHHHHHHHHhc----C-CCeEEEccCCCchhHHhHHHHHHHHHhcC--CCCCCCCCeEEEEcccHHHHHHHH-HH
Q 010709          142 TRPTSIQAQAMPVALS----G-RDLLGCAETGSGKTAAFTIPMIQHCVAQT--PVGRGDGPLALVLAPTRELAQQIE-KE  213 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~----~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~--~~~~~~~~~~lil~Ptr~La~q~~-~~  213 (503)
                      ..|+++|.++++.+++    + ++++++++||+|||+++ ++++..+....  ......++++|||+|+++|+.|+. +.
T Consensus       177 ~~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~-~~~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~  255 (590)
T 3h1t_A          177 YSPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVA-FQISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKT  255 (590)
T ss_dssp             --CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHHHTTCCSSCSSSCCCEEEEEC-----------C
T ss_pred             CCchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHH-HHHHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHH
Confidence            3799999999999875    4 55999999999999996 44555544432  111124688999999999999999 77


Q ss_pred             HHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc----CCCCCCCccEEEecchhHHhhCCCHHH
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ----GNTSLSRVSFVILDEADRMLDMGFEPQ  289 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~----~~~~l~~~~~vViDEaH~l~~~~~~~~  289 (503)
                      ++.++.     .+..+.++        ....+.+|+|+|+++|......    ..+....+++|||||||++...+ ...
T Consensus       256 ~~~~~~-----~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~  321 (590)
T 3h1t_A          256 FTPFGD-----ARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSN  321 (590)
T ss_dssp             CTTTCS-----SEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------
T ss_pred             HHhcch-----hhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHH
Confidence            776542     22333222        1345689999999999877642    23456779999999999987542 355


Q ss_pred             HHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEE-----------------eCCCCCCCC--------------
Q 010709          290 IREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVK-----------------VGKVSSPTA--------------  338 (503)
Q Consensus       290 ~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~--------------  338 (503)
                      +..++..++. .++++||||+..........+++.+....                 .........              
T Consensus       322 ~~~il~~~~~-~~~l~lTATP~~~~~~~~~~~f~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  400 (590)
T 3h1t_A          322 WREILEYFEP-AFQIGMTATPLREDNRDTYRYFGNPIYTYSLRQGIDDGFLAPYRVHRVISEVDAAGWRPSKGDVDRFGR  400 (590)
T ss_dssp             CHHHHHHSTT-SEEEEEESSCSCTTTHHHHHHSCSCSEEECHHHHHHHTSSCCEEEEEEEETTCC---------------
T ss_pred             HHHHHHhCCc-ceEEEeccccccccchhHHHHcCCceEecCHHHHhhCCccCCcEEEEeeeeeecccccccccccccccc
Confidence            6778888764 57999999997544333344444332211                 000000000              


Q ss_pred             ceEEEEEEcCh-------hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCC--------eEEE
Q 010709          339 NVIQILEKVSE-------NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGL--------HAVA  403 (503)
Q Consensus       339 ~~~~~~~~~~~-------~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~--------~v~~  403 (503)
                      .+.........       ..+...+...+......    ..+.+++||||+++..|+.+++.|.+.+.        .+..
T Consensus       401 ~~~~~~~~~~~~~~~~~~~~r~~~i~~~l~~~l~~----~~~~~k~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~  476 (590)
T 3h1t_A          401 EIPDGEYQTKDFERVIALKARTDAFAKHLTDFMKR----TDRFAKTIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVAR  476 (590)
T ss_dssp             --------CCSHHHHHHHHHTHHHHHHHHHHHHHH----HCTTSEEEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEE
T ss_pred             ccccccCCHHHhhhHhcChHHHHHHHHHHHHHHHh----cCCCccEEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEE
Confidence            00000000000       11222222223222111    14557899999999999999999987643        2778


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCc---EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeeee
Q 010709          404 LHGGRNQSDRESALRDFRNGSTN---ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNIT  470 (503)
Q Consensus       404 lh~~~~~~~r~~~~~~f~~g~~~---vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~  470 (503)
                      +||.+++ +|.++++.|++|+.+   |||||+++++|+|+|++++||++++|++...|+||+||+||..-
T Consensus       477 i~g~~~~-~r~~~l~~F~~~~~~~~~ilvtt~~l~~GiDip~v~~Vi~~~~~~s~~~~~Q~iGR~~R~~~  545 (590)
T 3h1t_A          477 VTSEEGK-IGKGHLSRFQELETSTPVILTTSQLLTTGVDAPTCKNVVLARVVNSMSEFKQIVGRGTRLRE  545 (590)
T ss_dssp             CSSTTHH-HHHHHHHHHHCTTCCCCCEEEESSTTTTTCCCTTEEEEEEESCCCCHHHHHHHHTTSCCCBG
T ss_pred             EeCCChH-HHHHHHHHHhCCCCCCCEEEEECChhhcCccchheeEEEEEecCCChHHHHHHHhhhcccCc
Confidence            8998764 799999999998866   89999999999999999999999999999999999999999653

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=100.00  E-value=1.9e-38  Score=332.37  Aligned_cols=280  Identities=16%  Similarity=0.228  Sum_probs=197.2

Q ss_pred             HHHCCCC-----CCcHHHH-----HHHHHHh------cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          136 IEFHEYT-----RPTSIQA-----QAMPVAL------SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       136 l~~~~~~-----~~~~~Q~-----~~i~~i~------~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      +...||.     .|+++|.     ++++.++      .++++++++|||+|||++|++|++..+...       ++++||
T Consensus       203 l~~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~~-------~~~~li  275 (673)
T 2wv9_A          203 LYGNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQK-------RLRTAV  275 (673)
T ss_dssp             EEEEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHHT-------TCCEEE
T ss_pred             eeeccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHhC-------CCcEEE
Confidence            3445555     8999999     9999888      899999999999999999999999876653       578999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++||++||.|+++.++.+.     +.  .. .+. ..   .....+.-+-+++.+.+.+.+.. ...+.++++|||||||
T Consensus       276 laPTr~La~Q~~~~l~~~~-----i~--~~-~~~-l~---~v~tp~~ll~~l~~~~l~~~l~~-~~~l~~l~lvViDEaH  342 (673)
T 2wv9_A          276 LAPTRVVAAEMAEALRGLP-----VR--YL-TPA-VQ---REHSGNEIVDVMCHATLTHRLMS-PLRVPNYNLFVMDEAH  342 (673)
T ss_dssp             EESSHHHHHHHHHHTTTSC-----CE--EC-CC-------CCCCSCCCEEEEEHHHHHHHHHS-SSCCCCCSEEEEESTT
T ss_pred             EccHHHHHHHHHHHHhcCC-----ee--ee-ccc-cc---ccCCHHHHHHHHHhhhhHHHHhc-ccccccceEEEEeCCc
Confidence            9999999999998887542     21  10 110 00   00112233455566666555554 3568899999999999


Q ss_pred             HHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLA  358 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~  358 (503)
                      ++ +..+...+..+...+ ++..|+++||||++..+..+...  ..|......              ..+.. +...++.
T Consensus       343 ~~-~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~~--~~~i~~v~~--------------~~~~~-~~~~~l~  404 (673)
T 2wv9_A          343 FT-DPASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPDT--NSPVHDVSS--------------EIPDR-AWSSGFE  404 (673)
T ss_dssp             CC-CHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCCC--SSCEEEEEC--------------CCCSS-CCSSCCH
T ss_pred             cc-CccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhccc--CCceEEEee--------------ecCHH-HHHHHHH
Confidence            87 111122222232222 26789999999998654322111  111111110              01111 1111112


Q ss_pred             HHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCC
Q 010709          359 LLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGL  438 (503)
Q Consensus       359 ~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gl  438 (503)
                      .+.+          ..+++||||++++.++.+++.|+..++.+..+||+    +|.++++.|++|+.+|||||+++++||
T Consensus       405 ~l~~----------~~~~~lVF~~s~~~~e~la~~L~~~g~~v~~lHg~----eR~~v~~~F~~g~~~VLVaTdv~e~GI  470 (673)
T 2wv9_A          405 WITD----------YAGKTVWFVASVKMSNEIAQCLQRAGKRVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGA  470 (673)
T ss_dssp             HHHS----------CCSCEEEECSSHHHHHHHHHHHHTTTCCEEEECSS----SHHHHGGGGGTCCCSEEEECGGGGTTC
T ss_pred             HHHh----------CCCCEEEEECCHHHHHHHHHHHHhCCCeEEEeChH----HHHHHHHHHHCCCceEEEECchhhcce
Confidence            2211          24579999999999999999999999999999994    789999999999999999999999999


Q ss_pred             CCCCCCEEEE--------------------ccCCCChhHHHHhhCcceee
Q 010709          439 DVMGVAHVVN--------------------LDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       439 dip~v~~VI~--------------------~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+| +++||+                    |++|.+.++|+||+||+||.
T Consensus       471 Dip-v~~VI~~g~~~~p~vi~da~~r~~ll~d~P~s~~~y~Qr~GRaGR~  519 (673)
T 2wv9_A          471 NFG-ASRVIDCRKSVKPTILDEGEGRVILSVPSAITSASAAQRRGRVGRN  519 (673)
T ss_dssp             CCC-CSEEEECCEECCEEEECSTTCEEEECCSEECCHHHHHHHHTTSSCC
T ss_pred             eeC-CcEEEECCCcccceeeecccccceecccCCCCHHHHHHHhhccCCC
Confidence            999 999998                    56899999999999999996

>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=8.7e-36  Score=270.25  Aligned_cols=203  Identities=34%  Similarity=0.640  Sum_probs=186.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .+|+++++++.+++.+..+|+..|+++|.++++.+++++++++++|||+|||++|++|++..+...     ..++++||+
T Consensus         3 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~-----~~~~~~lil   77 (206)
T 1vec_A            3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVI   77 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc-----CCCeeEEEE
Confidence            469999999999999999999999999999999999999999999999999999999999875432     235789999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++|+.|+++.++++.....+..+..++|+....+....+..+++|+|+||+++.+.+.+....+.++++||+||||+
T Consensus        78 ~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDEah~  157 (206)
T 1vec_A           78 VPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADK  157 (206)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHH
T ss_pred             eCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHcCCcCcccCCEEEEEChHH
Confidence            99999999999999999877656889999999988887777778899999999999999988777889999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEE
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQV  328 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~  328 (503)
                      +.+.+|...+..++..++++.|+++||||+++.+..+++.++.+|..+
T Consensus       158 ~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          158 LLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hHhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            999999999999999999899999999999999999999999999765

>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=100.00  E-value=1.3e-39  Score=328.05  Aligned_cols=253  Identities=17%  Similarity=0.206  Sum_probs=173.1

Q ss_pred             HHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCc
Q 010709          154 VALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT  233 (503)
Q Consensus       154 ~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~  233 (503)
                      ++++|+++++++|||||||++|++|++..+...       +++++|++||++||.|+++.++.+.       +....+..
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~~-------~~~~lil~Ptr~La~Q~~~~l~~~~-------v~~~~~~~   69 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR-------RLRTLVLAPTRVVLSEMKEAFHGLD-------VKFHTQAF   69 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTTSC-------EEEESSCC
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHhc-------CCeEEEEcchHHHHHHHHHHHhcCC-------eEEecccc
Confidence            356889999999999999999999999876653       5789999999999999998887432       22111110


Q ss_pred             cHHHHHHHhhCCCcEEEECcHHHH---------HHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcE
Q 010709          234 NIAEQRSELRGGVSIVVATPGRFL---------DHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQT  303 (503)
Q Consensus       234 ~~~~~~~~~~~~~~Ilv~Tp~~l~---------~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~  303 (503)
                      .              .++||+++.         ..+. ....+.++++|||||||++ +.++...+..+.... +++.|+
T Consensus        70 ~--------------~v~Tp~~l~~~l~~~~l~~~~~-~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~  133 (440)
T 1yks_A           70 S--------------AHGSGREVIDAMCHATLTYRML-EPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESAT  133 (440)
T ss_dssp             C--------------CCCCSSCCEEEEEHHHHHHHHT-SSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEE
T ss_pred             e--------------eccCCccceeeecccchhHhhh-CcccccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceE
Confidence            0              255655443         2222 2345889999999999987 222222222222222 357899


Q ss_pred             EEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcc
Q 010709          304 LLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVER  383 (503)
Q Consensus       304 i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~  383 (503)
                      ++||||+++.+..+...  ..+....              ...++... ...++..+.+          ..+++||||++
T Consensus       134 l~~SAT~~~~~~~~~~~--~~~~~~~--------------~~~~~~~~-~~~~~~~l~~----------~~~~~lVF~~s  186 (440)
T 1yks_A          134 ILMTATPPGTSDEFPHS--NGEIEDV--------------QTDIPSEP-WNTGHDWILA----------DKRPTAWFLPS  186 (440)
T ss_dssp             EEECSSCTTCCCSSCCC--SSCEEEE--------------ECCCCSSC-CSSSCHHHHH----------CCSCEEEECSC
T ss_pred             EEEeCCCCchhhhhhhc--CCCeeEe--------------eeccChHH-HHHHHHHHHh----------cCCCEEEEeCC
Confidence            99999997764322211  1111111              01111111 1111222221          13579999999


Q ss_pred             hhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE---------------
Q 010709          384 KTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN---------------  448 (503)
Q Consensus       384 ~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~---------------  448 (503)
                      ++.++.+++.|+..++.+..+||    ++|.++++.|++|+.+|||||+++++|||+| +++||+               
T Consensus       187 ~~~a~~l~~~L~~~~~~v~~lhg----~~R~~~~~~F~~g~~~vLVaT~v~e~GiDip-v~~VI~~g~~~~pv~~~~~~~  261 (440)
T 1yks_A          187 IRAANVMAASLRKAGKSVVVLNR----KTFEREYPTIKQKKPDFILATDIAEMGANLC-VERVLDCRTAFKPVLVDEGRK  261 (440)
T ss_dssp             HHHHHHHHHHHHHTTCCEEECCS----SSCC--------CCCSEEEESSSTTCCTTCC-CSEEEECCEEEEEEEETTTTE
T ss_pred             HHHHHHHHHHHHHcCCCEEEecc----hhHHHHHhhhcCCCceEEEECChhheeeccC-ceEEEeCCccceeeecccccc
Confidence            99999999999999999999999    4688999999999999999999999999999 999996               


Q ss_pred             ----ccCCCChhHHHHhhCcceee
Q 010709          449 ----LDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       449 ----~~~p~s~~~~~Qr~GR~gR~  468 (503)
                          ++.|.+.++|.||+||+||.
T Consensus       262 ~vi~~~~p~~~~~~~Qr~GR~GR~  285 (440)
T 1yks_A          262 VAIKGPLRISASSAAQRRGRIGRN  285 (440)
T ss_dssp             EEEEEEEECCHHHHHHHHTTSSCC
T ss_pred             eeeccccccCHHHHHHhccccCCC
Confidence                88899999999999999995

>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=100.00  E-value=3.2e-38  Score=319.85  Aligned_cols=260  Identities=17%  Similarity=0.229  Sum_probs=185.4

Q ss_pred             HHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEEC
Q 010709          152 MPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVG  231 (503)
Q Consensus       152 i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~  231 (503)
                      ...+..++++++++|||+|||++|++|++..+...       ++++||++|||+|+.|+++.++.       ..+....+
T Consensus        15 ~~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~~-------~~~~lvl~Ptr~La~Q~~~~l~g-------~~v~~~~~   80 (459)
T 2z83_A           15 PNMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQ-------RLRTAVLAPTRVVAAEMAEALRG-------LPVRYQTS   80 (459)
T ss_dssp             CGGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHHT-------TCCEEEEECSHHHHHHHHHHTTT-------SCEEECC-
T ss_pred             HHHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHhC-------CCcEEEECchHHHHHHHHHHhcC-------ceEeEEec
Confidence            34456788899999999999999999999887653       57899999999999999988862       22221111


Q ss_pred             CccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH-----HhhCCCHHHHHHHHHhCCCCCcEEEE
Q 010709          232 GTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR-----MLDMGFEPQIREVMQNLPDKHQTLLF  306 (503)
Q Consensus       232 ~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~-----l~~~~~~~~~~~il~~~~~~~q~i~~  306 (503)
                      ....     ....+..+.++|.+.+.+.+.. ...+.++++|||||||+     +...++....   .  ..++.|+++|
T Consensus        81 ~~~~-----~~t~~~~i~~~~~~~l~~~l~~-~~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~---~--~~~~~~~il~  149 (459)
T 2z83_A           81 AVQR-----EHQGNEIVDVMCHATLTHRLMS-PNRVPNYNLFVMDEAHFTDPASIAARGYIATK---V--ELGEAAAIFM  149 (459)
T ss_dssp             ------------CCCSEEEEEHHHHHHHHHS-CC-CCCCSEEEESSTTCCSHHHHHHHHHHHHH---H--HTTSCEEEEE
T ss_pred             cccc-----CCCCCcEEEEEchHHHHHHhhc-cccccCCcEEEEECCccCCchhhHHHHHHHHH---h--ccCCccEEEE
Confidence            1100     0123456788999998877765 35688999999999997     4433332221   1  1367899999


Q ss_pred             EeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhh
Q 010709          307 SATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTR  386 (503)
Q Consensus       307 SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~  386 (503)
                      |||++..+..+...  ..|........              +. .+...++..+.+          ..+++||||++++.
T Consensus       150 SAT~~~~~~~~~~~--~~pi~~~~~~~--------------~~-~~~~~~~~~l~~----------~~~~~LVF~~s~~~  202 (459)
T 2z83_A          150 TATPPGTTDPFPDS--NAPIHDLQDEI--------------PD-RAWSSGYEWITE----------YAGKTVWFVASVKM  202 (459)
T ss_dssp             CSSCTTCCCSSCCC--SSCEEEEECCC--------------CS-SCCSSCCHHHHH----------CCSCEEEECSCHHH
T ss_pred             EcCCCcchhhhccC--CCCeEEecccC--------------Cc-chhHHHHHHHHh----------cCCCEEEEeCChHH
Confidence            99998654322111  22332211100              00 000011112211          14579999999999


Q ss_pred             HHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEE------------------
Q 010709          387 CDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVN------------------  448 (503)
Q Consensus       387 ~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~------------------  448 (503)
                      |+.+++.|+..++.+..+|+.    +|.++++.|++|+.+|||||+++++|+|+|+ ++||+                  
T Consensus       203 ~~~l~~~L~~~g~~v~~lh~~----~R~~~~~~f~~g~~~iLVaT~v~~~GiDip~-~~VI~~G~~~~~~~~~~~~~~~~  277 (459)
T 2z83_A          203 GNEIAMCLQRAGKKVIQLNRK----SYDTEYPKCKNGDWDFVITTDISEMGANFGA-SRVIDCRKSVKPTILEEGEGRVI  277 (459)
T ss_dssp             HHHHHHHHHHTTCCEEEESTT----CCCCCGGGSSSCCCSEEEESSCC---CCCSC-SEEEECCEECCEEEECSSSCEEE
T ss_pred             HHHHHHHHHhcCCcEEecCHH----HHHHHHhhccCCCceEEEECChHHhCeecCC-CEEEECCcccccccccccccccc
Confidence            999999999999999999995    6788999999999999999999999999999 99999                  


Q ss_pred             --ccCCCChhHHHHhhCcceee
Q 010709          449 --LDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       449 --~~~p~s~~~~~Qr~GR~gR~  468 (503)
                        |+.|.+..+|+||+||+||.
T Consensus       278 ~~~d~p~s~~~~~QR~GRaGR~  299 (459)
T 2z83_A          278 LGNPSPITSASAAQRRGRVGRN  299 (459)
T ss_dssp             ECSCEECCHHHHHHHHTTSSCC
T ss_pred             cccCCCCCHHHHHHhccccCCC
Confidence              67999999999999999995

>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=5.5e-36  Score=276.13  Aligned_cols=210  Identities=29%  Similarity=0.512  Sum_probs=184.7

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      ..|.+..+|+++++++.+.+.+..+||..|+++|.++++.+++|+++++++|||+|||++|++|++..+...     ..+
T Consensus        18 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~-----~~~   92 (230)
T 2oxc_A           18 VLLAEPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE-----NLS   92 (230)
T ss_dssp             ------CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----SCS
T ss_pred             CCCCCCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----CCC
Confidence            455667789999999999999999999999999999999999999999999999999999999999876542     235


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      +++||++|+++|+.|+++.+++++....++.+..+.|+.........+ .+++|+|+||++|.+.+....+.+.++++||
T Consensus        93 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~~~lV  171 (230)
T 2oxc_A           93 TQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDYLNPGSIRLFI  171 (230)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHTTSSCGGGCCEEE
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhcCCcccccCCEEE
Confidence            789999999999999999999998765568899999998877665554 4699999999999999988777888999999


Q ss_pred             ecchhHHhhCC-CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEe
Q 010709          275 LDEADRMLDMG-FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV  330 (503)
Q Consensus       275 iDEaH~l~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~  330 (503)
                      +||||++.+++ |...+..++..+++..|++++|||+++.+..++..++.+|..+.+
T Consensus       172 iDEah~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~  228 (230)
T 2oxc_A          172 LDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRL  228 (230)
T ss_dssp             ESSHHHHHSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC
T ss_pred             eCCchHhhcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEc
Confidence            99999999987 999999999999989999999999999999999999999987753

>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=1.2e-35  Score=276.63  Aligned_cols=208  Identities=38%  Similarity=0.683  Sum_probs=189.1

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeE
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLA  197 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~  197 (503)
                      .+..+|+++++++.+.+.+..+|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+....     .++++
T Consensus        40 ~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~-----~~~~~  114 (249)
T 3ber_A           40 EETKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP-----QRLFA  114 (249)
T ss_dssp             HHHCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC-----CSSCE
T ss_pred             cccCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC-----CCceE
Confidence            3456799999999999999999999999999999999999999999999999999999999998876642     35789


Q ss_pred             EEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-CCCCCCCccEEEec
Q 010709          198 LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-GNTSLSRVSFVILD  276 (503)
Q Consensus       198 lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~~~~vViD  276 (503)
                      ||++|+++|+.|+++.+++++... ++.+..++|+.....+...+..+++|+|+||++|.+.+.+ ..+.+.++++||+|
T Consensus       115 lil~Ptr~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lViD  193 (249)
T 3ber_A          115 LVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMD  193 (249)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEEC
T ss_pred             EEEeCCHHHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEEc
Confidence            999999999999999999998665 4788999999988877777788899999999999998876 45678899999999


Q ss_pred             chhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       277 EaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      |||++.+++|...+..++..++++.|+++||||+++.+..+++.++.+|..+.+.
T Consensus       194 Eah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          194 EADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             SHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             ChhhhhccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            9999999999999999999999999999999999999999999999999887653

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=4.5e-36  Score=274.67  Aligned_cols=208  Identities=31%  Similarity=0.548  Sum_probs=185.4

Q ss_pred             cCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          120 IESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       120 ~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      ..+|+++++++.+.+.+..+|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+...     ..++++||
T Consensus         3 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~-----~~~~~~li   77 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAVI   77 (219)
T ss_dssp             -CCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEE
T ss_pred             CCCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC-----cCCceEEE
Confidence            4579999999999999999999999999999999999999999999999999999999999876532     23578999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCC---CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEec
Q 010709          200 LAPTRELAQQIEKEVKALSRSLD---SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD  276 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViD  276 (503)
                      ++|+++|+.|+++.++++.....   ++.+..++|+.........+..+++|+|+||+++.+.+.+....+.++++||+|
T Consensus        78 l~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~~lViD  157 (219)
T 1q0u_A           78 TAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVD  157 (219)
T ss_dssp             ECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEEC
T ss_pred             EcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHcCCCCcCcceEEEEc
Confidence            99999999999999999986542   477888888887766555555678999999999999998877788999999999


Q ss_pred             chhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCC
Q 010709          277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK  332 (503)
Q Consensus       277 EaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  332 (503)
                      |||++.+++|...+..++..++++.|++++|||+++++.++++.++.+|..+.+..
T Consensus       158 Eah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~  213 (219)
T 1q0u_A          158 EADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLE  213 (219)
T ss_dssp             SHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC-
T ss_pred             CchHHhhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeec
Confidence            99999999999999999999998999999999999999999999999998886553

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=100.00  E-value=5.6e-37  Score=308.27  Aligned_cols=259  Identities=16%  Similarity=0.180  Sum_probs=185.1

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA  236 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~  236 (503)
                      +|+++++++|||+|||++|++|++..+...       +++++|++||++|+.|+++.++       ++.+....++... 
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~~-------g~~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~~~-   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVKK-------RLRTVILAPTRVVASEMYEALR-------GEPIRYMTPAVQS-   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTT-------TSCEEEC-------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHhC-------CCCEEEECcHHHHHHHHHHHhC-------CCeEEEEecCccc-
Confidence            378899999999999999999999776553       5789999999999999987775       2344444333211 


Q ss_pred             HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHH
Q 010709          237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL-PDKHQTLLFSATMPVEIE  315 (503)
Q Consensus       237 ~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~  315 (503)
                          ....+..+.++|.+.+.+.+.. ...+.++++|||||+|++ +.++......+.... +++.|+++||||+++.+.
T Consensus        66 ----~~~~~~~~~~~~~~~l~~~l~~-~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~  139 (431)
T 2v6i_A           66 ----ERTGNEIVDFMCHSTFTMKLLQ-GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTE  139 (431)
T ss_dssp             -------CCCSEEEEEHHHHHHHHHH-TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCC
T ss_pred             ----cCCCCceEEEEchHHHHHHHhc-CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchh
Confidence                1223456778899988777766 566889999999999986 332333333333332 567899999999986432


Q ss_pred             HHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHH
Q 010709          316 ALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALV  395 (503)
Q Consensus       316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~  395 (503)
                      .+...  ..|... ..             ...+ ..+...++..+.+          ..+++||||++++.++.+++.|+
T Consensus       140 ~~~~~--~~~i~~-~~-------------~~~~-~~~~~~~~~~l~~----------~~~~~lVF~~~~~~~~~l~~~L~  192 (431)
T 2v6i_A          140 AFPPS--NSPIID-EE-------------TRIP-DKAWNSGYEWITE----------FDGRTVWFVHSIKQGAEIGTCLQ  192 (431)
T ss_dssp             SSCCC--SSCCEE-EE-------------CCCC-SSCCSSCCHHHHS----------CSSCEEEECSSHHHHHHHHHHHH
T ss_pred             hhcCC--CCceee-cc-------------ccCC-HHHHHHHHHHHHc----------CCCCEEEEeCCHHHHHHHHHHHH
Confidence            21110  111111 10             0011 0111112222211          24579999999999999999999


Q ss_pred             HCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCE-----------------EEEccCCCChhHH
Q 010709          396 AEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAH-----------------VVNLDLPKVLLAA  458 (503)
Q Consensus       396 ~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~-----------------VI~~~~p~s~~~~  458 (503)
                      +.++.+..+||+    +|.++++.|++|+.+|||||+++++|+|+| +.+                 ||+++.|.+..+|
T Consensus       193 ~~~~~v~~lhg~----~r~~~~~~f~~g~~~vLVaT~v~e~GiDip-~~~VI~~g~~~~~v~d~~~~vi~~~~p~~~~~~  267 (431)
T 2v6i_A          193 KAGKKVLYLNRK----TFESEYPKCKSEKWDFVITTDISEMGANFK-ADRVIDPRKTIKPILLDGRVSMQGPIAITPASA  267 (431)
T ss_dssp             HTTCCEEEESTT----THHHHTTHHHHSCCSEEEECGGGGTSCCCC-CSEEEECCEEEEEEEETTEEEEEEEEECCHHHH
T ss_pred             HcCCeEEEeCCc----cHHHHHHhhcCCCCeEEEECchHHcCcccC-CcEEEecCccccceecccceeecccccCCHHHH
Confidence            999999999997    578899999999999999999999999999 766                 5778889999999


Q ss_pred             HHhhCcceee
Q 010709          459 SESLCTTSFN  468 (503)
Q Consensus       459 ~Qr~GR~gR~  468 (503)
                      .||+||+||.
T Consensus       268 ~Qr~GR~GR~  277 (431)
T 2v6i_A          268 AQRRGRIGRN  277 (431)
T ss_dssp             HHHHTTSSCC
T ss_pred             HHhhhccCCC
Confidence            9999999995

>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=285.37  Aligned_cols=207  Identities=30%  Similarity=0.494  Sum_probs=184.2

Q ss_pred             CCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       117 ~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      .....+|+++++++.+++.|..+||..|+++|.++|+.++.|  +|+++++|||+|||++|++|++..+...     ..+
T Consensus        88 ~~~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~-----~~~  162 (300)
T 3fmo_B           88 LYSVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA-----NKY  162 (300)
T ss_dssp             CCCCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTT-----SCS
T ss_pred             cCCcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhcc-----CCC
Confidence            345788999999999999999999999999999999999987  8999999999999999999999886543     346


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHc-CCCCCCCccEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQ-GNTSLSRVSFV  273 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~~~~v  273 (503)
                      +++||++|||+||.|+++.++.++....++.+....|+......   ...+++|+|+||++|.+++.+ ..+.+.++++|
T Consensus       163 ~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~l  239 (300)
T 3fmo_B          163 PQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG---QKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVF  239 (300)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTT---CCCCCSEEEECHHHHHHHHTTTCCCCGGGCSEE
T ss_pred             ceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhh---hcCCCCEEEECHHHHHHHHHhcCCCChhhceEE
Confidence            78999999999999999999999877667888888887754332   245689999999999999976 45678999999


Q ss_pred             EecchhHHhh-CCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          274 ILDEADRMLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       274 ViDEaH~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      ||||||++++ .+|...+..++..+++.+|+++||||+++.+..+++.++.+|..+.+.
T Consensus       240 VlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~  298 (300)
T 3fmo_B          240 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLK  298 (300)
T ss_dssp             EETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEEC
T ss_pred             EEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEec
Confidence            9999999998 689999999999999999999999999999999999999999988764

>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=4.3e-35  Score=271.46  Aligned_cols=212  Identities=36%  Similarity=0.606  Sum_probs=185.9

Q ss_pred             CCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCe
Q 010709          117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPL  196 (503)
Q Consensus       117 ~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~  196 (503)
                      +.+..+|+++++++.+.+.|..+|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+..... ....+++
T Consensus        21 ~~~~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~-~~~~~~~   99 (236)
T 2pl3_A           21 VNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW-TSTDGLG   99 (236)
T ss_dssp             GGGCSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC-CGGGCCC
T ss_pred             CcccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc-cccCCce
Confidence            456778999999999999999999999999999999999999999999999999999999999988765321 1224678


Q ss_pred             EEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEe
Q 010709          197 ALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVIL  275 (503)
Q Consensus       197 ~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vVi  275 (503)
                      +||++|+++|+.|+++.+++++... ++.+..++|+.........+ .+++|+|+||++|.+.+.+. .+.+.++++||+
T Consensus       100 ~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lVi  177 (236)
T 2pl3_A          100 VLIISPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVL  177 (236)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEE
Confidence            9999999999999999999998654 47888889988776655555 57999999999999988764 466789999999


Q ss_pred             cchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          276 DEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       276 DEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      ||||++.+++|...+..++..+++..|+++||||+++.+..+++.++.+|..+.+.
T Consensus       178 DEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~  233 (236)
T 2pl3_A          178 DEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVH  233 (236)
T ss_dssp             TTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECC
T ss_pred             eChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeC
Confidence            99999999999999999999999999999999999999999999999999888654

>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=7.7e-36  Score=276.37  Aligned_cols=211  Identities=36%  Similarity=0.579  Sum_probs=177.4

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      ..+.+..+|+++++++.+.+.+..+||..|+++|.++++.+++|+++++++|||+|||++|++|++..+...     ..+
T Consensus        24 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~-----~~~   98 (237)
T 3bor_A           24 NWNEIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE-----FKE   98 (237)
T ss_dssp             ---CCCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT-----SCS
T ss_pred             CCCCccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc-----CCC
Confidence            455677889999999999999999999999999999999999999999999999999999999999876432     235


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCC-CcEEEECcHHHHHHHHcCCCCCCCccEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGG-VSIVVATPGRFLDHLQQGNTSLSRVSFV  273 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~Ilv~Tp~~l~~~l~~~~~~l~~~~~v  273 (503)
                      +++||++|+++|+.|+++.+++++... ++.+..++|+.........+..+ ++|+|+||++|.+.+.+....+.++++|
T Consensus        99 ~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~~~~l  177 (237)
T 3bor_A           99 TQALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMF  177 (237)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEEEECHHHHHHHHHTTSSCSTTCCEE
T ss_pred             ceEEEEECcHHHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHhCCcCcccCcEE
Confidence            789999999999999999999998654 47788888888766665555544 8999999999999998877788899999


Q ss_pred             EecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          274 ILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       274 ViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      |+||||++.+++|...+..++..+++..|++++|||+++++..+++.++.+|..+.+.
T Consensus       178 ViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~  235 (237)
T 3bor_A          178 VLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVK  235 (237)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC--
T ss_pred             EECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEec
Confidence            9999999999999999999999999999999999999999999999999999887543

>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=100.00  E-value=5e-35  Score=265.45  Aligned_cols=204  Identities=47%  Similarity=0.734  Sum_probs=184.7

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      +|+++++++.+.+.+...|+..|+++|.++++.+++++++++++|||+|||++|++|++..+....  ....++++||++
T Consensus         2 ~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~--~~~~~~~~lil~   79 (207)
T 2gxq_A            2 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQ--ERGRKPRALVLT   79 (207)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCC--CTTCCCSEEEEC
T ss_pred             ChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhcc--ccCCCCcEEEEE
Confidence            589999999999999999999999999999999999999999999999999999999998865422  123468899999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                      |+++|+.|+++.++++...   +.+..++|+.........+..+++|+|+||+++.+.+.+....+.++++||+||||++
T Consensus        80 P~~~L~~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~iViDEah~~  156 (207)
T 2gxq_A           80 PTRELALQVASELTAVAPH---LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEM  156 (207)
T ss_dssp             SSHHHHHHHHHHHHHHCTT---SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHHTSSCCTTCSEEEEESHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhc---ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHcCCcchhhceEEEEEChhHh
Confidence            9999999999999998743   6788888988877777777778999999999999999887788899999999999999


Q ss_pred             hhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEe
Q 010709          282 LDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV  330 (503)
Q Consensus       282 ~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~  330 (503)
                      .+.+|...+..++..++++.|++++|||+++.+..+++.++.+|..+.+
T Consensus       157 ~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~  205 (207)
T 2gxq_A          157 LSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINV  205 (207)
T ss_dssp             HHTTCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEEC
T ss_pred             hccchHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEc
Confidence            9999999999999999999999999999999999999999999988754

>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=100.00  E-value=4.8e-35  Score=268.96  Aligned_cols=211  Identities=36%  Similarity=0.587  Sum_probs=180.8

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      ..+.++.+|+++++++.+.+.+..+|+..|+++|.++++.+++|+++++++|||+|||++|++|++..+...     ..+
T Consensus         8 ~~~~~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~-----~~~   82 (224)
T 1qde_A            8 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKA   82 (224)
T ss_dssp             SCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCS
T ss_pred             ccCcccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc-----CCC
Confidence            456677889999999999999999999999999999999999999999999999999999999999876442     236


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      +++||++|+++|+.|+++.+++++... ++.+..+.|+.........+.. ++|+|+||++|.+.+.+....+.++++||
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~-~~iiv~Tp~~l~~~~~~~~~~~~~~~~iV  160 (224)
T 1qde_A           83 PQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD-AQIVVGTPGRVFDNIQRRRFRTDKIKMFI  160 (224)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------CTT-CSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             ceEEEEECCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcCCC-CCEEEECHHHHHHHHHhCCcchhhCcEEE
Confidence            789999999999999999999988655 5788888888876665544443 89999999999999988878889999999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCC
Q 010709          275 LDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK  332 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  332 (503)
                      +||||++.+++|...+..++..+++..|++++|||+++++..+++.++.+|..+.+..
T Consensus       161 iDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~  218 (224)
T 1qde_A          161 LDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKK  218 (224)
T ss_dssp             EETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             EcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecC
Confidence            9999999999999999999999999999999999999999999999999998876543

>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=100.00  E-value=4.9e-35  Score=272.67  Aligned_cols=230  Identities=31%  Similarity=0.531  Sum_probs=192.1

Q ss_pred             HHHHHHHHcCceEEecCCCCCCCCCcCCcccC----CCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCc
Q 010709           95 QIEEVRLRLNVDVTVASGSVPAPAPIESFTDM----CLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSG  170 (503)
Q Consensus        95 ~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~----~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsG  170 (503)
                      +++.++...++.+...    ..|.++.+|+++    ++++.+++.+...||..|+++|.++++.+++|+++++++|||+|
T Consensus         3 ~~~~~~~~~~i~~~~~----~~p~~~~~f~~l~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsG   78 (245)
T 3dkp_A            3 KINFLRNKHKIHVQGT----DLPDPIATFQQLDQEYKINSRLLQNILDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSG   78 (245)
T ss_dssp             HHHHHHHHTTEEEESS----SCCCCCSSHHHHHHHHCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSC
T ss_pred             hHHHHHHhCceEecCC----CCCCcccCHHHhhhccCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCc
Confidence            4567788888877754    678889999987    89999999999999999999999999999999999999999999


Q ss_pred             hhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH-HHhhCCCcEE
Q 010709          171 KTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR-SELRGGVSIV  249 (503)
Q Consensus       171 KTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~Il  249 (503)
                      ||++|++|++..+...    ...++++||++|+++|+.|+++.+++++... ++.+..+.++....... .....+++|+
T Consensus        79 KT~~~~l~~l~~l~~~----~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~I~  153 (245)
T 3dkp_A           79 KTLAFSIPILMQLKQP----ANKGFRALIISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKFGPKSSKKFDIL  153 (245)
T ss_dssp             HHHHHHHHHHHHHCSC----CSSSCCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTTSTTSCCCCCEE
T ss_pred             HHHHHHHHHHHHHhhc----ccCCceEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHhhhhhcCCCCEE
Confidence            9999999999887542    2346789999999999999999999998654 46666665544322211 1223568999


Q ss_pred             EECcHHHHHHHHcC--CCCCCCccEEEecchhHHhh---CCCHHHHHHHHHhC-CCCCcEEEEEeeCCHHHHHHHHHhcC
Q 010709          250 VATPGRFLDHLQQG--NTSLSRVSFVILDEADRMLD---MGFEPQIREVMQNL-PDKHQTLLFSATMPVEIEALAQEYLT  323 (503)
Q Consensus       250 v~Tp~~l~~~l~~~--~~~l~~~~~vViDEaH~l~~---~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~~~~~~~~~~~  323 (503)
                      |+||++|.+.+.+.  ...+.++++||+||||++.+   .+|...+..++..+ +++.|+++||||+++++..+++.++.
T Consensus       154 v~Tp~~l~~~l~~~~~~~~~~~~~~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~  233 (245)
T 3dkp_A          154 VTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLD  233 (245)
T ss_dssp             EECHHHHHHHHHSSSCSCCCTTCCEEEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSS
T ss_pred             EECHHHHHHHHHhCCCCcccccCcEEEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCC
Confidence            99999999999876  46788999999999999988   46888898888776 45789999999999999999999999


Q ss_pred             CCeEEEeCCC
Q 010709          324 DPVQVKVGKV  333 (503)
Q Consensus       324 ~~~~~~~~~~  333 (503)
                      +|..+.++..
T Consensus       234 ~p~~i~~~~~  243 (245)
T 3dkp_A          234 NVISVSIGAR  243 (245)
T ss_dssp             SCEEEEECC-
T ss_pred             CCEEEEeCCC
Confidence            9999987653

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=100.00  E-value=2.9e-35  Score=307.22  Aligned_cols=263  Identities=18%  Similarity=0.157  Sum_probs=197.5

Q ss_pred             HHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCc
Q 010709          154 VALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGT  233 (503)
Q Consensus       154 ~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~  233 (503)
                      ..+++++++++||||+|||+    +++..+...        +..+|++|||+||.|+++.+++.     ++.+..++|+.
T Consensus       151 r~l~rk~vlv~apTGSGKT~----~al~~l~~~--------~~gl~l~PtR~LA~Qi~~~l~~~-----g~~v~lltG~~  213 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTY----HAIQKYFSA--------KSGVYCGPLKLLAHEIFEKSNAA-----GVPCDLVTGEE  213 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHH----HHHHHHHHS--------SSEEEEESSHHHHHHHHHHHHHT-----TCCEEEECSSC
T ss_pred             HhcCCCEEEEEcCCCCCHHH----HHHHHHHhc--------CCeEEEeCHHHHHHHHHHHHHhc-----CCcEEEEECCe
Confidence            44578899999999999997    334443332        33599999999999999999886     36788888876


Q ss_pred             cHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC-CCCcEEEEEeeCCH
Q 010709          234 NIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP-DKHQTLLFSATMPV  312 (503)
Q Consensus       234 ~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~  312 (503)
                      ....  ..-....+++++|++.+.        ....+++|||||||++.+.+++..+..++..++ ...+++++|||. +
T Consensus       214 ~~iv--~TpGr~~~il~~T~e~~~--------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~-~  282 (677)
T 3rc3_A          214 RVTV--QPNGKQASHVSCTVEMCS--------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAI-D  282 (677)
T ss_dssp             EECC--STTCCCCSEEEEEGGGCC--------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-H
T ss_pred             eEEe--cCCCcccceeEecHhHhh--------hcccCCEEEEecceecCCccchHHHHHHHHccCccceEEEeccchH-H
Confidence            4310  000012567778775542        246789999999999999999999999999887 688999999996 3


Q ss_pred             HHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHH
Q 010709          313 EIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSE  392 (503)
Q Consensus       313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~  392 (503)
                      .+..+.... .....+........   ...   .......+       .          ...++.+|||+++++++.+++
T Consensus       283 ~i~~l~~~~-~~~~~v~~~~r~~~---l~~---~~~~l~~l-------~----------~~~~g~iIf~~s~~~ie~la~  338 (677)
T 3rc3_A          283 LVMELMYTT-GEEVEVRDYKRLTP---ISV---LDHALESL-------D----------NLRPGDCIVCFSKNDIYSVSR  338 (677)
T ss_dssp             HHHHHHHHH-TCCEEEEECCCSSC---EEE---CSSCCCSG-------G----------GCCTTEEEECSSHHHHHHHHH
T ss_pred             HHHHHHHhc-CCceEEEEeeecch---HHH---HHHHHHHH-------H----------hcCCCCEEEEcCHHHHHHHHH
Confidence            455444443 33444322211100   000   00000000       0          011246899999999999999


Q ss_pred             HHHHCCCeEEEEcCCCCHHHHHHHHHHHhc--CCCcEEEEccccccCCCCCCCCEEEEccC--------------CCChh
Q 010709          393 ALVAEGLHAVALHGGRNQSDRESALRDFRN--GSTNILVATDVASRGLDVMGVAHVVNLDL--------------PKVLL  456 (503)
Q Consensus       393 ~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~--g~~~vLvaT~~~~~Gldip~v~~VI~~~~--------------p~s~~  456 (503)
                      .|.+.++.+..+||+|++.+|.++++.|++  |..+|||||+++++|||+ ++++||++|+              |.+..
T Consensus       339 ~L~~~g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi~e~GlDi-~v~~VI~~~~~k~~~~~~G~~~~~p~s~~  417 (677)
T 3rc3_A          339 QIEIRGLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDAIGMGLNL-SIRRIIFYSLIKPSINEKGERELEPITTS  417 (677)
T ss_dssp             HHHHTTCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGGGGSSCCC-CBSEEEESCSBC-----------CBCCHH
T ss_pred             HHHhcCCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcHHHCCcCc-CccEEEECCccccccccCCccccccCCHH
Confidence            999999999999999999999999999999  889999999999999999 8999999999              77899


Q ss_pred             HHHHhhCcceeee
Q 010709          457 AASESLCTTSFNI  469 (503)
Q Consensus       457 ~~~Qr~GR~gR~~  469 (503)
                      +|+||+|||||.-
T Consensus       418 ~~~QR~GRAGR~g  430 (677)
T 3rc3_A          418 QALQIAGRAGRFS  430 (677)
T ss_dssp             HHHHHHTTBTCTT
T ss_pred             HHHHHhcCCCCCC
Confidence            9999999999965

>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=1.8e-34  Score=270.94  Aligned_cols=204  Identities=38%  Similarity=0.616  Sum_probs=179.2

Q ss_pred             CCcccCC--CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          121 ESFTDMC--LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       121 ~~~~~~~--l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ..|++++  +++.+++.+..+||..|+++|.++++.++.|+|+++++|||+|||++|++|++..+...... ...++++|
T Consensus        52 ~~f~~l~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~-~~~~~~~l  130 (262)
T 3ly5_A           52 TSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM-PRNGTGVL  130 (262)
T ss_dssp             GCC-----CCCHHHHHHHHHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCC-GGGCCCEE
T ss_pred             CChhHhccccCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhcccc-ccCCceEE
Confidence            3466665  99999999999999999999999999999999999999999999999999999887764311 12367899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcC-CCCCCCccEEEecc
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQG-NTSLSRVSFVILDE  277 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~-~~~l~~~~~vViDE  277 (503)
                      |++||++|+.|+++.+++++... +..+..++|+.........+..+++|+|+||+++.+.+.+. .+.+.++++|||||
T Consensus       131 il~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~lViDE  209 (262)
T 3ly5_A          131 ILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDE  209 (262)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCEEEECS
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCEEEEcC
Confidence            99999999999999999998765 57888999999888887777778999999999999988775 36788999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCe
Q 010709          278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPV  326 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~  326 (503)
                      ||++.+++|...+..++..+++.+|+++||||+++.+..+++.++.++.
T Consensus       210 ah~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          210 ADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             hHHHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            9999999999999999999999999999999999999999999987653

>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=2e-34  Score=264.08  Aligned_cols=206  Identities=32%  Similarity=0.552  Sum_probs=181.9

Q ss_pred             CcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEE
Q 010709          119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLAL  198 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~l  198 (503)
                      ....|+++++++.+.+.+..+|+..|+++|.++++.+++++++++++|||+|||++|++|++..+...     ..++++|
T Consensus        12 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~-----~~~~~~l   86 (220)
T 1t6n_A           12 HSSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVL   86 (220)
T ss_dssp             --CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCCEE
T ss_pred             cCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc-----CCCEEEE
Confidence            34569999999999999999999999999999999999999999999999999999999998875332     2346899


Q ss_pred             EEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecc
Q 010709          199 VLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE  277 (503)
Q Consensus       199 il~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDE  277 (503)
                      |++|+++|+.|+++.++++.....++.+..++|+.........+. ..++|+|+||+++.+.+.+....+.++++||+||
T Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~lViDE  166 (220)
T 1t6n_A           87 VMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDE  166 (220)
T ss_dssp             EECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEES
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHhCCCCcccCCEEEEcC
Confidence            999999999999999999987665688999999988766655554 4579999999999999988777889999999999


Q ss_pred             hhHHhh-CCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEE
Q 010709          278 ADRMLD-MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVK  329 (503)
Q Consensus       278 aH~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~  329 (503)
                      ||++.+ .+|...+..++..++++.|++++|||+++.+..+++.++.+|..+.
T Consensus       167 ah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~  219 (220)
T 1t6n_A          167 CDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  219 (220)
T ss_dssp             HHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             HHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEe
Confidence            999987 4788889999999988999999999999999999999999998764

>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=100.00  E-value=2.4e-33  Score=289.02  Aligned_cols=298  Identities=13%  Similarity=0.177  Sum_probs=205.4

Q ss_pred             CCCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          142 TRPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..|+|+|.+++.++.    .++++|++++||+|||++++ +++..+...     ....++|||+|+ .|+.||.++++++
T Consensus        36 ~~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai-~~i~~~~~~-----~~~~~~LIv~P~-~l~~qw~~e~~~~  108 (500)
T 1z63_A           36 ANLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTI-AVFSDAKKE-----NELTPSLVICPL-SVLKNWEEELSKF  108 (500)
T ss_dssp             SCCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHH-HHHHHHHHT-----TCCSSEEEEECS-TTHHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHH-HHHHHHHhc-----CCCCCEEEEccH-HHHHHHHHHHHHH
Confidence            379999999998874    57789999999999999874 455554432     224679999995 5889999999998


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                      ..   +..+..+.|+...     ......+|+|+|++++.+...   +....+++||+||||++.+..  ....+.+..+
T Consensus       109 ~~---~~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~---l~~~~~~~vIvDEaH~~kn~~--~~~~~~l~~l  175 (500)
T 1z63_A          109 AP---HLRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQ--TKIFKAVKEL  175 (500)
T ss_dssp             CT---TSCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTT--SHHHHHHHTS
T ss_pred             CC---CceEEEEecCchh-----ccccCCcEEEeeHHHHhccch---hcCCCcCEEEEeCccccCCHh--HHHHHHHHhh
Confidence            74   3556666555421     122457999999999965443   334578999999999987653  2345566666


Q ss_pred             CCCCcEEEEEeeCCHH-HHHH------------------------------------HHHhcCCCeEEEeCCCC----CC
Q 010709          298 PDKHQTLLFSATMPVE-IEAL------------------------------------AQEYLTDPVQVKVGKVS----SP  336 (503)
Q Consensus       298 ~~~~q~i~~SAT~~~~-~~~~------------------------------------~~~~~~~~~~~~~~~~~----~~  336 (503)
                      +. .+.+++||||..+ ..++                                    +..++ .|..+......    ..
T Consensus       176 ~~-~~~l~LTaTP~~n~~~el~~ll~~l~p~~~~~~~~f~~~~~~~~~~~~~~~~~~l~~~l-~~~~lrr~k~~~~~~~~  253 (500)
T 1z63_A          176 KS-KYRIALTGTPIENKVDDLWSIMTFLNPGLLGSYSEFKSKFATPIKKGDNMAKEELKAII-SPFILRRTKYDKAIIND  253 (500)
T ss_dssp             CE-EEEEEECSSCSTTCHHHHHHHHHHHSTTTTCCHHHHHTTTHHHHHTTCHHHHHHHHHHH-TTTEECCCTTCHHHHTT
T ss_pred             cc-CcEEEEecCCCCCCHHHHHHHHHHhCCCcCCCHHHHHHHhccccccccHHHHHHHHHHH-hhHeeeecccccchhhc
Confidence            43 4679999999432 1111                                    11111 12222211110    01


Q ss_pred             CCceEEEEEEcC--hh-------------------------------------------------------hHHHHHHHH
Q 010709          337 TANVIQILEKVS--EN-------------------------------------------------------EKVDRLLAL  359 (503)
Q Consensus       337 ~~~~~~~~~~~~--~~-------------------------------------------------------~k~~~l~~~  359 (503)
                      .+........+.  ..                                                       .|...+..+
T Consensus       254 lp~~~~~~v~~~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lr~~~~~p~l~~~~~~~~~~s~K~~~l~~~  333 (500)
T 1z63_A          254 LPDKIETNVYCNLTPEQAAMYKAEVENLFNNIDSVTGIKRKGMILSTLLKLKQIVDHPALLKGGEQSVRRSGKMIRTMEI  333 (500)
T ss_dssp             SCSEEEEEEEECCCHHHHHHHHHHHHHHTTTTTTCCTHHHHHHHHHHHHHHHHHTTCTHHHHCSCCCSTTCHHHHHHHHH
T ss_pred             CCCCeEEEEEcCCCHHHHHHHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhCCHHHhcCccchhhcchhHHHHHHH
Confidence            111222222222  11                                                       111122222


Q ss_pred             HHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcC-CCc-EEEEcccccc
Q 010709          360 LVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFRNG-STN-ILVATDVASR  436 (503)
Q Consensus       360 l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~~g-~~~-vLvaT~~~~~  436 (503)
                      +.+..       ....++||||++...++.+++.|... |+.+..+||++++.+|.++++.|++| ..+ +|++|+++++
T Consensus       334 l~~~~-------~~~~k~lvF~~~~~~~~~l~~~l~~~~~~~~~~~~g~~~~~~R~~~~~~F~~~~~~~vil~st~~~~~  406 (500)
T 1z63_A          334 IEEAL-------DEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGF  406 (500)
T ss_dssp             HHHHH-------TTTCCEEEECSCHHHHHHHHHHHHHHHTCCCCEEETTSCHHHHHHHHHHHHHCTTCCCCEEECCCC-C
T ss_pred             HHHHH-------ccCCcEEEEEehHHHHHHHHHHHHHhhCCCeEEEECCCCHHHHHHHHHHhcCCCCCCEEEEecccccC
Confidence            22111       24568999999999999999999885 99999999999999999999999998 454 7999999999


Q ss_pred             CCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          437 GLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       437 Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+|+|++++||++|+|+++..|.||+||++|.
T Consensus       407 Glnl~~~~~vi~~d~~~~~~~~~Q~~gR~~R~  438 (500)
T 1z63_A          407 GINLTSANRVIHFDRWWNPAVEDQATDRVYRI  438 (500)
T ss_dssp             CCCCTTCSEEEESSCCSCC---CHHHHTTTTT
T ss_pred             CCchhhCCEEEEeCCCCCcchHHHHHHHHHHc
Confidence            99999999999999999999999999999994

>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=100.00  E-value=3e-34  Score=314.25  Aligned_cols=307  Identities=18%  Similarity=0.165  Sum_probs=207.4

Q ss_pred             CCCcHHHHHHHHHHhcC--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          142 TRPTSIQAQAMPVALSG--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      ..|+|+|.+++..++..  .++|++++||+|||++++..+...+ ..     +...++|||+|+ .|+.||.+++.+.+ 
T Consensus       152 ~~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~-~~-----g~~~rvLIVvP~-sLl~Qw~~E~~~~f-  223 (968)
T 3dmq_A          152 TSLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQL-LS-----GAAERVLIIVPE-TLQHQWLVEMLRRF-  223 (968)
T ss_dssp             SCCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHH-HT-----SSCCCEEEECCT-TTHHHHHHHHHHHS-
T ss_pred             CCCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHH-Hh-----CCCCeEEEEeCH-HHHHHHHHHHHHHh-
Confidence            47999999999998864  4699999999999999866554443 32     123579999999 99999999997765 


Q ss_pred             cCCCceEEEEECCccHHHHHH--HhhCCCcEEEECcHHHHHHHHc-CCCCCCCccEEEecchhHHhhCCCH-HHHHHHHH
Q 010709          220 SLDSFKTAIVVGGTNIAEQRS--ELRGGVSIVVATPGRFLDHLQQ-GNTSLSRVSFVILDEADRMLDMGFE-PQIREVMQ  295 (503)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~Ilv~Tp~~l~~~l~~-~~~~l~~~~~vViDEaH~l~~~~~~-~~~~~il~  295 (503)
                         ++.+.++.++........  ......+|+|+|++.+.+.... ..+...++++|||||||++.+.+.. ....+.+.
T Consensus       224 ---~l~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l~  300 (968)
T 3dmq_A          224 ---NLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAIE  300 (968)
T ss_dssp             ---CCCCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHHH
T ss_pred             ---CCCEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHHH
Confidence               344554443322211110  1123578999999988642211 1123457999999999998655321 11122222


Q ss_pred             hC-CCCCcEEEEEeeCCH----HHHHHH----------------------------HHhcC-------------------
Q 010709          296 NL-PDKHQTLLFSATMPV----EIEALA----------------------------QEYLT-------------------  323 (503)
Q Consensus       296 ~~-~~~~q~i~~SAT~~~----~~~~~~----------------------------~~~~~-------------------  323 (503)
                      .+ ....+++++||||-.    ++..++                            ..+..                   
T Consensus       301 ~L~~~~~~~L~LTATPi~n~~~el~sll~~L~p~~~~~~~~f~~~~~~~~~i~~~~~~l~~~~~~~~~~~~~L~~~l~~~  380 (968)
T 3dmq_A          301 QLAEHVPGVLLLTATPEQLGMESHFARLRLLDPNRFHDFAQFVEEQKNYCPVADAVAMLLAGNKLSNDELNMLGEMIGEQ  380 (968)
T ss_dssp             HHHTTCSSEEESCSSCSSSCSSCTHHHHHHHCTTTCSSTHHHHHHHHHHHHHHHHHHTTTTSCCCCGGGTTSSTTTTCTT
T ss_pred             HHhhcCCcEEEEEcCCccCCHHHHHHHHHhcCccccCCHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHhcch
Confidence            22 234569999999832    000000                            00000                   


Q ss_pred             ---------------------------------CCeEEEeCCC---CCCCCceEEEEE----------------------
Q 010709          324 ---------------------------------DPVQVKVGKV---SSPTANVIQILE----------------------  345 (503)
Q Consensus       324 ---------------------------------~~~~~~~~~~---~~~~~~~~~~~~----------------------  345 (503)
                                                       ....+.....   ..+.........                      
T Consensus       381 ~~~~l~~~~~~~~~~~~~~~~~~i~~lld~~g~~~~l~r~~r~~i~~~p~r~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  460 (968)
T 3dmq_A          381 DIEPLLQAANSDSEDAQSARQELVSMLMDRHGTSRVLFRNTRNGVKGFPKRELHTIKLPLPTQYQTAIKVSGIMGARKSA  460 (968)
T ss_dssp             CSSTTGGGTCCCSSCSTTTHHHHHHHHGGGCTTTTTEECCCTTTCCCCCCCCCCEEEECCCHHHHHHHHHHHHTTCCSSG
T ss_pred             hhHHHHhcccchhhhhHHHHHHHHHHHHHhhCcchhhhhhhhhhhcccChhheEeeecCCCHHHHHHHHHHhhhhhhhhh
Confidence                                             0000000000   000111111111                      


Q ss_pred             -----------------------EcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHH-CCCeE
Q 010709          346 -----------------------KVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA-EGLHA  401 (503)
Q Consensus       346 -----------------------~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~-~~~~v  401 (503)
                                             .+....|...+..++..         .+..++||||+++..++.+++.|.. .|+.+
T Consensus       461 ~~~~~~~l~pe~~~~~l~~~~~~~~~~~~K~~~L~~ll~~---------~~~~k~iVF~~~~~~~~~l~~~L~~~~g~~~  531 (968)
T 3dmq_A          461 EDRARDMLYPERIYQEFEGDNATWWNFDPRVEWLMGYLTS---------HRSQKVLVICAKAATALQLEQVLREREGIRA  531 (968)
T ss_dssp             GGGTHHHHCSGGGTTTTTSSSCCTTTTSHHHHHHHHHHHH---------TSSSCCCEECSSTHHHHHHHHHHHTTTCCCE
T ss_pred             HHHHhhhcChHHHHHHhhhhhhcccCccHHHHHHHHHHHh---------CCCCCEEEEeCcHHHHHHHHHHHHHHcCCcE
Confidence                                   11223355555555543         3556899999999999999999995 59999


Q ss_pred             EEEcCCCCHHHHHHHHHHHhcCC--CcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          402 VALHGGRNQSDRESALRDFRNGS--TNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       402 ~~lh~~~~~~~r~~~~~~f~~g~--~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ..+||++++.+|..+++.|++|+  .+|||||+++++|+|+|++++||+||+|+++..|.||+||+||.
T Consensus       532 ~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~v~~~GlDl~~~~~VI~~d~p~~~~~~~Q~~GR~~R~  600 (968)
T 3dmq_A          532 AVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRI  600 (968)
T ss_dssp             EEECTTSCTTHHHHHHHHHHSTTSSCEEEECSCCTTCSSCCTTCCEEECSSCCSSHHHHHHHHHTTSCS
T ss_pred             EEEeCCCCHHHHHHHHHHHhCCCCcccEEEecchhhcCCCcccCcEEEEecCCCCHHHHHHHhhccccC
Confidence            99999999999999999999998  99999999999999999999999999999999999999999994

>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=100.00  E-value=1.6e-30  Score=273.90  Aligned_cols=317  Identities=15%  Similarity=0.155  Sum_probs=208.3

Q ss_pred             CCcHHHHHHHHHHh---------cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVAL---------SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~---------~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      .++|+|.+++.++.         .++.+|++.+||+|||++++.. +..+............++|||+|+ .|+.||.++
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~-i~~l~~~~~~~~p~~~~~LiV~P~-sll~qW~~E  132 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITL-IWTLLKQSPDCKPEIDKVIVVSPS-SLVRNWYNE  132 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHH-HHHHHHCCTTSSCSCSCEEEEECH-HHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHH-HHHHHHhCccccCCCCcEEEEecH-HHHHHHHHH
Confidence            68999999999875         3456999999999999987554 444444332222334579999997 788999999


Q ss_pred             HHHHhccCCCceEEEEECCccHHHH--HHHh-h-----CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQ--RSEL-R-----GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~-----~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      +.++...  .+.+..++++......  .... .     ...+|+|+|++.+.....  .+....+++||+||||++.+..
T Consensus       133 ~~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~--~l~~~~~~~vI~DEaH~ikn~~  208 (644)
T 1z3i_X          133 VGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD  208 (644)
T ss_dssp             HHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC
T ss_pred             HHHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH--HhhcCCccEEEEECceecCChh
Confidence            9999754  2556666665533211  1111 1     147899999999976432  3445678999999999986543


Q ss_pred             CHHHHHHHHHhCCCCCcEEEEEeeCCHHH----H---------------HHHHHhc------------------------
Q 010709          286 FEPQIREVMQNLPDKHQTLLFSATMPVEI----E---------------ALAQEYL------------------------  322 (503)
Q Consensus       286 ~~~~~~~il~~~~~~~q~i~~SAT~~~~~----~---------------~~~~~~~------------------------  322 (503)
                        ....+.+..++. .+.+++||||-.+-    .               .+.+.|.                        
T Consensus       209 --~~~~~al~~l~~-~~rl~LTgTPiqN~l~El~sll~fl~p~~l~~~~~F~~~f~~pi~~~~~~~~~~~~~~~~~~~~~  285 (644)
T 1z3i_X          209 --NQTYLALNSMNA-QRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRAAGEQKLQ  285 (644)
T ss_dssp             --HHHHHHHHHHCC-SEEEEECSSCSGGGGGGCHHHHHHHHHHHHCCHHHHHHHTHHHHHHHHSTTCCSHHHHHHHHHHH
T ss_pred             --hHHHHHHHhccc-CcEEEEecCcccCCHHHHHHHHHhhCCCcCCCHHHHHHhhcchhhhcCCcCCCHHHHHHHHHHHH
Confidence              233444444543 45799999983221    0               0000000                        


Q ss_pred             -----CCCeEEEeCCCC--CCCCceEEEEEEcChhhHHHHHHHHHHHHH-------------------------------
Q 010709          323 -----TDPVQVKVGKVS--SPTANVIQILEKVSENEKVDRLLALLVEEA-------------------------------  364 (503)
Q Consensus       323 -----~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~-------------------------------  364 (503)
                           ..|..+......  ...+........+.....-..++..+....                               
T Consensus       286 ~L~~~l~~~~lRR~k~~v~~~LP~k~~~~v~~~ls~~q~~lY~~~~~~~~~~~~~~~g~~~~~~l~~l~~Lrk~c~hp~l  365 (644)
T 1z3i_X          286 ELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLFLKQAKPVESLQTGKISVSSLSSITSLKKLCNHPAL  365 (644)
T ss_dssp             HHHHHHHHHEECCCGGGGGGTSCCEEEEEEEECCCHHHHHHHHHHHHHHCGGGSSCTTCCCHHHHHHHHHHHHHHHCTHH
T ss_pred             HHHHHHHHHHHHhhHHhHhhhCCCceEEEEEeCCCHHHHHHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHhCCHHH
Confidence                 001111110000  011111122222211111111111000000                               


Q ss_pred             -----H------------------------------------hhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEE
Q 010709          365 -----F------------------------------------LAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVA  403 (503)
Q Consensus       365 -----~------------------------------------~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~  403 (503)
                           .                                    .......+..++||||+....++.+.+.|...|+.+..
T Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~K~~~l~~ll~~~~~~~~~k~lIFs~~~~~~~~l~~~l~~~g~~~~~  445 (644)
T 1z3i_X          366 IYEKCLTGEEGFDGALDLFPQNYSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVR  445 (644)
T ss_dssp             HHHHHHHTCTTCTTGGGTSCSSCCSSSCCGGGSHHHHHHHHHHHHHHHHCCCEEEEEESCHHHHHHHHHHHHHHTCCEEE
T ss_pred             HHHHHhcccchhhhHHhhccccccccccCcccChHHHHHHHHHHHHhhcCCCEEEEEEccHHHHHHHHHHHHHCCCCEEE
Confidence                 0                                    00000013568999999999999999999999999999


Q ss_pred             EcCCCCHHHHHHHHHHHhcCCCc---EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          404 LHGGRNQSDRESALRDFRNGSTN---ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       404 lh~~~~~~~r~~~~~~f~~g~~~---vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +||++++.+|.++++.|++|...   +|++|.++++|||++++++||+||+|+++..+.|++||++|.
T Consensus       446 l~G~~~~~~R~~~i~~F~~~~~~~~v~L~st~a~g~Glnl~~a~~Vi~~d~~wnp~~~~Qa~gR~~R~  513 (644)
T 1z3i_X          446 LDGTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRD  513 (644)
T ss_dssp             ECSSCCHHHHHHHHHHHHSTTCCCCEEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSST
T ss_pred             EeCCCCHHHHHHHHHHhcCCCCCcEEEEEecccccCCcccccCCEEEEECCCCCccHHHHHHHhhhhc
Confidence            99999999999999999998754   899999999999999999999999999999999999999983

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.4e-31  Score=287.18  Aligned_cols=360  Identities=16%  Similarity=0.202  Sum_probs=237.2

Q ss_pred             CCCCCCCcccCCCHHHHHHHHHHcCceEEecCCCCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHh---
Q 010709           80 NNWKPSDRVLRFNPEQIEEVRLRLNVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL---  156 (503)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~---  156 (503)
                      ..|.....+....++.++.+..+.+........ ...+.....|..+...+...      .-..++++|.+++.+++   
T Consensus       180 ~tWe~~~~~~~~~~~~i~~~~~r~~~~~~~~~~-~~~~~~~~~~~~~~~~p~~~------~~~~Lr~yQ~egv~~l~~~~  252 (800)
T 3mwy_W          180 ATWENATDIVKLAPEQVKHFQNRENSKILPQYS-SNYTSQRPRFEKLSVQPPFI------KGGELRDFQLTGINWMAFLW  252 (800)
T ss_dssp             CBCCBHHHHTTTCHHHHHHHHHTTTCTTCSTTC-CCCCSCCCCCCCCSSCCTTC------CSSCCCTHHHHHHHHHHHHH
T ss_pred             ccccchhhhhhhhHHHHHHHHHhhhcccCCcch-hcccccCCcccccccCCCcc------CCCCcCHHHHHHHHHHHHHh
Confidence            356555555667777888887765433221110 01112222344443322221      12479999999998876   


Q ss_pred             -cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccH
Q 010709          157 -SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI  235 (503)
Q Consensus       157 -~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (503)
                       .++++|++.+||+|||++++..+...+...     ...+.+||||| ..|+.||.+++.+++.   ++.+.+++|+...
T Consensus       253 ~~~~~~ILademGlGKT~~ai~~i~~l~~~~-----~~~~~~LIV~P-~sll~qW~~E~~~~~p---~~~v~~~~g~~~~  323 (800)
T 3mwy_W          253 SKGDNGILADEMGLGKTVQTVAFISWLIFAR-----RQNGPHIIVVP-LSTMPAWLDTFEKWAP---DLNCICYMGNQKS  323 (800)
T ss_dssp             TTTCCEEECCCTTSSTTHHHHHHHHHHHHHH-----SCCSCEEEECC-TTTHHHHHHHHHHHST---TCCEEECCCSSHH
T ss_pred             hcCCCEEEEeCCCcchHHHHHHHHHHHHHhc-----CCCCCEEEEEC-chHHHHHHHHHHHHCC---CceEEEEeCCHHH
Confidence             788999999999999998754443332222     12456899999 5788999999999873   4667777776655


Q ss_pred             HHHHHHh------------hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcE
Q 010709          236 AEQRSEL------------RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQT  303 (503)
Q Consensus       236 ~~~~~~~------------~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~  303 (503)
                      .......            ....+|+|+|++.+......  +....+++|||||||++.+.  .....+.+..++.. ..
T Consensus       324 r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--l~~~~w~~vIvDEaH~lkn~--~s~~~~~l~~l~~~-~r  398 (800)
T 3mwy_W          324 RDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--LGSIKWQFMAVDEAHRLKNA--ESSLYESLNSFKVA-NR  398 (800)
T ss_dssp             HHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--HHTSEEEEEEETTGGGGCCS--SSHHHHHHTTSEEE-EE
T ss_pred             HHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--HhcCCcceeehhhhhhhcCc--hhHHHHHHHHhhhc-cE
Confidence            4443322            23578999999999765432  22346899999999998654  33456666666544 46


Q ss_pred             EEEEeeCC----HHHHHHHHHhcC-----------------------------CCeEEEeCCCC--CCCCceEEEEEEcC
Q 010709          304 LLFSATMP----VEIEALAQEYLT-----------------------------DPVQVKVGKVS--SPTANVIQILEKVS  348 (503)
Q Consensus       304 i~~SAT~~----~~~~~~~~~~~~-----------------------------~~~~~~~~~~~--~~~~~~~~~~~~~~  348 (503)
                      +++||||-    .++..++.....                             .|..+......  ...+........+.
T Consensus       399 l~LTgTPiqN~l~el~~ll~fL~p~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~p~~lRR~k~dv~~~LP~k~~~~v~v~  478 (800)
T 3mwy_W          399 MLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVE  478 (800)
T ss_dssp             EEECSCCCSSCSHHHHHHHHHHCSCCC---------CCTTHHHHHHHHHHHTTGGGEEECCGGGGTTTSCCEEEEEEEEC
T ss_pred             EEeeCCcCCCCHHHHHHHHHHhCccccCchhhhcccccchhHHHHHHHHHHHHhHHHhhhhHHhhhhccCCcEEEEEEeC
Confidence            88999982    222222221111                             11122111100  00111112222221


Q ss_pred             hh---------------------------------------------------------------------------hHH
Q 010709          349 EN---------------------------------------------------------------------------EKV  353 (503)
Q Consensus       349 ~~---------------------------------------------------------------------------~k~  353 (503)
                      ..                                                                           .|+
T Consensus       479 ls~~q~~~Y~~i~~~~~~~l~~~~~~~~~~~l~~l~~Lrk~~~hp~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~K~  558 (800)
T 3mwy_W          479 LSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKM  558 (800)
T ss_dssp             CCHHHHHHHHHHHHHCCC----------CTHHHHHHHHHHHHHCGGGSSSHHHHHCCCC----CCSHHHHHHHHHTCHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHhhccccchhhHHHHHHHHHHHhcChhhhcchHHHHHHhcccccccHHHHHHHhhhcChHH
Confidence            11                                                                           122


Q ss_pred             HHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC---cEEEE
Q 010709          354 DRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGST---NILVA  430 (503)
Q Consensus       354 ~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~---~vLva  430 (503)
                      ..+..++...       ...+.++||||+....++.|.++|...|+.+..+||+++..+|.++++.|++|..   .+|++
T Consensus       559 ~~L~~lL~~~-------~~~g~kvLIFsq~~~~ld~L~~~L~~~g~~~~~i~G~~~~~eR~~~i~~F~~~~~~~~v~LlS  631 (800)
T 3mwy_W          559 VLLDQLLTRL-------KKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLS  631 (800)
T ss_dssp             HHHHHHHHHH-------TTTTCCEEEEESCHHHHHHHHHHHHHHTCCCEEESTTSCHHHHHHHHHTTSSTTCSCCCEEEE
T ss_pred             HHHHHHHHHH-------hhCCCeEEEEechHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHHhhCCCCCceEEEEe
Confidence            2222222211       1245689999999999999999999999999999999999999999999998654   49999


Q ss_pred             ccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          431 TDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       431 T~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      |.++++|||++.+++||+||+|+++..+.||+||++|
T Consensus       632 t~agg~GlNL~~a~~VI~~D~~wnp~~~~Qa~gR~~R  668 (800)
T 3mwy_W          632 TRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHR  668 (800)
T ss_dssp             HHHHTTTCCCTTCCEEEESSCCSCSHHHHHHHTTTSC
T ss_pred             cccccCCCCccccceEEEecCCCChhhHHHHHHHHHh
Confidence            9999999999999999999999999999999999999

>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=99.98  E-value=2e-31  Score=289.57  Aligned_cols=311  Identities=12%  Similarity=0.068  Sum_probs=209.2

Q ss_pred             CCCcHHHHHHHHHHhc--------------CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          142 TRPTSIQAQAMPVALS--------------GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~--------------~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      ..|+++|.+|++.++.              +++++++++||||||+++ ++++..+...     ...+++|||+|+++|+
T Consensus       270 ~~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~-----~~~~rvLvlvpr~eL~  343 (1038)
T 2w00_A          270 LVMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATEL-----DFIDKVFFVVDRKDLD  343 (1038)
T ss_dssp             EECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTC-----TTCCEEEEEECGGGCC
T ss_pred             ccCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhc-----CCCceEEEEeCcHHHH
Confidence            3599999999999875              367999999999999997 6666443221     2246899999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhh-CCCcEEEECcHHHHHHHHcCC--CCCCCccEEEecchhHHhhC
Q 010709          208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELR-GGVSIVVATPGRFLDHLQQGN--TSLSRVSFVILDEADRMLDM  284 (503)
Q Consensus       208 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~Ilv~Tp~~l~~~l~~~~--~~l~~~~~vViDEaH~l~~~  284 (503)
                      .|+.+.++.+....       +.++.........+. .+.+|+|+|+++|...+....  ..+..+.+||+||||++.. 
T Consensus       344 ~Q~~~~f~~f~~~~-------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~-  415 (1038)
T 2w00_A          344 YQTMKEYQRFSPDS-------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF-  415 (1038)
T ss_dssp             HHHHHHHHTTSTTC-------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH-
T ss_pred             HHHHHHHHHhcccc-------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc-
Confidence            99999998876421       224444444444453 568999999999998876532  2456789999999999763 


Q ss_pred             CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHH----HHHHHhcCC-----------------CeEEEeCCCCCCCC--ceE
Q 010709          285 GFEPQIREVMQNLPDKHQTLLFSATMPVEIE----ALAQEYLTD-----------------PVQVKVGKVSSPTA--NVI  341 (503)
Q Consensus       285 ~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~----~~~~~~~~~-----------------~~~~~~~~~~~~~~--~~~  341 (503)
                        ...+..+...+++ .++++|||||.....    .....++++                 |..+..........  ...
T Consensus       416 --~~~~~~I~~~~p~-a~~lgfTATP~~~~~~~~~~~t~~~FG~~i~~Y~l~~AI~dg~l~p~~v~y~~v~~~~~~~~~e  492 (1038)
T 2w00_A          416 --GEAQKNLKKKFKR-YYQFGFTGTPIFPENALGSETTASVFGRELHSYVITDAIRDEKVLKFKVDYNDVRPQFKSLETE  492 (1038)
T ss_dssp             --HHHHHHHHHHCSS-EEEEEEESSCCCSTTCTTSCCHHHHHCSEEEEECHHHHHHHTSSCCEEEEECCCCGGGHHHHTC
T ss_pred             --hHHHHHHHHhCCc-ccEEEEeCCccccccchhhhHHHHHhCCeeEeecHHHHHhCCCcCCeEEEEEeccchhhhcccc
Confidence              3345667777754 689999999964321    112222232                 22221111000000  000


Q ss_pred             ---------EEEEEcChhhHHHHHHHHHHHHHHhhhcc---CCCCCcEEEEEcchhhHHHHHHHHHHCC-----------
Q 010709          342 ---------QILEKVSENEKVDRLLALLVEEAFLAEKS---CHPFPLTIVFVERKTRCDEVSEALVAEG-----------  398 (503)
Q Consensus       342 ---------~~~~~~~~~~k~~~l~~~l~~~~~~~~~~---~~~~~~~lIF~~~~~~~~~l~~~L~~~~-----------  398 (503)
                               ..........++..+...+..+.......   .....++||||.++..|..+++.|.+.+           
T Consensus       493 ~d~~~~~~i~~~~~l~~~~ri~~I~~~Il~~~~~~~~~~~~~~~g~kamVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~  572 (1038)
T 2w00_A          493 TDEKKLSAAENQQAFLHPMRIQEITQYILNNFRQKTHRTFPGSKGFNAMLAVSSVDAAKAYYATFKRLQEEAANKSATYK  572 (1038)
T ss_dssp             CCHHHHHHTCSTTTTTCHHHHHHHHHHHHHHHHHHTTCSSSSCCCCEEEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCC
T ss_pred             ccHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhhhcccCCCCcEEEEECCHHHHHHHHHHHHhhhhhhcccccccc
Confidence                     00000012223334444343332221110   1123579999999999999999997754           


Q ss_pred             -CeEE-EEcCC----------C----------CH-----------------------------HHHHHHHHHHhcCCCcE
Q 010709          399 -LHAV-ALHGG----------R----------NQ-----------------------------SDRESALRDFRNGSTNI  427 (503)
Q Consensus       399 -~~v~-~lh~~----------~----------~~-----------------------------~~r~~~~~~f~~g~~~v  427 (503)
                       +++. .+|++          +          ++                             .+|..+++.|++|+.+|
T Consensus       573 ~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dyn~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~I  652 (1038)
T 2w00_A          573 PLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREYNSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDL  652 (1038)
T ss_dssp             CCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHHHHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSE
T ss_pred             cCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHHHHHHHHhcccccccchhhhHHHHHHHHHHHcCCCeE
Confidence             4554 45542          2          22                             14788999999999999


Q ss_pred             EEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeeee
Q 010709          428 LVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNIT  470 (503)
Q Consensus       428 LvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~~  470 (503)
                      ||+|+++.+|+|+|.+ .|+++|.|.+...|+||+||++|..-
T Consensus       653 LIvvd~lltGfDiP~l-~tlylDkpl~~~~liQaIGRtnR~~~  694 (1038)
T 2w00_A          653 LIVVGMFLTGFDAPTL-NTLFVDKNLRYHGLMQAFSRTNRIYD  694 (1038)
T ss_dssp             EEESSTTSSSCCCTTE-EEEEEESCCCHHHHHHHHHTTCCCCC
T ss_pred             EEEcchHHhCcCcccc-cEEEEccCCCccceeehhhccCcCCC
Confidence            9999999999999999 78899999999999999999999764

>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=99.97  E-value=5.6e-30  Score=259.89  Aligned_cols=301  Identities=17%  Similarity=0.178  Sum_probs=221.1

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+++|..+...+..|+  |..+.||.|||+++.+|++...+.        |..+.|++|++.||.|-++.+..+...+ 
T Consensus        75 r~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~--------G~~vhVvT~ndyLA~rdae~m~~l~~~L-  143 (822)
T 3jux_A           75 RPFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI--------GKGVHLVTVNDYLARRDALWMGPVYLFL-  143 (822)
T ss_dssp             CCCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHHHHT-
T ss_pred             CCcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc--------CCceEEEeccHHHHHhHHHHHHHHHHHh-
Confidence            79999999999888886  899999999999999999876554        5679999999999999999999998877 


Q ss_pred             CceEEEEECC--------------------------------------------------ccHHHHHHHhhCCCcEEEEC
Q 010709          223 SFKTAIVVGG--------------------------------------------------TNIAEQRSELRGGVSIVVAT  252 (503)
Q Consensus       223 ~~~~~~~~~~--------------------------------------------------~~~~~~~~~~~~~~~Ilv~T  252 (503)
                      ++.+++++..                                                  ....+  +.....++|+++|
T Consensus       144 glsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~e--rr~aY~~DItYgT  221 (822)
T 3jux_A          144 GLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEIT--RKEAYLCDVTYGT  221 (822)
T ss_dssp             TCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCBCC--HHHHHHSSEEEEE
T ss_pred             CCEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCHHH--HHHHhcCCCEEcc
Confidence            5999998872                                                  11111  1122348999999


Q ss_pred             cHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hCC------------CH---HH--------------------
Q 010709          253 PGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DMG------------FE---PQ--------------------  289 (503)
Q Consensus       253 p~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~~------------~~---~~--------------------  289 (503)
                      ..-| .+.+..+      ....+.+.+.||||+|.++ +..            -.   ..                    
T Consensus       222 n~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiLIDeArtPLiISg~~~~~~~~y~~~~~~v~~l~~~~dy~vdek~  301 (822)
T 3jux_A          222 NNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKA  301 (822)
T ss_dssp             HHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHHTTGGGSCEEEECCCCSCHHHHHHHHHHTTSSCBTTTEEECCSS
T ss_pred             CcchhhHhHHhhccCCHHHhccCCCCeEEEecccceeecCCCCCceeeCCCCCccHHHHHHHHHHHhcCcCCcEEEEccc
Confidence            9887 3444322      2234678999999999632 100            00   00                    


Q ss_pred             ---------------------------------HHHHHH---hCCC----------------------------------
Q 010709          290 ---------------------------------IREVMQ---NLPD----------------------------------  299 (503)
Q Consensus       290 ---------------------------------~~~il~---~~~~----------------------------------  299 (503)
                                                       +...++   .+..                                  
T Consensus       302 ~~v~lTe~G~~~~E~~l~i~nly~~~n~~l~~~i~~AL~A~~l~~~d~dYiV~dg~V~iVDe~TGR~m~grr~s~GLHQa  381 (822)
T 3jux_A          302 RTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQA  381 (822)
T ss_dssp             SCEEECHHHHHHHHHHHTCSCTTSGGGHHHHHHHHHHHHHHHHSTTTSSEEEETTEEEECSSSSCSCCCSCCCGGGHHHH
T ss_pred             CeEEECHHHHHHHHHHhCCccccchhhhHHHHHHHHHHHHHHHHcCCCcEEEECCEEEEEECCCCcCCCCCcCchHHHHH
Confidence                                             000000   0100                                  


Q ss_pred             ---------------------------CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEE-EEEEcChhh
Q 010709          300 ---------------------------KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQ-ILEKVSENE  351 (503)
Q Consensus       300 ---------------------------~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  351 (503)
                                                 -.++.+||+|...+...+.+.|-.+  .+.+ +...+.....+ .........
T Consensus       382 iEaKEgv~i~~e~~tla~IT~Qn~Fr~Y~kL~GMTGTa~te~~Ef~~iY~l~--vv~I-Ptnkp~~R~d~~d~vy~t~~e  458 (822)
T 3jux_A          382 IEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGME--VVVI-PTHKPMIRKDHDDLVFRTQKE  458 (822)
T ss_dssp             HHHHHSSCCCCCCCEEEEECHHHHHTTSSEEEEEESSCGGGHHHHHHHSCCC--EEEC-CCSSCCCCEECCCEEESSHHH
T ss_pred             HHHHcCCCCCCCcchhHHHHHHHHHHHhhHHeEECCCCchHHHHHHHHhCCe--EEEE-CCCCCcceeecCcEEEecHHH
Confidence                                       0268999999988777766655333  2323 22223223322 345667788


Q ss_pred             HHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc
Q 010709          352 KVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVAT  431 (503)
Q Consensus       352 k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT  431 (503)
                      |...+...+......       ..++||||++++.++.+++.|.+.|+.+..+||+..+.++..+.+.++.|  .|+|||
T Consensus       459 K~~al~~~I~~~~~~-------gqpVLVFt~S~e~sE~Ls~~L~~~Gi~~~vLhgkq~~rE~~ii~~ag~~g--~VtVAT  529 (822)
T 3jux_A          459 KYEKIVEEIEKRYKK-------GQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKG--MVTIAT  529 (822)
T ss_dssp             HHHHHHHHHHHHHHH-------TCCEEEEESSHHHHHHHHHHHHTTTCCCEEECSCHHHHHHHHHHHHHSTT--CEEEEE
T ss_pred             HHHHHHHHHHHHhhC-------CCCEEEEECCHHHHHHHHHHHHHCCCCEEEeeCCchHHHHHHHHhCCCCC--eEEEEc
Confidence            888888888765322       23699999999999999999999999999999997666666666666655  699999


Q ss_pred             cccccCCCCC--------CCCEEEEccCCCChhHHHHhhCcceee
Q 010709          432 DVASRGLDVM--------GVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       432 ~~~~~Gldip--------~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ++++||+||+        +..+||++++|.+...|.||+||+||.
T Consensus       530 dmAgRGtDI~lg~~V~~~GglhVInte~Pes~r~y~qriGRTGRq  574 (822)
T 3jux_A          530 NMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQ  574 (822)
T ss_dssp             TTTTTTCCCCCCTTTTTTTSCEEEESSCCSSHHHHHHHHTTSSCS
T ss_pred             chhhCCcCccCCcchhhcCCCEEEecCCCCCHHHHHHhhCccccC
Confidence            9999999998        667999999999999999999999994

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.95  E-value=1.4e-25  Score=232.03  Aligned_cols=131  Identities=21%  Similarity=0.273  Sum_probs=112.4

Q ss_pred             HCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          138 FHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       138 ~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ..|+ .|+++|..+++.+++|+  |..+.||+|||++|.+|++...+.        +..++|++||++||.|.++.+..+
T Consensus        75 ~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~--------G~qv~VvTPTreLA~Qdae~m~~l  143 (997)
T 2ipc_A           75 YLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT--------GKGVHVVTVNDYLARRDAEWMGPV  143 (997)
T ss_dssp             HTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT--------CSCCEEEESSHHHHHHHHHHHHHH
T ss_pred             HhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh--------CCCEEEEeCCHHHHHHHHHHHHHH
Confidence            4788 99999999999999998  999999999999999999765443        457999999999999999999999


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcCC------CCCC---CccEEEecchhHHh
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQGN------TSLS---RVSFVILDEADRML  282 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~------~~l~---~~~~vViDEaH~l~  282 (503)
                      ...+ ++++.+++||.....  +....+++|+|+||+.| ++++..+.      +.+.   .+.++||||+|.++
T Consensus       144 ~~~l-GLsv~~i~Gg~~~~~--r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          144 YRGL-GLSVGVIQHASTPAE--RRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             HHTT-TCCEEECCTTCCHHH--HHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHHHT
T ss_pred             HHhc-CCeEEEEeCCCCHHH--HHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHHHH
Confidence            9877 699999999987543  33345699999999999 78887652      4567   89999999999876

>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=99.95  E-value=2.9e-26  Score=241.24  Aligned_cols=154  Identities=22%  Similarity=0.177  Sum_probs=116.5

Q ss_pred             CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEE
Q 010709          300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIV  379 (503)
Q Consensus       300 ~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lI  379 (503)
                      ..|++++|||++......    ..  ..+.............  +.......+...++..+.....       ...++||
T Consensus       380 ~~q~i~~SAT~~~~~~~~----~~--~~~~~~~r~~~l~~p~--i~v~~~~~~~~~Ll~~l~~~~~-------~~~~vlV  444 (664)
T 1c4o_A          380 VSQVVFVSATPGPFELAH----SG--RVVEQIIRPTGLLDPL--VRVKPTENQILDLMEGIRERAA-------RGERTLV  444 (664)
T ss_dssp             CSEEEEEESSCCHHHHHH----CS--EEEEECSCTTCCCCCE--EEEECSTTHHHHHHHHHHHHHH-------TTCEEEE
T ss_pred             cCCEEEEecCCCHHHHHh----hh--CeeeeeeccCCCCCCe--EEEecccchHHHHHHHHHHHHh-------cCCEEEE
Confidence            578999999997643211    11  1111111110000111  1122333455566555544332       2347999


Q ss_pred             EEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC-----CCC
Q 010709          380 FVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL-----PKV  454 (503)
Q Consensus       380 F~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~-----p~s  454 (503)
                      ||+++..++.+++.|...|+.+..+||++++.+|.++++.|+.|+.+|||||+++++|+|+|++++||++|.     |.+
T Consensus       445 f~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l~~GlDip~v~lVI~~d~d~~G~p~s  524 (664)
T 1c4o_A          445 TVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADKEGFLRS  524 (664)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCCCTTCCCTTEEEEEETTTTSCSGGGS
T ss_pred             EECCHHHHHHHHHHHHhcCCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChhhcCccCCCCCEEEEeCCcccCCCCC
Confidence            999999999999999999999999999999999999999999999999999999999999999999999997     899


Q ss_pred             hhHHHHhhCcceee
Q 010709          455 LLAASESLCTTSFN  468 (503)
Q Consensus       455 ~~~~~Qr~GR~gR~  468 (503)
                      ..+|+||+||+||.
T Consensus       525 ~~~~iQr~GRagR~  538 (664)
T 1c4o_A          525 ERSLIQTIGRAARN  538 (664)
T ss_dssp             HHHHHHHHGGGTTS
T ss_pred             HHHHHHHHCccCcC
Confidence            99999999999995

>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=99.94  E-value=6.9e-25  Score=230.64  Aligned_cols=155  Identities=18%  Similarity=0.204  Sum_probs=117.5

Q ss_pred             CCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEE
Q 010709          299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTI  378 (503)
Q Consensus       299 ~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~l  378 (503)
                      ...|++++|||++......    ................. .   +.......+...++..+....       ....++|
T Consensus       385 ~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~~l~~p-~---i~v~~~~~~~~~Ll~~l~~~~-------~~~~~vl  449 (661)
T 2d7d_A          385 HMHNIVYVSATPGPYEIEH----TDEMVEQIIRPTGLLDP-L---IDVRPIEGQIDDLIGEIQARI-------ERNERVL  449 (661)
T ss_dssp             TCSEEEEECSSCCHHHHHH----CSSCEEECCCTTCCCCC-E---EEEECSTTHHHHHHHHHHHHH-------TTTCEEE
T ss_pred             cCCCEEEEecCCChhHHHh----hhCeeeeeecccCCCCC-e---EEEecccchHHHHHHHHHHHH-------hcCCeEE
Confidence            3578999999997653221    11222211111111111 1   112233345555655554432       1335799


Q ss_pred             EEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccC-----CC
Q 010709          379 VFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDL-----PK  453 (503)
Q Consensus       379 IF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~-----p~  453 (503)
                      |||+++..++.+++.|...|+.+..+||++++.+|.++++.|+.|+.+|||||+++++|+|+|++++||++|.     |.
T Consensus       450 Vf~~t~~~ae~L~~~L~~~gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~~l~~GlDip~v~lVi~~d~d~~G~p~  529 (661)
T 2d7d_A          450 VTTLTKKMSEDLTDYLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLR  529 (661)
T ss_dssp             EECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCCCSTTCCCTTEEEEEETTTTCCTTTT
T ss_pred             EEECCHHHHHHHHHHHHhcCCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecchhhCCcccCCCCEEEEeCcccccCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999997     99


Q ss_pred             ChhHHHHhhCcceee
Q 010709          454 VLLAASESLCTTSFN  468 (503)
Q Consensus       454 s~~~~~Qr~GR~gR~  468 (503)
                      +..+|+||+||+||.
T Consensus       530 s~~~~iQr~GRagR~  544 (661)
T 2d7d_A          530 SERSLIQTIGRAARN  544 (661)
T ss_dssp             SHHHHHHHHHTTTTS
T ss_pred             CHHHHHHHhCcccCC
Confidence            999999999999995

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=99.92  E-value=1.1e-24  Score=193.26  Aligned_cols=140  Identities=34%  Similarity=0.535  Sum_probs=113.2

Q ss_pred             HHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCC
Q 010709          319 QEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEG  398 (503)
Q Consensus       319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~  398 (503)
                      ..|+.+|..+.+........++.+.+..+....|...+..++..          ..+++||||+++..++.+++.|...|
T Consensus         9 ~~~~~~p~~i~v~~~~~~~~~i~q~~~~~~~~~K~~~L~~~l~~----------~~~~~lVF~~~~~~~~~l~~~L~~~g   78 (191)
T 2p6n_A            9 SGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQK----------TPPPVLIFAEKKADVDAIHEYLLLKG   78 (191)
T ss_dssp             -------------------CCSEEEEEECCGGGHHHHHHHHHTT----------SCSCEEEECSCHHHHHHHHHHHHHHT
T ss_pred             ccccCCCEEEEECCCCCCCcCceEEEEEcChHHHHHHHHHHHHh----------CCCCEEEEECCHHHHHHHHHHHHHcC
Confidence            35778898888877777788899999999999999888877643          23479999999999999999999999


Q ss_pred             CeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          399 LHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       399 ~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.+..+||++++.+|.++++.|++|+.+|||||+++++|+|+|++++||+||+|.+...|+||+||+||.
T Consensus        79 ~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~~~~~Gldi~~v~~VI~~d~p~~~~~~~qr~GR~gR~  148 (191)
T 2p6n_A           79 VEAVAIHGGKDQEERTKAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCS  148 (191)
T ss_dssp             CCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECHHHHTTCCCCCCSEEEESSCCSSHHHHHHHHTTSCC-
T ss_pred             CcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcCchhcCCCcccCCEEEEeCCCCCHHHHHHHhCccccC
Confidence            9999999999999999999999999999999999999999999999999999999999999999999995

>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=99.91  E-value=8.7e-25  Score=199.20  Aligned_cols=167  Identities=20%  Similarity=0.231  Sum_probs=120.3

Q ss_pred             CCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH-HHHHHHHH
Q 010709          139 HEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ-IEKEVKAL  217 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q-~~~~~~~~  217 (503)
                      .....|+++|.++++.+++++++++++|||+|||++|+++++..+.....  ...++++||++|+++|+.| +.+.++.+
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~--~~~~~~~lil~p~~~L~~q~~~~~~~~~  106 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK--ASEPGKVIVLVNKVLLVEQLFRKEFQPF  106 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH--TTCCCCEEEEESSHHHHHHHHHHTHHHH
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc--ccCCCcEEEEECHHHHHHHHHHHHHHHH
Confidence            34568999999999999999999999999999999999988876554211  1235779999999999999 88888888


Q ss_pred             hccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCC------CCCCCccEEEecchhHHhhCCCHHHHH
Q 010709          218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGN------TSLSRVSFVILDEADRMLDMGFEPQIR  291 (503)
Q Consensus       218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~------~~l~~~~~vViDEaH~l~~~~~~~~~~  291 (503)
                      ...  ++.+..+.|+............+++|+|+||++|.+.+....      ..+.++++|||||||++.+.++...+.
T Consensus       107 ~~~--~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~~  184 (216)
T 3b6e_A          107 LKK--WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIM  184 (216)
T ss_dssp             HTT--TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHHH
T ss_pred             hcc--CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHHH
Confidence            754  467777777765443333344468999999999999887643      567889999999999998765555443


Q ss_pred             -HHHHhC-------------CCCCcEEEEEee
Q 010709          292 -EVMQNL-------------PDKHQTLLFSAT  309 (503)
Q Consensus       292 -~il~~~-------------~~~~q~i~~SAT  309 (503)
                       .++...             .+..++|+||||
T Consensus       185 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          185 RHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHHhcccccccccccCCCCcceEEEeecC
Confidence             322211             157889999998

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=99.91  E-value=1.9e-23  Score=181.01  Aligned_cols=125  Identities=30%  Similarity=0.410  Sum_probs=115.7

Q ss_pred             CCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHH
Q 010709          335 SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRE  414 (503)
Q Consensus       335 ~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~  414 (503)
                      ....++.+.+..++...|...+..++...         ..+++||||+++..++.+++.|...|+.+..+||++++.+|.
T Consensus         5 ~~~~~i~~~~~~~~~~~K~~~L~~ll~~~---------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~   75 (163)
T 2hjv_A            5 LTTRNIEHAVIQVREENKFSLLKDVLMTE---------NPDSCIIFCRTKEHVNQLTDELDDLGYPCDKIHGGMIQEDRF   75 (163)
T ss_dssp             -CCCCEEEEEEECCGGGHHHHHHHHHHHH---------CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHH
T ss_pred             cCcccceEEEEECChHHHHHHHHHHHHhc---------CCCcEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHH
Confidence            34556889999999999999988887653         345799999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          415 SALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       415 ~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .+++.|++|+.+|||||+++++|+|+|++++||+||+|.+...|+||+||+||.
T Consensus        76 ~~~~~f~~g~~~vlv~T~~~~~Gld~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~  129 (163)
T 2hjv_A           76 DVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRA  129 (163)
T ss_dssp             HHHHHHHTTSCSEEEECGGGTTTCCCSCCSEEEESSCCSSHHHHHHHTTTSSCT
T ss_pred             HHHHHHHcCCCeEEEECChhhcCCchhcCCEEEEeCCCCCHHHHHHhccccCcC
Confidence            999999999999999999999999999999999999999999999999999995

>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=99.90  E-value=1.7e-23  Score=182.86  Aligned_cols=122  Identities=29%  Similarity=0.415  Sum_probs=113.7

Q ss_pred             CceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHH
Q 010709          338 ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL  417 (503)
Q Consensus       338 ~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~  417 (503)
                      ..+.+.+..++...|...+..++...         +.+++||||+++..++.+++.|...|+.+..+||++++.+|..++
T Consensus         4 ~~i~q~~~~~~~~~K~~~L~~ll~~~---------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~hg~~~~~~r~~~~   74 (172)
T 1t5i_A            4 HGLQQYYVKLKDNEKNRKLFDLLDVL---------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRY   74 (172)
T ss_dssp             -CCEEEEEECCGGGHHHHHHHHHHHS---------CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CCeEEEEEECChHHHHHHHHHHHHhC---------CCCcEEEEECCHHHHHHHHHHHHhcCCCEEEEECCCCHHHHHHHH
Confidence            46788899999999999888887642         456899999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       418 ~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|++|+.+|||||+++++|+|+|++++||+||+|++...|+||+||+||.
T Consensus        75 ~~f~~g~~~vLvaT~~~~~Gldi~~~~~Vi~~d~p~~~~~~~qr~GR~~R~  125 (172)
T 1t5i_A           75 QQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRF  125 (172)
T ss_dssp             HHHHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGG
T ss_pred             HHHHCCCCcEEEECCchhcCcchhhCCEEEEECCCCCHHHHHHHhcccccC
Confidence            999999999999999999999999999999999999999999999999995

>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=99.90  E-value=4.8e-23  Score=182.00  Aligned_cols=127  Identities=41%  Similarity=0.561  Sum_probs=102.5

Q ss_pred             CCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHH
Q 010709          334 SSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR  413 (503)
Q Consensus       334 ~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r  413 (503)
                      .....++.+.+..++...|...|..++...        .+.+++||||+++..++.+++.|...|+.+..+||++++.+|
T Consensus        14 ~~~~~~i~q~~~~v~~~~K~~~L~~ll~~~--------~~~~k~lVF~~~~~~~~~l~~~L~~~g~~~~~lhg~~~~~~r   85 (185)
T 2jgn_A           14 GSTSENITQKVVWVEESDKRSFLLDLLNAT--------GKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDR   85 (185)
T ss_dssp             --CCTTEEEEEEECCGGGHHHHHHHHHHHC---------CCSCEEEEESCHHHHHHHHHHHHHTTCCEEEEC--------
T ss_pred             CCCCCCceEEEEEeCcHHHHHHHHHHHHhc--------CCCCeEEEEECCHHHHHHHHHHHHHcCCceEEEeCCCCHHHH
Confidence            345668999999999999999888887652        245679999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          414 ESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       414 ~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ..+++.|++|+.+|||||+++++|+|+|++++||+||+|++..+|+||+||+||.
T Consensus        86 ~~~~~~f~~g~~~vLvaT~~~~~Gldi~~~~~VI~~d~p~s~~~~~Qr~GR~~R~  140 (185)
T 2jgn_A           86 EEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV  140 (185)
T ss_dssp             CHHHHHHHHTSSSEEEEEC------CCCSBSEEEESSCCSSHHHHHHHHTTBCCT
T ss_pred             HHHHHHHHcCCCeEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHccccCCC
Confidence            9999999999999999999999999999999999999999999999999999994

>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=99.90  E-value=2.1e-23  Score=192.32  Aligned_cols=182  Identities=18%  Similarity=0.217  Sum_probs=131.4

Q ss_pred             HHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHH
Q 010709          130 PSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQ  209 (503)
Q Consensus       130 ~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q  209 (503)
                      +.+.+.+.......++++|.++++.+..|++++++||||+|||+++.++++........   ..+.++++++|+++++.|
T Consensus        48 ~~~~~~~~~~~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~---~~~~~~l~~~p~~~la~q  124 (235)
T 3llm_A           48 HDLQAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR---AAECNIVVTQPRRISAVS  124 (235)
T ss_dssp             HHHHHHHHHHHTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC---GGGCEEEEEESSHHHHHH
T ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC---CCceEEEEeccchHHHHH
Confidence            33444444444556799999999999999999999999999999988888877665421   234589999999999999


Q ss_pred             HHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH-hhCCCH-
Q 010709          210 IEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM-LDMGFE-  287 (503)
Q Consensus       210 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l-~~~~~~-  287 (503)
                      +++.+.......-+..++.......     .....+++|+|+|||+|.+++..   .+.++++||+||||++ .+.+|. 
T Consensus       125 ~~~~~~~~~~~~~~~~~g~~~~~~~-----~~~~~~~~Ivv~Tpg~l~~~l~~---~l~~~~~lVlDEah~~~~~~~~~~  196 (235)
T 3llm_A          125 VAERVAFERGEEPGKSCGYSVRFES-----ILPRPHASIMFCTVGVLLRKLEA---GIRGISHVIVDEIHERDINTDFLL  196 (235)
T ss_dssp             HHHHHHHTTTCCTTSSEEEEETTEE-----ECCCSSSEEEEEEHHHHHHHHHH---CCTTCCEEEECCTTSCCHHHHHHH
T ss_pred             HHHHHHHHhccccCceEEEeechhh-----ccCCCCCeEEEECHHHHHHHHHh---hhcCCcEEEEECCccCCcchHHHH
Confidence            9988876653322233332222111     00124588999999999999876   4889999999999985 666666 


Q ss_pred             HHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCC
Q 010709          288 PQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDP  325 (503)
Q Consensus       288 ~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~  325 (503)
                      ..+..++... ++.|+++||||++.+.  +.+.+...|
T Consensus       197 ~~l~~i~~~~-~~~~~il~SAT~~~~~--~~~~~~~~p  231 (235)
T 3llm_A          197 VVLRDVVQAY-PEVRIVLMSATIDTSM--FCEYFFNCP  231 (235)
T ss_dssp             HHHHHHHHHC-TTSEEEEEECSSCCHH--HHHHTTSCC
T ss_pred             HHHHHHHhhC-CCCeEEEEecCCCHHH--HHHHcCCCC
Confidence            3556666655 5789999999998775  444444444

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=99.90  E-value=5.9e-23  Score=178.39  Aligned_cols=121  Identities=26%  Similarity=0.412  Sum_probs=109.5

Q ss_pred             ceEEEEEEcChhh-HHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHH
Q 010709          339 NVIQILEKVSENE-KVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL  417 (503)
Q Consensus       339 ~~~~~~~~~~~~~-k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~  417 (503)
                      ++.+.+..+.... |...+..++...         +.+++||||+++..++.+++.|...++.+..+||++++.+|..++
T Consensus         3 ~i~~~~~~~~~~~~K~~~l~~ll~~~---------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~~   73 (165)
T 1fuk_A            3 GIKQFYVNVEEEEYKYECLTDLYDSI---------SVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIM   73 (165)
T ss_dssp             -CEEEEEEEESGGGHHHHHHHHHHHT---------TCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHH
T ss_pred             CcEEEEEECCcchhHHHHHHHHHHhC---------CCCCEEEEECCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHH
Confidence            5677788887776 888888777652         456799999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       418 ~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|++|+.+|||||+++++|+|+|++++||++|+|++...|.||+||+||.
T Consensus        74 ~~f~~g~~~vlv~T~~~~~G~d~~~~~~Vi~~~~p~~~~~~~qr~GR~gR~  124 (165)
T 1fuk_A           74 KEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRF  124 (165)
T ss_dssp             HHHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC--
T ss_pred             HHHHcCCCEEEEEcChhhcCCCcccCCEEEEeCCCCCHHHHHHHhcccccC
Confidence            999999999999999999999999999999999999999999999999995

>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=99.90  E-value=5.6e-23  Score=180.35  Aligned_cols=124  Identities=23%  Similarity=0.350  Sum_probs=110.4

Q ss_pred             CCCceEEEEEEcChhh-HHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHH
Q 010709          336 PTANVIQILEKVSENE-KVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRE  414 (503)
Q Consensus       336 ~~~~~~~~~~~~~~~~-k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~  414 (503)
                      ...++.+.+..++... |...+..++..         .+.+++||||+++..++.+++.|...|+.+..+||++++.+|.
T Consensus         4 ~~~~i~q~~~~~~~~~~K~~~L~~ll~~---------~~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~R~   74 (175)
T 2rb4_A            4 TLNNIRQYYVLCEHRKDKYQALCNIYGS---------ITIGQAIIFCQTRRNAKWLTVEMIQDGHQVSLLSGELTVEQRA   74 (175)
T ss_dssp             CBCCEEEEEEECSSHHHHHHHHHHHHTT---------SCCSEEEEECSCHHHHHHHHHHHHTTTCCEEEECSSCCHHHHH
T ss_pred             ccCCceEEEEEcCChHhHHHHHHHHHHh---------CCCCCEEEEECCHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHH
Confidence            3457888898888765 88777776643         2456899999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCC------CChhHHHHhhCcceee
Q 010709          415 SALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP------KVLLAASESLCTTSFN  468 (503)
Q Consensus       415 ~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p------~s~~~~~Qr~GR~gR~  468 (503)
                      .+++.|++|+.+|||||+++++|+|+|++++||+||+|      .+..+|+||+||+||.
T Consensus        75 ~~~~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~d~p~~~~~~~~~~~~~qr~GR~gR~  134 (175)
T 2rb4_A           75 SIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRF  134 (175)
T ss_dssp             HHHHHHHTTSCSEEEECCSCCTTTCCTTEEEEEESSCCC--CCSCCHHHHHHHHCBC---
T ss_pred             HHHHHHHcCCCeEEEEecchhcCCCcccCCEEEEeCCCCCccccCCHHHHHHHhcccccC
Confidence            99999999999999999999999999999999999999      9999999999999995

>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=99.89  E-value=1.1e-22  Score=183.90  Aligned_cols=120  Identities=33%  Similarity=0.400  Sum_probs=110.0

Q ss_pred             eEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHH
Q 010709          340 VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRD  419 (503)
Q Consensus       340 ~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~  419 (503)
                      +.+....++...|...+..++...         +.+++||||+++..++.+++.|...|+.+..+||++++.+|..+++.
T Consensus         6 ~~~~~~~~~~~~k~~~l~~ll~~~---------~~~~~lVF~~~~~~~~~l~~~L~~~~~~~~~lhg~~~~~~r~~~~~~   76 (212)
T 3eaq_A            6 YEEEAVPAPVRGRLEVLSDLLYVA---------SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDLSQGERERVLGA   76 (212)
T ss_dssp             BCCEEEECCTTSHHHHHHHHHHHH---------CCSCEEEECSSHHHHHHHHHHHHHHTCCEEEECSSSCHHHHHHHHHH
T ss_pred             eeeeEEeCCHHHHHHHHHHHHHhC---------CCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCCHHHHHHHHHH
Confidence            345556677788998888887643         35679999999999999999999999999999999999999999999


Q ss_pred             HhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          420 FRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       420 f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |++|+.+|||||+++++|+|+|++++||+||+|++...|+||+||+||.
T Consensus        77 f~~g~~~vlvaT~~~~~Gidi~~v~~Vi~~~~p~~~~~~~qr~GR~gR~  125 (212)
T 3eaq_A           77 FRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRA  125 (212)
T ss_dssp             HHSSSCCEEEECTTTTCSSSCCCBSEEEESSCCSSHHHHHHHHTTBCCC
T ss_pred             HHCCCCeEEEecChhhcCCCCccCcEEEECCCCcCHHHHHHHhcccCCC
Confidence            9999999999999999999999999999999999999999999999995

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.89  E-value=2e-22  Score=207.87  Aligned_cols=126  Identities=19%  Similarity=0.204  Sum_probs=86.6

Q ss_pred             CCCCCCcHHHHHHHHH----HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHH
Q 010709          139 HEYTRPTSIQAQAMPV----ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEV  214 (503)
Q Consensus       139 ~~~~~~~~~Q~~~i~~----i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~  214 (503)
                      .|| .|+++|.+++..    +..|+++++.+|||+|||++|++|++..           +++++|++||++|+.|+.+.+
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~-----------~~~~~~~~~t~~l~~q~~~~~   71 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL-----------KKKVLIFTRTHSQLDSIYKNA   71 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH-----------TCEEEEEESCHHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC-----------CCcEEEEcCCHHHHHHHHHHH
Confidence            456 899999998765    4578899999999999999999998764           578999999999999999888


Q ss_pred             HHHhccCCCceEEEEECCccH--------H------------------------HH---------------HHHhhCCCc
Q 010709          215 KALSRSLDSFKTAIVVGGTNI--------A------------------------EQ---------------RSELRGGVS  247 (503)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~~~--------~------------------------~~---------------~~~~~~~~~  247 (503)
                      ..+.     +++..+.|....        .                        +.               .+.....++
T Consensus        72 ~~l~-----~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~ad  146 (540)
T 2vl7_A           72 KLLG-----LKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKD  146 (540)
T ss_dssp             GGGT-----CCEEEC---------------------------------------------------------CTTGGGCS
T ss_pred             HhcC-----CcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcCC
Confidence            7752     333333221100        0                        00               011124579


Q ss_pred             EEEECcHHHHHHHHcCCC-------CCCCccEEEecchhHH
Q 010709          248 IVVATPGRFLDHLQQGNT-------SLSRVSFVILDEADRM  281 (503)
Q Consensus       248 Ilv~Tp~~l~~~l~~~~~-------~l~~~~~vViDEaH~l  281 (503)
                      |+|+|+..|++......+       .+.+..++||||||++
T Consensus       147 iVV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl  187 (540)
T 2vl7_A          147 VIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNL  187 (540)
T ss_dssp             EEEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGG
T ss_pred             EEEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccH
Confidence            999999999875543221       2456789999999986

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=99.88  E-value=4.8e-22  Score=188.15  Aligned_cols=120  Identities=31%  Similarity=0.395  Sum_probs=110.6

Q ss_pred             eEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHH
Q 010709          340 VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRD  419 (503)
Q Consensus       340 ~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~  419 (503)
                      +.+.+..++...|...+..++...         ..+++||||++++.++.+++.|...++.+..+||++++.+|..+++.
T Consensus         3 v~~~~i~~~~~~K~~~L~~ll~~~---------~~~~~LVF~~t~~~~~~l~~~L~~~g~~~~~lhg~l~~~~r~~~~~~   73 (300)
T 3i32_A            3 YEEEAVPAPVRGRLEVLSDLLYVA---------SPDRAMVFTRTKAETEEIAQGLLRLGHPAQALHGDMSQGERERVMGA   73 (300)
T ss_dssp             SEEEEEECCSSSHHHHHHHHHHHH---------CCSSEEEECSSHHHHHHHHHHHHTTTCCEEEECSCCCTHHHHHHHHH
T ss_pred             eEEEEEECCHHHHHHHHHHHHHhc---------CCCCEEEEECCHHHHHHHHHHHHhCCCCEEEEeCCCCHHHHHHHHHH
Confidence            567788888889999988887653         34679999999999999999999999999999999999999999999


Q ss_pred             HhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          420 FRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       420 f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |++|+.+|||||+++++|+|+|++++||+||+|++...|+||+||+||.
T Consensus        74 f~~g~~~vLVaT~va~~Gidi~~v~~VI~~d~p~s~~~y~Qr~GRagR~  122 (300)
T 3i32_A           74 FRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRA  122 (300)
T ss_dssp             HHHTSCCEEEECSTTTCSTTCCCCSEEEESSCCSSTTHHHHHHTCCC--
T ss_pred             hhcCCceEEEEechhhcCccccceeEEEEcCCCCCHHHHHHHccCcCcC
Confidence            9999999999999999999999999999999999999999999999995

>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=99.88  E-value=9.1e-23  Score=193.61  Aligned_cols=155  Identities=15%  Similarity=0.138  Sum_probs=123.6

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|+++|.++++.++.+++.++++|||+|||+++++++...+...       +.++||++|+++|+.|+.+++++++...
T Consensus       112 ~~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~-------~~~~lil~Pt~~L~~q~~~~l~~~~~~~  184 (282)
T 1rif_A          112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY-------EGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC-------SSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             cCccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC-------CCeEEEEECCHHHHHHHHHHHHHhcccc
Confidence            379999999999999888899999999999999977766654431       3479999999999999999999987432


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                       ...+..++++.....   ....+.+|+|+||+.+.+.   ....+.++++||+||||++.    ...+..++..+.+..
T Consensus       185 -~~~~~~~~~~~~~~~---~~~~~~~I~v~T~~~l~~~---~~~~~~~~~~vIiDEaH~~~----~~~~~~il~~~~~~~  253 (282)
T 1rif_A          185 -HAMIKKIGGGASKDD---KYKNDAPVVVGTWQTVVKQ---PKEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCM  253 (282)
T ss_dssp             -GGGEEECSTTCSSTT---CCCTTCSEEEECHHHHTTS---CGGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCC
T ss_pred             -cceEEEEeCCCcchh---hhccCCcEEEEchHHHHhh---HHHHHhhCCEEEEECCccCC----cccHHHHHHHhhcCC
Confidence             356777777764322   2225689999999987543   22346789999999999986    347888888887889


Q ss_pred             cEEEEEeeCCHHH
Q 010709          302 QTLLFSATMPVEI  314 (503)
Q Consensus       302 q~i~~SAT~~~~~  314 (503)
                      +++++|||+++..
T Consensus       254 ~~l~lSATp~~~~  266 (282)
T 1rif_A          254 FKFGLSGSLRDGK  266 (282)
T ss_dssp             EEEEECSSCCTTS
T ss_pred             eEEEEeCCCCCcc
Confidence            9999999997654

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.85  E-value=1.8e-19  Score=186.66  Aligned_cols=285  Identities=14%  Similarity=0.126  Sum_probs=180.5

Q ss_pred             CCcHHHHHHHHHH----hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVA----LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i----~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .|++.|.+++..+    ..|+++++.+|||+|||++|++|++..           +++++|++||++|+.|+.+++..+.
T Consensus         3 ~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~-----------~~~v~i~~pt~~l~~q~~~~~~~l~   71 (551)
T 3crv_A            3 KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV-----------KPKVLFVVRTHNEFYPIYRDLTKIR   71 (551)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH-----------CSEEEEEESSGGGHHHHHHHHTTCC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC-----------CCeEEEEcCCHHHHHHHHHHHHHHh
Confidence            6899999987754    478999999999999999999999972           5789999999999999999998886


Q ss_pred             ccCCCceEEEEECCccH---------------------------------HHH------------------HHHhhCCCc
Q 010709          219 RSLDSFKTAIVVGGTNI---------------------------------AEQ------------------RSELRGGVS  247 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~---------------------------------~~~------------------~~~~~~~~~  247 (503)
                      ... ++++.++.|....                                 ...                  .+.....++
T Consensus        72 ~~~-~~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~~~ad  150 (551)
T 3crv_A           72 EKR-NITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSLYKAD  150 (551)
T ss_dssp             CSS-CCCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHGGGCS
T ss_pred             hhc-CccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhhhcCC
Confidence            554 4677766653211                                 111                  122335689


Q ss_pred             EEEECcHHHHHHHHcCCCCC-CCccEEEecchhHHhhCC-----------------------------------------
Q 010709          248 IVVATPGRFLDHLQQGNTSL-SRVSFVILDEADRMLDMG-----------------------------------------  285 (503)
Q Consensus       248 Ilv~Tp~~l~~~l~~~~~~l-~~~~~vViDEaH~l~~~~-----------------------------------------  285 (503)
                      |+|+|++.|++...+..+.+ .+..+|||||||++.+ .                                         
T Consensus       151 IVV~~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d-~~~~~s~~ls~~~l~~~~~~l~~~~~~~~l~~l~~~l~~~~~  229 (551)
T 3crv_A          151 VIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK-VNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVVL  229 (551)
T ss_dssp             EEEEETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG-GGGGGCEEEEHHHHHHHHHHCSCHHHHHHHHHHHHHHTTSCC
T ss_pred             EEEeCchHhcCHHHHHhcCCCcCCeEEEEecccchHH-HHHhhceecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            99999999988765544333 4678999999998654 1                                         


Q ss_pred             --------------CHHHHHHH----------------------------HH----------------------------
Q 010709          286 --------------FEPQIREV----------------------------MQ----------------------------  295 (503)
Q Consensus       286 --------------~~~~~~~i----------------------------l~----------------------------  295 (503)
                                    +...+..+                            +.                            
T Consensus       230 ~~~~~~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~v~~~~~~l~~~pl~~~~~l~  309 (551)
T 3crv_A          230 PDEKYIKVENVPKLSKEELEILADDYEDIRKDSLKQGKVNKIHIGSILRFFSLLSIGSFIPFSYSKRLVIKNPEISYYLN  309 (551)
T ss_dssp             SCSSCEECSCCCCCCHHHHHHHHHHHHHHHHHHHHTTCBCCCHHHHHHHHHHHHHHSSCEEEEETTEEEEECCCTHHHHG
T ss_pred             ccccccccccChHHHHHHHHHHHHHHHHHHHhhhhcCCcccchHHHHHHHHHHHhccCCeEeccCCEEEEEECCHHHHHH
Confidence                          01111000                            00                            


Q ss_pred             hCCCC-CcEEEEEeeCCHHHHHHHHHhcCC-CeEEE--eCCCCCCCCceEEEEEE--cCh------hhHHHHHHHHHHHH
Q 010709          296 NLPDK-HQTLLFSATMPVEIEALAQEYLTD-PVQVK--VGKVSSPTANVIQILEK--VSE------NEKVDRLLALLVEE  363 (503)
Q Consensus       296 ~~~~~-~q~i~~SAT~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~~--~~~------~~k~~~l~~~l~~~  363 (503)
                      .+... ..+|++|||+.+ ...+.+.+..+ +....  ......+...-...+..  ++.      ......+...+.+.
T Consensus       310 ~~~~~~~svIltSaTL~~-~~~~~~~lGl~~~~~~~~~~~~~~spf~~~~~l~v~~~~~~~~~~r~~~~~~~l~~~i~~l  388 (551)
T 3crv_A          310 LLNDNELSIILMSGTLPP-REYMEKVWGIKRNMLYLDVEREIQKRVSGSYECYIGVDVTSKYDMRSDNMWKRYADYLLKI  388 (551)
T ss_dssp             GGGCTTCEEEEEESSCCC-HHHHHHTSCCCSCEEEEEHHHHTTSCCSCEEEEEEECSCCCCTTTCCHHHHHHHHHHHHHH
T ss_pred             HHhccCceEEEEeeCCCc-HHHHHHHhCCCCccccccceeecCCcCCCceEEEEeCCCCCccccCCHHHHHHHHHHHHHH
Confidence            01122 678999999976 33333333222 22210  00011111111122221  111      11233444444433


Q ss_pred             HHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc--cccccCCCCC
Q 010709          364 AFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVAT--DVASRGLDVM  441 (503)
Q Consensus       364 ~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT--~~~~~Gldip  441 (503)
                      ...      .++.+|||+++....+.+++.   .+..+..=..+++.   .++++.|+.+...||++|  ..+.+|||+|
T Consensus       389 ~~~------~~g~~lvlF~Sy~~l~~v~~~---~~~~v~~q~~~~~~---~~~~~~~~~~~~~vl~~v~gg~~~EGiD~~  456 (551)
T 3crv_A          389 YFQ------AKANVLVVFPSYEIMDRVMSR---ISLPKYVESEDSSV---EDLYSAISANNKVLIGSVGKGKLAEGIELR  456 (551)
T ss_dssp             HHH------CSSEEEEEESCHHHHHHHHTT---CCSSEEECCSSCCH---HHHHHHTTSSSSCEEEEESSCCSCCSSCCE
T ss_pred             HHh------CCCCEEEEecCHHHHHHHHHh---cCCcEEEcCCCCCH---HHHHHHHHhcCCeEEEEEecceeccccccc
Confidence            221      345799999999999998873   34444433334453   456777754445899998  6999999999


Q ss_pred             ---C--CCEEEEccCCC
Q 010709          442 ---G--VAHVVNLDLPK  453 (503)
Q Consensus       442 ---~--v~~VI~~~~p~  453 (503)
                         +  ++.||..++|-
T Consensus       457 d~~g~~l~~viI~~lPf  473 (551)
T 3crv_A          457 NNDRSLISDVVIVGIPY  473 (551)
T ss_dssp             ETTEESEEEEEEESCCC
T ss_pred             ccCCcceeEEEEEcCCC
Confidence               3  78999999874

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=99.75  E-value=5.8e-23  Score=179.31  Aligned_cols=121  Identities=31%  Similarity=0.463  Sum_probs=108.0

Q ss_pred             ceEEEEEEcCh-hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHH
Q 010709          339 NVIQILEKVSE-NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL  417 (503)
Q Consensus       339 ~~~~~~~~~~~-~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~  417 (503)
                      ++.+.+..++. ..|...+..++...         +.+++||||+++..++.+++.|...++.+..+||++++.+|..++
T Consensus         3 ~i~~~~~~~~~~~~k~~~l~~ll~~~---------~~~~~iVF~~~~~~~~~l~~~L~~~~~~~~~~~g~~~~~~r~~~~   73 (170)
T 2yjt_D            3 KIHQWYYRADDLEHKTALLVHLLKQP---------EATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAI   73 (170)
Confidence            34556666666 67777776666542         335799999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       418 ~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|++|+.+|||||+++++|+|+|++++||++|+|++...|+||+||+||.
T Consensus        74 ~~f~~g~~~vLvaT~~~~~Gid~~~~~~Vi~~~~p~~~~~~~qr~GR~~R~  124 (170)
T 2yjt_D           74 KRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARA  124 (170)
Confidence            999999999999999999999999999999999999999999999999995

>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=99.81  E-value=1.5e-19  Score=166.17  Aligned_cols=139  Identities=19%  Similarity=0.144  Sum_probs=109.5

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..|+++|.+++..+++++++++++|||+|||++++.++...           +.+++|++|+++|+.|+.+.++++    
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            48999999999999999899999999999999887665432           456999999999999999999884    


Q ss_pred             CCce-EEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCC
Q 010709          222 DSFK-TAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK  300 (503)
Q Consensus       222 ~~~~-~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~  300 (503)
                       ++. +..+.|+..         ...+|+|+|++.+......   ...++++|||||||++.+..    +..++..++ .
T Consensus       157 -~~~~v~~~~g~~~---------~~~~i~v~T~~~l~~~~~~---~~~~~~llIiDEaH~l~~~~----~~~i~~~~~-~  218 (237)
T 2fz4_A          157 -GEEYVGEFSGRIK---------ELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAES----YVQIAQMSI-A  218 (237)
T ss_dssp             -CGGGEEEESSSCB---------CCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTTT----HHHHHHTCC-C
T ss_pred             -CCCeEEEEeCCCC---------CcCCEEEEeHHHHHhhHHH---hcccCCEEEEECCccCCChH----HHHHHHhcc-C
Confidence             355 666666653         3579999999999776653   12468999999999987654    345555555 5


Q ss_pred             CcEEEEEeeCCHH
Q 010709          301 HQTLLFSATMPVE  313 (503)
Q Consensus       301 ~q~i~~SAT~~~~  313 (503)
                      .+++++|||+++.
T Consensus       219 ~~~l~LSATp~r~  231 (237)
T 2fz4_A          219 PFRLGLTATFERE  231 (237)
T ss_dssp             SEEEEEEESCC--
T ss_pred             CEEEEEecCCCCC
Confidence            6789999999754

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.77  E-value=4.1e-17  Score=170.18  Aligned_cols=81  Identities=22%  Similarity=0.227  Sum_probs=66.6

Q ss_pred             CCcHHHHHHHHH----HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPV----ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~----i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      +|++.|.+.+..    +.+|+++++.||||+|||++|++|++.++...       +++++|++||++++.|+.+.++.+.
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~-------~~kvli~t~T~~l~~Qi~~el~~l~   75 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER-------KLKVLYLVRTNSQEEQVIKELRSLS   75 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH-------TCEEEEEESSHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc-------CCeEEEECCCHHHHHHHHHHHHHHh
Confidence            589999998865    45789999999999999999999999987653       5789999999999999999999887


Q ss_pred             ccCCCceEEEEEC
Q 010709          219 RSLDSFKTAIVVG  231 (503)
Q Consensus       219 ~~~~~~~~~~~~~  231 (503)
                      ... .+++..+.|
T Consensus        76 ~~~-~~~~~~l~g   87 (620)
T 4a15_A           76 STM-KIRAIPMQG   87 (620)
T ss_dssp             HHS-CCCEEECCC
T ss_pred             hcc-CeEEEEEEC
Confidence            654 455555554

>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination, hydrolase-recombination complex; 2.00A {Sulfolobus solfataricus} SCOP: c.37.1.19

Probab=99.70  E-value=6.5e-17  Score=151.16  Aligned_cols=114  Identities=13%  Similarity=0.144  Sum_probs=93.4

Q ss_pred             ChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcC-CC
Q 010709          348 SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFRNG-ST  425 (503)
Q Consensus       348 ~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~~g-~~  425 (503)
                      ....|+..+..++.....       ...++||||++...++.+.+.|... |+.+..+||++++.+|.++++.|++| +.
T Consensus        93 ~~s~K~~~L~~ll~~~~~-------~~~kvlIFs~~~~~~~~l~~~L~~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~  165 (271)
T 1z5z_A           93 RRSGKMIRTMEIIEEALD-------EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSV  165 (271)
T ss_dssp             TTCHHHHHHHHHHHHHHH-------TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTC
T ss_pred             ccCHHHHHHHHHHHHHHh-------CCCeEEEEeccHHHHHHHHHHHHHhcCCcEEEEECCCCHHHHHHHHHHhcCCCCC
Confidence            456788888888776532       2357999999999999999999885 99999999999999999999999998 67


Q ss_pred             c-EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          426 N-ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       426 ~-vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      + +|++|+++++|+|++++++||+||+|+++..|.||+||++|.
T Consensus       166 ~v~L~st~~~g~Glnl~~a~~VI~~d~~wnp~~~~Q~~gR~~R~  209 (271)
T 1z5z_A          166 KFIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI  209 (271)
T ss_dssp             CEEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC----------
T ss_pred             CEEEEehhhhcCCcCcccCCEEEEECCCCChhHHHHHHHhcccc
Confidence            7 789999999999999999999999999999999999999984

>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=98.89  E-value=4.9e-09  Score=109.23  Aligned_cols=145  Identities=21%  Similarity=0.292  Sum_probs=88.9

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchh--HHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKT--AAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKT--l~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .+.|.++++.++.++.+++.|++|+|||  +.++++.+.....      ..+.++++++||..+|.++.+.+........
T Consensus       151 ~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~------~~~~~vll~APTg~AA~~L~e~~~~~~~~l~  224 (608)
T 1w36_D          151 INWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD------GERCRIRLAAPTGKAAARLTESLGKALRQLP  224 (608)
T ss_dssp             CCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS------SCCCCEEEEBSSHHHHHHHHHHHTHHHHHSS
T ss_pred             CHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh------cCCCeEEEEeCChhHHHHHHHHHHHHHhcCC
Confidence            7899999999999999999999999999  4455555443211      2356799999999999999888876654331


Q ss_pred             CceEEEEECCccHHHHHHHhhCCC-cEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGV-SIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~-~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                       +..... .+...      ..... .++-.+|+.. . +.........+++||||||+ |++   ...+..++..++...
T Consensus       225 -l~~~~~-~~~~~------~~~Tih~ll~~~~~~~-~-~~~~~~~~l~~d~lIIDEAs-ml~---~~~~~~Ll~~l~~~~  290 (608)
T 1w36_D          225 -LTDEQK-KRIPE------DASTLHRLLGAQPGSQ-R-LRHHAGNPLHLDVLVVDEAS-MID---LPMMSRLIDALPDHA  290 (608)
T ss_dssp             -CCSCCC-CSCSC------CCBTTTSCC-------------CTTSCCSCSEEEECSGG-GCB---HHHHHHHHHTCCTTC
T ss_pred             -CCHHHH-hccch------hhhhhHhhhccCCCch-H-HHhccCCCCCCCEEEEechh-hCC---HHHHHHHHHhCCCCC
Confidence             110000 00000      00001 1111222221 0 11112222378999999999 543   556788899998889


Q ss_pred             cEEEEEee
Q 010709          302 QTLLFSAT  309 (503)
Q Consensus       302 q~i~~SAT  309 (503)
                      |+|++.-.
T Consensus       291 ~liLvGD~  298 (608)
T 1w36_D          291 RVIFLGDR  298 (608)
T ss_dssp             EEEEEECT
T ss_pred             EEEEEcch
Confidence            98887644

>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=98.43  E-value=1.1e-06  Score=90.55  Aligned_cols=126  Identities=17%  Similarity=0.202  Sum_probs=80.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..+++.|.+++..++.++.++|.|+.|+|||+.. ..++..+...       +.++++++||...+..+.+.+.      
T Consensus       188 ~~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~~-------g~~Vl~~ApT~~Aa~~L~e~~~------  253 (574)
T 3e1s_A          188 KGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAESL-------GLEVGLCAPTGKAARRLGEVTG------  253 (574)
T ss_dssp             TTCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHT------
T ss_pred             CCCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHhc-------CCeEEEecCcHHHHHHhHhhhc------
Confidence            3578999999999998889999999999999753 3344443332       5679999999988877655431      


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                        .....+      .    .+.   ..   .+..    ..........+++|||||++.+.    ...+..++..++...
T Consensus       254 --~~a~Ti------h----~ll---~~---~~~~----~~~~~~~~~~~dvlIIDEasml~----~~~~~~Ll~~~~~~~  307 (574)
T 3e1s_A          254 --RTASTV------H----RLL---GY---GPQG----FRHNHLEPAPYDLLIVDEVSMMG----DALMLSLLAAVPPGA  307 (574)
T ss_dssp             --SCEEEH------H----HHT---TE---ETTE----ESCSSSSCCSCSEEEECCGGGCC----HHHHHHHHTTSCTTC
T ss_pred             --ccHHHH------H----HHH---cC---Ccch----hhhhhcccccCCEEEEcCccCCC----HHHHHHHHHhCcCCC
Confidence              111100      0    000   00   0000    01112234468999999999653    456777888888777


Q ss_pred             cEEEEE
Q 010709          302 QTLLFS  307 (503)
Q Consensus       302 q~i~~S  307 (503)
                      +++++.
T Consensus       308 ~lilvG  313 (574)
T 3e1s_A          308 RVLLVG  313 (574)
T ss_dssp             EEEEEE
T ss_pred             EEEEEe
Confidence            777654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.40  E-value=7.9e-07  Score=93.62  Aligned_cols=69  Identities=25%  Similarity=0.314  Sum_probs=55.9

Q ss_pred             CCCcHHHHHHHHHHhcCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          142 TRPTSIQAQAMPVALSGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..+.+-|.+|+..++..++ .||.||+|+|||.+. +-++.++...       +.++|+++||...+.++.+.+....
T Consensus       188 ~~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti-~~~I~~l~~~-------~~~ILv~a~TN~AvD~i~erL~~~~  257 (646)
T 4b3f_X          188 TCLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTV-VEIILQAVKQ-------GLKVLCCAPSNIAVDNLVERLALCK  257 (646)
T ss_dssp             TTCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHH-HHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHH-HHHHHHHHhC-------CCeEEEEcCchHHHHHHHHHHHhcC
Confidence            3578899999999987776 899999999999875 4455555553       5789999999999999988886543

>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=98.37  E-value=1.5e-06  Score=87.58  Aligned_cols=138  Identities=12%  Similarity=0.107  Sum_probs=80.5

Q ss_pred             HHHCCCCCCcHHHHHHHHHHhc----CC-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHH
Q 010709          136 IEFHEYTRPTSIQAQAMPVALS----GR-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQI  210 (503)
Q Consensus       136 l~~~~~~~~~~~Q~~~i~~i~~----~~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~  210 (503)
                      .....|..+++-|.+++..++.    ++ .++|.|+.|+|||... ..++..+...+      ...+++++||...+..+
T Consensus        18 ~~p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~------~~~il~~a~T~~Aa~~l   90 (459)
T 3upu_A           18 GSHMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTG------ETGIILAAPTHAAKKIL   90 (459)
T ss_dssp             ---CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTT------CCCEEEEESSHHHHHHH
T ss_pred             cCCCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcC------CceEEEecCcHHHHHHH
Confidence            3456788899999999997753    24 7999999999999754 44555555531      13689999999887766


Q ss_pred             HHHHHHHhccCCCceEEEEECCccHHHHHHHh--hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHH
Q 010709          211 EKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL--RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEP  288 (503)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~  288 (503)
                      .+.+.        .....++      ......  .......+..         .....+..+++|||||++.+.    ..
T Consensus        91 ~~~~~--------~~~~T~h------~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~iiiDE~~~~~----~~  143 (459)
T 3upu_A           91 SKLSG--------KEASTIH------SILKINPVTYEENVLFEQ---------KEVPDLAKCRVLICDEVSMYD----RK  143 (459)
T ss_dssp             HHHHS--------SCEEEHH------HHHTEEEEECSSCEEEEE---------CSCCCCSSCSEEEESCGGGCC----HH
T ss_pred             Hhhhc--------cchhhHH------HHhccCcccccccchhcc---------cccccccCCCEEEEECchhCC----HH
Confidence            55441        1111100      000000  0000001100         112345678999999999542    34


Q ss_pred             HHHHHHHhCCCCCcEEEEE
Q 010709          289 QIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       289 ~~~~il~~~~~~~q~i~~S  307 (503)
                      .+..++..++...+++++.
T Consensus       144 ~~~~l~~~~~~~~~~~~vG  162 (459)
T 3upu_A          144 LFKILLSTIPPWCTIIGIG  162 (459)
T ss_dssp             HHHHHHHHSCTTCEEEEEE
T ss_pred             HHHHHHHhccCCCEEEEEC
Confidence            5666666666556555554

>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=98.24  E-value=8.1e-05  Score=78.48  Aligned_cols=71  Identities=20%  Similarity=0.211  Sum_probs=54.2

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ..+++-|.+++..  .+..++|.|+.|||||.+. +--+.+++...   +....++|++++|+..+.++.+++.++.
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l-~~ri~~l~~~~---~~~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVL-VHRIAWLMSVE---NCSPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHH-HHHHHHHHHTS---CCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHH-HHHHHHHHHhC---CCChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            4688999999973  3567999999999999865 33444555432   1124579999999999999999998775

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.23  E-value=1.3e-05  Score=85.84  Aligned_cols=70  Identities=21%  Similarity=0.255  Sum_probs=56.2

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      +..+++.|.+|+..++.+..++|.||+|+|||... ..++..+...      .+.++|+++||...+.++.+.+.+.
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-ATIVYHLSKI------HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             SCCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHH-HHHHHHHHHH------HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHH-HHHHHHHHhC------CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            45688999999999988777999999999999864 3444444432      1467999999999999999988765

>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=98.22  E-value=7.6e-06  Score=85.62  Aligned_cols=70  Identities=21%  Similarity=0.210  Sum_probs=56.1

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ...+++.|.+|+..++.+..++|.||+|+|||... ..++..+...      .+.++++++||...+.++.+.+.+.
T Consensus       178 ~~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~-~~~i~~l~~~------~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          178 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTS-ATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             SCCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHH-HHHHHHHHTS------SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHH-HHHHHHHHHc------CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            45689999999999888777999999999999864 4455554432      2567999999999999998887654

>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=98.17  E-value=1.6e-05  Score=85.00  Aligned_cols=70  Identities=21%  Similarity=0.210  Sum_probs=56.1

Q ss_pred             CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       141 ~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      ...+++.|.+|+..++.+..++|.||+|+|||... ..++..+...      .+.++++++||...+.++.+.+...
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-ATIVYHLARQ------GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             SCCCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHH-HHHHHHHHTT------CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             ccCCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHH-HHHHHHHHHc------CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            45689999999999988777999999999999864 4455555442      2567999999999999998887654

>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=97.43  E-value=0.00092  Score=64.76  Aligned_cols=73  Identities=15%  Similarity=0.118  Sum_probs=55.7

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      .++|+|...+..+...+-+++..+-+.|||......++..+...      .+..+++++|++.-|..+.+.++.+....
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~~------~g~~v~~vA~t~~qA~~vf~~i~~mi~~~  235 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN------KDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHSS------SSCEEEEEESSHHHHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHhC------CCCeEEEEeCCHHHHHHHHHHHHHHHHhC
Confidence            68999999998775556689999999999987655444333332      25679999999999988888888776543

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=97.33  E-value=0.00047  Score=67.66  Aligned_cols=107  Identities=21%  Similarity=0.188  Sum_probs=63.1

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR  239 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  239 (503)
                      -.++.|+.|+|||....     ....        ....+|++||++++..+.+.+.+.+..                   
T Consensus       163 v~~I~G~aGsGKTt~I~-----~~~~--------~~~~lVlTpT~~aa~~l~~kl~~~~~~-------------------  210 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEIL-----SRVN--------FEEDLILVPGRQAAEMIRRRANASGII-------------------  210 (446)
T ss_dssp             EEEEEECTTSCHHHHHH-----HHCC--------TTTCEEEESCHHHHHHHHHHHTTTSCC-------------------
T ss_pred             EEEEEcCCCCCHHHHHH-----HHhc--------cCCeEEEeCCHHHHHHHHHHhhhcCcc-------------------
Confidence            37899999999997431     1111        134799999999998888776432100                   


Q ss_pred             HHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          240 SELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       240 ~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                          .....-|.|.+.++.  .......-.+++||||||- |++.   ..+..++...+. .+++++.-+
T Consensus       211 ----~~~~~~V~T~dsfL~--~~~~~~~~~~d~liiDE~s-m~~~---~~l~~l~~~~~~-~~vilvGD~  269 (446)
T 3vkw_A          211 ----VATKDNVRTVDSFLM--NYGKGARCQFKRLFIDEGL-MLHT---GCVNFLVEMSLC-DIAYVYGDT  269 (446)
T ss_dssp             ----CCCTTTEEEHHHHHH--TTTSSCCCCCSEEEEETGG-GSCH---HHHHHHHHHTTC-SEEEEEECT
T ss_pred             ----ccccceEEEeHHhhc--CCCCCCCCcCCEEEEeCcc-cCCH---HHHHHHHHhCCC-CEEEEecCc
Confidence                012233678776653  1112222348999999998 4332   234445555544 556655443

>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain, chromatin regulator, coiled coil, nucleus, repressor, transcription; 2.20A {Saccharomyces cerevisiae} PDB: 3hgq_A

Probab=97.19  E-value=0.0013  Score=61.57  Aligned_cols=102  Identities=13%  Similarity=0.025  Sum_probs=73.7

Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      ...|+..|-+++....       ..+.++|||++..+..+-+.+++...++....+.|.....++ +    -.++...|.
T Consensus       107 ~SGKf~~L~~LL~~l~-------~~~~kVLIfsq~t~~LDilE~~l~~~~~~y~RlDG~~~~~~~-k----~~~~~~~i~  174 (328)
T 3hgt_A          107 NSGKFSVLRDLINLVQ-------EYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHSIKSAA-A----ANDFSCTVH  174 (328)
T ss_dssp             TCHHHHHHHHHHHHHT-------TSCEEEEEEECSTHHHHHHHHHHTTSSCEEEESSSCCC------------CCSEEEE
T ss_pred             cCccHHHHHHHHHHHH-------hCCCEEEEEECChhHHHHHHHHHhcCCCceEeCCCCchhhhh-h----cccCCceEE
Confidence            4567776666665543       234579999999999999999999999999999998554322 1    124556666


Q ss_pred             EEccccccCCC-----CCCCCEEEEccCCCChhH-HHHhh
Q 010709          429 VATDVASRGLD-----VMGVAHVVNLDLPKVLLA-ASESL  462 (503)
Q Consensus       429 vaT~~~~~Gld-----ip~v~~VI~~~~p~s~~~-~~Qr~  462 (503)
                      +.|..+.-|+|     +...+.||.||..+++.. .+|.+
T Consensus       175 Lltsag~~gin~~~~nl~~aD~VI~~DsdwNp~~d~iQa~  214 (328)
T 3hgt_A          175 LFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQYL  214 (328)
T ss_dssp             EEESSCCCTTTSCCCCCSCCSEEEECSTTCCTTSHHHHHH
T ss_pred             EEECCCCCCcCcccccCCCCCEEEEECCCCCCCChHHHHH
Confidence            66777777776     678999999999998866 36644

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.11  E-value=0.00026  Score=61.40  Aligned_cols=39  Identities=18%  Similarity=0.152  Sum_probs=26.7

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      |+-.++.|++|+|||+..+ -++..+...       +.+++++.|..
T Consensus         3 g~i~vi~G~~gsGKTT~ll-~~~~~~~~~-------g~~v~~~~~~~   41 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELL-SFVEIYKLG-------KKKVAVFKPKI   41 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHH-HHHHHHHHT-------TCEEEEEEEC-
T ss_pred             cEEEEEECCCCCCHHHHHH-HHHHHHHHC-------CCeEEEEeecc
Confidence            4557899999999998653 334333332       46788888884

>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=97.10  E-value=0.00034  Score=62.41  Aligned_cols=90  Identities=16%  Similarity=0.137  Sum_probs=51.3

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      |.-+++.|++|+|||+.. +-++..+...       +.+++++.|...--   .  ...+...+ ++.            
T Consensus        12 G~i~litG~mGsGKTT~l-l~~~~r~~~~-------g~kVli~~~~~d~r---~--~~~i~srl-G~~------------   65 (223)
T 2b8t_A           12 GWIEFITGPMFAGKTAEL-IRRLHRLEYA-------DVKYLVFKPKIDTR---S--IRNIQSRT-GTS------------   65 (223)
T ss_dssp             CEEEEEECSTTSCHHHHH-HHHHHHHHHT-------TCCEEEEEECCCGG---G--CSSCCCCC-CCS------------
T ss_pred             cEEEEEECCCCCcHHHHH-HHHHHHHHhc-------CCEEEEEEeccCch---H--HHHHHHhc-CCC------------
Confidence            445889999999999865 4344444432       56788888765210   0  00111111 000            


Q ss_pred             HHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                             -..+.+.+...++..+... ..-.++++|||||++.+
T Consensus        66 -------~~~~~~~~~~~i~~~i~~~-~~~~~~dvViIDEaQ~l  101 (223)
T 2b8t_A           66 -------LPSVEVESAPEILNYIMSN-SFNDETKVIGIDEVQFF  101 (223)
T ss_dssp             -------SCCEEESSTHHHHHHHHST-TSCTTCCEEEECSGGGS
T ss_pred             -------ccccccCCHHHHHHHHHHH-hhCCCCCEEEEecCccC
Confidence                   0123345666676666542 23346899999999964

>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=97.04  E-value=0.0027  Score=67.49  Aligned_cols=109  Identities=21%  Similarity=0.216  Sum_probs=71.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ..+++-|.+++..  .+..++|.|+.|||||.+. +--+.+++...   +.....+|+|+.|+..|.++.+++..+....
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL-~~ri~~ll~~~---~~~p~~IL~vTFTnkAA~Em~~Rl~~~l~~~   83 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVL-THRIAYLMAEK---HVAPWNILAITFTNKAAREMRERVQSLLGGA   83 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHH-HHHHHHHHHTT---CCCGGGEEEEESSHHHHHHHHHHHHHHHGGG
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHH-HHHHHHHHHhc---CCCHHHeEEEeccHHHHHHHHHHHHHHhccc
Confidence            4689999999876  3567999999999999865 33344444431   1124679999999999999999998775220


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCC-CCC-CccEEEecchh
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNT-SLS-RVSFVILDEAD  279 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~-~l~-~~~~vViDEaH  279 (503)
                                             ...+-|+|...+...+.+... .+. .-.+-|+|+.+
T Consensus        84 -----------------------~~~~~v~Tfhs~~~~ilr~~~~~~g~~~~f~i~d~~d  120 (724)
T 1pjr_A           84 -----------------------AEDVWISTFHSMCVRILRRDIDRIGINRNFSILDPTD  120 (724)
T ss_dssp             -----------------------GTTSEEEEHHHHHHHHHHHHGGGGTCCTTCEECCHHH
T ss_pred             -----------------------ccCcEEeeHHHHHHHHHHHHHHHhCCCCCCEECCHHH
Confidence                                   023567888777544433111 110 12356778766

>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=97.01  E-value=0.0018  Score=57.41  Aligned_cols=39  Identities=15%  Similarity=0.089  Sum_probs=27.9

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      |+=.+++|++|+|||+..+- .+.....       .+.+++++.|..
T Consensus        19 g~l~v~~G~MgsGKTT~lL~-~~~r~~~-------~g~kvli~kp~~   57 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMR-RVRRFQI-------AQYKCLVIKYAK   57 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHH-HHHHHHT-------TTCCEEEEEETT
T ss_pred             eEEEEEECCCCCcHHHHHHH-HHHHHHH-------CCCeEEEEeecC
Confidence            45578999999999987543 3433333       267799999875

>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=97.01  E-value=0.0014  Score=56.49  Aligned_cols=19  Identities=32%  Similarity=0.379  Sum_probs=16.2

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|+.+++.||+|+|||+.+
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4677999999999999854

>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=97.00  E-value=0.00094  Score=58.69  Aligned_cols=40  Identities=20%  Similarity=0.248  Sum_probs=27.0

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      |+=.+++|++|+|||+..+ -.+......       +.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL-~~a~r~~~~-------g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELI-RRVRRTQFA-------KQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHH-HHHHHHHHT-------TCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHH-HHHHHHHHC-------CCEEEEEEeccC
Confidence            3346789999999998754 344443432       577999998763

>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=96.97  E-value=0.0062  Score=63.10  Aligned_cols=73  Identities=15%  Similarity=0.118  Sum_probs=56.5

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      .++++|...+..+...+.+++.++-|.|||......++..+...      .+..++++.|++..|..+.+.++.+....
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~~------~~~~i~~va~t~~qA~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCFN------KDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHTS------SSCEEEEEESSHHHHHHHHHHHHHHHTTS
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHhC------CCCeEEEEECCHHHHHHHHHHHHHHHHhC
Confidence            57999999998775556799999999999987654444443332      24579999999999999988888877554

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.78  E-value=0.0015  Score=57.22  Aligned_cols=40  Identities=18%  Similarity=0.163  Sum_probs=27.1

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      |.-.+++|++|+|||+.. +-.+......       +.+++++.|...
T Consensus        28 G~I~vitG~M~sGKTT~L-lr~~~r~~~~-------g~kvli~kp~~D   67 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEEL-IRRLRRGIYA-------KQKVVVFKPAID   67 (219)
T ss_dssp             CEEEEEEECTTSCHHHHH-HHHHHHHHHT-------TCCEEEEEEC--
T ss_pred             ceEEEEECCCCCCHHHHH-HHHHHHHHHc-------CCceEEEEeccC
Confidence            445789999999999865 3344444332       567899999753

>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=96.68  E-value=0.00072  Score=58.81  Aligned_cols=39  Identities=21%  Similarity=0.148  Sum_probs=27.6

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      |+=.++.|++|+|||+.. +-++......       +.+++++.|..
T Consensus         8 g~i~v~~G~mgsGKTT~l-l~~a~r~~~~-------g~kV~v~k~~~   46 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEEL-IRRIRRAKIA-------KQKIQVFKPEI   46 (191)
T ss_dssp             CEEEEEECSTTSSHHHHH-HHHHHHHHHT-------TCCEEEEEEC-
T ss_pred             CEEEEEECCCCCcHHHHH-HHHHHHHHHC-------CCEEEEEEecc
Confidence            445789999999999865 4444444432       57799999884

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.65  E-value=0.0078  Score=56.66  Aligned_cols=25  Identities=8%  Similarity=-0.036  Sum_probs=18.3

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      +.++++.||+|+|||++. -.++..+
T Consensus        45 ~~~lli~GpPGTGKT~~v-~~v~~~L   69 (318)
T 3te6_A           45 NKLFYITNADDSTKFQLV-NDVMDEL   69 (318)
T ss_dssp             CCEEEEECCCSHHHHHHH-HHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHH
Confidence            456999999999999865 3344444

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.59  E-value=0.0066  Score=52.39  Aligned_cols=38  Identities=16%  Similarity=0.109  Sum_probs=26.4

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      ++=.++.|++|+|||+-. +-.+......       +.+++++.|.
T Consensus        20 g~l~fiyG~MgsGKTt~L-l~~i~n~~~~-------~~kvl~~kp~   57 (195)
T 1w4r_A           20 GQIQVILGPMFSGKSTEL-MRRVRRFQIA-------QYKCLVIKYA   57 (195)
T ss_dssp             CEEEEEEECTTSCHHHHH-HHHHHHHHHT-------TCCEEEEEET
T ss_pred             eEEEEEECCCCCcHHHHH-HHHHHHHHHc-------CCeEEEEccc
Confidence            445889999999999654 3344433332       4678999887

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.52  E-value=0.00081  Score=56.05  Aligned_cols=18  Identities=28%  Similarity=0.425  Sum_probs=15.9

Q ss_pred             cCCCeEEEccCCCchhHH
Q 010709          157 SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~  174 (503)
                      .++.+++.||+|+|||..
T Consensus        35 ~g~~~~l~G~~G~GKTtL   52 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHL   52 (149)
T ss_dssp             CCSEEEEESSSTTTTCHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            577899999999999974

>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=96.47  E-value=0.0094  Score=56.62  Aligned_cols=18  Identities=22%  Similarity=0.307  Sum_probs=15.2

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++.+++.||+|+|||..+
T Consensus        37 ~~~lll~G~~GtGKT~la   54 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL   54 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            357999999999999854

>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=96.37  E-value=0.049  Score=50.11  Aligned_cols=17  Identities=35%  Similarity=0.178  Sum_probs=14.6

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      ..+++.||+|+|||..+
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            35999999999999754

>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=96.32  E-value=0.0025  Score=57.53  Aligned_cols=19  Identities=16%  Similarity=0.135  Sum_probs=15.8

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .++.+++.||+|+|||..+
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3567999999999999743

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.30  E-value=0.0073  Score=62.33  Aligned_cols=112  Identities=21%  Similarity=0.329  Sum_probs=73.1

Q ss_pred             CCcHHHHHHHHHHhc--CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhcc
Q 010709          143 RPTSIQAQAMPVALS--GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRS  220 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~--~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~  220 (503)
                      .+|.-|.+++..+..  ....++.|+-|.|||.+.  -++.....         ..++|++|+.+-+..+.+    +...
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~l--G~~~a~~~---------~~~~vtAP~~~a~~~l~~----~~~~  239 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALA--GQLISRIA---------GRAIVTAPAKASTDVLAQ----FAGE  239 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHH--HHHHHHSS---------SCEEEECSSCCSCHHHHH----HHGG
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHH--HHHHHHHH---------hCcEEECCCHHHHHHHHH----HhhC
Confidence            689999999998876  334899999999999643  33322221         236899999977654332    2210


Q ss_pred             CCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCC
Q 010709          221 LDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK  300 (503)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~  300 (503)
                                                .|-+..|+.+..       ...+.++||||||=.+-    .+.+.+++...+  
T Consensus       240 --------------------------~i~~~~Pd~~~~-------~~~~~dlliVDEAAaIp----~pll~~ll~~~~--  280 (671)
T 2zpa_A          240 --------------------------KFRFIAPDALLA-------SDEQADWLVVDEAAAIP----APLLHQLVSRFP--  280 (671)
T ss_dssp             --------------------------GCCBCCHHHHHH-------SCCCCSEEEEETGGGSC----HHHHHHHHTTSS--
T ss_pred             --------------------------CeEEeCchhhhh-------CcccCCEEEEEchhcCC----HHHHHHHHhhCC--
Confidence                                      133446655431       23458999999997542    566777776443  


Q ss_pred             CcEEEEEeeC
Q 010709          301 HQTLLFSATM  310 (503)
Q Consensus       301 ~q~i~~SAT~  310 (503)
                        .++||.|+
T Consensus       281 --~v~~~tTv  288 (671)
T 2zpa_A          281 --RTLLTTTV  288 (671)
T ss_dssp             --EEEEEEEB
T ss_pred             --eEEEEecC
Confidence              57888887

>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=96.25  E-value=0.0071  Score=63.84  Aligned_cols=71  Identities=24%  Similarity=0.164  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhc
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSR  219 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~  219 (503)
                      .+++-|.+++..  .+..++|.|+.|||||.+..- -+.+++...   +....++|+|+.|+..|.++.+++.....
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~-ri~~ll~~~---~~~~~~IL~lTfT~~Aa~em~~Rl~~~l~   72 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITN-KIAHLIRGC---GYQARHIAAVTFTNKAAREMKERVGQTLG   72 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHH-HHHHHHHHH---CCCGGGEEEEESSHHHHHHHHHHHHHHSC
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHH-HHHHHHHhc---CCCHHHeEEEeccHHHHHHHHHHHHHHcC
Confidence            468889999975  366799999999999986533 333444321   11246799999999999999999987753

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=96.23  E-value=0.1  Score=44.59  Aligned_cols=17  Identities=35%  Similarity=0.399  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||..+
T Consensus        44 ~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           44 NNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             CEEEEECCTTSCHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            56999999999999754

>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=96.22  E-value=0.014  Score=57.42  Aligned_cols=130  Identities=16%  Similarity=0.178  Sum_probs=69.3

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      .++++|++|+|||+...  .+...+..      .+.+++++.  +.|.-+.   +.+..++... ++.+.....+.    
T Consensus        99 vI~lvG~~GsGKTTt~~--kLA~~l~~------~G~kVllv~~D~~r~~a~---eqL~~~~~~~-gv~~~~~~~~~----  162 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAG--KLAYFYKK------RGYKVGLVAADVYRPAAY---DQLLQLGNQI-GVQVYGEPNNQ----  162 (433)
T ss_dssp             EEEECCCTTSCHHHHHH--HHHHHHHH------TTCCEEEEEECCSCHHHH---HHHHHHHHTT-TCCEECCTTCS----
T ss_pred             EEEEECCCCCCHHHHHH--HHHHHHHH------cCCeEEEEecCccchhHH---HHHHHHHHhc-CCceeeccccC----
Confidence            48899999999998542  33333332      245566655  4444332   2333333322 23222111111    


Q ss_pred             HHHHhhCCCcEEEECcHHH-HHHHHcCCCCCCCccEEEecchhHHh---hCCCHHHHHHHHHhCCCCCcEEEEEeeCCHH
Q 010709          238 QRSELRGGVSIVVATPGRF-LDHLQQGNTSLSRVSFVILDEADRML---DMGFEPQIREVMQNLPDKHQTLLFSATMPVE  313 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l-~~~l~~~~~~l~~~~~vViDEaH~l~---~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  313 (503)
                                    .|..+ ...+..  ....++++||||++-++.   +..+...+..+.....++.-++.++|+...+
T Consensus       163 --------------dp~~i~~~al~~--a~~~~~DvvIIDTaGr~~~~~d~~lm~el~~i~~~~~pd~vlLVlDa~~gq~  226 (433)
T 3kl4_A          163 --------------NPIEIAKKGVDI--FVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQK  226 (433)
T ss_dssp             --------------CHHHHHHHHHHH--TTTTTCSEEEEEECCCSSSCCTTHHHHHHHHHHHHHCCSEEEEEEEGGGGGG
T ss_pred             --------------CHHHHHHHHHHH--HHhcCCCEEEEECCCCccccCCHHHHHHHHHHHHhhCCcceEEEEeCccchH
Confidence                          11111 122221  223578999999997543   2234566666766666666677888887665


Q ss_pred             HHHHHHHh
Q 010709          314 IEALAQEY  321 (503)
Q Consensus       314 ~~~~~~~~  321 (503)
                      ....+..|
T Consensus       227 a~~~a~~f  234 (433)
T 3kl4_A          227 AYDLASRF  234 (433)
T ss_dssp             GHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555544

>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=96.16  E-value=0.035  Score=52.92  Aligned_cols=32  Identities=25%  Similarity=0.180  Sum_probs=23.5

Q ss_pred             CcHHHHHHHHHHh----cCC--C-eEEEccCCCchhHHh
Q 010709          144 PTSIQAQAMPVAL----SGR--D-LLGCAETGSGKTAAF  175 (503)
Q Consensus       144 ~~~~Q~~~i~~i~----~~~--~-vii~~~TGsGKTl~~  175 (503)
                      .+|+|.+++..+.    +|+  + +++.||.|+|||..+
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a   41 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALI   41 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHH
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHH
Confidence            3677777776544    343  3 899999999999865

>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=96.11  E-value=0.048  Score=47.98  Aligned_cols=40  Identities=20%  Similarity=0.306  Sum_probs=25.8

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEe
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA  308 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SA  308 (503)
                      .+..+|||||+|.+... ....+..++...+....+|+.+.
T Consensus       101 ~~~~vliiDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~~~  140 (226)
T 2chg_A          101 APFKIIFLDEADALTAD-AQAALRRTMEMYSKSCRFILSCN  140 (226)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             cCceEEEEeChhhcCHH-HHHHHHHHHHhcCCCCeEEEEeC
Confidence            45679999999976432 34456666666666665555443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.96  E-value=0.026  Score=48.20  Aligned_cols=18  Identities=28%  Similarity=0.351  Sum_probs=15.1

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+++++.||+|+|||..+
T Consensus        43 ~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCEEEEESCGGGCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            356999999999999754

>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=95.91  E-value=0.026  Score=48.76  Aligned_cols=52  Identities=17%  Similarity=0.218  Sum_probs=36.5

Q ss_pred             CCCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHH
Q 010709          267 LSRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATMPVEIEALA  318 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~  318 (503)
                      -.++++||+||+-..+..+  -...+..++...+...-+|+.+--.|+.+.+.+
T Consensus       118 ~~~yDlvILDEi~~al~~g~l~~~ev~~~l~~Rp~~~~vIlTGr~ap~~l~e~A  171 (196)
T 1g5t_A          118 DPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  171 (196)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             cCCCCEEEEeCCCccccCCCCCHHHHHHHHHhCcCCCEEEEECCCCcHHHHHhC
Confidence            3679999999998665554  345677777777777766666666677766544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.88  E-value=0.011  Score=57.40  Aligned_cols=18  Identities=39%  Similarity=0.355  Sum_probs=15.3

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++.+++.||+|+|||..+
T Consensus        44 ~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           44 PSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCEEECBCTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            457999999999999754

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=95.84  E-value=0.04  Score=51.08  Aligned_cols=53  Identities=17%  Similarity=0.135  Sum_probs=28.9

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHH--hcCCCeEEEccCCCchhHHh
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVA--LSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i--~~~~~vii~~~TGsGKTl~~  175 (503)
                      ..|+++.-.+...+.+...-. .+ -...+.+...  ...+.+++.||+|+|||..+
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~-~~-~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVE-LP-LKHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTH-HH-HHCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCHHHhcCHHHHHHHHHHHHH-HH-hhCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            457777655666666543210 00 0001111111  23456999999999999743

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.83  E-value=0.02  Score=53.83  Aligned_cols=17  Identities=24%  Similarity=0.266  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||..+
T Consensus        68 ~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           68 LHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CEEEEEECTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            46999999999999854

>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=95.79  E-value=0.017  Score=65.15  Aligned_cols=71  Identities=30%  Similarity=0.287  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .+++-|.+++..-  +++++|.|..|||||.+.+--++..+....  ......++|++++|+..|..+.+++...
T Consensus        10 ~~t~eQ~~~i~~~--~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~--~~~~~~~il~~Tft~~aa~e~~~ri~~~   80 (1232)
T 3u4q_A           10 TWTDDQWNAIVST--GQDILVAAAAGSGKTAVLVERMIRKITAEE--NPIDVDRLLVVTFTNASAAEMKHRIAEA   80 (1232)
T ss_dssp             CCCHHHHHHHHCC--SSCEEEEECTTCCHHHHHHHHHHHHHSCSS--SCCCGGGEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCC--CCCEEEEecCCCcHHHHHHHHHHHHHhcCC--CCCCccceEEEeccHHHHHHHHHHHHHH
Confidence            5789999999764  779999999999999875444444333211  1113457999999999999999888764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.71  E-value=0.039  Score=48.16  Aligned_cols=17  Identities=29%  Similarity=0.317  Sum_probs=14.9

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||..+
T Consensus        55 ~~~~l~G~~GtGKT~la   71 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLL   71 (202)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            67999999999999854

>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=95.69  E-value=0.052  Score=53.88  Aligned_cols=41  Identities=15%  Similarity=0.398  Sum_probs=23.7

Q ss_pred             CccEEEecchhHHhhC-CCHHHHHHHHHhC-CCCCcEEEEEee
Q 010709          269 RVSFVILDEADRMLDM-GFEPQIREVMQNL-PDKHQTLLFSAT  309 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~-~~~~~~~~il~~~-~~~~q~i~~SAT  309 (503)
                      +.++|+|||+|.+.+. .....+..++..+ ....++|+.|..
T Consensus       194 ~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          194 KVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             TCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            4679999999987653 2233444444433 334555554433

>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=95.65  E-value=0.013  Score=55.68  Aligned_cols=40  Identities=18%  Similarity=0.286  Sum_probs=26.1

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ...++|||||+|.+........+..++...+...++|+.+
T Consensus       104 ~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~~~iI~~~  143 (324)
T 3u61_B          104 GRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSNCSIIITA  143 (324)
T ss_dssp             SCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGGCEEEEEE
T ss_pred             CCCeEEEEECCcccCcHHHHHHHHHHHHhCCCCcEEEEEe
Confidence            3678999999998752223455666666655566555543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=95.62  E-value=0.024  Score=53.34  Aligned_cols=18  Identities=22%  Similarity=0.338  Sum_probs=15.6

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++++++.||+|+|||..+
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            567999999999999754

>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=95.51  E-value=0.077  Score=52.17  Aligned_cols=40  Identities=28%  Similarity=0.179  Sum_probs=24.8

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELA  207 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La  207 (503)
                      .++++|++|+|||+.. .-+..++...       +.+++++.  |.|.-+
T Consensus       102 vIlivG~~G~GKTTt~-~kLA~~l~~~-------G~kVllv~~D~~R~aa  143 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTV-AKLARYFQKR-------GYKVGVVCSDTWRPGA  143 (443)
T ss_dssp             EEEEECCTTSSHHHHH-HHHHHHHHTT-------TCCEEEEECCCSSTHH
T ss_pred             EEEEECcCCCCHHHHH-HHHHHHHHHC-------CCeEEEEeCCCcchhH
Confidence            4889999999999864 2233333322       45566665  555544

>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=95.50  E-value=0.017  Score=56.17  Aligned_cols=16  Identities=25%  Similarity=0.322  Sum_probs=14.2

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            6999999999999853

>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=95.31  E-value=0.046  Score=53.03  Aligned_cols=37  Identities=14%  Similarity=0.243  Sum_probs=22.2

Q ss_pred             EEEecchhHHhhCCCHHH-HHHHHHhCCCCCcEEEEEee
Q 010709          272 FVILDEADRMLDMGFEPQ-IREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       272 ~vViDEaH~l~~~~~~~~-~~~il~~~~~~~q~i~~SAT  309 (503)
                      +|||||+|.+........ +..++... .+..+|+.|..
T Consensus       136 vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~~iI~~t~~  173 (384)
T 2qby_B          136 IIYLDEVDTLVKRRGGDIVLYQLLRSD-ANISVIMISND  173 (384)
T ss_dssp             EEEEETTHHHHHSTTSHHHHHHHHTSS-SCEEEEEECSS
T ss_pred             EEEEECHHHhccCCCCceeHHHHhcCC-cceEEEEEECC
Confidence            999999999876532333 45555444 44444444433

>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=95.26  E-value=0.18  Score=47.68  Aligned_cols=49  Identities=12%  Similarity=0.122  Sum_probs=28.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHh-----cCCCeEEEccCCCchhHHh
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL-----SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~-----~~~~vii~~~TGsGKTl~~  175 (503)
                      ..|+++.-.+...+.+...-.   .+   ...+.+.     ..+.+++.||+|+|||+.+
T Consensus        15 ~~~~di~G~~~~~~~l~~~i~---~~---~~~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           15 VKWEDVAGLEGAKEALKEAVI---LP---VKFPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTH---HH---HHCGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCHHHhcChHHHHHHHHHHHH---HH---HhCHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            458888666666666643210   00   0011111     1345999999999999754

>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=95.22  E-value=0.17  Score=45.08  Aligned_cols=39  Identities=15%  Similarity=0.246  Sum_probs=22.3

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+-.+|||||+|.+... ....+...+...+....+|+.|
T Consensus       125 ~~~~vlviDe~~~l~~~-~~~~l~~~l~~~~~~~~~i~~t  163 (250)
T 1njg_A          125 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  163 (250)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEE
T ss_pred             CCceEEEEECcccccHH-HHHHHHHHHhcCCCceEEEEEe
Confidence            34579999999975322 2334445555444455444444

>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=95.19  E-value=0.11  Score=55.11  Aligned_cols=74  Identities=18%  Similarity=0.261  Sum_probs=64.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      .+++|.++++.-+.++++.+.+.    ++.+..+||+++..+|...++.+.+|+.+|+|+|. .+...+.+.++++||.
T Consensus       418 ~qvlvlaPtr~La~Q~~~~l~~~~~~~gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~~~~~~~l~lVVI  496 (780)
T 1gm5_A          418 FQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVII  496 (780)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEE
T ss_pred             CeEEEEeCcHHHHHHHHHHHHHHhhhcCceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhhhhhccCCceEEe
Confidence            46999999999999888877654    78999999999999999999999999999999994 5556788888888874

>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=94.90  E-value=0.21  Score=46.56  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=15.7

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .++.+++.||+|+|||+.+
T Consensus        48 ~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           48 PSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCSEEEEECSSSSSHHHHH
T ss_pred             CCceEEEECCCCcCHHHHH
Confidence            3566999999999999743

>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=94.78  E-value=0.1  Score=49.79  Aligned_cols=40  Identities=25%  Similarity=0.340  Sum_probs=26.2

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEe
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA  308 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SA  308 (503)
                      ...++|+|||+|.+... ....+.+++...+....+|+.+.
T Consensus       132 ~~~~vliiDE~~~l~~~-~~~~Ll~~le~~~~~~~~il~~~  171 (353)
T 1sxj_D          132 PPYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICN  171 (353)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEES
T ss_pred             CCceEEEEECCCccCHH-HHHHHHHHHHhcCCCceEEEEeC
Confidence            35689999999976432 24456666776666665665443

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=94.72  E-value=0.093  Score=51.52  Aligned_cols=76  Identities=16%  Similarity=0.138  Sum_probs=63.3

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc-cc---cCCCCCCCCE
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVA---EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV-AS---RGLDVMGVAH  445 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~---~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~-~~---~Gldip~v~~  445 (503)
                      ..+++||.++++.-+.++++.++.   .++.+..+||+.+..++...++.+..|..+|+|+|.- +.   .-++...+++
T Consensus        63 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~  142 (414)
T 3oiy_A           63 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDF  142 (414)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHHHCCSSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHHHTTCCCSE
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHHccCCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHHhccccccE
Confidence            345799999999999999999998   5889999999999999988999999999999999942 21   1255667888


Q ss_pred             EEE
Q 010709          446 VVN  448 (503)
Q Consensus       446 VI~  448 (503)
                      ||.
T Consensus       143 iVi  145 (414)
T 3oiy_A          143 VFV  145 (414)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            875

>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=94.66  E-value=0.17  Score=47.61  Aligned_cols=39  Identities=21%  Similarity=0.345  Sum_probs=25.6

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .+.++|||||+|.+... ....+.+++...+....+|+.+
T Consensus       109 ~~~~vliiDe~~~l~~~-~~~~L~~~le~~~~~~~~i~~~  147 (327)
T 1iqp_A          109 ASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILSC  147 (327)
T ss_dssp             CSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             CCCeEEEEeCCCcCCHH-HHHHHHHHHHhcCCCCeEEEEe
Confidence            45789999999987432 2445666666666666555544

>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=94.65  E-value=0.2  Score=48.30  Aligned_cols=18  Identities=33%  Similarity=0.444  Sum_probs=15.3

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      +..+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            456999999999999854

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=94.54  E-value=0.088  Score=50.09  Aligned_cols=17  Identities=29%  Similarity=0.321  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||+.+
T Consensus        56 ~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           56 DHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECcCCCCHHHHH
Confidence            47999999999999754

>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=94.40  E-value=0.1  Score=50.02  Aligned_cols=43  Identities=21%  Similarity=0.387  Sum_probs=28.5

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ..+.+++|+||+|. ++......+.+++...++...+|+.|-.+
T Consensus       132 ~~~~~vlilDE~~~-L~~~~~~~L~~~le~~~~~~~~Il~t~~~  174 (354)
T 1sxj_E          132 AHRYKCVIINEANS-LTKDAQAALRRTMEKYSKNIRLIMVCDSM  174 (354)
T ss_dssp             --CCEEEEEECTTS-SCHHHHHHHHHHHHHSTTTEEEEEEESCS
T ss_pred             CCCCeEEEEeCccc-cCHHHHHHHHHHHHhhcCCCEEEEEeCCH
Confidence            34678999999997 44444566777777776666566555444

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=94.27  E-value=0.2  Score=46.81  Aligned_cols=40  Identities=18%  Similarity=0.314  Sum_probs=25.6

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+.+++||||||.|... -.+.+.+.+..-++...+|+.+
T Consensus        80 ~~~~kvviIdead~lt~~-a~naLLk~LEep~~~t~fIl~t  119 (305)
T 2gno_A           80 LYTRKYVIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNT  119 (305)
T ss_dssp             SSSSEEEEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEE
T ss_pred             cCCceEEEeccHHHhCHH-HHHHHHHHHhCCCCCeEEEEEE
Confidence            456899999999987533 2344566666655555444444

>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=94.23  E-value=0.27  Score=44.58  Aligned_cols=18  Identities=28%  Similarity=0.233  Sum_probs=15.0

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+.+++.||+|+|||+.+
T Consensus        39 ~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A           39 PKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCEEEEESCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            356999999999999754

>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=93.97  E-value=0.14  Score=51.95  Aligned_cols=41  Identities=17%  Similarity=0.177  Sum_probs=26.5

Q ss_pred             CCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          268 SRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ....+|||||+|.+....  ....+..++...  ...+|+++++.
T Consensus       147 ~~~~vliIDEid~l~~~~~~~l~~L~~~l~~~--~~~iIli~~~~  189 (516)
T 1sxj_A          147 GKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKT--STPLILICNER  189 (516)
T ss_dssp             TTSEEEEECSGGGCCTTSTTHHHHHHHHHHHC--SSCEEEEESCT
T ss_pred             CCCeEEEEECCCccchhhHHHHHHHHHHHHhc--CCCEEEEEcCC
Confidence            456799999999876432  234555666553  34577777764

>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=93.88  E-value=0.076  Score=52.00  Aligned_cols=16  Identities=25%  Similarity=0.372  Sum_probs=13.6

Q ss_pred             CeEE--EccCCCchhHHh
Q 010709          160 DLLG--CAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii--~~~TGsGKTl~~  175 (503)
                      .++|  .|+.|+|||...
T Consensus        52 ~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           52 NMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             EEEEECTTCCSSSHHHHH
T ss_pred             EEEEeCcCcCCCCHHHHH
Confidence            4888  899999999754

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.85  E-value=0.18  Score=50.26  Aligned_cols=38  Identities=16%  Similarity=0.149  Sum_probs=23.8

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|.-++|.|++|+|||+..+. +...+...      .+..++|+.
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~-ia~~~~~~------~g~~Vl~~s  239 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALN-IAQNVATK------TNENVAIFS  239 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHH-HHHHHHHH------SSCCEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHH-HHHHHHHh------CCCcEEEEE
Confidence            445599999999999975433 33333321      134577776

>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=93.84  E-value=0.27  Score=47.24  Aligned_cols=40  Identities=15%  Similarity=0.222  Sum_probs=24.0

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..+..+|||||+|.+... ....+.+.+...+....+|+.+
T Consensus       117 ~~~~~vliiDe~~~l~~~-~~~~Ll~~le~~~~~~~~Il~~  156 (373)
T 1jr3_A          117 RGRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLAT  156 (373)
T ss_dssp             SSSSEEEEEECGGGSCHH-HHHHHHHHHHSCCSSEEEEEEE
T ss_pred             cCCeEEEEEECcchhcHH-HHHHHHHHHhcCCCceEEEEEe
Confidence            445789999999976432 2344555555555555444443

>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=93.84  E-value=0.083  Score=50.75  Aligned_cols=17  Identities=24%  Similarity=0.307  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||+.+
T Consensus        85 ~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           85 SGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             CCEEEECSTTSCHHHHH
T ss_pred             ceEEEECCCCCcHHHHH
Confidence            56999999999999854

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=93.64  E-value=0.13  Score=48.56  Aligned_cols=17  Identities=35%  Similarity=0.346  Sum_probs=14.9

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      ..+++.||+|+|||+.+
T Consensus        39 ~~vll~G~~GtGKT~la   55 (324)
T 1hqc_A           39 EHLLLFGPPGLGKTTLA   55 (324)
T ss_dssp             CCCEEECCTTCCCHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57999999999999743

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=93.64  E-value=0.25  Score=44.30  Aligned_cols=51  Identities=18%  Similarity=0.207  Sum_probs=29.7

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA  216 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~  216 (503)
                      .|.-+++.|++|+|||+.+. -++......       +..++++.-. .-..++.+.+..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~-~~~~~~~~~-------~~~v~~~~~e-~~~~~~~~~~~~   72 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQ-QFLWNGLKM-------GEPGIYVALE-EHPVQVRQNMAQ   72 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHH-HHHHHHHHT-------TCCEEEEESS-SCHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHH-HHHHHHHhc-------CCeEEEEEcc-CCHHHHHHHHHH
Confidence            46679999999999998543 233333322       3457776633 223445554443

>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=93.59  E-value=0.16  Score=47.72  Aligned_cols=38  Identities=26%  Similarity=0.333  Sum_probs=24.4

Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      +..+|||||+|.+... ....+.+++...+....+|+.+
T Consensus       107 ~~~viiiDe~~~l~~~-~~~~L~~~le~~~~~~~~il~~  144 (323)
T 1sxj_B          107 KHKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFAC  144 (323)
T ss_dssp             CCEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEE
T ss_pred             CceEEEEECcccCCHH-HHHHHHHHHhccCCCceEEEEe
Confidence            4789999999986432 2334556666655566555554

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=93.53  E-value=0.33  Score=46.60  Aligned_cols=17  Identities=41%  Similarity=0.554  Sum_probs=14.9

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||..+
T Consensus        71 ~~vLl~GppGtGKT~la   87 (368)
T 3uk6_A           71 RAVLIAGQPGTGKTAIA   87 (368)
T ss_dssp             CEEEEEESTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46999999999999854

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=93.47  E-value=0.23  Score=44.00  Aligned_cols=19  Identities=32%  Similarity=0.256  Sum_probs=15.8

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|.-+++.||+|+|||+..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~   40 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFS   40 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            4567899999999999743

>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=93.39  E-value=0.32  Score=46.21  Aligned_cols=39  Identities=23%  Similarity=0.425  Sum_probs=26.3

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ...+++||||+|.+... ....+.+++...+....+++.+
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            45789999999976432 3455667777766666555443

>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=93.37  E-value=0.19  Score=50.36  Aligned_cols=42  Identities=19%  Similarity=0.344  Sum_probs=26.7

Q ss_pred             ccEEEecchhHHhhCC----------CHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          270 VSFVILDEADRMLDMG----------FEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       270 ~~~vViDEaH~l~~~~----------~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      ..+|+|||+|.+....          ....+..++..+.....++++.||=.
T Consensus       298 p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~~~~v~vIaaTn~  349 (489)
T 3hu3_A          298 PAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNR  349 (489)
T ss_dssp             SEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCTTSCEEEEEEESC
T ss_pred             CcEEEecchhhhccccccccchHHHHHHHHHHHHhhccccCCceEEEEecCC
Confidence            3689999999876531          22344555565555566777777753

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=93.28  E-value=0.13  Score=51.07  Aligned_cols=16  Identities=25%  Similarity=0.382  Sum_probs=14.1

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+++.||+|+|||+.+
T Consensus        52 ~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           52 SMILWGPPGTGKTTLA   67 (447)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCcHHHHH
Confidence            5999999999999854

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=93.13  E-value=0.28  Score=47.70  Aligned_cols=18  Identities=39%  Similarity=0.442  Sum_probs=15.4

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+.+++.||+|+|||+.+
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            467999999999999754

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=93.11  E-value=0.17  Score=50.26  Aligned_cols=39  Identities=21%  Similarity=0.145  Sum_probs=23.8

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      .|.-++|.|++|+|||...+ -+.......      .+..++++.-
T Consensus       199 ~G~l~ii~G~pg~GKT~lal-~ia~~~a~~------~g~~vl~~sl  237 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFAL-TIAQNAALK------EGVGVGIYSL  237 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHH-HHHHHHHHT------TCCCEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHHH-HHHHHHHHh------CCCeEEEEEC
Confidence            34458999999999997543 333333321      1345777653

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=92.50  E-value=0.21  Score=55.40  Aligned_cols=75  Identities=15%  Similarity=0.150  Sum_probs=63.2

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHH---CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-c----cccCCCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVA---EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-V----ASRGLDVMGVA  444 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~---~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~----~~~Gldip~v~  444 (503)
                      ..+++||.++++.-+.++++.+.+   .++.+..+||+.+..+|...++.+..|..+|+|+|. .    +.. ++..+++
T Consensus       120 ~~~~~Lil~PtreLa~Q~~~~l~~l~~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~-l~~~~l~  198 (1104)
T 4ddu_A          120 KGKKSALVFPTVTLVKQTLERLQKLADEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK-LSQKRFD  198 (1104)
T ss_dssp             TTCCEEEEESSHHHHHHHHHHHHTTSCTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH-HHTSCCS
T ss_pred             cCCeEEEEechHHHHHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh-hcccCcC
Confidence            345699999999999999999998   577999999999998888899999999999999994 2    222 4566788


Q ss_pred             EEEE
Q 010709          445 HVVN  448 (503)
Q Consensus       445 ~VI~  448 (503)
                      +||.
T Consensus       199 ~lVi  202 (1104)
T 4ddu_A          199 FVFV  202 (1104)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8886

>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=91.87  E-value=5.9  Score=37.19  Aligned_cols=51  Identities=20%  Similarity=0.436  Sum_probs=29.3

Q ss_pred             HHHHHHHHcCCCCCCCccEEEecchhHHhh---CCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          254 GRFLDHLQQGNTSLSRVSFVILDEADRMLD---MGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       254 ~~l~~~l~~~~~~l~~~~~vViDEaH~l~~---~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      ..+.+.+.....   +--+|||||+|.+..   ..+...+..+....+ +..+| ++++
T Consensus       125 ~~l~~~l~~~~~---~~~vlvlDe~~~~~~~~~~~~~~~l~~~~~~~~-~~~~i-~~g~  178 (357)
T 2fna_A          125 ANLLESFEQASK---DNVIIVLDEAQELVKLRGVNLLPALAYAYDNLK-RIKFI-MSGS  178 (357)
T ss_dssp             HHHHHHHHHTCS---SCEEEEEETGGGGGGCTTCCCHHHHHHHHHHCT-TEEEE-EEES
T ss_pred             HHHHHHHHhcCC---CCeEEEEECHHHhhccCchhHHHHHHHHHHcCC-CeEEE-EEcC
Confidence            445555543211   234899999998764   356666776666542 44444 4444

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=91.84  E-value=1.4  Score=43.07  Aligned_cols=54  Identities=17%  Similarity=0.142  Sum_probs=28.8

Q ss_pred             CcCCcccCCCCHHHHHHHHHC---CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHh
Q 010709          119 PIESFTDMCLHPSIMKDIEFH---EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~---~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      |-.+|++.+=-+...+.|...   .+..|--++...   +...+.+++.||+|+|||+.+
T Consensus       167 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          167 PDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            345688886555555555421   011111111100   012345999999999999743

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=91.72  E-value=0.17  Score=42.81  Aligned_cols=120  Identities=13%  Similarity=0.161  Sum_probs=70.2

Q ss_pred             cHHHHHHHHHHhcCC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          145 TSIQAQAMPVALSGR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .+-|..++..++...  -.+|.+.-|++||...+.-++.....       .|..+.+|+|+..-.....+....      
T Consensus        36 ~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~-------~Gr~V~vLAp~~~s~~~l~~~~~l------  102 (189)
T 2l8b_A           36 TAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE-------QGREVQIIAADRRSQMNMKQDERL------  102 (189)
T ss_dssp             HHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH-------TTCCEEEECSTTHHHHHHSCTTTC------
T ss_pred             CccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh-------cCeEEEEEcCchHHHHHHHhhcCc------
Confidence            456888888887544  38899999999998754433333222       378899999998665543322111      


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh-CCCCC
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN-LPDKH  301 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~-~~~~~  301 (503)
                        .                    .+++  |-    ..+......+..=+++|||||-.|.    ...+..++.. ...+.
T Consensus       103 --~--------------------~~t~--t~----~~ll~~~~~~tp~s~lIVD~AekLS----~kE~~~Lld~A~~~na  150 (189)
T 2l8b_A          103 --S--------------------GELI--TG----RRQLLEGMAFTPGSTVIVDQGEKLS----LKETLTLLDGAARHNV  150 (189)
T ss_dssp             --S--------------------SCSS--ST----TTTTTTSCCCCCCCEEEEEESSSHH----HHHHHHHHHHHHHTTC
T ss_pred             --C--------------------ccee--eh----hhhhcCCCCCCCCCEEEEechhhcC----HHHHHHHHHHHHhcCC
Confidence              0                    0000  11    1112223333445689999999886    3344444433 23457


Q ss_pred             cEEEEEee
Q 010709          302 QTLLFSAT  309 (503)
Q Consensus       302 q~i~~SAT  309 (503)
                      |+|++--+
T Consensus       151 qvvll~~~  158 (189)
T 2l8b_A          151 QVLITDSG  158 (189)
T ss_dssp             CEEEEESS
T ss_pred             EEEEeCCc
Confidence            78777544

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=91.62  E-value=0.53  Score=43.71  Aligned_cols=18  Identities=28%  Similarity=0.185  Sum_probs=14.1

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++.+.++++.|+|||+..
T Consensus        98 ~~~i~i~g~~G~GKTT~~  115 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTA  115 (295)
T ss_dssp             SEEEEEECCTTTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            445778899999999754

>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=91.61  E-value=0.41  Score=53.41  Aligned_cols=75  Identities=11%  Similarity=0.181  Sum_probs=64.6

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-cccccCCCCCCCCEEEE
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-DVASRGLDVMGVAHVVN  448 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-~~~~~Gldip~v~~VI~  448 (503)
                      ..+++|.|+++.-+.+.++.+.+.    ++.+..+++..+..++...++.+..|..+|+|+| ..+...+.+.++++||.
T Consensus       652 g~~vlvlvPt~~La~Q~~~~~~~~~~~~~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~~~~~~~~l~lvIi  731 (1151)
T 2eyq_A          652 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV  731 (1151)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             CCeEEEEechHHHHHHHHHHHHHHhhcCCCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhCCccccccceEEE
Confidence            347999999999999998888753    6789999999999999999999999999999999 56666788888887774

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=91.48  E-value=0.68  Score=46.15  Aligned_cols=62  Identities=11%  Similarity=0.044  Sum_probs=43.5

Q ss_pred             cEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEc
Q 010709          376 LTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNL  449 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~  449 (503)
                      +++|.|.+...++.+.+.|...++.+...... .         .+.  ...|.|+..-++.|+-+|+.+++|..
T Consensus       384 rVvi~a~s~~r~erL~~~L~~~~i~~~~~~~~-~---------~~~--~g~v~i~~g~L~~GF~~p~~klaVIT  445 (483)
T 3hjh_A          384 PVVFSVESEGRREALGELLARIKIAPQRIMRL-D---------EAS--DRGRYLMIGAAEHGFVDTVRNLALIC  445 (483)
T ss_dssp             CEEEEESCSSTTTTTHHHHGGGTCCCEECSCG-G---------GCC--TTCEEEEESCCCSCEEETTTTEEEEE
T ss_pred             eEEEEeCChHHHHHHHHHHHHcCCCceecCch-h---------hcC--CCcEEEEEcccccCcccCCCCEEEEE
Confidence            58888888888888888888877765443221 1         112  23566777788999999988887764

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=91.26  E-value=0.16  Score=41.52  Aligned_cols=19  Identities=16%  Similarity=0.069  Sum_probs=16.2

Q ss_pred             hcCCCeEEEccCCCchhHH
Q 010709          156 LSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~  174 (503)
                      ..+.++++.||+|+|||..
T Consensus        25 ~~~~~vll~G~~GtGKt~l   43 (143)
T 3co5_A           25 KRTSPVFLTGEAGSPFETV   43 (143)
T ss_dssp             TCSSCEEEEEETTCCHHHH
T ss_pred             CCCCcEEEECCCCccHHHH
Confidence            4567899999999999964

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=91.19  E-value=0.17  Score=41.46  Aligned_cols=38  Identities=5%  Similarity=0.086  Sum_probs=23.2

Q ss_pred             cEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          271 SFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       271 ~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      ..++|||+|.+... ....+..++...+.+.++|+.|..
T Consensus        78 g~l~ldei~~l~~~-~q~~Ll~~l~~~~~~~~~I~~t~~  115 (145)
T 3n70_A           78 GTLVLSHPEHLTRE-QQYHLVQLQSQEHRPFRLIGIGDT  115 (145)
T ss_dssp             SCEEEECGGGSCHH-HHHHHHHHHHSSSCSSCEEEEESS
T ss_pred             cEEEEcChHHCCHH-HHHHHHHHHhhcCCCEEEEEECCc
Confidence            47999999976432 334455555555556666555443

>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=90.97  E-value=1.9  Score=38.45  Aligned_cols=72  Identities=15%  Similarity=0.216  Sum_probs=54.5

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----ccc-cCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVA----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VAS-RGLDVMG  442 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~-~Gldip~  442 (503)
                      ..+++||.+++++.+.++++.+..    .++.+..++|+.+..++...+..    ..+|+|+|.     .+. ..+++.+
T Consensus       101 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~----~~~I~v~Tp~~l~~~l~~~~~~~~~  176 (242)
T 3fe2_A          101 DGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLER----GVEICIATPGRLIDFLECGKTNLRR  176 (242)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHHTSCCCTT
T ss_pred             CCCEEEEEeCcHHHHHHHHHHHHHHHhhcCceEEEEECCCChHHHHHHhcC----CCCEEEECHHHHHHHHHcCCCCccc
Confidence            345699999999999988777765    38899999999998776655542    478999994     222 3457788


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       177 ~~~lVi  182 (242)
T 3fe2_A          177 TTYLVL  182 (242)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            888775

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=90.71  E-value=2.9  Score=35.71  Aligned_cols=73  Identities=19%  Similarity=0.311  Sum_probs=53.1

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      ++++||.++++.-+..+++.++..     ++.+..++|+....+....+    .+..+|+|+|     +.+.. .+++..
T Consensus        54 ~~~~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT-----~~~~~-Gldi~~  122 (191)
T 2p6n_A           54 PPPVLIFAEKKADVDAIHEYLLLK-----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVAT-----DVASK-GLDFPA  122 (191)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEEC-----HHHHT-TCCCCC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEc-----Cchhc-CCCccc
Confidence            456999999999999998888775     36788889987765443322    2568999999     33443 566778


Q ss_pred             ccEEEecc
Q 010709          270 VSFVILDE  277 (503)
Q Consensus       270 ~~~vViDE  277 (503)
                      +++||.=+
T Consensus       123 v~~VI~~d  130 (191)
T 2p6n_A          123 IQHVINYD  130 (191)
T ss_dssp             CSEEEESS
T ss_pred             CCEEEEeC
Confidence            88887633

>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=90.70  E-value=1.3  Score=38.78  Aligned_cols=71  Identities=14%  Similarity=0.257  Sum_probs=54.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHC-----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc-c-----ccCCCCCCC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAE-----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV-A-----SRGLDVMGV  443 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~-~-----~~Gldip~v  443 (503)
                      .++||.++++..+.++++.+++.     ++.+..++|+.+..++...   +..+..+|+|+|.- +     ...+++..+
T Consensus        83 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~---~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~  159 (220)
T 1t6n_A           83 VSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKHI  159 (220)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTTC
T ss_pred             EEEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHH---HhcCCCCEEEeCHHHHHHHHHhCCCCcccC
Confidence            47999999999999998888764     7889999999987665543   44567899999941 1     234677788


Q ss_pred             CEEEE
Q 010709          444 AHVVN  448 (503)
Q Consensus       444 ~~VI~  448 (503)
                      ++||.
T Consensus       160 ~~lVi  164 (220)
T 1t6n_A          160 KHFIL  164 (220)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            88775

>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=90.59  E-value=0.25  Score=50.29  Aligned_cols=19  Identities=32%  Similarity=0.286  Sum_probs=16.0

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .+..+++.||+|+|||+.+
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            3667999999999999843

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=90.56  E-value=0.74  Score=49.78  Aligned_cols=17  Identities=35%  Similarity=0.399  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      ++++++||+|+|||..+
T Consensus       192 ~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCEEEECTTSCHHHHH
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            46999999999999754

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=90.55  E-value=1.6  Score=38.57  Aligned_cols=70  Identities=16%  Similarity=0.170  Sum_probs=50.2

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-c----ccc--CCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-V----ASR--GLDVMG  442 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~----~~~--Gldip~  442 (503)
                      ..++||.++++..+.++++.+...    ++.+..++|+.+...+...+     +..+|+|+|. .    +..  .++..+
T Consensus        97 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~iiv~Tp~~l~~~l~~~~~~~~~~  171 (236)
T 2pl3_A           97 GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERI-----NNINILVCTPGRLLQHMDETVSFHATD  171 (236)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTSSCCEEEECCC--CHHHHHHH-----TTCSEEEECHHHHHHHHHHCSSCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhCCCCeeEEEEECCCCHHHHHHhC-----CCCCEEEECHHHHHHHHHhcCCccccc
Confidence            456999999999999999988765    47889999988765544333     4689999994 2    222  366777


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       172 ~~~lVi  177 (236)
T 2pl3_A          172 LQMLVL  177 (236)
T ss_dssp             CCEEEE
T ss_pred             ccEEEE
Confidence            887775

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=90.29  E-value=1.5  Score=41.33  Aligned_cols=53  Identities=13%  Similarity=0.193  Sum_probs=32.5

Q ss_pred             CccEEEecchhHHh-hCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh
Q 010709          269 RVSFVILDEADRML-DMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       269 ~~~~vViDEaH~l~-~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                      .++++++|.+-+.- .......+..+.+.+.++..++.+.++...+....++.+
T Consensus       211 ~~d~vliDtaG~~~~~~~l~~eL~~i~ral~~de~llvLDa~t~~~~~~~~~~~  264 (328)
T 3e70_C          211 GIDVVLIDTAGRSETNRNLMDEMKKIARVTKPNLVIFVGDALAGNAIVEQARQF  264 (328)
T ss_dssp             TCSEEEEEECCSCCTTTCHHHHHHHHHHHHCCSEEEEEEEGGGTTHHHHHHHHH
T ss_pred             cchhhHHhhccchhHHHHHHHHHHHHHHHhcCCCCEEEEecHHHHHHHHHHHHH
Confidence            35677888776432 122444555555555666667788888776666666555

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=89.75  E-value=1.5  Score=36.38  Aligned_cols=74  Identities=22%  Similarity=0.342  Sum_probs=52.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..+++.+...     ++.+..++|+....+....+    .+..+|+|+|     +.+.. .+++..
T Consensus        35 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T-----~~~~~-Gld~~~  103 (163)
T 2hjv_A           35 PDSCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVAT-----DVAAR-GIDIEN  103 (163)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEC-----GGGTT-TCCCSC
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEC-----Chhhc-CCchhc
Confidence            457999999999999988888775     36788889887665433322    2467899999     22222 566778


Q ss_pred             ccEEEecch
Q 010709          270 VSFVILDEA  278 (503)
Q Consensus       270 ~~~vViDEa  278 (503)
                      +++||.-+.
T Consensus       104 ~~~Vi~~~~  112 (163)
T 2hjv_A          104 ISLVINYDL  112 (163)
T ss_dssp             CSEEEESSC
T ss_pred             CCEEEEeCC
Confidence            888886443

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=89.39  E-value=0.92  Score=48.33  Aligned_cols=18  Identities=39%  Similarity=0.399  Sum_probs=15.3

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++++++.||+|+|||..+
T Consensus       207 ~~~vlL~G~~GtGKT~la  224 (758)
T 1r6b_X          207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_dssp             SCEEEEECCTTSSHHHHH
T ss_pred             CCCeEEEcCCCCCHHHHH
Confidence            456999999999999754

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=88.86  E-value=0.77  Score=44.87  Aligned_cols=27  Identities=22%  Similarity=0.271  Sum_probs=18.6

Q ss_pred             HHHHHHHHh--cCCCeEEEccCCCchhHH
Q 010709          148 QAQAMPVAL--SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       148 Q~~~i~~i~--~~~~vii~~~TGsGKTl~  174 (503)
                      +...+..++  .+.-++|+||||||||+.
T Consensus       155 ~~~~L~~l~~~~ggii~I~GpnGSGKTTl  183 (418)
T 1p9r_A          155 NHDNFRRLIKRPHGIILVTGPTGSGKSTT  183 (418)
T ss_dssp             HHHHHHHHHTSSSEEEEEECSTTSCHHHH
T ss_pred             HHHHHHHHHHhcCCeEEEECCCCCCHHHH
Confidence            344444444  334589999999999984

>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=88.78  E-value=0.99  Score=45.70  Aligned_cols=58  Identities=19%  Similarity=0.290  Sum_probs=54.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD  432 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~  432 (503)
                      +.+||.++++.-+....+.|...|+.+..+||+.+..++..++..+..|..+|+++|.
T Consensus        66 g~~lvi~P~~aL~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tp  123 (523)
T 1oyw_A           66 GLTVVVSPLISLMKDQVDQLQANGVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAP  123 (523)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECH
T ss_pred             CCEEEECChHHHHHHHHHHHHHcCCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECH
Confidence            5699999999999999999999999999999999999999999999999999999994

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=88.16  E-value=0.56  Score=49.79  Aligned_cols=53  Identities=15%  Similarity=0.216  Sum_probs=31.1

Q ss_pred             CcCCcccCCCCHHHHHHHHHCC---CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHH
Q 010709          119 PIESFTDMCLHPSIMKDIEFHE---YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~---~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~  174 (503)
                      +-..|++++--+...+.|...-   ...|..++...   +...+.+++.||+|+|||+.
T Consensus       472 p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g---~~~~~gvLl~GPPGtGKT~l  527 (806)
T 3cf2_A          472 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG---MTPSKGVLFYGPPGCGKTLL  527 (806)
T ss_dssp             CCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSC---CCCCSCCEEESSTTSSHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEecCCCCCchHH
Confidence            3456888877777777775531   11221111000   01234699999999999974

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=87.87  E-value=2.1  Score=35.45  Aligned_cols=73  Identities=19%  Similarity=0.327  Sum_probs=51.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..+++.++..     ++.+..++|+....+....+    .+..+|+|+|     +.+.. .+++..
T Consensus        30 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T-----~~~~~-G~d~~~   98 (165)
T 1fuk_A           30 VTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILIST-----DLLAR-GIDVQQ   98 (165)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEE-----GGGTT-TCCCCS
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEc-----Chhhc-CCCccc
Confidence            467999999999999888888764     36788888887765443322    2567899999     22222 456777


Q ss_pred             ccEEEecc
Q 010709          270 VSFVILDE  277 (503)
Q Consensus       270 ~~~vViDE  277 (503)
                      +++||.-+
T Consensus        99 ~~~Vi~~~  106 (165)
T 1fuk_A           99 VSLVINYD  106 (165)
T ss_dssp             CSEEEESS
T ss_pred             CCEEEEeC
Confidence            88887644

>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=87.59  E-value=2.2  Score=37.22  Aligned_cols=71  Identities=23%  Similarity=0.343  Sum_probs=52.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..+++.+...     ++.+..++|+....+....+    .+..+|+|+|     +.+.. .+++..
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT-----~~~~~-Gidi~~   99 (212)
T 3eaq_A           31 PDRAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVAT-----DVAAR-GLDIPQ   99 (212)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEEC-----TTTTC-SSSCCC
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEec-----Chhhc-CCCCcc
Confidence            467999999999999888888775     36788899988765544333    2568899999     33333 567778


Q ss_pred             ccEEEe
Q 010709          270 VSFVIL  275 (503)
Q Consensus       270 ~~~vVi  275 (503)
                      +++||.
T Consensus       100 v~~Vi~  105 (212)
T 3eaq_A          100 VDLVVH  105 (212)
T ss_dssp             BSEEEE
T ss_pred             CcEEEE
Confidence            888875

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=87.56  E-value=0.46  Score=55.28  Aligned_cols=39  Identities=21%  Similarity=0.202  Sum_probs=26.8

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTR  204 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr  204 (503)
                      ++.++++||+|+|||..+.. +......       .+.+++++..-.
T Consensus      1427 g~~vll~GppGtGKT~LA~a-la~ea~~-------~G~~v~Fi~~e~ 1465 (2050)
T 3cmu_A         1427 GRIVEIYGPESSGKTTLTLQ-VIAAAQR-------EGKTCAFIDAEH 1465 (2050)
T ss_dssp             TSEEEEECCTTSSHHHHHHH-HHHHHHT-------TTCCEEEECTTS
T ss_pred             CeEEEEECCCCCCHHHHHHH-HHHHHHH-------cCCcEEEEEccc
Confidence            67899999999999986533 3333222       256788887553

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=87.53  E-value=0.55  Score=46.35  Aligned_cols=44  Identities=20%  Similarity=0.366  Sum_probs=31.9

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      ...+++|.|+||+|||... ..++..++..       +..++|+=|..++..
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~~~~-------g~~viv~Dpkge~~~   95 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTGLLR-------GDRMVIVDPNGDMLS   95 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHHHHT-------TCEEEEEEETTHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHHHHC-------CCcEEEEeCCCchhH
Confidence            4578999999999999864 4455555543       456777778888754

>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=87.46  E-value=1  Score=46.26  Aligned_cols=58  Identities=14%  Similarity=0.194  Sum_probs=53.5

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHH--hcCCCcEEEEcc
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDF--RNGSTNILVATD  432 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f--~~g~~~vLvaT~  432 (503)
                      +.+||.++++.-+.+.++.|...|+.+..++|+++..++..++..+  ..+..+||++|.
T Consensus        85 g~~lVisP~~~L~~q~~~~l~~~gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tp  144 (591)
T 2v1x_A           85 GFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTP  144 (591)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHHTCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECH
T ss_pred             CcEEEEeCHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEECh
Confidence            5799999999999999999999999999999999999999998888  568899999996

>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=87.45  E-value=2.3  Score=38.11  Aligned_cols=71  Identities=20%  Similarity=0.323  Sum_probs=53.7

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----ccc--cCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VAS--RGLDVMG  442 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~--~Gldip~  442 (503)
                      ..++||.++++..+.++++.+++.    ++.+..++|+....++...+    .+..+|+|+|.     .+.  .++++..
T Consensus       111 ~~~~lil~Ptr~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~I~v~Tp~~l~~~l~~~~~~~l~~  186 (249)
T 3ber_A          111 RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDSMSQSLAL----AKKPHIIIATPGRLIDHLENTKGFNLRA  186 (249)
T ss_dssp             SSCEEEECSSHHHHHHHHHHHHHHHGGGTCCEEEECTTSCHHHHHHHH----HTCCSEEEECHHHHHHHHHHSTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhccCCeeEEEEECCCChHHHHHHh----cCCCCEEEECHHHHHHHHHcCCCcCccc
Confidence            346999999999999998887764    78899999999876554433    24689999993     222  4567888


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       187 ~~~lVi  192 (249)
T 3ber_A          187 LKYLVM  192 (249)
T ss_dssp             CCEEEE
T ss_pred             cCEEEE
Confidence            888775

>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=87.33  E-value=1.6  Score=38.57  Aligned_cols=70  Identities=14%  Similarity=0.170  Sum_probs=53.0

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC-----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc-c-----ccCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE-----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV-A-----SRGLDVMG  442 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~-~-----~~Gldip~  442 (503)
                      ..++||.+++++.+.++++.++..     ++.+..++|+....++...+     ...+|+|+|.- +     ...+++..
T Consensus        92 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-----~~~~Iiv~Tp~~l~~~~~~~~~~~~~  166 (230)
T 2oxc_A           92 STQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-----KKCHIAVGSPGRIKQLIELDYLNPGS  166 (230)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-----TSCSEEEECHHHHHHHHHTTSSCGGG
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-----cCCCEEEECHHHHHHHHhcCCccccc
Confidence            457999999999999999988764     67889999999877655443     25799999942 1     23456777


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       167 ~~~lVi  172 (230)
T 2oxc_A          167 IRLFIL  172 (230)
T ss_dssp             CCEEEE
T ss_pred             CCEEEe
Confidence            877774

>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=87.30  E-value=2.2  Score=36.64  Aligned_cols=72  Identities=26%  Similarity=0.277  Sum_probs=53.1

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----ccc-cCCCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VAS-RGLDVMGVA  444 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~-~Gldip~v~  444 (503)
                      ...++||.++++..+.++++.+...  ++.+..++|+.....+...+.    ...+|+|+|.     .+. ..+++.+++
T Consensus        71 ~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~i~v~T~~~l~~~~~~~~~~~~~~~  146 (207)
T 2gxq_A           71 RKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALL----RGADAVVATPGRALDYLRQGVLDLSRVE  146 (207)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCTTSCEEEECSSSCSHHHHHHHH----HCCSEEEECHHHHHHHHHHTSSCCTTCS
T ss_pred             CCCcEEEEECCHHHHHHHHHHHHHHhhcceEEEEECCCChHHHHHHhh----CCCCEEEECHHHHHHHHHcCCcchhhce
Confidence            3457999999999999999999876  468888999887655444332    2578999994     222 346677888


Q ss_pred             EEEE
Q 010709          445 HVVN  448 (503)
Q Consensus       445 ~VI~  448 (503)
                      +||.
T Consensus       147 ~iVi  150 (207)
T 2gxq_A          147 VAVL  150 (207)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8775

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=87.28  E-value=0.69  Score=40.42  Aligned_cols=30  Identities=27%  Similarity=0.207  Sum_probs=24.8

Q ss_pred             cHHHHHHHHHHhcCCCeEEEccCCCchhHH
Q 010709          145 TSIQAQAMPVALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~  174 (503)
                      +.-|..++..+..|.-+.+.||.|+|||+.
T Consensus         9 ~~g~~~~l~~i~~Ge~~~liG~nGsGKSTL   38 (208)
T 3b85_A            9 TLGQKHYVDAIDTNTIVFGLGPAGSGKTYL   38 (208)
T ss_dssp             SHHHHHHHHHHHHCSEEEEECCTTSSTTHH
T ss_pred             CHhHHHHHHhccCCCEEEEECCCCCCHHHH
Confidence            344667888888888899999999999984

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=87.05  E-value=0.62  Score=46.92  Aligned_cols=40  Identities=20%  Similarity=-0.026  Sum_probs=25.5

Q ss_pred             HHHHHHCCCCCCcHHHHHHHH-HHhcCCCeEEEccCCCchhHH
Q 010709          133 MKDIEFHEYTRPTSIQAQAMP-VALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       133 ~~~l~~~~~~~~~~~Q~~~i~-~i~~~~~vii~~~TGsGKTl~  174 (503)
                      ...+...|.  +.+.+...+. .+..|..++++||||||||+.
T Consensus       236 ~~~l~~~G~--~~~~~l~~l~~~v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          236 PIDLIEKGT--VPSGVLAYLWLAIEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHHHHTTS--SCHHHHHHHHHHHHTTCCEEEEESTTSSHHHH
T ss_pred             hhhHHhcCC--CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHH
Confidence            344555553  2333334343 345778899999999999983

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=87.04  E-value=1.2  Score=41.61  Aligned_cols=41  Identities=15%  Similarity=0.031  Sum_probs=26.7

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      -++|.||+|+|||+..+ .++......     ..+.+++++..-..+
T Consensus        30 iteI~G~pGsGKTtL~L-q~~~~~~~~-----g~g~~vlyId~E~s~   70 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGL-TMVSSYMRQ-----YPDAVCLFYDSEFGI   70 (333)
T ss_dssp             EEEEEESSSSSHHHHHH-HHHHHHHHH-----CTTCEEEEEESSCCC
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHHhc-----CCCceEEEEeccchh
Confidence            58999999999998653 334333332     124678888765444

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=86.90  E-value=0.76  Score=43.88  Aligned_cols=18  Identities=33%  Similarity=0.375  Sum_probs=15.2

Q ss_pred             cCCCeEEEccCCCchhHH
Q 010709          157 SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~  174 (503)
                      .+..++|+||||||||+.
T Consensus       122 ~~g~i~I~GptGSGKTTl  139 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTT  139 (356)
T ss_dssp             SSEEEEEECSTTSCHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            445699999999999984

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=86.84  E-value=0.42  Score=45.24  Aligned_cols=38  Identities=18%  Similarity=0.188  Sum_probs=24.7

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      .|.-++|.|++|+|||..++ -+.......       +..++|+..
T Consensus        45 ~G~LiiIaG~pG~GKTt~al-~ia~~~a~~-------g~~Vl~fSl   82 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMM-NMVLSALND-------DRGVAVFSL   82 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHH-HHHHHHHHT-------TCEEEEEES
T ss_pred             CCcEEEEEeCCCCCHHHHHH-HHHHHHHHc-------CCeEEEEeC
Confidence            45559999999999997543 333333332       456777763

>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=86.57  E-value=2.7  Score=40.23  Aligned_cols=72  Identities=14%  Similarity=0.247  Sum_probs=55.1

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC-----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-cc-----ccCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE-----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VA-----SRGLDVMG  442 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~-----~~Gldip~  442 (503)
                      ..++||.|+++..+.++++.+.+.     ++.+..++|+.+..++...   +..+..+|+|+|. .+     ...+++..
T Consensus        76 ~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~---~~~~~~~iiv~T~~~l~~~~~~~~~~~~~  152 (391)
T 1xti_A           76 QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV---LKKNCPHIVVGTPGRILALARNKSLNLKH  152 (391)
T ss_dssp             CCCEEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHH---HHHSCCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CeeEEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHH---HhcCCCCEEEECHHHHHHHHHcCCccccc
Confidence            457999999999999998888764     7889999999987665544   3457789999993 22     23456778


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       153 ~~~vVi  158 (391)
T 1xti_A          153 IKHFIL  158 (391)
T ss_dssp             CSEEEE
T ss_pred             cCEEEE
Confidence            888775

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=86.46  E-value=0.69  Score=49.28  Aligned_cols=16  Identities=31%  Similarity=0.324  Sum_probs=14.1

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      ++++.||||+|||..+
T Consensus       523 ~~Ll~Gp~GtGKT~lA  538 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELA  538 (758)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4999999999999754

>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=86.37  E-value=1.7  Score=36.44  Aligned_cols=71  Identities=15%  Similarity=0.237  Sum_probs=51.5

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++..+..+++.+...     ++.+..++|+....+....+    .+..+|+|+|.     .+. ..+++..
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~~-~Gid~~~  102 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN-----VCA-RGIDVKQ  102 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC-----SCC-TTTCCTT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec-----chh-cCCCccc
Confidence            568999999999999888877764     46788889988765543332    24689999992     222 2456778


Q ss_pred             ccEEEe
Q 010709          270 VSFVIL  275 (503)
Q Consensus       270 ~~~vVi  275 (503)
                      +++||.
T Consensus       103 ~~~Vi~  108 (175)
T 2rb4_A          103 VTIVVN  108 (175)
T ss_dssp             EEEEEE
T ss_pred             CCEEEE
Confidence            888885

>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=86.36  E-value=6  Score=35.64  Aligned_cols=71  Identities=21%  Similarity=0.170  Sum_probs=52.6

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----ccc--cCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VAS--RGLDVMG  442 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~--~Gldip~  442 (503)
                      ..++||.++++.-+.++++.+++.    +..+..++|+.....+...+   ..| .+|+|+|.     .+.  .++++.+
T Consensus       126 ~~~~lil~Pt~~La~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~~~-~~Iiv~Tp~~l~~~~~~~~~~~~~~  201 (262)
T 3ly5_A          126 GTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKL---GNG-INIIVATPGRLLDHMQNTPGFMYKN  201 (262)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTCCSCEEEECSSSCHHHHHHHH---HHC-CSEEEECHHHHHHHHHHCTTCCCTT
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHHhhcCceEEEEECCCCHHHHHHHh---cCC-CCEEEEcHHHHHHHHHccCCccccc
Confidence            456999999999999999888763    56788899988866554433   333 89999993     222  2467888


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       202 l~~lVi  207 (262)
T 3ly5_A          202 LQCLVI  207 (262)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            888775

>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=86.35  E-value=1.8  Score=38.02  Aligned_cols=72  Identities=18%  Similarity=0.316  Sum_probs=49.3

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC---CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----c-cccCCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE---GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----V-ASRGLDVMGV  443 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~---~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~-~~~Gldip~v  443 (503)
                      ...++||.+++++.+.++++.+...   ++.+..++|+....++...+   . ...+|+|+|.     . ....+++.++
T Consensus        93 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~iiv~Tp~~l~~~~~~~~~~~~~~  168 (228)
T 3iuy_A           93 NGPGMLVLTPTRELALHVEAECSKYSYKGLKSICIYGGRNRNGQIEDI---S-KGVDIIIATPGRLNDLQMNNSVNLRSI  168 (228)
T ss_dssp             CCCSEEEECSSHHHHHHHHHHHHHHCCTTCCEEEECC------CHHHH---H-SCCSEEEECHHHHHHHHHTTCCCCTTC
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHhcccCceEEEEECCCChHHHHHHh---c-CCCCEEEECHHHHHHHHHcCCcCcccc
Confidence            4457999999999999999998874   77889999988765544333   2 3489999993     1 2235677888


Q ss_pred             CEEEE
Q 010709          444 AHVVN  448 (503)
Q Consensus       444 ~~VI~  448 (503)
                      ++||.
T Consensus       169 ~~lVi  173 (228)
T 3iuy_A          169 TYLVI  173 (228)
T ss_dssp             CEEEE
T ss_pred             eEEEE
Confidence            88775

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=86.06  E-value=0.59  Score=45.81  Aligned_cols=55  Identities=16%  Similarity=0.243  Sum_probs=33.4

Q ss_pred             CCcCCcccCCCCHHHHHHHHHC---CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHh
Q 010709          118 APIESFTDMCLHPSIMKDIEFH---EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~---~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      .|..+|++++-.+...+.|...   -+..|.-++...+   ...+.+++.||+|+|||+.+
T Consensus       175 ~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          175 KPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            4556799998777777776532   1112222221111   12356999999999999743

>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=85.91  E-value=3  Score=35.81  Aligned_cols=71  Identities=23%  Similarity=0.265  Sum_probs=51.7

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC-----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----cccc-CCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE-----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VASR-GLDVMG  442 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~~-Gldip~  442 (503)
                      ..++||.++++..+.++++.+...     +..+..++|+....++...+    .+..+|+|+|.     .+.. .+++.+
T Consensus        71 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~i~v~T~~~l~~~~~~~~~~~~~  146 (206)
T 1vec_A           71 NIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL----DDTVHVVIATPGRILDLIKKGVAKVDH  146 (206)
T ss_dssp             SCCEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT----TSCCSEEEECHHHHHHHHHTTCSCCTT
T ss_pred             CeeEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhc----CCCCCEEEeCHHHHHHHHHcCCcCccc
Confidence            356999999999999998888653     57889999998866543322    35688999994     2223 346677


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       147 ~~~lVi  152 (206)
T 1vec_A          147 VQMIVL  152 (206)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            888774

>2l82_A Designed protein OR32; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, de novo protein; NMR {Artificial gene}

Probab=85.79  E-value=4.4  Score=30.21  Aligned_cols=49  Identities=18%  Similarity=0.359  Sum_probs=41.4

Q ss_pred             EEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCC
Q 010709          377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGST  425 (503)
Q Consensus       377 ~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~  425 (503)
                      .+||....+-..++...++..|+.++.++++...+.|.+-++.|.....
T Consensus         5 fvvfssdpeilkeivreikrqgvrvvllysdqdekrrrerleefekqgv   53 (162)
T 2l82_A            5 FVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGV   53 (162)
T ss_dssp             EEEEESCHHHHHHHHHHHHHTTCEEEEEECCSCHHHHHHHHHHHHTTTC
T ss_pred             EEEecCCHHHHHHHHHHHHhCCeEEEEEecCchHHHHHHHHHHHHHcCC
Confidence            5678777788888999999999999999999999999998888865433

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=85.75  E-value=0.4  Score=43.62  Aligned_cols=20  Identities=30%  Similarity=0.258  Sum_probs=16.6

Q ss_pred             HhcCCCeEEEccCCCchhHH
Q 010709          155 ALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~  174 (503)
                      +..|.-++++||||+|||+.
T Consensus        22 i~~g~~v~i~Gp~GsGKSTl   41 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTT   41 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHH
T ss_pred             hCCCCEEEEECCCCccHHHH
Confidence            34666799999999999984

>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=85.49  E-value=1.9  Score=38.22  Aligned_cols=73  Identities=19%  Similarity=0.286  Sum_probs=46.5

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEc-----ccccc-CCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVAT-----DVASR-GLDVMG  442 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT-----~~~~~-Gldip~  442 (503)
                      ...++||.++++..+.++++.++..    ++.+..++|+......   .+.+..+...|+|+|     +.+.+ .+++..
T Consensus        97 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~Ilv~Tp~~l~~~l~~~~~~~~~  173 (237)
T 3bor_A           97 KETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNE---MQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKW  173 (237)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECC----------------CCCSEEEECHHHHHHHHHTTSSCSTT
T ss_pred             CCceEEEEECcHHHHHHHHHHHHHHhhhcCceEEEEECCCchHHH---HHHHhcCCCCEEEECHHHHHHHHHhCCcCccc
Confidence            3457999999999999999988764    5678888888764432   334556778999999     33333 356777


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       174 ~~~lVi  179 (237)
T 3bor_A          174 IKMFVL  179 (237)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            888774

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=85.31  E-value=0.53  Score=45.16  Aligned_cols=20  Identities=40%  Similarity=0.439  Sum_probs=17.4

Q ss_pred             HhcCCCeEEEccCCCchhHH
Q 010709          155 ALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~  174 (503)
                      +..|..++++||||+|||+.
T Consensus       172 i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHH
Confidence            44788999999999999983

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=84.70  E-value=0.89  Score=48.25  Aligned_cols=16  Identities=38%  Similarity=0.526  Sum_probs=14.2

Q ss_pred             CCeEEEccCCCchhHH
Q 010709          159 RDLLGCAETGSGKTAA  174 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~  174 (503)
                      +.+++.||+|+|||+.
T Consensus       239 ~GILL~GPPGTGKT~L  254 (806)
T 3cf2_A          239 RGILLYGPPGTGKTLI  254 (806)
T ss_dssp             CEEEEECCTTSCHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4699999999999974

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=84.36  E-value=0.7  Score=39.94  Aligned_cols=24  Identities=17%  Similarity=0.337  Sum_probs=17.0

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQH  182 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~  182 (503)
                      .|+-++++||+|+|||+.  +-++..
T Consensus         3 ~g~~i~lvGpsGaGKSTL--l~~L~~   26 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTL--LKKLFQ   26 (198)
T ss_dssp             --CCEEEECCTTSSHHHH--HHHHHH
T ss_pred             CCCEEEEECCCCCCHHHH--HHHHHh
Confidence            467799999999999984  334443

>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=84.28  E-value=2.5  Score=35.36  Aligned_cols=74  Identities=14%  Similarity=0.111  Sum_probs=52.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..+++.+...     ++.+..++|+....+....+    .+..+|+|+|. .    +. ..+++..
T Consensus        31 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~-~----~~-~Gldi~~   99 (172)
T 1t5i_A           31 FNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-L----FG-RGMDIER   99 (172)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-C----CS-TTCCGGG
T ss_pred             CCcEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC-c----hh-cCcchhh
Confidence            467999999999999888888775     36788888887765443322    25689999993 2    22 2456777


Q ss_pred             ccEEEecch
Q 010709          270 VSFVILDEA  278 (503)
Q Consensus       270 ~~~vViDEa  278 (503)
                      +++||.-+.
T Consensus       100 ~~~Vi~~d~  108 (172)
T 1t5i_A          100 VNIAFNYDM  108 (172)
T ss_dssp             CSEEEESSC
T ss_pred             CCEEEEECC
Confidence            888876443

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=84.01  E-value=2.1  Score=41.52  Aligned_cols=18  Identities=22%  Similarity=0.091  Sum_probs=14.9

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      |.-+.|.||+|+|||+..
T Consensus       178 Gei~~I~G~sGsGKTTLl  195 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLC  195 (400)
T ss_dssp             TSEEEEEESTTSSHHHHH
T ss_pred             CcEEEEEcCCCCChHHHH
Confidence            455899999999999743

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=83.88  E-value=1.1  Score=40.02  Aligned_cols=51  Identities=22%  Similarity=0.282  Sum_probs=28.3

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVK  215 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~  215 (503)
                      .|.-+++.|++|+|||..++-.+.+.....       +..++|+.-. .-..++.+.+.
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~-------~~~v~~~s~E-~~~~~~~~~~~   79 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEY-------GEPGVFVTLE-ERARDLRREMA   79 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHH-------CCCEEEEESS-SCHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-------CCCceeeccc-CCHHHHHHHHH
Confidence            355699999999999975433233322332       3446666532 22334444443

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=83.84  E-value=1.3  Score=42.32  Aligned_cols=19  Identities=37%  Similarity=0.378  Sum_probs=15.9

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      ...++++.||+|+|||+.+
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3467999999999999854

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=83.81  E-value=0.48  Score=40.26  Aligned_cols=18  Identities=17%  Similarity=0.252  Sum_probs=15.5

Q ss_pred             cCCCeEEEccCCCchhHH
Q 010709          157 SGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~  174 (503)
                      .|+-++++||+|+|||+.
T Consensus         4 ~g~~i~i~GpsGsGKSTL   21 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHI   21 (180)
T ss_dssp             CCCEEEEECCTTSSHHHH
T ss_pred             CCCEEEEECCCCCCHHHH
Confidence            466789999999999984

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=83.81  E-value=9  Score=37.30  Aligned_cols=42  Identities=24%  Similarity=0.233  Sum_probs=24.6

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHH
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQ  208 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~  208 (503)
                      +.++++|+.|+|||+...  .+...+..      .+.+++++.  +.+..+.
T Consensus        99 ~vi~i~G~~GsGKTT~~~--~LA~~l~~------~g~~Vllvd~D~~r~aa~  142 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAA--KLALYYKG------KGRRPLLVAADTQRPAAR  142 (425)
T ss_dssp             EEEEEECCTTSSHHHHHH--HHHHHHHT------TTCCEEEEECCSSCHHHH
T ss_pred             eEEEEECCCCCCHHHHHH--HHHHHHHH------cCCeEEEeeccccCchhH
Confidence            347788999999998542  33333332      145566654  4444443

>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=83.24  E-value=2.2  Score=36.25  Aligned_cols=72  Identities=22%  Similarity=0.282  Sum_probs=43.3

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHH---HHh-hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQR---SEL-RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..+++.++..     ++.+..++|+....+..   ..+ .+..+|+|+|. .+    .. .+++..
T Consensus        46 ~~k~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-~~----~~-Gldi~~  114 (185)
T 2jgn_A           46 DSLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-VA----AR-GLDISN  114 (185)
T ss_dssp             CSCEEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSEEEEEC------------CCCS
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-hh----hc-CCCccc
Confidence            567999999999999888888764     36788888876544322   222 35688999992 22    22 456677


Q ss_pred             ccEEEec
Q 010709          270 VSFVILD  276 (503)
Q Consensus       270 ~~~vViD  276 (503)
                      +++||.=
T Consensus       115 ~~~VI~~  121 (185)
T 2jgn_A          115 VKHVINF  121 (185)
T ss_dssp             BSEEEES
T ss_pred             CCEEEEe
Confidence            8877763

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=83.21  E-value=5.3  Score=37.06  Aligned_cols=17  Identities=24%  Similarity=0.327  Sum_probs=14.0

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +-++++|++|+|||+..
T Consensus       105 ~vi~ivG~~GsGKTTl~  121 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSC  121 (306)
T ss_dssp             EEEEEECCTTSSHHHHH
T ss_pred             eEEEEEcCCCChHHHHH
Confidence            34789999999999853

>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=83.21  E-value=4.3  Score=39.78  Aligned_cols=71  Identities=13%  Similarity=0.142  Sum_probs=53.3

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----cccc-CCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VASR-GLDVMGV  443 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~~-Gldip~v  443 (503)
                      ..++||.+++++.+.++++.+++.    ++.+..++|+.+..++...+    ....+|+|+|.     .+.+ .+++..+
T Consensus       129 ~~~~lil~PtreLa~Q~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l----~~~~~Ivv~Tp~~l~~~l~~~~~~l~~~  204 (434)
T 2db3_A          129 RPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECI----TRGCHVVIATPGRLLDFVDRTFITFEDT  204 (434)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHTTTSSCCCCEECTTSCHHHHHHHH----TTCCSEEEECHHHHHHHHHTTSCCCTTC
T ss_pred             CccEEEEecCHHHHHHHHHHHHHHhccCCcEEEEEECCCCHHHHHHHh----hcCCCEEEEChHHHHHHHHhCCcccccC
Confidence            457999999999999999888764    57788899999876655433    24689999993     2333 3567788


Q ss_pred             CEEEE
Q 010709          444 AHVVN  448 (503)
Q Consensus       444 ~~VI~  448 (503)
                      ++||.
T Consensus       205 ~~lVl  209 (434)
T 2db3_A          205 RFVVL  209 (434)
T ss_dssp             CEEEE
T ss_pred             CeEEE
Confidence            88774

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=83.13  E-value=2.1  Score=39.59  Aligned_cols=18  Identities=33%  Similarity=0.423  Sum_probs=15.5

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ..++++.||+|+|||..+
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            567999999999999754

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=83.02  E-value=0.53  Score=40.71  Aligned_cols=19  Identities=21%  Similarity=0.118  Sum_probs=16.4

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .++.++++|++|+|||+..
T Consensus        24 ~~~~i~l~G~~GsGKsTl~   42 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLG   42 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHH
Confidence            5678999999999999854

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=82.95  E-value=1.4  Score=44.14  Aligned_cols=26  Identities=23%  Similarity=0.271  Sum_probs=20.9

Q ss_pred             HHHHHHHhcCCCeEEEccCCCchhHH
Q 010709          149 AQAMPVALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       149 ~~~i~~i~~~~~vii~~~TGsGKTl~  174 (503)
                      ..++..+..+.++++.||+|+|||..
T Consensus        32 ~~l~~al~~~~~VLL~GpPGtGKT~L   57 (500)
T 3nbx_X           32 RLCLLAALSGESVFLLGPPGIAKSLI   57 (500)
T ss_dssp             HHHHHHHHHTCEEEEECCSSSSHHHH
T ss_pred             HHHHHHHhcCCeeEeecCchHHHHHH
Confidence            44555566888999999999999973

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=82.79  E-value=6  Score=38.17  Aligned_cols=72  Identities=24%  Similarity=0.310  Sum_probs=53.7

Q ss_pred             CCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCC
Q 010709          193 DGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLS  268 (503)
Q Consensus       193 ~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~  268 (503)
                      .+.++||.++++.-+..+++.+++.     ++.+..++|+....+....+    .+..+|+|+|     +.+.. .+++.
T Consensus       275 ~~~~~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT-----~~~~~-Gidip  343 (417)
T 2i4i_A          275 KDSLTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVAT-----AVAAR-GLDIS  343 (417)
T ss_dssp             TTCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEEC-----HHHHT-TSCCC
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHC-----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEEC-----Chhhc-CCCcc
Confidence            3678999999999999988888774     46788889888765443332    2568999999     34444 56778


Q ss_pred             CccEEEe
Q 010709          269 RVSFVIL  275 (503)
Q Consensus       269 ~~~~vVi  275 (503)
                      .+++||.
T Consensus       344 ~v~~Vi~  350 (417)
T 2i4i_A          344 NVKHVIN  350 (417)
T ss_dssp             CEEEEEE
T ss_pred             cCCEEEE
Confidence            8888875

>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=82.74  E-value=4  Score=36.49  Aligned_cols=71  Identities=13%  Similarity=0.173  Sum_probs=51.4

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-cc-----ccCCCCCCC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VA-----SRGLDVMGV  443 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~-----~~Gldip~v  443 (503)
                      ..++||.+++++.+.++++.+...    ++.+..++|+....++...+    ....+|+|+|. .+     ...+++..+
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~  175 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREV----QMGCHLLVATPGRLVDFIEKNKISLEFC  175 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSSCCEEEECSSSCSHHHHHHH----SSCCSEEEECHHHHHHHHHTTSBCCTTC
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCCceEEEEECCCCHHHHHHHh----CCCCCEEEECHHHHHHHHHcCCCChhhC
Confidence            357999999999999988887653    57788899988765544332    34679999994 22     224577788


Q ss_pred             CEEEE
Q 010709          444 AHVVN  448 (503)
Q Consensus       444 ~~VI~  448 (503)
                      ++||.
T Consensus       176 ~~lVi  180 (253)
T 1wrb_A          176 KYIVL  180 (253)
T ss_dssp             CEEEE
T ss_pred             CEEEE
Confidence            88774

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=82.36  E-value=0.95  Score=41.04  Aligned_cols=19  Identities=26%  Similarity=0.310  Sum_probs=16.0

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .+..+++.||+|+|||..+
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            4567999999999999743

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.33  E-value=1.5  Score=42.31  Aligned_cols=54  Identities=15%  Similarity=0.167  Sum_probs=30.0

Q ss_pred             CcCCcccCCCCHHHHHHHHHCC---CCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHh
Q 010709          119 PIESFTDMCLHPSIMKDIEFHE---YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       119 ~~~~~~~~~l~~~l~~~l~~~~---~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      |--+|++.+=-+...+.|+..=   +..|.-++...   +...+.+++.||+|+|||+.+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g---i~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG---IAQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCCCEEEESCSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCCceEEeCCCCCCHHHHH
Confidence            3456888864456666654321   11111111111   112367999999999999743

>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=82.02  E-value=12  Score=37.85  Aligned_cols=77  Identities=16%  Similarity=0.128  Sum_probs=56.7

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..+++.+++....  ++.+..++|+....+....+    .+..+|+|+|.     .+.. .+++.+
T Consensus       339 ~~~~iVF~~s~~~~~~l~~~L~~~~~~--~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~~~-GiDip~  410 (563)
T 3i5x_A          339 NYKAIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGAR-GMDFPN  410 (563)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGTS-SCCCTT
T ss_pred             CCcEEEEcCcHHHHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc-----hhhc-CCCccc
Confidence            578999999999999999999877532  47788888888765543332    25689999993     3333 567888


Q ss_pred             ccEEEecch
Q 010709          270 VSFVILDEA  278 (503)
Q Consensus       270 ~~~vViDEa  278 (503)
                      +++||.-..
T Consensus       411 v~~VI~~~~  419 (563)
T 3i5x_A          411 VHEVLQIGV  419 (563)
T ss_dssp             CCEEEEESC
T ss_pred             CCEEEEECC
Confidence            888886553

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=81.82  E-value=1.3  Score=42.97  Aligned_cols=42  Identities=21%  Similarity=0.389  Sum_probs=28.3

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      .+.+++|.|+||+|||+..-. ++......       +.+++++=|..+.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~-~~~~~~~~-------~~~~~~~D~~~~~   75 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKM-LLLREYMQ-------GSRVIIIDPEREY   75 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHH-HHHHHHTT-------TCCEEEEESSCCS
T ss_pred             ccCceEEEcCCCCCHHHHHHH-HHHHHHHC-------CCEEEEEeCCcCH
Confidence            567899999999999975432 33333322       4667777787653

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=81.77  E-value=0.62  Score=39.57  Aligned_cols=18  Identities=22%  Similarity=0.150  Sum_probs=15.4

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++.++++|++|+|||+..
T Consensus         5 ~~~i~l~G~~GsGKst~a   22 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVG   22 (185)
T ss_dssp             CCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEECCCCCCHHHHH
Confidence            456999999999999854

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=81.38  E-value=1.5  Score=40.63  Aligned_cols=18  Identities=28%  Similarity=0.484  Sum_probs=15.1

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++.++++|++|+|||+..
T Consensus       105 g~vi~lvG~~GsGKTTl~  122 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTL  122 (296)
T ss_dssp             SSEEEEEESTTSSHHHHH
T ss_pred             CcEEEEECCCCCCHHHHH
Confidence            456889999999999854

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=81.37  E-value=0.7  Score=43.56  Aligned_cols=24  Identities=21%  Similarity=0.153  Sum_probs=19.0

Q ss_pred             HHHHhcCCCeEEEccCCCchhHHh
Q 010709          152 MPVALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       152 i~~i~~~~~vii~~~TGsGKTl~~  175 (503)
                      ...+..++++++.||+|+|||..+
T Consensus        40 ~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           40 LIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHcCCeEEEECCCCCcHHHHH
Confidence            344456889999999999999743

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=81.36  E-value=0.57  Score=39.62  Aligned_cols=19  Identities=26%  Similarity=0.165  Sum_probs=16.3

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .++.++++|++|+|||+..
T Consensus        10 ~~~~i~i~G~~GsGKst~~   28 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLG   28 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHH
Confidence            4567999999999999854

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=81.34  E-value=0.69  Score=43.56  Aligned_cols=17  Identities=29%  Similarity=0.335  Sum_probs=14.5

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.++|+||||+|||...
T Consensus        41 ~lIvI~GPTgsGKTtLa   57 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLS   57 (339)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             ceEEEECCCCCCHHHHH
Confidence            35899999999999854

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=81.17  E-value=0.66  Score=38.75  Aligned_cols=16  Identities=31%  Similarity=0.272  Sum_probs=13.7

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .++++|++|+|||+..
T Consensus         3 ~I~l~G~~GsGKsT~a   18 (179)
T 3lw7_A            3 VILITGMPGSGKSEFA   18 (179)
T ss_dssp             EEEEECCTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999854

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=81.16  E-value=0.79  Score=44.09  Aligned_cols=19  Identities=32%  Similarity=0.286  Sum_probs=16.0

Q ss_pred             hcCCCeEEEccCCCchhHH
Q 010709          156 LSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~  174 (503)
                      ..|..++++||||+|||+.
T Consensus       134 ~~g~~i~ivG~~GsGKTTl  152 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTT  152 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHH
T ss_pred             cCCCEEEEECCCCCCHHHH
Confidence            3566799999999999984

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=81.08  E-value=0.73  Score=43.55  Aligned_cols=19  Identities=42%  Similarity=0.779  Sum_probs=16.9

Q ss_pred             HhcCCCeEEEccCCCchhH
Q 010709          155 ALSGRDLLGCAETGSGKTA  173 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl  173 (503)
                      +..|+.++++||||+|||+
T Consensus       168 i~~g~~v~i~G~~GsGKTT  186 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTT  186 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHH
T ss_pred             ccCCCEEEEECCCCCCHHH
Confidence            3478899999999999998

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=81.06  E-value=0.68  Score=38.98  Aligned_cols=18  Identities=17%  Similarity=0.257  Sum_probs=15.0

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      ++-++++|++|+|||+..
T Consensus         3 ~~~i~l~G~~GsGKST~a   20 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            445899999999999854

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=80.97  E-value=0.89  Score=39.62  Aligned_cols=19  Identities=21%  Similarity=0.244  Sum_probs=15.5

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|+-++++||+|+|||+..
T Consensus         7 ~g~~i~l~GpsGsGKsTl~   25 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVR   25 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHH
T ss_pred             CCcEEEEECcCCCCHHHHH
Confidence            4556899999999999843

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=80.81  E-value=0.66  Score=40.26  Aligned_cols=20  Identities=25%  Similarity=0.380  Sum_probs=16.6

Q ss_pred             hcCCCeEEEccCCCchhHHh
Q 010709          156 LSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~  175 (503)
                      ..++-++++||+|+|||+..
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~   29 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLI   29 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHH
T ss_pred             ccCCEEEEECCCCCCHHHHH
Confidence            35677999999999999843

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.75  E-value=1.2  Score=43.70  Aligned_cols=17  Identities=29%  Similarity=0.384  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.||+|+|||+.+
T Consensus       216 rGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          216 KGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CEEEEESCTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            56999999999999843

>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=80.72  E-value=7.6  Score=38.08  Aligned_cols=90  Identities=17%  Similarity=0.133  Sum_probs=61.9

Q ss_pred             ChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-CC---eEEEEcCCCCHHHHHHHHHHHhcC
Q 010709          348 SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-GL---HAVALHGGRNQSDRESALRDFRNG  423 (503)
Q Consensus       348 ~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-~~---~v~~lh~~~~~~~r~~~~~~f~~g  423 (503)
                      ....|.......+.....      .+.+++||.|+++..+.+.++.+.+. +.   .+..+||+....++.....     
T Consensus        32 tG~GKT~~~~~~~~~~~~------~~~~~~liv~P~~~L~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~-----  100 (494)
T 1wp9_A           32 TGLGKTLIAMMIAEYRLT------KYGGKVLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWA-----  100 (494)
T ss_dssp             TTSCHHHHHHHHHHHHHH------HSCSCEEEECSSHHHHHHHHHHHHHHBCSCGGGEEEECSCSCHHHHHHHHH-----
T ss_pred             CCCCHHHHHHHHHHHHHh------cCCCeEEEEECCHHHHHHHHHHHHHHhCcchhheEEeeCCcchhhhhhhcc-----
Confidence            344565555444443322      13457999999999999999988875 55   8999999999887665543     


Q ss_pred             CCcEEEEcc-ccc-----cCCCCCCCCEEEE
Q 010709          424 STNILVATD-VAS-----RGLDVMGVAHVVN  448 (503)
Q Consensus       424 ~~~vLvaT~-~~~-----~Gldip~v~~VI~  448 (503)
                      ...|+|+|. .+.     ..+....+++||.
T Consensus       101 ~~~ivv~T~~~l~~~~~~~~~~~~~~~~vIi  131 (494)
T 1wp9_A          101 RAKVIVATPQTIENDLLAGRISLEDVSLIVF  131 (494)
T ss_dssp             HCSEEEECHHHHHHHHHTTSCCTTSCSEEEE
T ss_pred             CCCEEEecHHHHHHHHhcCCcchhhceEEEE
Confidence            468999993 222     2456677787774

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=80.45  E-value=1.2  Score=39.05  Aligned_cols=19  Identities=26%  Similarity=0.333  Sum_probs=16.0

Q ss_pred             hcCCCeEEEccCCCchhHH
Q 010709          156 LSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~  174 (503)
                      ..|+-+.++||+|+|||+.
T Consensus        21 ~~G~~~~lvGpsGsGKSTL   39 (218)
T 1z6g_A           21 NNIYPLVICGPSGVGKGTL   39 (218)
T ss_dssp             -CCCCEEEECSTTSSHHHH
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3677899999999999983

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=80.33  E-value=5.7  Score=37.74  Aligned_cols=18  Identities=28%  Similarity=0.300  Sum_probs=15.2

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+.+++.||+|+|||+.+
T Consensus       117 ~~~vLl~GppGtGKT~la  134 (357)
T 3d8b_A          117 PKGILLFGPPGTGKTLIG  134 (357)
T ss_dssp             CSEEEEESSTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            456999999999999754

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=80.31  E-value=0.7  Score=39.98  Aligned_cols=20  Identities=20%  Similarity=0.190  Sum_probs=16.4

Q ss_pred             hcCCCeEEEccCCCchhHHh
Q 010709          156 LSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~  175 (503)
                      ..|.-++++||+|+|||+..
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~   23 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVR   23 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHH
Confidence            35667899999999999843

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=80.31  E-value=1.7  Score=40.40  Aligned_cols=26  Identities=31%  Similarity=0.419  Sum_probs=18.6

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      +.-+.+.||+|+|||+.  +..+..+..
T Consensus       102 g~vi~lvG~nGsGKTTl--l~~Lagll~  127 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTT--IAKLGRYYQ  127 (304)
T ss_dssp             SSEEEEECSTTSSHHHH--HHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHH--HHHHHHHHH
Confidence            44588999999999984  445555444

>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=80.27  E-value=2.7  Score=36.75  Aligned_cols=71  Identities=15%  Similarity=0.239  Sum_probs=45.8

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc------cccCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV------ASRGLDVMG  442 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~------~~~Gldip~  442 (503)
                      ...++||.++++..+.++++.+...    ++.+..++|+....++...+   .  ..+|+|+|.-      ....+++..
T Consensus        81 ~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~---~--~~~iiv~Tp~~l~~~~~~~~~~~~~  155 (224)
T 1qde_A           81 KAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGL---R--DAQIVVGTPGRVFDNIQRRRFRTDK  155 (224)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTSCCCEEEECC----------C---T--TCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHHhcccCceEEEEeCCcchHHHHhcC---C--CCCEEEECHHHHHHHHHhCCcchhh
Confidence            3457999999999999998888753    67889999988765544332   2  3789999942      134566777


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      +++||.
T Consensus       156 ~~~iVi  161 (224)
T 1qde_A          156 IKMFIL  161 (224)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            888774

---

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	503
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-56
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	2e-53
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	5e-53
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	1e-51
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	1e-49
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	1e-49
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-43
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	2e-41
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	8e-36
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	2e-35
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-34
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	3e-28
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	4e-25
d1a1va2	299	c.37.1.14 (A:326-624) HCV helicase domain {Human h	7e-21
d1wp9a2	286	c.37.1.19 (A:201-486) putative ATP-dependent RNA h	2e-18
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	2e-17
d1gkub2	248	c.37.1.16 (B:251-498) Helicase-like "domain" of re	2e-17
d1t5la2	181	c.37.1.19 (A:415-595) Nucleotide excision repair e	2e-12
d1fuka_	162	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	6e-11
d1c4oa2	174	c.37.1.19 (A:410-583) Nucleotide excision repair e	3e-09
d1hv8a2	155	c.37.1.19 (A:211-365) Putative DEAD box RNA helica	1e-08
d2j0sa2	168	c.37.1.19 (A:244-411) Probable ATP-dependent RNA h	6e-08
d1jr6a_	138	c.37.1.14 (A:) HCV helicase domain {Human hepatiti	9e-08
d2fwra1	200	c.37.1.19 (A:257-456) DNA repair protein RAD25 {Ar	5e-06
d1yksa2	299	c.37.1.14 (A:325-623) YFV helicase domain {Yellow	3e-05
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	9e-05
d2fz4a1	206	c.37.1.19 (A:24-229) DNA repair protein RAD25 {Arc	2e-04
d1a1va1	136	c.37.1.14 (A:190-325) HCV helicase domain {Human h	0.003

>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 =  184 bits (468), Expect = 3e-56
 Identities = 80/210 (38%), Positives = 123/210 (58%), Gaps = 9/210 (4%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMI 180
           +F ++ L  +I+  I    + +PT IQ + +P+ L+   +++  A TGSGKTA+F IP+I
Sbjct: 5   NFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 181 QHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS 240
           +           +G  A++L PTRELA Q+  E+++L  +  + K A + GG  I  Q  
Sbjct: 65  ELVNEN------NGIEAIILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIK 117

Query: 241 ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDK 300
            L+   +IVV TPGR LDH+ +G  +L  V + ILDEAD ML+MGF   + +++      
Sbjct: 118 ALKN-ANIVVGTPGRILDHINRGTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKD 176

Query: 301 HQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
            + LLFSATMP EI  LA++Y+ D   +K 
Sbjct: 177 KRILLFSATMPREILNLAKKYMGDYSFIKA 206

>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 =  178 bits (452), Expect = 2e-53
 Identities = 99/236 (41%), Positives = 142/236 (60%), Gaps = 9/236 (3%)

Query: 104 NVDVTVASGSVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLG 163
           ++ V+V      A   IE+F ++ L P+I  +I    Y RPT IQ  A+P  L  RD++ 
Sbjct: 4   SIPVSVTGPDYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMA 63

Query: 164 CAETGSGKTAAFTIPMIQHCVAQTPV----GRGDGPLALVLAPTRELAQQIEKEVKALSR 219
           CA+TGSGKTAAF IP+I H V Q        +   P  L+LAPTRELA QI  E +  S 
Sbjct: 64  CAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSL 123

Query: 220 SLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD 279
           +    ++ +V GG +   Q  E++ G  ++VATPGR +D +++   SL    +++LDEAD
Sbjct: 124 NTP-LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLEFCKYIVLDEAD 182

Query: 280 RMLDMGFEPQIREVMQNL----PDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG 331
           RMLDMGFEPQIR++++          QTL+FSAT P EI+ LA ++L + + + VG
Sbjct: 183 RMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG 238

>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 =  176 bits (447), Expect = 5e-53
 Identities = 77/216 (35%), Positives = 120/216 (55%), Gaps = 5/216 (2%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
              ++SF DM L  S+++ I  + + +P++IQ +A+   + G D++  A++G+GKTA F 
Sbjct: 8   NEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFA 67

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           I ++Q               ALVLAPTRELAQQI+K V AL   + +   A + G    A
Sbjct: 68  ISILQQIELDLK-----ATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRA 122

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
           E +        I+V TPGR  D L +   S   +   +LDEAD ML  GF+ QI ++ Q 
Sbjct: 123 EVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQK 182

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           L    Q +L SATMP ++  + ++++ DP+++ V K
Sbjct: 183 LNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 218

>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 =  172 bits (437), Expect = 1e-51
 Identities = 74/214 (34%), Positives = 125/214 (58%), Gaps = 6/214 (2%)

Query: 119 PIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIP 178
              +F  M L   +++ I  + + +P++IQ +A+   + GRD++  +++G+GKTA F+I 
Sbjct: 15  VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSIS 74

Query: 179 MIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ 238
           ++Q    Q          AL+LAPTRELA QI+K + AL     + +    +GGTN+ E 
Sbjct: 75  VLQCLDIQVR-----ETQALILAPTRELAVQIQKGLLALGDY-MNVQCHACIGGTNVGED 128

Query: 239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP 298
             +L  G  +V  TPGR  D +++ +     +  ++LDEAD ML+ GF+ QI +V + LP
Sbjct: 129 IRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLP 188

Query: 299 DKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
              Q +L SAT+P EI  +  +++TDP+++ V +
Sbjct: 189 PATQVVLISATLPHEILEMTNKFMTDPIRILVKR 222

>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 =  167 bits (423), Expect = 1e-49
 Identities = 67/211 (31%), Positives = 113/211 (53%), Gaps = 7/211 (3%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D  L P +++ I    +  P+ +Q + +P A+ G D+L  A++G GKTA F +  +Q
Sbjct: 2   GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
                T          LV+  TRELA QI KE +  S+ + + K A+  GG +I +    
Sbjct: 62  QLEPVTG-----QVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEV 116

Query: 242 L-RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLD-MGFEPQIREVMQNLPD 299
           L +    IVV TPGR L   +  + +L  +   ILDE D+ML+ +     ++E+ +  P 
Sbjct: 117 LKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPH 176

Query: 300 KHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           + Q ++FSAT+  EI  + ++++ DP+++ V
Sbjct: 177 EKQVMMFSATLSKEIRPVCRKFMQDPMEIFV 207

>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 =  167 bits (423), Expect = 1e-49
 Identities = 69/214 (32%), Positives = 111/214 (51%), Gaps = 7/214 (3%)

Query: 117 PAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFT 176
              +  F DM L  ++++ +  + +  P++IQ +A+   + G D+L  A++G+GKT  F+
Sbjct: 6   DKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS 65

Query: 177 IPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA 236
           I  +Q             P AL+LAPTRE      ++V          K    +GGT+  
Sbjct: 66  IAALQRIDTS-----VKAPQALMLAPTRE-LALQIQKVVMALAFHMDIKVHACIGGTSFV 119

Query: 237 EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN 296
           E    LR    IVV TPGR  D++Q+      ++   ILDEAD ML  GF+ QI ++   
Sbjct: 120 EDAEGLRDAQ-IVVGTPGRVFDNIQRRRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTL 178

Query: 297 LPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           LP   Q +L SATMP ++  +  +++ +PV++ V
Sbjct: 179 LPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV 212

>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 =  150 bits (380), Expect = 2e-43
 Identities = 69/207 (33%), Positives = 117/207 (56%), Gaps = 5/207 (2%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            F D CL   ++  I    + +P+ IQ +++P+ALSGRD+L  A+ G+GK+ A+ IP+++
Sbjct: 4   EFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
                    + D   A+V+ PTRELA Q+ +    +S+ +   K     GGTN+ +    
Sbjct: 64  RLDL-----KKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMR 118

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L   V +V+ATPGR LD +++G   +  V  ++LDEAD++L   F   + +++  LP   
Sbjct: 119 LDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNR 178

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQV 328
           Q LL+SAT P+ ++     +L  P ++
Sbjct: 179 QILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 =  145 bits (365), Expect = 2e-41
 Identities = 75/211 (35%), Positives = 118/211 (55%), Gaps = 6/211 (2%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
           +F D  L   ++  I    + +P+ IQ +A+PVA++GRD+L  A+ G+GKTAAF IP ++
Sbjct: 2   TFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               +    +     AL++ PTRELA Q  + V+ L +        +  GGTN+ +    
Sbjct: 62  KVKPKLNKIQ-----ALIMVPTRELALQTSQVVRTLGKHCG-ISCMVTTGGTNLRDDILR 115

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L   V I+V TPGR LD   +    LS  S  I+DEAD+ML   F+  I +++  LP  H
Sbjct: 116 LNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTH 175

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKVGK 332
           Q+LLFSAT P+ ++    ++L  P ++ + +
Sbjct: 176 QSLLFSATFPLTVKEFMVKHLHKPYEINLME 206

>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 =  133 bits (334), Expect = 8e-36
 Identities = 44/297 (14%), Positives = 92/297 (30%), Gaps = 52/297 (17%)

Query: 157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKA 216
             R  +     G+GKT  +   +++  + +       G   L+LAPTR +A ++E+ ++ 
Sbjct: 8   KKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRG 60

Query: 217 LSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD 276
           L                     R+E  G   + +     F   L      +   + +I+D
Sbjct: 61  LP------------IRYQTPAIRAEHTGREIVDLMCHATFTMRLL-SPIRVPNYNLIIMD 107

Query: 277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVSSP 336
           EA          +     +    +   +  +AT P   +   Q       + +      P
Sbjct: 108 EAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRDPFPQSNAPIMDEERE----IP 163

Query: 337 TANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVA 396
             +     E V++ +                         T+ FV      ++++  L  
Sbjct: 164 ERSWNSGHEWVTDFKGK-----------------------TVWFVPSIKAGNDIAACLRK 200

Query: 397 EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            G   + L      S+        R    + +V TD++  G +      V++     
Sbjct: 201 NGKKVIQLSRKTFDSEYI----KTRTNDWDFVVTTDISEMGAN-FKAERVIDPRRCM 252

>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 =  129 bits (324), Expect = 2e-35
 Identities = 57/209 (27%), Positives = 105/209 (50%), Gaps = 2/209 (0%)

Query: 122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQ 181
            FT     P I++ I+   + +PT IQ + +P AL G  ++G ++TG+GKT A+ +P+++
Sbjct: 2   QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 61

Query: 182 HCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE 241
               +          A       ++  +  K  K   +         ++GGT+  +   +
Sbjct: 62  KIKPERA-EVQAVITAPTRELATQIYHETLKITKFCPKDRM-IVARCLIGGTDKQKALEK 119

Query: 242 LRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH 301
           L     IV+ TPGR  D +++    +     +++DEAD MLDMGF   + ++   +P   
Sbjct: 120 LNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDL 179

Query: 302 QTLLFSATMPVEIEALAQEYLTDPVQVKV 330
           Q L+FSAT+P +++   ++Y+ +P  V V
Sbjct: 180 QMLVFSATIPEKLKPFLKKYMENPTFVHV 208

>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 =  127 bits (319), Expect = 2e-34
 Identities = 42/235 (17%), Positives = 74/235 (31%), Gaps = 35/235 (14%)

Query: 110 ASGSVPAPAPIESFTDMCLHPSIMKDIEFHE-----YTRPTSIQAQAMPVALSGRDLLGC 164
           A+ +  A A   +   +CL P      EF E        P +IQ       L        
Sbjct: 5   AAAAAAAAAAAAAAASLCLFPEDFLLKEFVEFFRKCVGEPRAIQKMWAKRILRKESFAAT 64

Query: 165 AETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSF 224
           A TG GKT+      +   +              V+ PT  L  Q  + ++  +      
Sbjct: 65  APTGVGKTSFGLAMSLFLALKGKRC--------YVIFPTSLLVIQAAETIRKYAEKAG-V 115

Query: 225 KTAIVVGGTNIAEQRSEL------RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA 278
            T  ++G  +    + E            IV+ T      H ++    L    F+ +D+ 
Sbjct: 116 GTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE----LGHFDFIFVDDV 171

Query: 279 DRMLD-----------MGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYL 322
           D +L            +GF   ++        +   ++ +AT     +A     L
Sbjct: 172 DAILKASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKAELFRQL 226

>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 =  109 bits (272), Expect = 3e-28
 Identities = 33/193 (17%), Positives = 67/193 (34%), Gaps = 20/193 (10%)

Query: 141 YTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL 200
           Y +    Q + +   LSGRD L    TG GK+  + IP +               L +V+
Sbjct: 23  YQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN-----------GLTVVV 71

Query: 201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHL 260
           +P   L +    +++A   +  +   +       +        G + ++   P R +   
Sbjct: 72  SPLISLMKDQVDQLQANGVA-AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDN 130

Query: 261 QQGNTSLSRVSFVILDEADRMLDMGFEP-----QIREVMQNLPDKHQTLLFSATMPVEIE 315
              + +      + +DEA  +   G +       + ++ Q  P     +  +AT      
Sbjct: 131 FLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTL-PFMALTATADDTTR 189

Query: 316 A--LAQEYLTDPV 326
              +    L DP+
Sbjct: 190 QDIVRLLGLNDPL 202

>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 =  100 bits (249), Expect = 4e-25
 Identities = 33/195 (16%), Positives = 72/195 (36%), Gaps = 17/195 (8%)

Query: 128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQT 187
           +    +  ++          QA+A+    SG++LL    T +GKT    + M++  +   
Sbjct: 10  ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKG- 68

Query: 188 PVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVS 247
                    +L + P R LA +  +  K   +     +  I  G     ++         
Sbjct: 69  -------GKSLYVVPLRALAGEKYESFKKWEK--IGLRIGISTGDYESRDEHLGDC---D 116

Query: 248 IVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQ---IREVMQNLPDKHQTL 304
           I+V T  +    ++   + +  VS +++DE   +           +   M+ +    + +
Sbjct: 117 IIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVI 176

Query: 305 LFSATMPVEIEALAQ 319
             SAT P  +  +A+
Sbjct: 177 GLSATAP-NVTEIAE 190

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 299

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]

 Score = 90.7 bits (225), Expect = 7e-21
 Identities = 25/136 (18%), Positives = 49/136 (36%), Gaps = 22/136 (16%)

Query: 331 GKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEV 390
           G V+ P  N+ +    +S   ++      +  E     +        ++F   K +CDE+
Sbjct: 2   GSVTVPHPNIEE--VALSTTGEIPFYGKAIPLEVIKGGR-------HLIFCHSKKKCDEL 52

Query: 391 SEALVAEGLHAVALHGGRNQSDR----------ESALRDFRNGSTNILVATDVASRG--- 437
           +  LVA G++AVA + G + S              AL     G  + ++  +        
Sbjct: 53  AAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVD 112

Query: 438 LDVMGVAHVVNLDLPK 453
             +     +    LP+
Sbjct: 113 FSLDPTFTIETTTLPQ 128

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 286

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 = 83.8 bits (206), Expect = 2e-18
 Identities = 38/187 (20%), Positives = 72/187 (38%), Gaps = 28/187 (14%)

Query: 275 LDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVGKVS 334
           L  A  +L+      +R  ++ L ++ +     A         ++E  +D       ++ 
Sbjct: 82  LHHAIELLETQGLSALRAYIKKLYEEAKAGSTKA---------SKEIFSDK------RMK 126

Query: 335 SPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEAL 394
              + ++Q  E   ++ K+D+L  ++     L           IVF   +    ++   L
Sbjct: 127 KAISLLVQAKEIGLDHPKMDKLKEII--REQLQR---KQNSKIIVFTNYRETAKKIVNEL 181

Query: 395 VAEGLHAVALHGGRNQSDR--------ESALRDFRNGSTNILVATDVASRGLDVMGVAHV 446
           V +G+ A    G  ++ +         +  L +F  G  N+LVAT V   GLDV  V  V
Sbjct: 182 VKDGIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLV 241

Query: 447 VNLDLPK 453
           V  +   
Sbjct: 242 VFYEPVP 248

>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 = 78.7 bits (192), Expect = 2e-17
 Identities = 39/198 (19%), Positives = 66/198 (33%), Gaps = 11/198 (5%)

Query: 140 EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV 199
           +  +P   Q           + L    TG GKT    +                G   L+
Sbjct: 6   DLIQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRL-------TKYGGKVLM 57

Query: 200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDH 259
           LAPT+ L  Q  +  + L         A+    +    +RS+      ++VATP    + 
Sbjct: 58  LAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSPE--ERSKAWARAKVIVATPQTIEND 115

Query: 260 LQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQ 319
           L  G  SL  VS ++ DEA R +       I    +        +  +A+     E + +
Sbjct: 116 LLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIME 175

Query: 320 EYLT-DPVQVKVGKVSSP 336
                    ++    +SP
Sbjct: 176 VINNLGIEHIEYRSENSP 193

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 248

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 = 79.8 bits (196), Expect = 2e-17
 Identities = 18/116 (15%), Positives = 38/116 (32%), Gaps = 21/116 (18%)

Query: 342 QILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHA 401
            + +    +E +  L ++L +               I++       +E+ E+L       
Sbjct: 3   NVEDVAVNDESISTLSSILEKLG----------TGGIIYARTGEEAEEIYESLKN----- 47

Query: 402 VALHGGRNQSDRESALRDFRNGSTNILVAT----DVASRGLDVM-GVAHVVNLDLP 452
                G   + ++     F  G  + L+ T        RGLD+   +   V +  P
Sbjct: 48  -KFRIGIVTATKKGDYEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCP 102

>d1t5la2 c.37.1.19 (A:415-595) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]} Length = 181

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]

 Score = 63.7 bits (154), Expect = 2e-12
 Identities = 30/124 (24%), Positives = 52/124 (41%), Gaps = 8/124 (6%)

Query: 343 ILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAV 402
            ++      ++D L+  + E     E+       T+V    K   +++++ L   G+   
Sbjct: 7   TIDVRPTKGQIDDLIGEIRERVERNER-------TLVTTLTKKMAEDLTDYLKEAGIKVA 59

Query: 403 ALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAAS-ES 461
            LH      +R   +RD R G  ++LV  ++   GLD+  V+ V  LD  K     S  S
Sbjct: 60  YLHSEIKTLERIEIIRDLRLGKYDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERS 119

Query: 462 LCTT 465
           L  T
Sbjct: 120 LIQT 123

>d1fuka_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 162

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 = 58.8 bits (141), Expect = 6e-11
 Identities = 30/112 (26%), Positives = 56/112 (50%), Gaps = 8/112 (7%)

Query: 342 QILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHA 401
           Q    V E E     L  L +               ++F   + + +E++  L  +    
Sbjct: 3   QFYVNVEEEEYKYECLTDLYDS--------ISVTQAVIFCNTRRKVEELTTKLRNDKFTV 54

Query: 402 VALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
            A++    Q +R++ +++FR+GS+ IL++TD+ +RG+DV  V+ V+N DLP 
Sbjct: 55  SAIYSDLPQQERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPA 106

>d1c4oa2 c.37.1.19 (A:410-583) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]} Length = 174

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]

 Score = 54.3 bits (130), Expect = 3e-09
 Identities = 29/101 (28%), Positives = 47/101 (46%), Gaps = 7/101 (6%)

Query: 353 VDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSD 412
           +  L+  + E A   E+       T+V V      +E++  LV  G+ A  LH   +   
Sbjct: 17  ILDLMEGIRERAARGER-------TLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFK 69

Query: 413 RESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           R++ +RD R G  + LV  ++   GLD+  V+ V  LD  K
Sbjct: 70  RQALIRDLRLGHYDCLVGINLLREGLDIPEVSLVAILDADK 110

>d1hv8a2 c.37.1.19 (A:211-365) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 155

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 = 52.3 bits (124), Expect = 1e-08
 Identities = 42/116 (36%), Positives = 61/116 (52%), Gaps = 10/116 (8%)

Query: 338 ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE 397
           AN+ Q   +V+ENE+ + L  LL  + F            +VF + K    E++  L   
Sbjct: 2   ANIEQSYVEVNENERFEALCRLLKNKEFYG----------LVFCKTKRDTKELASMLRDI 51

Query: 398 GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
           G  A A+HG  +QS RE  +R F+     IL+ATDV SRG+DV  +  V+N  LP+
Sbjct: 52  GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQ 107

>d2j0sa2 c.37.1.19 (A:244-411) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]} Length = 168

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 = 50.3 bits (119), Expect = 6e-08
 Identities = 34/116 (29%), Positives = 57/116 (49%), Gaps = 10/116 (8%)

Query: 339 NVIQILEKV-SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE 397
            + Q    V  E  K D L  L                  ++F   K + D ++E +   
Sbjct: 7   GIKQFFVAVEREEWKFDTLCDLY---------DTLTITQAVIFCNTKRKVDWLTEKMREA 57

Query: 398 GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
                ++HG   Q +RES +++FR+G++ +L++TDV +RGLDV  V+ ++N DLP 
Sbjct: 58  NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPN 113

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 138

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]

 Score = 48.9 bits (116), Expect = 9e-08
 Identities = 24/126 (19%), Positives = 47/126 (37%), Gaps = 19/126 (15%)

Query: 331 GKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEV 390
           G V+ P  N+ ++    +   ++      +  E     +        ++F   K +CDE+
Sbjct: 1   GSVTVPHPNIEEVALSTTG--EIPFYGKAIPLEVIKGGR-------HLIFCHSKKKCDEL 51

Query: 391 SEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVA---HVV 447
           +  LVA G++AVA + G +                 ++VATD    G      +      
Sbjct: 52  AAKLVALGINAVAYYRGLDV-------SVIPTNGDVVVVATDALMTGFTGDFDSVIDCNT 104

Query: 448 NLDLPK 453
           +   P+
Sbjct: 105 SDGKPQ 110

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 45.3 bits (106), Expect = 5e-06
 Identities = 19/107 (17%), Positives = 36/107 (33%), Gaps = 14/107 (13%)

Query: 347 VSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG 406
            +   K+ +L  +L           H     I+F         +     ++     A+  
Sbjct: 75  FNSKNKIRKLREILER---------HRKDKIIIFTRHNELVYRI-----SKVFLIPAITH 120

Query: 407 GRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK 453
             ++ +RE  L  FR G    +V++ V   G+DV      V +    
Sbjct: 121 RTSREEREEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSG 167

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 299

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]

 Score = 43.8 bits (103), Expect = 3e-05
 Identities = 14/94 (14%), Positives = 33/94 (35%), Gaps = 5/94 (5%)

Query: 377 TIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASR 436
           T  F+      + ++ +L   G   V L+    + +  +     +    + ++ATD+A  
Sbjct: 39  TAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPT----IKQKKPDFILATDIAEM 94

Query: 437 GLDVMGVAHVVNLDLPKVLLAASESLCTTSFNIT 470
           G ++  V  V++       +   E          
Sbjct: 95  GANL-CVERVLDCRTAFKPVLVDEGRKVAIKGPL 127

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

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]

 Score = 40.4 bits (93), Expect = 9e-05
 Identities = 27/154 (17%), Positives = 51/154 (33%), Gaps = 20/154 (12%)

Query: 158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL 217
           G   +     G+GKT  F   ++  C              LVLAPTR +  ++++    L
Sbjct: 7   GMTTVLDFHPGAGKTRRFLPQILAEC-------ARRRLRTLVLAPTRVVLSEMKEAFHGL 59

Query: 218 SRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE 277
                +   +    G  + +                   L +     T +     +I+DE
Sbjct: 60  DVKFHTQAFSAHGSGREVIDAMCH-------------ATLTYRMLEPTRVVNWEVIIMDE 106

Query: 278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP 311
           A  +       +     +   ++  T+L +AT P
Sbjct: 107 AHFLDPASIAARGWAAHRARANESATILMTATPP 140

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 40.6 bits (94), Expect = 2e-04
 Identities = 27/182 (14%), Positives = 49/182 (26%), Gaps = 38/182 (20%)

Query: 129 HPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP 188
            P    +I   +Y      Q +A+   L  +       TGSGKT      + +       
Sbjct: 62  TPYFDAEISLRDY------QEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------ 109

Query: 189 VGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSI 248
                    L++ PT  LA+Q ++ +                                 +
Sbjct: 110 -----STPTLIVVPTLALAEQWKERLGI----------------FGEEYVGEFSGRIKEL 148

Query: 249 VVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA 308
              T   +           +R   +I DE   +          ++ Q      + L  +A
Sbjct: 149 KPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPA----ESYVQIAQMSIAPFR-LGLTA 203

Query: 309 TM 310
           T 
Sbjct: 204 TF 205

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]} Length = 136

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]

 Score = 35.6 bits (81), Expect = 0.003
 Identities = 25/149 (16%), Positives = 40/149 (26%), Gaps = 30/149 (20%)

Query: 164 CAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDS 223
            A TGSGK+                     G   LVL P+          +        +
Sbjct: 14  HAPTGSGKSTKVPAAYAAQ-----------GYKVLVLNPSVAATLGFGAYMSKAHGVDPN 62

Query: 224 FKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA---DR 280
            +T +    T      S               +   L  G  S      +I DE    D 
Sbjct: 63  IRTGVRTITTGSPITYS--------------TYGKFLADGGCSGGAYDIIICDECHSTDA 108

Query: 281 MLDMGFEPQIREVMQNLPDKHQTLLFSAT 309
              +G    + +  +    +   +L +AT
Sbjct: 109 TSILGIG-TVLDQAETAGARL-VVLATAT 135

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	503
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
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	100.0
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.94
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.94
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	99.94
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.93
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	99.93
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.93
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	99.93
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.92
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.92
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	99.92
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	99.92
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	99.92
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	99.91
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	99.83
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.81
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.8
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.79
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.79
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.78
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.76
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	99.73
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.72
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.71
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.7
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	99.68
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	99.63
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	99.61
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.53
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	99.49
d1z3ix1	346	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.41
d1z5za1	244	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.34
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.29
d1tf5a4	175	Translocation ATPase SecA, nucleotide-binding doma	98.95
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	98.88
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	98.83
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.42
d1nkta4	219	Translocation ATPase SecA, nucleotide-binding doma	98.18
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.64
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.35
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.33
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.13
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	97.06
d1okkd2	207	GTPase domain of the signal recognition particle r	96.86
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	96.81
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.8
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.67
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.67
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.66
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.5
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.47
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	96.2
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.14
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.96
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	95.9
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.89
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	95.85
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.84
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	95.83
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	95.8
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.79
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.6
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	95.45
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.14
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	94.78
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	94.47
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	94.43
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	94.26
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	93.92
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	93.62
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	93.12
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	93.07
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	92.82
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	92.6
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	92.08
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	91.89
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	91.34
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	91.31
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	91.24
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	91.21
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	91.13
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	90.5
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	90.5
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	90.13
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	89.64
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	89.35
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	89.13
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	88.92
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	88.78
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	88.67
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	88.29
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	87.96
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	87.93
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	87.77
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	87.63
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	87.59
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	87.35
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	87.26
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	87.2
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	86.55
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	86.35
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	86.11
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	85.5
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	85.12
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	85.03
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	84.98
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	84.38
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	84.21
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	83.48
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	83.07
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	82.94
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	82.75
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	82.34
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	82.31
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	82.28
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	82.27
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	82.22
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	81.72
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	81.57
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	81.51
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	81.49
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	81.25
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	80.95
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	80.55
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	80.35
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	80.29
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	80.14

>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=6.3e-42  Score=308.15  Aligned_cols=208  Identities=36%  Similarity=0.596  Sum_probs=193.9

Q ss_pred             CCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeE
Q 010709          118 APIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLA  197 (503)
Q Consensus       118 ~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~  197 (503)
                      ....+|++++|++.++++|..+||..|+++|.++||.+++|+|+++.|+||||||++|++|+++++...     ..++++
T Consensus        14 ~~~~sF~~l~L~~~l~~~L~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~-----~~~~~~   88 (222)
T d2j0sa1          14 DVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ-----VRETQA   88 (222)
T ss_dssp             CCCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT-----SCSCCE
T ss_pred             CCCCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccc-----ccCcee
Confidence            445689999999999999999999999999999999999999999999999999999999999886543     346789


Q ss_pred             EEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecc
Q 010709          198 LVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDE  277 (503)
Q Consensus       198 lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDE  277 (503)
                      +|++|||+||.|+++.++.++... ++++..++|+.....+...+..+++|+|+|||+|.+++.+....+++++++|+||
T Consensus        89 lil~PtreLa~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~~~~~~~~l~~lVlDE  167 (222)
T d2j0sa1          89 LILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDE  167 (222)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEET
T ss_pred             EEecchHHHHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccccccccccceeeeecc
Confidence            999999999999999999998765 5899999999999988888888999999999999999999888999999999999


Q ss_pred             hhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          278 ADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       278 aH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      ||+|++.+|...+..+++.+++.+|++++|||+++++.++++.++.+|+.+.++
T Consensus       168 aD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         168 ADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             HHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             hhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            999999999999999999999999999999999999999999999999887654

>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=4.9e-41  Score=300.30  Aligned_cols=203  Identities=34%  Similarity=0.640  Sum_probs=190.7

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .+|++++|++.++++|..+||..|+++|.++||.+++|+|++++||||+|||++|++|++.++...     .++++++|+
T Consensus         3 ~~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~-----~~~~~~lil   77 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK-----KDNIQAMVI   77 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChhccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc-----ccCcceEEE
Confidence            579999999999999999999999999999999999999999999999999999999999886543     357889999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++|+.|+++.+..+.............|+.........+..+++|+|+||+++.+++..+...+.+++++|+||||+
T Consensus        78 ~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~~~~~~~~l~~lVlDEaD~  157 (206)
T d1veca_          78 VPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADK  157 (206)
T ss_dssp             CSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEETHHH
T ss_pred             eecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccchhccccccceEEEecccc
Confidence            99999999999999999877767888889999988888888889999999999999999999888999999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEE
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQV  328 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~  328 (503)
                      |++.+|...+..++..+++++|++++|||+++++.++++.++.+|..+
T Consensus       158 ll~~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         158 LLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             ccccchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            999999999999999999999999999999999999999999999765

>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=3.3e-40  Score=295.15  Aligned_cols=203  Identities=32%  Similarity=0.558  Sum_probs=186.6

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|++++|++.++++|..+||..|+++|.++||.+++|+|++++||||||||++|++|++..+...     ..+++++|++
T Consensus         2 ~F~dl~L~~~l~~~l~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~-----~~~~~~lil~   76 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV-----TGQVSVLVMC   76 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC-----TTCCCEEEEC
T ss_pred             CccccCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc-----CCCceEEEEe
Confidence            59999999999999999999999999999999999999999999999999999999999875432     3467899999


Q ss_pred             ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh-hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          202 PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL-RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      |+|+|+.|+.+.++.+......+...+++|+.....+...+ ..+++|+|+||+++.+++.++.+.+++++++|+||||+
T Consensus        77 PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~~~~~l~~l~~lVlDEaD~  156 (207)
T d1t6na_          77 HTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDK  156 (207)
T ss_dssp             SCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHTTSSCCTTCCEEEEESHHH
T ss_pred             ccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccCCceeccccceeehhhhhh
Confidence            99999999999999999877777888899998877766655 46799999999999999999888999999999999999


Q ss_pred             HhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEE
Q 010709          281 MLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVK  329 (503)
Q Consensus       281 l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~  329 (503)
                      |++. +|...+..+++.+++++|++++|||++++++++++.++++|..+.
T Consensus       157 ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~  206 (207)
T d1t6na_         157 MLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIF  206 (207)
T ss_dssp             HHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEE
T ss_pred             hhhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEe
Confidence            9985 799999999999999999999999999999999999999998774

>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=2.2e-40  Score=297.96  Aligned_cols=211  Identities=36%  Similarity=0.563  Sum_probs=187.7

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      +.++++.+|+++++++.++++|..+||..|+++|.++||.++.|+|++++||||||||++|++|+++++...     ..+
T Consensus         6 ~~~e~i~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~~-----~~~   80 (218)
T d2g9na1           6 NWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD-----LKA   80 (218)
T ss_dssp             CCCCCCCCGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCS
T ss_pred             CCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheeccc-----ccC
Confidence            456788999999999999999999999999999999999999999999999999999999999999987442     357


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHH-HhhCCCcEEEECcHHHHHHHHcCCCCCCCccEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS-ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFV  273 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~v  273 (503)
                      +++||++||++||.|+++.++.+.... ...+..+.++........ .....++|+|+||+++.+++.++...+.+++++
T Consensus        81 ~~alil~Pt~eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~~~~~~~~l~~l  159 (218)
T d2g9na1          81 TQALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMF  159 (218)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHTTSSCSTTCCEE
T ss_pred             ccEEEEcccchhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhcCCcccccceEE
Confidence            889999999999999999999998776 466666666554433322 233568999999999999999988899999999


Q ss_pred             EecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          274 ILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       274 ViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      |+||||++.+.+|...+..+++.++++.|++++|||+++++..+++.++.+|..+.+.
T Consensus       160 VlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         160 VLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999999999999999999999999999999988764

>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=1.8e-39  Score=290.97  Aligned_cols=208  Identities=36%  Similarity=0.577  Sum_probs=183.5

Q ss_pred             CCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCC
Q 010709          115 PAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDG  194 (503)
Q Consensus       115 ~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~  194 (503)
                      +.|.++.+|+++++++.++++|..+||.+|+++|.++|+.++.|+|+++++|||+|||++|++|+++++...     ..+
T Consensus         4 ~~~~~~~sF~~l~l~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~~-----~~~   78 (212)
T d1qdea_           4 NYDKVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS-----VKA   78 (212)
T ss_dssp             SCCCCCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT-----CCS
T ss_pred             CCcccccChhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhcc-----CCC
Confidence            677889999999999999999999999999999999999999999999999999999999999999987432     357


Q ss_pred             CeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEE
Q 010709          195 PLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVI  274 (503)
Q Consensus       195 ~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vV  274 (503)
                      ++++|++||++|+.|....+..+.... ........++....++...+ .+++|+|+||+++.+++..+.+.+.+++++|
T Consensus        79 ~~~lil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~IvI~TP~~l~~~~~~~~~~l~~l~~lV  156 (212)
T d1qdea_          79 PQALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQRRRFRTDKIKMFI  156 (212)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------C-TTCSEEEECHHHHHHHHHTTSSCCTTCCEEE
T ss_pred             cceEEEcccHHHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHh-cCCcEEEECCCccccccccCceecCcceEEe
Confidence            899999999999999999999888665 46777777776666555544 4689999999999999999999999999999


Q ss_pred             ecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEE
Q 010709          275 LDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVK  329 (503)
Q Consensus       275 iDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~  329 (503)
                      +||||++++.+|...+.++++.+++.+|++++|||+++++..+++.++.+|+.+.
T Consensus       157 lDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~  211 (212)
T d1qdea_         157 LDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRIL  211 (212)
T ss_dssp             EETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC
T ss_pred             ehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEe
Confidence            9999999999999999999999999999999999999999999999999998764

>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=1.6e-39  Score=296.67  Aligned_cols=218  Identities=44%  Similarity=0.728  Sum_probs=197.1

Q ss_pred             CCCCCCCcCCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCC----
Q 010709          113 SVPAPAPIESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTP----  188 (503)
Q Consensus       113 ~~~~~~~~~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~----  188 (503)
                      ....+.++.+|+++++++++.++|..+||..|+++|.++||.+++|+|+++++|||+|||++|++|++.++.....    
T Consensus        13 ~~~~~~~~~~F~~l~l~~~l~~~L~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~   92 (238)
T d1wrba1          13 DYSATNVIENFDELKLDPTIRNNILLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQR   92 (238)
T ss_dssp             SSSCCSCCCSSGGGSCCCSTTTTTTTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC----
T ss_pred             CCCCCCccCCHHHCCCCHHHHHHHHHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhccccccc
Confidence            3366778999999999999999999999999999999999999999999999999999999999999999876432    


Q ss_pred             CCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCC
Q 010709          189 VGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLS  268 (503)
Q Consensus       189 ~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~  268 (503)
                      .....++++||++|+++||.|+.+.+..++... ++++..+.|+.....+.+....+++|+|+||++|.+++..+...+.
T Consensus        93 ~~~~~~~~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~~~~~l~  171 (238)
T d1wrba1          93 YSKTAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEKNKISLE  171 (238)
T ss_dssp             --CCBCCSEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHTTSBCCT
T ss_pred             ccCCCCceEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHccCceecc
Confidence            123457899999999999999999999998776 5889999999988888888888999999999999999999888999


Q ss_pred             CccEEEecchhHHhhCCCHHHHHHHHHhCCC----CCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          269 RVSFVILDEADRMLDMGFEPQIREVMQNLPD----KHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~~~~~~~~il~~~~~----~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      +++++|+||||++++.+|...+..+++.++.    ++|++++|||++++++.+++.|+++|..+.++
T Consensus       172 ~v~~lViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         172 FCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             TCCEEEEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             ccceeeeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence            9999999999999999999999999987642    57999999999999999999999999888653

>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=3.7e-38  Score=282.39  Aligned_cols=202  Identities=40%  Similarity=0.665  Sum_probs=185.3

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCC-CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGR-DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALV  199 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~-~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~li  199 (503)
                      .+|+++++++.++++|..+||..|+++|.++||.+++|+ |+++++|||+|||++|++|++.....      ..++++||
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~------~~~~~~li   77 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE------NNGIEAII   77 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS------SSSCCEEE
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc------ccCcceEE
Confidence            479999999999999999999999999999999999885 89999999999999999999886443      35789999


Q ss_pred             EcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          200 LAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       200 l~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ++||++||.|+.+.++.+.... +.++...+|+....++...+. +++|+|+||++|.+++.++.+.+++++++||||||
T Consensus        78 l~pt~~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l~-~~~IlV~TP~~l~~~l~~~~~~~~~l~~lViDEad  155 (208)
T d1hv8a1          78 LTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINRGTLNLKNVKYFILDEAD  155 (208)
T ss_dssp             ECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHTTCSCTTSCCEEEEETHH
T ss_pred             EeeccccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhcC-CCCEEEEChHHHHHHHHcCCCCcccCcEEEEEChH
Confidence            9999999999999999998765 578889999988877766554 69999999999999999988899999999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEe
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV  330 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~  330 (503)
                      ++++.++...+.+++..+++++|++++|||+++++.+++++++++|..+..
T Consensus       156 ~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         156 EMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             HHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             HhhcCCChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            999999999999999999999999999999999999999999999988764

>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=8.3e-38  Score=280.00  Aligned_cols=205  Identities=37%  Similarity=0.615  Sum_probs=190.9

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      .+|++++|++.++++|..+||..|+++|.++||.+++|+|+++.||||+|||++|++|++..+...     ..+.+++++
T Consensus         1 ~sF~~l~L~~~l~~~L~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~-----~~~~~~~~~   75 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK-----LNKIQALIM   75 (206)
T ss_dssp             CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT-----SCSCCEEEE
T ss_pred             CChHHcCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc-----cccccceee
Confidence            369999999999999999999999999999999999999999999999999999999999886543     346779999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +|+++++.|....+..+.... ++++...+|+.........+..+++|+|+||++|.+++....+.+.+++++|+||||+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~~~~~l~~l~~lV~DEaD~  154 (206)
T d1s2ma1          76 VPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADLSDCSLFIMDEADK  154 (206)
T ss_dssp             CSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHTTCSCCTTCCEEEEESHHH
T ss_pred             ccchhhhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHhcccceEEEECCcccccccccceeecccceEEEeechhh
Confidence            999999999999998888665 6999999999999988888889999999999999999999888999999999999999


Q ss_pred             HhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEeC
Q 010709          281 MLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKVG  331 (503)
Q Consensus       281 l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~~  331 (503)
                      |++.+|...+..+++.+++.+|++++|||+|+++..+++.|+.+|..+.+.
T Consensus       155 l~~~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         155 MLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             HSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             hhhhhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            999999999999999999999999999999999999999999999887543

>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=4.7e-36  Score=270.00  Aligned_cols=204  Identities=32%  Similarity=0.569  Sum_probs=182.1

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA  201 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~  201 (503)
                      .|++++|++.++++|++.||.+|+++|.++||.+++|+|++++||||||||++|++|+++.....     ......++++
T Consensus         2 ~F~~l~L~~~l~~~l~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~-----~~~~~~~~~~   76 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE-----RAEVQAVITA   76 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT-----SCSCCEEEEC
T ss_pred             ccccCCcCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccc-----cccccccccc
Confidence            69999999999999999999999999999999999999999999999999999999999876543     2456789999


Q ss_pred             ccHHHHHHHHHHHHHHhccCC---CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecch
Q 010709          202 PTRELAQQIEKEVKALSRSLD---SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEA  278 (503)
Q Consensus       202 Ptr~La~q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEa  278 (503)
                      |++.++.+.+..+........   ...+.+..++.....+......+++|+|+||+++..++.+....+.+++++|+|||
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~~~~~~~~l~~lViDEa  156 (209)
T d1q0ua_          77 PTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVDEA  156 (209)
T ss_dssp             SSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHTTCCCGGGCCEEEECSH
T ss_pred             cccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhhhccccccceEEEEeec
Confidence            999999999988877654432   35566677777666665566678999999999999999988888999999999999


Q ss_pred             hHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeEEEe
Q 010709          279 DRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQVKV  330 (503)
Q Consensus       279 H~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~~~~  330 (503)
                      |++++++|...+..++..++++.|++++|||+|+++.++++.++.+|..+.+
T Consensus       157 d~ll~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         157 DLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             HHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             ccccccccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999999999999999999999999999999999988764

>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=100.00  E-value=6.6e-36  Score=285.91  Aligned_cols=261  Identities=18%  Similarity=0.218  Sum_probs=180.2

Q ss_pred             HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCcc
Q 010709          155 ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTN  234 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~  234 (503)
                      +.+|+++++.||||+|||++|+++++......       ++++||++||++||.|+++.++.++........        
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~-------~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~--------   70 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR-------GLRTLILAPTRVVAAEMEEALRGLPIRYQTPAI--------   70 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH-------TCCEEEEESSHHHHHHHHHHTTTSCCBCCC-----------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc-------CCEEEEEccHHHHHHHHHHHHhcCCcceeeeEE--------
Confidence            34788899999999999999988888776654       577999999999999999888766432211111        


Q ss_pred             HHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHh--CCCCCcEEEEEeeCCH
Q 010709          235 IAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQN--LPDKHQTLLFSATMPV  312 (503)
Q Consensus       235 ~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~--~~~~~q~i~~SAT~~~  312 (503)
                          .........++++|++.|..++.. ...+.++++|||||||++..+++  ....++..  ..++.+++++|||++.
T Consensus        71 ----~~~~~~~~~i~~~t~~~l~~~~~~-~~~~~~~~~vViDE~H~~~~~~~--~~~~~l~~~~~~~~~~~v~~SAT~~~  143 (305)
T d2bmfa2          71 ----RAEHTGREIVDLMCHATFTMRLLS-PIRVPNYNLIIMDEAHFTDPASI--AARGYISTRVEMGEAAGIFMTATPPG  143 (305)
T ss_dssp             ---------CCCSEEEEEHHHHHHHHTS-SSCCCCCSEEEEESTTCCSHHHH--HHHHHHHHHHHHTSCEEEEECSSCTT
T ss_pred             ----eecccCccccccCCcHHHHHHHhc-CccccceeEEEeeeeeecchhhH--HHHHHHHHhhccccceEEEeecCCCc
Confidence                012234578999999999877664 45678899999999998765432  12222222  1356889999999965


Q ss_pred             HHHHHHHHhcCCCeEEEeCCCCCCCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHH
Q 010709          313 EIEALAQEYLTDPVQVKVGKVSSPTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSE  392 (503)
Q Consensus       313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~  392 (503)
                      .......  ...+...              .....+...+...+ ..+.          ...+++||||+++++++.+++
T Consensus       144 ~~~~~~~--~~~~~~~--------------~~~~~~~~~~~~~~-~~~~----------~~~~~~lvf~~~~~~~~~l~~  196 (305)
T d2bmfa2         144 SRDPFPQ--SNAPIMD--------------EEREIPERSWNSGH-EWVT----------DFKGKTVWFVPSIKAGNDIAA  196 (305)
T ss_dssp             CCCSSCC--CSSCEEE--------------EECCCCCSCCSSCC-HHHH----------SSCSCEEEECSCHHHHHHHHH
T ss_pred             ceeeecc--cCCcceE--------------EEEeccHHHHHHHH-HHHH----------hhCCCEEEEeccHHHHHHHHH
Confidence            3211000  0011111              11111111110000 0000          234679999999999999999


Q ss_pred             HHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEcc----------C----------C
Q 010709          393 ALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLD----------L----------P  452 (503)
Q Consensus       393 ~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~----------~----------p  452 (503)
                      .|++.++.+..+||++.+..+    ..|++|..+++|||+++++|+|++ +++||+++          .          |
T Consensus       197 ~L~~~~~~~~~l~~~~~~~~~----~~~~~~~~~~lvaT~~~~~G~~~~-~~~Vi~~~~~~~~~~~~~~~~~~~~~~~~~  271 (305)
T d2bmfa2         197 CLRKNGKKVIQLSRKTFDSEY----IKTRTNDWDFVVTTDISEMGANFK-AERVIDPRRCMKPVILTDGEERVILAGPMP  271 (305)
T ss_dssp             HHHHHTCCCEECCTTCHHHHG----GGGGTSCCSEEEECGGGGTTCCCC-CSEEEECCEEEEEEEECSSSCEEEEEEEEE
T ss_pred             HHHhCCCCEEEeCCcChHHHH----hhhhccchhhhhhhHHHHhcCCCC-ccEEEEcCCceeeeEecCCCCceEEecccc
Confidence            999999999999999875543    467899999999999999999995 67766433          3          4


Q ss_pred             CChhHHHHhhCcceeee
Q 010709          453 KVLLAASESLCTTSFNI  469 (503)
Q Consensus       453 ~s~~~~~Qr~GR~gR~~  469 (503)
                      -|..+|+||+||+||.-
T Consensus       272 ~s~~~~~Qr~GR~GR~~  288 (305)
T d2bmfa2         272 VTHSSAAQRRGRVGRNP  288 (305)
T ss_dssp             CCHHHHHHHHTTSSCSS
T ss_pred             CCHHHHhhhhcCcCcCC
Confidence            57889999999999964

>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=99.94  E-value=1.6e-27  Score=212.53  Aligned_cols=185  Identities=19%  Similarity=0.257  Sum_probs=144.7

Q ss_pred             CCHHHHHHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH
Q 010709          128 LHPSIMKDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA  207 (503)
Q Consensus       128 l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La  207 (503)
                      +++++...|...|+..|+|+|.++++.+++|+++++++|||+|||++++++++..+..        ++++|+++|+++|+
T Consensus        10 ~~~~~~~~l~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~--------~~~vl~l~P~~~L~   81 (202)
T d2p6ra3          10 ISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK--------GGKSLYVVPLRALA   81 (202)
T ss_dssp             HHHHHHHHHHCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT--------TCCEEEEESSHHHH
T ss_pred             hhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc--------cCcceeecccHHHH
Confidence            5678888999999999999999999999999999999999999999998888877654        46799999999999


Q ss_pred             HHHHHHHHHHhccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCH
Q 010709          208 QQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFE  287 (503)
Q Consensus       208 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~  287 (503)
                      .|+.+.++++....  ..+....++.....   .....+.++++||..+...+.+....+..+++||+||+|++.+..+.
T Consensus        82 ~q~~~~~~~~~~~~--~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~~~~~~~~~~~ii~DE~h~~~~~~r~  156 (202)
T d2p6ra3          82 GEKYESFKKWEKIG--LRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHLLDSEKRG  156 (202)
T ss_dssp             HHHHHHHTTTTTTT--CCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHTTCSGGGGCCEEEETTGGGGGCTTTH
T ss_pred             HHHHHHHHHHhhcc--ccceeeccCccccc---ccccccceeeeccHHHHHHHhccchhhhhhhhccccHHHHhcccccc
Confidence            99999998887543  45555555543322   12346889999999999998887778889999999999998877666


Q ss_pred             HHHHHHH---HhCCCCCcEEEEEeeCCHHHHHHHHHhcCCCeE
Q 010709          288 PQIREVM---QNLPDKHQTLLFSATMPVEIEALAQEYLTDPVQ  327 (503)
Q Consensus       288 ~~~~~il---~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~  327 (503)
                      ..+..++   ...+++.|+|+||||+++ .+++ ..|+..+..
T Consensus       157 ~~~~~~l~~i~~~~~~~~~l~lSATl~n-~~~~-~~~l~~~~~  197 (202)
T d2p6ra3         157 ATLEILVTKMRRMNKALRVIGLSATAPN-VTEI-AEWLDADYY  197 (202)
T ss_dssp             HHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHH-HHHTTCEEE
T ss_pred             hHHHHHHHHHHhcCCCCcEEEEcCCCCc-HHHH-HHHcCCCee
Confidence            5555444   445678899999999965 4544 466654433

>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=99.94  E-value=7e-28  Score=215.66  Aligned_cols=188  Identities=19%  Similarity=0.249  Sum_probs=141.8

Q ss_pred             CcccCCCCHHHHHHHHHC-CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          122 SFTDMCLHPSIMKDIEFH-EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~-~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      ..+.++|++...+.|+.. ||..++|+|.++++++++|+|+++++|||+|||++|.+|++..           ..+++++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~-----------~~~~~~v   71 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL-----------NGLTVVV   71 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS-----------SSEEEEE
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhc-----------cCceEEe
Confidence            356778888888888776 9999999999999999999999999999999999999988753           5679999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHH----HHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEec
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIA----EQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD  276 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViD  276 (503)
                      +|+++|++|+.+.++.++.     ............    ...........++++|++.+.............++++|+|
T Consensus        72 ~P~~~L~~q~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~v~~lviD  146 (206)
T d1oywa2          72 SPLISLMKDQVDQLQANGV-----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVD  146 (206)
T ss_dssp             CSCHHHHHHHHHHHHHTTC-----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHHHHHTTSCEEEEEES
T ss_pred             ccchhhhhhHHHHHHhhcc-----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhcccchhheeeeeeee
Confidence            9999999999999988763     223333333222    2222334668999999998855444434567789999999


Q ss_pred             chhHHhhCCC--HHH---HHHHHHhCCCCCcEEEEEeeCCHHHHH-HHHHh-cCCCe
Q 010709          277 EADRMLDMGF--EPQ---IREVMQNLPDKHQTLLFSATMPVEIEA-LAQEY-LTDPV  326 (503)
Q Consensus       277 EaH~l~~~~~--~~~---~~~il~~~~~~~q~i~~SAT~~~~~~~-~~~~~-~~~~~  326 (503)
                      |||++.++++  ...   +..+...+ ++.|++++|||+++.+.+ +.+.+ +.+|+
T Consensus       147 EaH~~~~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         147 EAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             SGGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eeeeeeccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            9998877652  222   23344444 468999999999998765 44443 67884

>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=99.94  E-value=3.2e-26  Score=194.78  Aligned_cols=120  Identities=25%  Similarity=0.398  Sum_probs=108.3

Q ss_pred             eEEEEEEcCh-hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHH
Q 010709          340 VIQILEKVSE-NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALR  418 (503)
Q Consensus       340 ~~~~~~~~~~-~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~  418 (503)
                      +.|++..+.. +.|...|..++..         .+..++||||+++..++.+++.|...++.+..+||++++.+|..+++
T Consensus         1 I~q~~~~v~~~e~K~~~L~~ll~~---------~~~~k~iIF~~s~~~~~~l~~~L~~~~~~~~~~~~~~~~~~r~~~l~   71 (162)
T d1fuka_           1 IKQFYVNVEEEEYKYECLTDLYDS---------ISVTQAVIFCNTRRKVEELTTKLRNDKFTVSAIYSDLPQQERDTIMK   71 (162)
T ss_dssp             CEEEEEEEESGGGHHHHHHHHHHH---------TTCSCEEEEESSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEEeCCcHHHHHHHHHHHHh---------CCCCcEEEEEEEEchHHHHHHHHhhcCceEEEeccCCchhhHHHHHH
Confidence            4577777754 4588888887754         34567999999999999999999999999999999999999999999


Q ss_pred             HHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          419 DFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       419 ~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .|+.|+.+|||||+++++|+|+|+|++||+||+|++...|+||+||+||.
T Consensus        72 ~f~~~~~~iLv~Tdv~~rGiDi~~v~~VI~~d~P~~~~~yihR~GR~gR~  121 (162)
T d1fuka_          72 EFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRF  121 (162)
T ss_dssp             HHHTTSCSEEEEEGGGTTTCCCCSCSEEEESSCCSSGGGGGGSSCSCC--
T ss_pred             HHhhcccceeeccccccccccCCCceEEEEeccchhHHHHHhhccccccC
Confidence            99999999999999999999999999999999999999999999999994

>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=99.93  E-value=4.7e-27  Score=214.93  Aligned_cols=169  Identities=18%  Similarity=0.173  Sum_probs=126.0

Q ss_pred             HHHHHCCCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          134 KDIEFHEYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       134 ~~l~~~~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      ..+...++.+|+++|.++++.++.|+|+++++|||+|||++++++++.....        ++++||++|+++|+.|++++
T Consensus        34 ~~~~~~~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~--------~~rvliv~Pt~~La~Q~~~~  105 (237)
T d1gkub1          34 VEFFRKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK--------GKRCYVIFPTSLLVIQAAET  105 (237)
T ss_dssp             HHHHHTTTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT--------SCCEEEEESCHHHHHHHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh--------cCeEEEEeccHHHHHHHHHH
Confidence            4556668889999999999999999999999999999999998888765432        57899999999999999999


Q ss_pred             HHHHhccCC---CceEEEEECCccHHHHHHHh--hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHH
Q 010709          214 VKALSRSLD---SFKTAIVVGGTNIAEQRSEL--RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEP  288 (503)
Q Consensus       214 ~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~--~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~  288 (503)
                      +++++...+   ...+....++.........+  ..+++|+|+||++|.+.    ...+.++++|||||||.+++.+.  
T Consensus       106 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~----~~~~~~~~~vVvDE~d~~l~~~~--  179 (237)
T d1gkub1         106 IRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH----YRELGHFDFIFVDDVDAILKASK--  179 (237)
T ss_dssp             HHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC----STTSCCCSEEEESCHHHHHTSTH--
T ss_pred             HHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHh----hhhcCCCCEEEEEChhhhhhccc--
Confidence            999986542   12234444444433333332  34578999999988653    33567899999999999887642  


Q ss_pred             HHHHHHHh-------------CCCCCcEEEEEeeCCHHHHH
Q 010709          289 QIREVMQN-------------LPDKHQTLLFSATMPVEIEA  316 (503)
Q Consensus       289 ~~~~il~~-------------~~~~~q~i~~SAT~~~~~~~  316 (503)
                      .+.+++..             .+...|++++|||+++.+..
T Consensus       180 ~~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  220 (237)
T d1gkub1         180 NVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKA  220 (237)
T ss_dssp             HHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTH
T ss_pred             chhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHH
Confidence            23333222             24567899999999865443

>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=99.93  E-value=7e-26  Score=193.75  Aligned_cols=124  Identities=27%  Similarity=0.419  Sum_probs=114.2

Q ss_pred             CCCceEEEEEEcChh-hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHH
Q 010709          336 PTANVIQILEKVSEN-EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRE  414 (503)
Q Consensus       336 ~~~~~~~~~~~~~~~-~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~  414 (503)
                      ...++.|++..+... .|+..|..++...         +..++||||++++.|+.+++.|...++.+..+||++++.+|.
T Consensus         4 tl~~i~q~~v~v~~~~~K~~~L~~ll~~~---------~~~k~iiF~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~r~   74 (168)
T d2j0sa2           4 TLEGIKQFFVAVEREEWKFDTLCDLYDTL---------TITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERE   74 (168)
T ss_dssp             SCTTEEEEEEEESSTTHHHHHHHHHHHHH---------TSSEEEEECSSHHHHHHHHHHHHHTTCCCEEECTTSCHHHHH
T ss_pred             CCCCcEEEEEEecChHHHHHHHHHHHHhC---------CCCceEEEeeeHHHHHHHHHHhhhcccchhhhhhhhhHHHHH
Confidence            457889999888765 5888888887553         345799999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          415 SALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       415 ~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      .+++.|++|+.++||||+++++|+|+|++++|||||+|++...|+||+||+||.
T Consensus        75 ~~~~~fk~g~~~iLv~Td~~~rGiDi~~v~~VIn~d~P~~~~~yihR~GR~gR~  128 (168)
T d2j0sa2          75 SIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRY  128 (168)
T ss_dssp             HHHHHHHHTSSCEEEECGGGSSSCCCTTEEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             HHHHHHhcCCccEEeccchhcccccccCcceEEEecCCcCHHHHHhhhcccccc
Confidence            999999999999999999999999999999999999999999999999999994

>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=99.93  E-value=1e-25  Score=194.08  Aligned_cols=124  Identities=23%  Similarity=0.376  Sum_probs=116.8

Q ss_pred             CCCceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHH
Q 010709          336 PTANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRES  415 (503)
Q Consensus       336 ~~~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~  415 (503)
                      ....+.|++..++...|...|..++..         .+..++||||+++..++.++..|...|+.+..+||++++.+|..
T Consensus         3 tl~~i~q~yi~v~~~~K~~~L~~ll~~---------~~~~k~iVF~~~~~~~~~l~~~L~~~g~~~~~~h~~~~~~~r~~   73 (171)
T d1s2ma2           3 TLKGITQYYAFVEERQKLHCLNTLFSK---------LQINQAIIFCNSTNRVELLAKKITDLGYSCYYSHARMKQQERNK   73 (171)
T ss_dssp             BCTTEEEEEEECCGGGHHHHHHHHHHH---------SCCSEEEEECSSHHHHHHHHHHHHHHTCCEEEECTTSCHHHHHH
T ss_pred             CccceEEEEEEcCHHHHHHHHHHHHHh---------CCCCceEEEEeeeehhhHhHHhhhcccccccccccccchhhhhh
Confidence            345788999999999999999998865         35678999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          416 ALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       416 ~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +++.|++|+.++||||+++++|+|+|++++||+||+|+++..|+||+||+||.
T Consensus        74 ~~~~f~~~~~~ilv~Td~~~~Gid~~~v~~VI~~d~p~~~~~y~qr~GR~gR~  126 (171)
T d1s2ma2          74 VFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRF  126 (171)
T ss_dssp             HHHHHHTTSSSEEEESSCSSSSCCCTTEEEEEESSCCSSHHHHHHHHCBSSCT
T ss_pred             hhhhcccCccccccchhHhhhccccceeEEEEecCCcchHHHHHHHhhhcccC
Confidence            99999999999999999999999999999999999999999999999999994

>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=99.93  E-value=1.4e-25  Score=190.08  Aligned_cols=121  Identities=35%  Similarity=0.443  Sum_probs=113.6

Q ss_pred             CceEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHH
Q 010709          338 ANVIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESAL  417 (503)
Q Consensus       338 ~~~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~  417 (503)
                      .++.+.+..++..+|...|..++..          ...++||||++++.|+.+++.|+..|+.+..+||++++.+|..++
T Consensus         2 ~nI~~~~i~v~~~~K~~~L~~ll~~----------~~~k~IIF~~s~~~~~~l~~~L~~~g~~~~~~~~~~~~~~r~~~~   71 (155)
T d1hv8a2           2 ANIEQSYVEVNENERFEALCRLLKN----------KEFYGLVFCKTKRDTKELASMLRDIGFKAGAIHGDLSQSQREKVI   71 (155)
T ss_dssp             SSSEEEEEECCGGGHHHHHHHHHCS----------TTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECSSSCHHHHHHHH
T ss_pred             CCeEEEEEEeChHHHHHHHHHHHcc----------CCCCEEEEECchHHHHHHHhhhcccccccccccccchhhhhhhhh
Confidence            4688999999999999998887742          345799999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          418 RDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       418 ~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +.|++|+.+|||||+++++|+|+|++++||+||+|+++..|+||+||+||.
T Consensus        72 ~~f~~~~~~ilv~T~~~~~Gid~~~v~~Vi~~d~p~~~~~y~qr~GR~gR~  122 (155)
T d1hv8a2          72 RLFKQKKIRILIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRA  122 (155)
T ss_dssp             HHHHTTSSSEEEECTTHHHHCCCSCCSEEEESSCCSCHHHHHHHSTTTCCS
T ss_pred             hhhhcccceeeeehhHHhhhhhhccCcEEEEecCCCCHHHHHHHHHhcCcC
Confidence            999999999999999999999999999999999999999999999999994

>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=99.92  E-value=1.8e-24  Score=192.43  Aligned_cols=166  Identities=22%  Similarity=0.210  Sum_probs=130.2

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      -+|+++|.+++..+. ++|+|+++|||+|||+++++++...+...       +.+++|++|+++|+.|+++.++++....
T Consensus         8 ~~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~-------~~~il~i~P~~~L~~q~~~~~~~~~~~~   79 (200)
T d1wp9a1           8 IQPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY-------GGKVLMLAPTKPLVLQHAESFRRLFNLP   79 (200)
T ss_dssp             HCCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS-------CSCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CCCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc-------CCcEEEEcCchHHHHHHHHHHHHhhccc
Confidence            479999999999875 56799999999999999887776665443       4679999999999999999999997544


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                       +..+....++....... ......+++++||+.+...+......+.++++||+||||++.+......+...+.......
T Consensus        80 -~~~v~~~~~~~~~~~~~-~~~~~~~i~i~t~~~~~~~~~~~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~~~  157 (200)
T d1wp9a1          80 -PEKIVALTGEKSPEERS-KAWARAKVIVATPQTIENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNP  157 (200)
T ss_dssp             -GGGEEEECSCSCHHHHH-HHHHHCSEEEECHHHHHHHHHTTSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCSSC
T ss_pred             -ccceeeeecccchhHHH-HhhhcccccccccchhHHHHhhhhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCCCC
Confidence             46777777766655443 3334478999999999999988888889999999999998876654444444444445667


Q ss_pred             cEEEEEeeCCHHHHHH
Q 010709          302 QTLLFSATMPVEIEAL  317 (503)
Q Consensus       302 q~i~~SAT~~~~~~~~  317 (503)
                      ++++||||++.....+
T Consensus       158 ~~l~~SATp~~~~~~~  173 (200)
T d1wp9a1         158 LVIGLTASPGSTPEKI  173 (200)
T ss_dssp             CEEEEESCSCSSHHHH
T ss_pred             cEEEEEecCCCcHHHH
Confidence            8999999986544433

>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=99.92  E-value=5.5e-25  Score=188.43  Aligned_cols=120  Identities=29%  Similarity=0.423  Sum_probs=113.5

Q ss_pred             eEEEEEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHH
Q 010709          340 VIQILEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRD  419 (503)
Q Consensus       340 ~~~~~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~  419 (503)
                      +.|++..+....|...|..++...         ...++||||++++.++.+++.|.+.|+.+..+||+|++.+|..+++.
T Consensus         2 l~q~~v~~~~~~K~~~L~~ll~~~---------~~~k~iIF~~~~~~~~~l~~~L~~~~~~~~~ihg~~~~~~r~~~l~~   72 (168)
T d1t5ia_           2 LQQYYVKLKDNEKNRKLFDLLDVL---------EFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQ   72 (168)
T ss_dssp             CEEEEEECCGGGHHHHHHHHHHHS---------CCSSEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHH
T ss_pred             cEEEEEEeChHHHHHHHHHHHHhC---------CCCeEEEEEeeeecchhhhhhhccccccccccccccchhhhhhhhhh
Confidence            578899999999999999988663         45679999999999999999999999999999999999999999999


Q ss_pred             HhcCCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          420 FRNGSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       420 f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |++|+.+|||||+++++|+|+|.+++||+||+|.+...|+||+||+||.
T Consensus        73 F~~g~~~iLv~T~~~~~Gid~~~~~~vi~~~~p~~~~~yiqr~GR~gR~  121 (168)
T d1t5ia_          73 FKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRF  121 (168)
T ss_dssp             HHTTSCSEEEESSCCSTTCCGGGCSEEEESSCCSSHHHHHHHHHHHTGG
T ss_pred             hccccceeeeccccccchhhcccchhhhhhhcccchhhHhhhhhhcccC
Confidence            9999999999999999999999999999999999999999999999994

>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=99.92  E-value=1.2e-24  Score=191.05  Aligned_cols=113  Identities=19%  Similarity=0.346  Sum_probs=104.4

Q ss_pred             cChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc
Q 010709          347 VSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTN  426 (503)
Q Consensus       347 ~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~  426 (503)
                      +....|+..|+.++..         .+..++||||++++.++.++..|...++.+..+||++++.+|.++++.|+.|+.+
T Consensus        12 ~~~~~k~~~L~~~l~~---------~~~~~~IIF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~~~~r~~~~~~f~~g~~~   82 (200)
T d1oywa3          12 MEKFKPLDQLMRYVQE---------QRGKSGIIYCNSRAKVEDTAARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQ   82 (200)
T ss_dssp             EECSSHHHHHHHHHHH---------TTTCCEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCHHHHHHHHHHHHTTSCS
T ss_pred             EcCCcHHHHHHHHHHh---------cCCCCEEEEEeeehhhHHhhhhhccCCceeEEecCCCcHHHHHHHHHHHhcccce
Confidence            4455678888877765         2445799999999999999999999999999999999999999999999999999


Q ss_pred             EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          427 ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       427 vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |||||+++++|||+|+|++||+||+|.++..|+||+||+||.
T Consensus        83 ilvaTd~~~~GiD~p~v~~VI~~~~P~~~~~y~qr~GR~gR~  124 (200)
T d1oywa3          83 IVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRD  124 (200)
T ss_dssp             EEEECTTSCTTTCCTTCCEEEESSCCSSHHHHHHHHTTSCTT
T ss_pred             EEEecchhhhccCCCCCCEEEECCCccchHHHHHHhhhhhcC
Confidence            999999999999999999999999999999999999999994

>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=99.92  E-value=1.2e-24  Score=183.69  Aligned_cols=114  Identities=25%  Similarity=0.283  Sum_probs=101.3

Q ss_pred             ChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcE
Q 010709          348 SENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNI  427 (503)
Q Consensus       348 ~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~v  427 (503)
                      +....++.++..+.+....       +.++||||++++.|+.+++.|.+.|+.+..+||++++.+|.++++.|++|+.+|
T Consensus        12 p~~~qv~dll~~i~~~~~~-------g~r~lvfc~t~~~~~~l~~~L~~~Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~v   84 (174)
T d1c4oa2          12 PTENQILDLMEGIRERAAR-------GERTLVTVLTVRMAEELTSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDC   84 (174)
T ss_dssp             CSTTHHHHHHHHHHHHHHT-------TCEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTCCHHHHHHHHHHHHTTSCSE
T ss_pred             eCCCCHHHHHHHHHHHHhc-------CCcEEEEEcchhHHHHHHHHHHhcCCceEEEecccchHHHHHHHHHHHCCCeEE
Confidence            3345566677776665432       346999999999999999999999999999999999999999999999999999


Q ss_pred             EEEccccccCCCCCCCCEEEEccCCCC-----hhHHHHhhCcceee
Q 010709          428 LVATDVASRGLDVMGVAHVVNLDLPKV-----LLAASESLCTTSFN  468 (503)
Q Consensus       428 LvaT~~~~~Gldip~v~~VI~~~~p~s-----~~~~~Qr~GR~gR~  468 (503)
                      ||||+++++|+|+|+|++||+||+|++     ..+|+||+||+||.
T Consensus        85 LVaT~v~~~GiDip~V~~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~  130 (174)
T d1c4oa2          85 LVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN  130 (174)
T ss_dssp             EEESCCCCTTCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTS
T ss_pred             EEeeeeeeeeccCCCCcEEEEeccccccccchhHHHHHHhhhhhhc
Confidence            999999999999999999999998774     47899999999994

>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=99.91  E-value=1.2e-24  Score=187.09  Aligned_cols=113  Identities=23%  Similarity=0.310  Sum_probs=101.2

Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEE
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNIL  428 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vL  428 (503)
                      ...+++.++..+.+....       ..++||||++++.++.++..|...|+.+..+||+|++.+|.++++.|++|+.+||
T Consensus        13 ~~~qvd~ll~~i~~~~~~-------~~~~iif~~~~~~~~~~~~~l~~~g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vL   85 (181)
T d1t5la2          13 TKGQIDDLIGEIRERVER-------NERTLVTTLTKKMAEDLTDYLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVL   85 (181)
T ss_dssp             STTHHHHHHHHHHHHHHT-------TCEEEEECSSHHHHHHHHHHHHTTTCCEEEECSSCCHHHHHHHHHHHHHTSCSEE
T ss_pred             CCCcHHHHHHHHHHHHhc-------CCeEEEEeehhhhhHHHHHHHHhCCcceeEecCCccHHHHHHHHHHHHCCCCCEE
Confidence            345566677766654332       3469999999999999999999999999999999999999999999999999999


Q ss_pred             EEccccccCCCCCCCCEEEEccCCC-----ChhHHHHhhCcceee
Q 010709          429 VATDVASRGLDVMGVAHVVNLDLPK-----VLLAASESLCTTSFN  468 (503)
Q Consensus       429 vaT~~~~~Gldip~v~~VI~~~~p~-----s~~~~~Qr~GR~gR~  468 (503)
                      |||+++++|||+|+|++|||||+|+     +...|+||+||+||.
T Consensus        86 VaTdv~~rGiDip~v~~VI~~d~p~~~~~~s~~~yi~R~GRagR~  130 (181)
T d1t5la2          86 VGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARN  130 (181)
T ss_dssp             EESCCCSSSCCCTTEEEEEETTTTSCSGGGSHHHHHHHHGGGTTS
T ss_pred             EehhHHHccCCCCCCCEEEEecCCcccccccHHHHHHHHHhhccc
Confidence            9999999999999999999999996     678999999999994

>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=99.83  E-value=2.4e-21  Score=158.50  Aligned_cols=86  Identities=26%  Similarity=0.355  Sum_probs=80.2

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEcc---
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLD---  450 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~---  450 (503)
                      .+++||||++++.|+.+++.|.+.|+.+..+|++++++       .|++|+.+|||||+++++|+| |++++||++|   
T Consensus        35 ~~k~IVFc~t~~~ae~la~~L~~~G~~~~~~H~~~~~~-------~~~~~~~~vlvaTd~~~~GiD-~~v~~Vi~~~~~~  106 (138)
T d1jr6a_          35 GGRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVS-------VIPTNGDVVVVATDALMTGFT-GDFDSVIDCNTSD  106 (138)
T ss_dssp             TSCEEEECSCHHHHHHHHHHHHHHTCEEEEECTTCCSC-------CCTTSSCEEEEESSSSCSSSC-CCBSEEEECSEET
T ss_pred             CCCEEEEeCcHHHHHHHHHHHhccccchhhhhccchhh-------hhhhhhcceeehhHHHHhccc-cccceEEEEEecC
Confidence            45799999999999999999999999999999999854       468899999999999999999 9999999865   


Q ss_pred             -CCCChhHHHHhhCccee
Q 010709          451 -LPKVLLAASESLCTTSF  467 (503)
Q Consensus       451 -~p~s~~~~~Qr~GR~gR  467 (503)
                       +|.++.+|+||+||+||
T Consensus       107 ~~P~~~~~y~qr~GR~gR  124 (138)
T d1jr6a_         107 GKPQDAVSRTQRRGRTGR  124 (138)
T ss_dssp             TEECCHHHHHHHHTTBCS
T ss_pred             CCCCCHHHHHhHhccccC
Confidence             69999999999999999

>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=99.81  E-value=8.4e-19  Score=155.47  Aligned_cols=172  Identities=20%  Similarity=0.180  Sum_probs=130.2

Q ss_pred             CCCHHHHHHHHHCCCCCCcHHHHHHHHHHh----cCC--CeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEE
Q 010709          127 CLHPSIMKDIEFHEYTRPTSIQAQAMPVAL----SGR--DLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVL  200 (503)
Q Consensus       127 ~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~----~~~--~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil  200 (503)
                      ..+....+.+...-.-.+++-|..++..+.    +++  +.+++|.||||||.+|+..++..+..        |.+++++
T Consensus        39 ~~~~~~~~~~~~~lP~~lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~--------g~qv~~l  110 (233)
T d2eyqa3          39 KHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN--------HKQVAVL  110 (233)
T ss_dssp             CCCHHHHHHHHHTCCSCCCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT--------TCEEEEE
T ss_pred             CCCHHHHHhhhhccccccchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc--------CCceEEE
Confidence            344666677766666689999999998876    233  58999999999999998877766533        7889999


Q ss_pred             cccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHH---Hh-hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEec
Q 010709          201 APTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS---EL-RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILD  276 (503)
Q Consensus       201 ~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViD  276 (503)
                      +|+..|+.|.++.+++++..+ ++.+.++++.....+...   .+ .+..+|+|+|-..+.     ..+.+.++++||||
T Consensus       111 ~Pt~~La~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~-----~~~~f~~LgLiIiD  184 (233)
T d2eyqa3         111 VPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ-----SDVKFKDLGLLIVD  184 (233)
T ss_dssp             CSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH-----SCCCCSSEEEEEEE
T ss_pred             ccHHHhHHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc-----cCCccccccceeee
Confidence            999999999999999988766 478888888887654332   22 356899999955443     35678899999999


Q ss_pred             chhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHH
Q 010709          277 EADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEAL  317 (503)
Q Consensus       277 EaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~  317 (503)
                      |-|+..     ..-+..+.....+..++++||||.+....+
T Consensus       185 EeH~fg-----~kQ~~~l~~~~~~~~~l~~SATPiprtl~~  220 (233)
T d2eyqa3         185 EEHRFG-----VRHKERIKAMRANVDILTLTATPIPRTLNM  220 (233)
T ss_dssp             SGGGSC-----HHHHHHHHHHHTTSEEEEEESSCCCHHHHH
T ss_pred             chhhhh-----hHHHHHHHhhCCCCCEEEEecchhHHHHHH
Confidence            999743     223344444455678999999996655433

>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=99.80  E-value=4.8e-20  Score=172.70  Aligned_cols=113  Identities=27%  Similarity=0.376  Sum_probs=97.5

Q ss_pred             hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcC--------CCCHHHHHHHHHHHhc
Q 010709          351 EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHG--------GRNQSDRESALRDFRN  422 (503)
Q Consensus       351 ~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~--------~~~~~~r~~~~~~f~~  422 (503)
                      .|+..+..++......     .+..++||||+++..++.+++.|.+.++.+..+||        ++++.+|..+++.|++
T Consensus       143 pK~~~l~~~l~~~~~~-----~~~~k~iiF~~~~~~~~~~~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~  217 (286)
T d1wp9a2         143 PKMDKLKEIIREQLQR-----KQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGLSQREQKLILDEFAR  217 (286)
T ss_dssp             HHHHHHHHHHHHHHHH-----CTTCCEEEECSCHHHHHHHHHHHHHTTCCEEEECCSSCC-------CCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHh-----CCCCcEEEEeCcHHhHHHHHHHHHHcCCceEEeeccccccccchhchHHHHHHHHHHHc
Confidence            4666666666544332     35568999999999999999999999999988876        5666789999999999


Q ss_pred             CCCcEEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          423 GSTNILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       423 g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      |+++|||||+++++|||+|+|++||+||+|+++..|+||+||+||.
T Consensus       218 g~~~vLv~T~~~~~Gld~~~~~~Vi~~d~~~~~~~~~Qr~GR~gR~  263 (286)
T d1wp9a2         218 GEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH  263 (286)
T ss_dssp             TSCSEEEECGGGGGGGGSTTCCEEEESSCCHHHHHHHHHHTTSCSC
T ss_pred             CCCcEEEEccceeccccCCCCCEEEEeCCCCCHHHHHHHHHhCCCC
Confidence            9999999999999999999999999999999999999999999994

>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=99.79  E-value=1.2e-19  Score=168.39  Aligned_cols=154  Identities=15%  Similarity=0.175  Sum_probs=114.2

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      -.|+++|.+++..++.++..++.+|||+|||+++.. ++..+...      .+.++||++|+++|+.|+++.+.+++...
T Consensus       112 ~~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~-i~~~~~~~------~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~  184 (282)
T d1rifa_         112 IEPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQAL-LARYYLEN------YEGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHH-HHHHHHHH------CSSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             cccchHHHHHHHHHHhcCCceeEEEcccCccHHHHH-HHHHhhhc------ccceEEEEEcCchhHHHHHHHHHHhhccc
Confidence            479999999999999999999999999999987644 33333332      14679999999999999999999987432


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCC
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKH  301 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~  301 (503)
                       ...+..+.+|.....   .......++++|++.+.+..   ...++++++||+||||++.    ...+..++..+.+..
T Consensus       185 -~~~~~~~~~g~~~~~---~~~~~~~i~i~t~qs~~~~~---~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~~~  253 (282)
T d1rifa_         185 -HAMIKKIGGGASKDD---KYKNDAPVVVGTWQTVVKQP---KEWFSQFGMMMNDECHLAT----GKSISSIISGLNNCM  253 (282)
T ss_dssp             -GGGEEECSTTCSSTT---CCCTTCSEEEECHHHHTTSC---GGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTTCC
T ss_pred             -cccceeecceecccc---cccccceEEEEeeehhhhhc---ccccCCCCEEEEECCCCCC----chhHHHHHHhccCCC
Confidence             234555555543221   12234789999988775432   2346789999999999864    566788888876555


Q ss_pred             cEEEEEeeCCHH
Q 010709          302 QTLLFSATMPVE  313 (503)
Q Consensus       302 q~i~~SAT~~~~  313 (503)
                      ..++||||++..
T Consensus       254 ~rlGlTaT~~~~  265 (282)
T d1rifa_         254 FKFGLSGSLRDG  265 (282)
T ss_dssp             EEEEECSSCCTT
T ss_pred             eEEEEEeecCCC
Confidence            569999998643

>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=99.79  E-value=1.7e-18  Score=156.41  Aligned_cols=167  Identities=23%  Similarity=0.296  Sum_probs=123.6

Q ss_pred             HHHHHH-HHCCCCCCcHHHHHHHHHHhc----C--CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEccc
Q 010709          131 SIMKDI-EFHEYTRPTSIQAQAMPVALS----G--RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPT  203 (503)
Q Consensus       131 ~l~~~l-~~~~~~~~~~~Q~~~i~~i~~----~--~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Pt  203 (503)
                      .+.+.+ ....| .+|..|.+++..+.+    +  .+.+++|.||||||.+|+..++..+..        |.++++++||
T Consensus        71 ~l~~~f~~~LPF-eLT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~--------g~q~~~m~Pt  141 (264)
T d1gm5a3          71 KLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA--------GFQTAFMVPT  141 (264)
T ss_dssp             HHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH--------TSCEEEECSC
T ss_pred             HHHHHHHhhccc-cCCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc--------ccceeEEeeh
Confidence            344444 44444 799999999999863    3  368999999999999998888776655        6789999999


Q ss_pred             HHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHH---h-hCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          204 RELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSE---L-RGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       204 r~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      ..||.|.++.+++++... ++.+.+++|+....+....   + .+..+|+|||-..+.+     .+.+.++++|||||-|
T Consensus       142 ~~La~Qh~~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~-----~~~f~~LglviiDEqH  215 (264)
T d1gm5a3         142 SILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE-----DVHFKNLGLVIIDEQH  215 (264)
T ss_dssp             HHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH-----CCCCSCCCEEEEESCC
T ss_pred             HhhhHHHHHHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC-----CCCccccceeeecccc
Confidence            999999999999999766 4788888888876543322   2 3569999999655542     5667899999999999


Q ss_pred             HHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHH
Q 010709          280 RMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEAL  317 (503)
Q Consensus       280 ~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~  317 (503)
                      +..-     .-+..+........+++|||||-+....+
T Consensus       216 ~fgv-----~Qr~~l~~~~~~~~~l~~SATPiprtl~~  248 (264)
T d1gm5a3         216 RFGV-----KQREALMNKGKMVDTLVMSATPIPRSMAL  248 (264)
T ss_dssp             CC----------CCCCSSSSCCCEEEEESSCCCHHHHH
T ss_pred             ccch-----hhHHHHHHhCcCCCEEEEECCCCHHHHHH
Confidence            7532     22333334445678999999986554433

>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=99.78  E-value=2e-19  Score=159.50  Aligned_cols=136  Identities=20%  Similarity=0.151  Sum_probs=102.6

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCC
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLD  222 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~  222 (503)
                      .|+++|.+++..++++++.++++|||+|||++++. ++..+          +.++||++|+++|+.||.+.++.++.   
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~-~~~~~----------~~~~Liv~p~~~L~~q~~~~~~~~~~---  135 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMA-AINEL----------STPTLIVVPTLALAEQWKERLGIFGE---  135 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHH-HHHHS----------CSCEEEEESSHHHHHHHHHHHGGGCG---
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHh-HHHHh----------cCceeEEEcccchHHHHHHHHHhhcc---
Confidence            68999999999999988899999999999987643 33321          35689999999999999999988753   


Q ss_pred             CceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCc
Q 010709          223 SFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQ  302 (503)
Q Consensus       223 ~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q  302 (503)
                       ..+....|+.         .....++++|.+.+......   ...++++||+||||++...    .+.+++..++. ..
T Consensus       136 -~~~~~~~~~~---------~~~~~i~i~t~~~~~~~~~~---~~~~~~lvIiDEaH~~~a~----~~~~i~~~~~~-~~  197 (206)
T d2fz4a1         136 -EYVGEFSGRI---------KELKPLTVSTYDSAYVNAEK---LGNRFMLLIFDEVHHLPAE----SYVQIAQMSIA-PF  197 (206)
T ss_dssp             -GGEEEESSSC---------BCCCSEEEEEHHHHHHTHHH---HTTTCSEEEEECSSCCCTT----THHHHHHTCCC-SE
T ss_pred             -cchhhccccc---------ccccccccceehhhhhhhHh---hCCcCCEEEEECCeeCCcH----HHHHHHhccCC-Cc
Confidence             2344444432         23467999999988765543   2357899999999987533    35667776654 34


Q ss_pred             EEEEEeeC
Q 010709          303 TLLFSATM  310 (503)
Q Consensus       303 ~i~~SAT~  310 (503)
                      .++||||+
T Consensus       198 ~lgLTATl  205 (206)
T d2fz4a1         198 RLGLTATF  205 (206)
T ss_dssp             EEEEEESC
T ss_pred             EEEEecCC
Confidence            78999998

>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=99.76  E-value=1.4e-19  Score=150.46  Aligned_cols=135  Identities=21%  Similarity=0.242  Sum_probs=91.1

Q ss_pred             hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccH
Q 010709          156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNI  235 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~  235 (503)
                      .+|+++++++|||+|||++++..++......       +.++++++|+++++.|+++.+....     ..+........ 
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~-------~~~vli~~p~~~l~~q~~~~~~~~~-----~~~~~~~~~~~-   71 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARR-------RLRTLVLAPTRVVLSEMKEAFHGLD-----VKFHTQAFSAH-   71 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT-------TCCEEEEESSHHHHHHHHHHTTTSC-----EEEESSCCCCC-
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhc-------CceeeeeecchhHHHHHHHHhhhhh-----hhhcccccccc-
Confidence            3678899999999999988866666665553       5779999999999999887764332     22211111110 


Q ss_pred             HHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCH-HHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          236 AEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFE-PQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       236 ~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~-~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                            ......+.++|...+...... ...+.++++||+||||++....+. ..+...+.. .++.++|+||||||
T Consensus        72 ------~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~lvIiDEaH~~~~~~~~~~~~~~~~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1          72 ------GSGREVIDAMCHATLTYRMLE-PTRVVNWEVIIMDEAHFLDPASIAARGWAAHRAR-ANESATILMTATPP  140 (140)
T ss_dssp             ------CCSSCCEEEEEHHHHHHHHTS-SSCCCCCSEEEETTTTCCSHHHHHHHHHHHHHHH-TTSCEEEEECSSCT
T ss_pred             ------cccccchhhhhHHHHHHHHhc-cccccceeEEEEccccccChhhHHHHHHHHHHhh-CCCCCEEEEEcCCC
Confidence                  113356778888887665543 567889999999999976433211 122222333 35789999999997

>d1a1va2 c.37.1.14 (A:326-624) 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=99.73  E-value=7.9e-19  Score=157.83  Aligned_cols=93  Identities=22%  Similarity=0.278  Sum_probs=84.7

Q ss_pred             CcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHH----------HHHHHHHhcCCCcEEEEcccccc---CCCCC
Q 010709          375 PLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDR----------ESALRDFRNGSTNILVATDVASR---GLDVM  441 (503)
Q Consensus       375 ~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r----------~~~~~~f~~g~~~vLvaT~~~~~---Gldip  441 (503)
                      +++||||++++.|++++..|++.|+++..+|++++++.|          ..+++.|..|+.++||+|+++++   |+|++
T Consensus        37 gk~LVFcnSR~~aE~La~~L~~~Gi~a~~~Hgglsq~~R~~~gd~~i~~~~aLe~f~~G~~dvVVaT~~~a~g~~giDid  116 (299)
T d1a1va2          37 GRHLIFCHSKKKCDELAAKLVALGINAVAYYRGLDVSVIPTSGDVVVVATDALMTGFTGDFDSVIDCNTCVTQTVDFSLD  116 (299)
T ss_dssp             SEEEEECSSHHHHHHHHHHHHHTTCCEEEECTTSCGGGSCSSSSEEEEECTTC---CCCCBSEEEECCEEEEEEEECCCS
T ss_pred             CCEEEECCcHHHHHHHHHHHHHCCCCEEEEeCCchHHHHHhccchHHHHHHHHHHHhcCCCcEEEEEeehhccCCCCCCC
Confidence            469999999999999999999999999999999999876          56788999999999999999988   77888


Q ss_pred             CCCEEEEccCCCChhHHHHhhCccee
Q 010709          442 GVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       442 ~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                      .+.+||++++|.+.++|+||+||+||
T Consensus       117 ~V~~VI~~d~P~SvesyIQRiGRTGR  142 (299)
T d1a1va2         117 PTFTIETTTLPQDAVSRTQRRGRTGR  142 (299)
T ss_dssp             SSCEEEEEEEECBHHHHHHHHTTBCS
T ss_pred             cceEEEeCCCCCCHHHHHhhccccCC
Confidence            88999999999999999999999999

>d2p6ra4 c.37.1.19 (A:203-403) 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=99.72  E-value=2.3e-18  Score=151.15  Aligned_cols=96  Identities=17%  Similarity=0.137  Sum_probs=85.2

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHC------------------------------CCeEEEEcCCCCHHHHHHHHHHHhcC
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAE------------------------------GLHAVALHGGRNQSDRESALRDFRNG  423 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~------------------------------~~~v~~lh~~~~~~~r~~~~~~f~~g  423 (503)
                      .+++||||++++.|+.++..|...                              ...+..+|++|++.+|..+++.|++|
T Consensus        40 ~~~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g  119 (201)
T d2p6ra4          40 NGGVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRG  119 (201)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTT
T ss_pred             CCcEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCC
Confidence            346999999999999988888642                              02378899999999999999999999


Q ss_pred             CCcEEEEccccccCCCCCCCCEEEE-------ccCCCChhHHHHhhCcceeee
Q 010709          424 STNILVATDVASRGLDVMGVAHVVN-------LDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       424 ~~~vLvaT~~~~~Gldip~v~~VI~-------~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      .++|||||+.+++|||+|..++||.       ++.|.+..+|.||+|||||..
T Consensus       120 ~i~vlvaT~~l~~Gin~p~~~vvi~~~~~~d~~~~~~~~~~~~q~~GRAGR~g  172 (201)
T d2p6ra4         120 NIKVVVATPTLAAGVNLPARRVIVRSLYRFDGYSKRIKVSEYKQMAGRAGRPG  172 (201)
T ss_dssp             SCCEEEECSTTTSSSCCCBSEEEECCSEEESSSEEECCHHHHHHHHTTBSCTT
T ss_pred             CceEEEechHHHhhcCCCCceEEEecceeccCCcCCCCHHHHHHHhcccCCCC
Confidence            9999999999999999998888886       677889999999999999953

>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=99.71  E-value=5.3e-18  Score=139.92  Aligned_cols=127  Identities=23%  Similarity=0.184  Sum_probs=87.4

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHH
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAE  237 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  237 (503)
                      .+..++.+|||+|||+.+..  +  +..       .+.+++|++|+++|++|+.+.+.++...    ......++..   
T Consensus         8 ~~~~ll~apTGsGKT~~~~~--~--~~~-------~~~~vli~~P~~~l~~q~~~~~~~~~~~----~~~~~~~~~~---   69 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPA--A--YAA-------QGYKVLVLNPSVAATLGFGAYMSKAHGV----DPNIRTGVRT---   69 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHH--H--HHT-------TTCCEEEEESCHHHHHHHHHHHHHHHSC----CCEEECSSCE---
T ss_pred             CCEEEEEeCCCCCHHHHHHH--H--HHH-------cCCcEEEEcChHHHHHHHHHHHHHHhhc----cccccccccc---
Confidence            34589999999999975422  2  122       2567999999999999999999987643    2233334332   


Q ss_pred             HHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhC--CCCCcEEEEEeeC
Q 010709          238 QRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNL--PDKHQTLLFSATM  310 (503)
Q Consensus       238 ~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~--~~~~q~i~~SAT~  310 (503)
                          ......++++|.+.+....   ...+.++++||+||+|++... ....+..++..+  .++.+++++||||
T Consensus        70 ----~~~~~~~~~~~~~~~~~~~---~~~~~~~~~vIiDE~H~~~~~-~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1          70 ----ITTGSPITYSTYGKFLADG---GCSGGAYDIIICDECHSTDAT-SILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             ----ECCCCSEEEEEHHHHHHTT---GGGGCCCSEEEEETTTCCSHH-HHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             ----cccccceEEEeeeeecccc---chhhhcCCEEEEecccccCHH-HHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence                1234678899988775433   345788999999999975322 223355555544  3566899999996

>d2fwra1 c.37.1.19 (A:257-456) 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=99.70  E-value=2.7e-18  Score=151.60  Aligned_cols=105  Identities=20%  Similarity=0.247  Sum_probs=92.6

Q ss_pred             hHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEE
Q 010709          351 EKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVA  430 (503)
Q Consensus       351 ~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLva  430 (503)
                      .|+..+..++..         ++..++||||++...++.+++.|.     +..+||++++.+|..+++.|++|+.+||||
T Consensus        79 ~K~~~l~~ll~~---------~~~~k~lvf~~~~~~~~~l~~~l~-----~~~i~g~~~~~~R~~~l~~F~~~~~~vLv~  144 (200)
T d2fwra1          79 NKIRKLREILER---------HRKDKIIIFTRHNELVYRISKVFL-----IPAITHRTSREEREEILEGFRTGRFRAIVS  144 (200)
T ss_dssp             HHHHHHHHHHHH---------TSSSCBCCBCSCHHHHHHHHHHTT-----CCBCCSSSCSHHHHTHHHHHHHSSCSBCBC
T ss_pred             HHHHHHHHHHHh---------CCCCcEEEEeCcHHHHHHHHhhcC-----cceeeCCCCHHHHHHHHHHhhcCCeeeeee
Confidence            466666666554         345679999999999999988763     345799999999999999999999999999


Q ss_pred             ccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceeee
Q 010709          431 TDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFNI  469 (503)
Q Consensus       431 T~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~~  469 (503)
                      |+++++|+|+|.+++||++++|+++..|+||+||++|..
T Consensus       145 ~~~~~~Gidl~~~~~vi~~~~~~s~~~~~Q~iGR~~R~~  183 (200)
T d2fwra1         145 SQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRPS  183 (200)
T ss_dssp             SSCCCSSSCSCCBSEEEEECCSSCCHHHHHHHHHSBCCC
T ss_pred             cchhhcccCCCCCCEEEEeCCCCCHHHHHHHHHhcCCCC
Confidence            999999999999999999999999999999999999953

>d1gkub2 c.37.1.16 (B:251-498) 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=99.68  E-value=1.1e-18  Score=159.46  Aligned_cols=99  Identities=18%  Similarity=0.270  Sum_probs=81.9

Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEE
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILV  429 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLv  429 (503)
                      .+++..+..++..          -++++||||++++.++.++++|...      +||++++.+|.++++.|++|+.+|||
T Consensus        11 ~~~~~~l~~~l~~----------~~~~~iif~~~~~~~~~l~~~l~~~------~hg~~~~~~R~~~~~~f~~g~~~vLV   74 (248)
T d1gkub2          11 DESISTLSSILEK----------LGTGGIIYARTGEEAEEIYESLKNK------FRIGIVTATKKGDYEKFVEGEIDHLI   74 (248)
T ss_dssp             CCCTTTTHHHHTT----------SCSCEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSSHHHHHHHHTSCSEEE
T ss_pred             chHHHHHHHHHHH----------hCCCEEEEECCHHHHHHHHHHHHHh------ccCCCCHHHHHHHHHHHHhCCCeEEE
Confidence            4455555555542          1246999999999999999999753      79999999999999999999999999


Q ss_pred             Ec----cccccCCCCCC-CCEEEEccCCCChhHHHHhhCcceee
Q 010709          430 AT----DVASRGLDVMG-VAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       430 aT----~~~~~Gldip~-v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ||    +++++|||+|+ |++|||||+|+    |.||+||+||.
T Consensus        75 aT~a~~~v~~rGlDip~~v~~VI~~d~P~----~~~r~gR~~R~  114 (248)
T d1gkub2          75 GTAHYYGTLVRGLDLPERIRFAVFVGCPS----FRVTIEDIDSL  114 (248)
T ss_dssp             EECC------CCSCCTTTCCEEEEESCCE----EEEECSCGGGS
T ss_pred             EeccccchhhhccCccccccEEEEeCCCc----chhhhhhhhcc
Confidence            99    78999999996 99999999995    88999999985

>d1gm5a4 c.37.1.19 (A:550-755) 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=99.63  E-value=1.5e-17  Score=144.54  Aligned_cols=143  Identities=17%  Similarity=0.219  Sum_probs=101.3

Q ss_pred             hhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHH--------HHHHHHHC---CCeEEEEcCCCCHHHHHHHHH
Q 010709          350 NEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDE--------VSEALVAE---GLHAVALHGGRNQSDRESALR  418 (503)
Q Consensus       350 ~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~--------l~~~L~~~---~~~v~~lh~~~~~~~r~~~~~  418 (503)
                      ..+...++..+.+...       ..+++-+.||..++.+.        .++.|.+.   ++++..+||.|++++|.++++
T Consensus        12 ~~~~~~v~~~I~~el~-------~g~QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~   84 (206)
T d1gm5a4          12 MDRVNEVYEFVRQEVM-------RGGQAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVML   84 (206)
T ss_dssp             SSTHHHHHHHHHHHTT-------TSCCBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHH
T ss_pred             cccHHHHHHHHHHHHH-------cCCCEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHH
Confidence            3456667777766543       34457788887665443        33333332   567888999999999999999


Q ss_pred             HHhcCCCcEEEEccccccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee--------eeeccC-chhhhhhHHHHHHH
Q 010709          419 DFRNGSTNILVATDVASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN--------ITTNLD-GDMKKLEFCLILAI  488 (503)
Q Consensus       419 ~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~--------~~~~~~-~~~~~~~~~~~~~~  488 (503)
                      .|++|+.+|||||+++++|||+|++++||+++.|. ..+++.|+.||+||.        ++...+ ...+++.......|
T Consensus        85 ~F~~g~~~iLVaTtViE~GIDip~a~~iii~~a~~fglsqlhQlrGRvGR~~~~~~~~l~~~~~~~~~~~rl~~~~~~~d  164 (206)
T d1gm5a4          85 EFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLHQLRGRVGRGGQEAYCFLVVGDVGEEAMERLRFFTLNTD  164 (206)
T ss_dssp             HHTTTSSSBCCCSSCCCSCSCCTTCCEEEBCSCSSSCTTHHHHHHHTSCCSSTTCEEECCCCSCCHHHHHHHHHHHTCCC
T ss_pred             HHHCCCEEEEEEehhhhccccccCCcEEEEEccCCccHHHHHhhhhheeeccccceeEeeeccccccchhhhhhccccCC
Confidence            99999999999999999999999999999999998 577778888999994        222222 44555655555556


Q ss_pred             HHHHHHHHHhh
Q 010709          489 TVLLFVIFLSI  499 (503)
Q Consensus       489 ~~~~~~~~~~~  499 (503)
                      .+.++...|-+
T Consensus       165 Gf~ia~~Dl~l  175 (206)
T d1gm5a4         165 GFKIAEYDLKT  175 (206)
T ss_dssp             SHHHHHHHHHS
T ss_pred             CchHHHHHHhc
Confidence            66666666543

>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=99.61  E-value=5.2e-15  Score=126.91  Aligned_cols=136  Identities=16%  Similarity=0.121  Sum_probs=108.4

Q ss_pred             HHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC--CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccc
Q 010709          356 LLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE--GLHAVALHGGRNQSDRESALRDFRNGSTNILVATDV  433 (503)
Q Consensus       356 l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~--~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~  433 (503)
                      ++..+....       ...+++-+.||..+.++.+++.+.+.  ++++..+||.|+.+++.+++..|.+|+.+|||||.+
T Consensus        20 i~~~I~~El-------~rGgQvy~V~p~I~~~e~~~~~l~~~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Ttv   92 (211)
T d2eyqa5          20 VREAILREI-------LRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI   92 (211)
T ss_dssp             HHHHHHHHH-------TTTCEEEEECCCSSCHHHHHHHHHHHCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST
T ss_pred             HHHHHHHHH-------HcCCeEEEEEcCccchhhHHHHHHHhCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehh
Confidence            455555444       34567999999999999999999875  779999999999999999999999999999999999


Q ss_pred             cccCCCCCCCCEEEEccCCC-ChhHHHHhhCcceee-------eeecc-----CchhhhhhHHHHHHH---HHHHHHHHH
Q 010709          434 ASRGLDVMGVAHVVNLDLPK-VLLAASESLCTTSFN-------ITTNL-----DGDMKKLEFCLILAI---TVLLFVIFL  497 (503)
Q Consensus       434 ~~~Gldip~v~~VI~~~~p~-s~~~~~Qr~GR~gR~-------~~~~~-----~~~~~~~~~~~~~~~---~~~~~~~~~  497 (503)
                      .+.|||+|+++++|..+... -.+++-|..||+||.       ++++.     +...+++.......|   .+.++...|
T Consensus        93 IEvGiDvpnA~~iiI~~a~rfGLaQLhQLRGRVGR~~~~s~c~l~~~~~~~~~~~a~~RL~~l~~~~dlg~GF~iA~~DL  172 (211)
T d2eyqa5          93 IETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDL  172 (211)
T ss_dssp             TGGGSCCTTEEEEEETTTTSSCHHHHHHHHTTCCBTTBCEEEEEEECCGGGSCHHHHHHHHHHTTCCSBSHHHHHHHHHH
T ss_pred             hhhccCCCCCcEEEEecchhccccccccccceeeecCccceEEEEecCCcCCCchHHHHHHHHHhcccCCcceeeeHhHH
Confidence            99999999999999999886 788888888999994       23322     233455555544444   666666666


Q ss_pred             h
Q 010709          498 S  498 (503)
Q Consensus       498 ~  498 (503)
                      -
T Consensus       173 ~  173 (211)
T d2eyqa5         173 E  173 (211)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.53  E-value=7.1e-14  Score=130.83  Aligned_cols=160  Identities=19%  Similarity=0.208  Sum_probs=107.0

Q ss_pred             CCcHHHHHHHHHHh---------cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVAL---------SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKE  213 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~---------~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~  213 (503)
                      .++|+|.+++.++.         .+..+|++.++|+|||++. +.++..+............++|||+|.. |+.||.++
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qa-ia~l~~l~~~~~~~~~~~~~~LIV~P~s-l~~qW~~E  132 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQC-ITLIWTLLKQSPDCKPEIDKVIVVSPSS-LVRNWYNE  132 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHH-HHHHHHHHHCCTTSSCSCSCEEEEECHH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHH-HHHHHHHHHhcccccCCCCcEEEEccch-hhHHHHHH
Confidence            68999999998764         2345999999999999876 4455555555433333446799999985 78899999


Q ss_pred             HHHHhccCCCceEEEEECCccHHHHHHH---hh-----CCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCC
Q 010709          214 VKALSRSLDSFKTAIVVGGTNIAEQRSE---LR-----GGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMG  285 (503)
Q Consensus       214 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-----~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~  285 (503)
                      +.++....  .....++++.........   ..     ...+++++|.+.+.....  .+.-.++++||+||+|++.+..
T Consensus       133 i~k~~~~~--~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~--~l~~~~~~~vI~DEaH~ikn~~  208 (298)
T d1z3ix2         133 VGKWLGGR--VQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE--VLHKGKVGLVICDEGHRLKNSD  208 (298)
T ss_dssp             HHHHHGGG--CCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT--TTTTSCCCEEEETTGGGCCTTC
T ss_pred             HHhhcCCc--eeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh--cccccceeeeeccccccccccc
Confidence            99988542  444455555433221111   11     235799999988865433  3334568899999999886553


Q ss_pred             CHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          286 FEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       286 ~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                        ....+.+..+.. ...+++||||-
T Consensus       209 --s~~~~a~~~l~~-~~rllLTGTPi  231 (298)
T d1z3ix2         209 --NQTYLALNSMNA-QRRVLISGTPI  231 (298)
T ss_dssp             --HHHHHHHHHHCC-SEEEEECSSCS
T ss_pred             --chhhhhhhcccc-ceeeeecchHH
Confidence              223333444443 45789999994

>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=99.49  E-value=1.6e-14  Score=132.80  Aligned_cols=90  Identities=17%  Similarity=0.188  Sum_probs=75.2

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEccccccCCCCCCCCEEEEccCC-
Q 010709          374 FPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTNILVATDVASRGLDVMGVAHVVNLDLP-  452 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~~~~~Gldip~v~~VI~~~~p-  452 (503)
                      .++++|||++.++++.+++.|++.|.+|+.+||.+...++.    +|++|+.+|||||+++++|+|+ ++++||+++++ 
T Consensus        36 ~g~~~~F~~s~~~~~~~a~~L~~~g~~V~~l~~~~~~~e~~----~~~~~~~~~~~~t~~~~~~~~~-~~~~vid~g~~~  110 (299)
T d1yksa2          36 KRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYP----TIKQKKPDFILATDIAEMGANL-CVERVLDCRTAF  110 (299)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCEEECCSSSCC------------CCCSEEEESSSTTCCTTC-CCSEEEECCEEE
T ss_pred             CCCEEEEeCCHHHHHHHHHHHHhcCCeEEEEcCcCcHhHHh----hhhcCCcCEEEEechhhhceec-CceEEEecCcee
Confidence            46799999999999999999999999999999999977755    4678999999999999999999 59999988753 


Q ss_pred             ------------------CChhHHHHhhCcceee
Q 010709          453 ------------------KVLLAASESLCTTSFN  468 (503)
Q Consensus       453 ------------------~s~~~~~Qr~GR~gR~  468 (503)
                                        -+.++..||.||+||+
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~qr~gr~gr~  144 (299)
T d1yksa2         111 KPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRN  144 (299)
T ss_dssp             EEEEETTTTEEEEEEEEECCHHHHHHHHTTSSCC
T ss_pred             ceeeecCCCCeeEEeeeecCHHHHHHhccccccc
Confidence                              2558889999999995

>d1z3ix1 c.37.1.19 (X:390-735) 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=99.41  E-value=1.1e-12  Score=124.11  Aligned_cols=113  Identities=14%  Similarity=0.124  Sum_probs=98.3

Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcCCCc--
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNGSTN--  426 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~--  426 (503)
                      ...|+..+..++......      ++.|+|||++.....+.+.+.|...|+.+..+||+++..+|..+++.|+++...  
T Consensus        99 ~S~Kl~~L~~ll~~~~~~------~g~KvlIFs~~~~~ld~l~~~l~~~g~~~~~l~G~~~~~~R~~~i~~F~~~~~~~~  172 (346)
T d1z3ix1          99 LSGKMLVLDYILAMTRTT------TSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEF  172 (346)
T ss_dssp             GSHHHHHHHHHHHHHHHH------CCCEEEEEESCHHHHHHHHHHHHHHTCCEEEECSSCCHHHHHHHHHHHHSTTCCCC
T ss_pred             cCHHHHHHHHHHHHHHHh------cCCceeEEeehhhhhHHHHHHHhhhhccccccccchhHHHHHHHHHhhhcccccce
Confidence            346777666666543222      345899999999999999999999999999999999999999999999987543  


Q ss_pred             -EEEEccccccCCCCCCCCEEEEccCCCChhHHHHhhCccee
Q 010709          427 -ILVATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSF  467 (503)
Q Consensus       427 -vLvaT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR  467 (503)
                       +|++|.+++.|+|+.++++||+||+++++..+.|++||+.|
T Consensus       173 vlLls~~agg~GlnL~~a~~vi~~d~~wnp~~~~Qa~~R~~R  214 (346)
T d1z3ix1         173 IFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWR  214 (346)
T ss_dssp             EEEEEGGGSCTTCCCTTEEEEEECSCCSSHHHHHHHHTTSSS
T ss_pred             eeeecchhhhhccccccceEEEEecCCCccchHhHhhhcccc
Confidence             67888999999999999999999999999999999999977

>d1z5za1 c.37.1.19 (A:663-906) 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=99.34  E-value=2.5e-12  Score=116.30  Aligned_cols=113  Identities=12%  Similarity=0.140  Sum_probs=88.0

Q ss_pred             hhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHC-CCeEEEEcCCCCHHHHHHHHHHHhcCC-Cc
Q 010709          349 ENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAE-GLHAVALHGGRNQSDRESALRDFRNGS-TN  426 (503)
Q Consensus       349 ~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~-~~~v~~lh~~~~~~~r~~~~~~f~~g~-~~  426 (503)
                      ...|+..+..++.....       .+.++||||+.....+.+...+... +..+..+||+++..+|..+++.|.++. ..
T Consensus        67 ~S~K~~~l~~~l~~~~~-------~g~kviIFs~~~~~~~~l~~~l~~~~~~~~~~i~G~~~~~~R~~~i~~F~~~~~~~  139 (244)
T d1z5za1          67 RSGKMIRTMEIIEEALD-------EGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVK  139 (244)
T ss_dssp             TCHHHHHHHHHHHHHHH-------TTCCEEEEESCHHHHHHHHHHHHHHHCSCCCEECTTSCHHHHHHHHHHHHHCTTCC
T ss_pred             hhhHHHHHHHHHHhhcc-------cccceEEEeeceehHHHHHHHHHhhccceEEEEecccchhccchhhhhhhccccch
Confidence            35688888888766442       3457999999999999999988755 889999999999999999999998764 56


Q ss_pred             EEE-EccccccCCCCCCCCEEEEccCCCChhHHHHhhCcceee
Q 010709          427 ILV-ATDVASRGLDVMGVAHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       427 vLv-aT~~~~~Gldip~v~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      +|+ +|.+++.|+|++.+++||++++|+++..+.|++||+.|.
T Consensus       140 vll~~~~~~g~Glnl~~a~~vi~~~~~wn~~~~~Qa~~R~~R~  182 (244)
T d1z5za1         140 FIVLSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRI  182 (244)
T ss_dssp             EEEEECCTTCCCCCCTTCSEEEECSCCSCTTTC----------
T ss_pred             hccccccccccccccchhhhhhhcCchhhhHHHhhhcceeeec
Confidence            665 558999999999999999999999999999999998883

>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=99.29  E-value=1.6e-12  Score=116.58  Aligned_cols=148  Identities=15%  Similarity=0.199  Sum_probs=97.9

Q ss_pred             CCcHHHHHHHHHHh----cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVAL----SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .++++|.+++..+.    .+..+|++.++|.|||++. +.++..+....     ...++||++|. .+..||.+++.++.
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~-i~~~~~~~~~~-----~~~~~LIv~p~-~l~~~W~~e~~~~~   84 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQT-IAVFSDAKKEN-----ELTPSLVICPL-SVLKNWEEELSKFA   84 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHH-HHHHHHHHHTT-----CCSSEEEEECS-TTHHHHHHHHHHHC
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHH-HHhhhhhhhcc-----cccccceecch-hhhhHHHHHHHhhc
Confidence            58999999998764    3456999999999999987 44455544432     23568999996 57788999999887


Q ss_pred             ccCCCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCC
Q 010709          219 RSLDSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLP  298 (503)
Q Consensus       219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~  298 (503)
                      ..   ..+..........     ...+.+|+++|.+.+.....   +.-.++.+||+||+|++.+...  ...+.+..+.
T Consensus        85 ~~---~~~~~~~~~~~~~-----~~~~~~vvi~~~~~~~~~~~---l~~~~~~~vI~DEah~~k~~~s--~~~~~~~~l~  151 (230)
T d1z63a1          85 PH---LRFAVFHEDRSKI-----KLEDYDIILTTYAVLLRDTR---LKEVEWKYIVIDEAQNIKNPQT--KIFKAVKELK  151 (230)
T ss_dssp             TT---SCEEECSSSTTSC-----CGGGSSEEEEEHHHHTTCHH---HHTCCEEEEEEETGGGGSCTTS--HHHHHHHTSC
T ss_pred             cc---ccceeeccccchh-----hccCcCEEEeeHHHHHhHHH---HhcccceEEEEEhhhcccccch--hhhhhhhhhc
Confidence            43   2333322221111     12347899999988754322   1223578999999998876532  2334445554


Q ss_pred             CCCcEEEEEeeCC
Q 010709          299 DKHQTLLFSATMP  311 (503)
Q Consensus       299 ~~~q~i~~SAT~~  311 (503)
                      . ...+++||||-
T Consensus       152 a-~~r~~LTgTPi  163 (230)
T d1z63a1         152 S-KYRIALTGTPI  163 (230)
T ss_dssp             E-EEEEEECSSCS
T ss_pred             c-ceEEEEecchH
Confidence            3 34689999983

>d1tf5a4 c.37.1.19 (A:396-570) 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=98.95  E-value=2.8e-09  Score=87.77  Aligned_cols=114  Identities=14%  Similarity=0.143  Sum_probs=91.1

Q ss_pred             EEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC-
Q 010709          345 EKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNG-  423 (503)
Q Consensus       345 ~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g-  423 (503)
                      ++....+|...+...+.+.....       .|+||++.+.+.++.+++.|.+.++....++.....++-. ++.  ..| 
T Consensus        12 vf~T~~eK~~AIi~eV~~~~~~g-------rPVLIgT~SIe~SE~ls~~L~~~gi~h~vLnAk~~~~Ea~-II~--~Ag~   81 (175)
T d1tf5a4          12 IYRTMEGKFKAVAEDVAQRYMTG-------QPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQ-IIE--EAGQ   81 (175)
T ss_dssp             EESSHHHHHHHHHHHHHHHHHHT-------CCEEEEESCHHHHHHHHHHHHTTTCCCEEECSSCHHHHHH-HHT--TTTS
T ss_pred             EEcCHHHHHHHHHHHHHHHHhcC-------CCEEEEeCcHHHHHHHHHHHHHcCCCceeehhhhHHHHHH-HHH--hccC
Confidence            44467788888888887655443       3699999999999999999999999999999887544433 222  233 


Q ss_pred             CCcEEEEccccccCCCCCC---C-----CEEEEccCCCChhHHHHhhCcceee
Q 010709          424 STNILVATDVASRGLDVMG---V-----AHVVNLDLPKVLLAASESLCTTSFN  468 (503)
Q Consensus       424 ~~~vLvaT~~~~~Gldip~---v-----~~VI~~~~p~s~~~~~Qr~GR~gR~  468 (503)
                      ...|.|||++++||.||.-   |     -|||...+|.+.....|..||+||.
T Consensus        82 ~g~VtIATNmAGRGtDikl~~~v~~~GGLhVI~t~~~~s~Rid~Ql~GR~gRQ  134 (175)
T d1tf5a4          82 KGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQ  134 (175)
T ss_dssp             TTCEEEEETTSSTTCCCCCCTTSGGGTSEEEEESSCCSSHHHHHHHHTTSSGG
T ss_pred             CCceeehhhHHHcCCCccchHHHHhCCCcEEEEeccCcchhHHHHHhcchhhh
Confidence            3569999999999999862   2     3799999999999999999999994

>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=98.88  E-value=2.2e-08  Score=87.87  Aligned_cols=164  Identities=19%  Similarity=0.248  Sum_probs=117.8

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      .+|++.|..+--.+.+|  -|..+.||-|||+++.+|+....+.        |+.+-|++..--||..=++++..+...+
T Consensus        79 ~RhyDVQLiGgi~L~~G--~iaem~TGEGKTL~a~l~a~l~al~--------g~~vhvvTvNdyLA~RDae~m~~iy~~l  148 (273)
T d1tf5a3          79 MFPFKVQLMGGVALHDG--NIAEMKTGEGKTLTSTLPVYLNALT--------GKGVHVVTVNEYLASRDAEQMGKIFEFL  148 (273)
T ss_dssp             CCCCHHHHHHHHHHHTT--SEEECCTTSCHHHHHHHHHHHHHTT--------SSCEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred             eEEehhHHHHHHHHHhh--hheeecCCCcchhHHHHHHHHHHhc--------CCCceEEecCccccchhhhHHhHHHHHc
Confidence            37899998888888777  5889999999999998888877655        5678999999999998888888888777


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHH-HHHHHcC------CCCCCCccEEEecchhHHh-hCCCH------
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRF-LDHLQQG------NTSLSRVSFVILDEADRML-DMGFE------  287 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l-~~~l~~~------~~~l~~~~~vViDEaH~l~-~~~~~------  287 (503)
                       ++.++++..+....+....  ..++|+++|..-+ .+.+..+      ....+.+.+.||||+|.++ +....      
T Consensus       149 -Glsvg~~~~~~~~~~r~~~--Y~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsiliDeartpliisg  225 (273)
T d1tf5a3         149 -GLTVGLNLNSMSKDEKREA--YAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISG  225 (273)
T ss_dssp             -TCCEEECCTTSCHHHHHHH--HHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCEEEEEE
T ss_pred             -CCCccccccccCHHHHHHH--hhCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhhhhccCCceEecc
Confidence             6999998887766554333  3589999999887 3444332      2235678999999999754 32100      


Q ss_pred             -------HHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh
Q 010709          288 -------PQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       288 -------~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                             -.+...++..   .++-+||+|...+..++.+-|
T Consensus       226 ~~~~~a~it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy  263 (273)
T d1tf5a3         226 QSMTLATITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIY  263 (273)
T ss_dssp             EEEEEEEEEHHHHHTTS---SEEEEEESCCGGGHHHHHHHH
T ss_pred             CccchhhhhHHHHHHHH---HHHhCCccccHHHHHHHHhcc
Confidence                   0122333332   357788888766666555554

>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=98.42  E-value=7.9e-07  Score=83.58  Aligned_cols=144  Identities=19%  Similarity=0.266  Sum_probs=88.3

Q ss_pred             CCCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccC
Q 010709          142 TRPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSL  221 (503)
Q Consensus       142 ~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~  221 (503)
                      ......|.+|+..++.++-++|.||.|+|||+.. ..++..+....   ...+.++++++||-..|..+.+.+.......
T Consensus       147 ~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i-~~~l~~l~~~~---~~~~~~I~l~ApTgkAA~~L~e~~~~~~~~~  222 (359)
T d1w36d1         147 SDEINWQKVAAAVALTRRISVISGGPGTGKTTTV-AKLLAALIQMA---DGERCRIRLAAPTGKAAARLTESLGKALRQL  222 (359)
T ss_dssp             TTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHH-HHHHHHHHHTC---SSCCCCEEEEBSSHHHHHHHHHHHTHHHHHS
T ss_pred             cccccHHHHHHHHHHcCCeEEEEcCCCCCceehH-HHHHHHHHHHH---hccCCeEEEecCcHHHHHHHHHHHHHHHhhc
Confidence            4467889999999999888999999999999864 33444433321   2346779999999998888877765544322


Q ss_pred             CCceEEEEECCccHHHHHHHhhCCCcEEEECcHHHHH------HHHcCCCCCCCccEEEecchhHHhhCCCHHHHHHHHH
Q 010709          222 DSFKTAIVVGGTNIAEQRSELRGGVSIVVATPGRFLD------HLQQGNTSLSRVSFVILDEADRMLDMGFEPQIREVMQ  295 (503)
Q Consensus       222 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~Tp~~l~~------~l~~~~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~  295 (503)
                      ...... .  .            ....-..|..++..      .+.........+++||||||-.+.    ...+..++.
T Consensus       223 ~~~~~~-~--~------------~~~~~~~t~~~ll~~~~~~~~~~~~~~~~l~~d~lIIDEaSmv~----~~l~~~ll~  283 (359)
T d1w36d1         223 PLTDEQ-K--K------------RIPEDASTLHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMID----LPMMSRLID  283 (359)
T ss_dssp             SCCSCC-C--C------------SCSCCCBTTTSCC-----------CTTSCCSCSEEEECSGGGCB----HHHHHHHHH
T ss_pred             Cchhhh-h--h------------hhhhhhhHHHHHHhhhhcchHHHHhhhcccccceeeehhhhccC----HHHHHHHHH
Confidence            100000 0  0            00000112111111      111223345568999999998542    456778888


Q ss_pred             hCCCCCcEEEEEe
Q 010709          296 NLPDKHQTLLFSA  308 (503)
Q Consensus       296 ~~~~~~q~i~~SA  308 (503)
                      .+++..++|++.-
T Consensus       284 ~~~~~~~lILvGD  296 (359)
T d1w36d1         284 ALPDHARVIFLGD  296 (359)
T ss_dssp             TCCTTCEEEEEEC
T ss_pred             HhcCCCEEEEECC
Confidence            8888888877653

>d1nkta4 c.37.1.19 (A:397-615) Translocation ATPase SecA, nucleotide-binding domains {Mycobacterium tuberculosis [TaxId: 1773]}

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: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.18  E-value=9.5e-06  Score=67.62  Aligned_cols=115  Identities=14%  Similarity=0.077  Sum_probs=89.3

Q ss_pred             EEEcChhhHHHHHHHHHHHHHHhhhccCCCCCcEEEEEcchhhHHHHHHHHHHCCCeEEEEcCCCCHHHHHHHHHHHhcC
Q 010709          344 LEKVSENEKVDRLLALLVEEAFLAEKSCHPFPLTIVFVERKTRCDEVSEALVAEGLHAVALHGGRNQSDRESALRDFRNG  423 (503)
Q Consensus       344 ~~~~~~~~k~~~l~~~l~~~~~~~~~~~~~~~~~lIF~~~~~~~~~l~~~L~~~~~~v~~lh~~~~~~~r~~~~~~f~~g  423 (503)
                      .++.....|...+...+......       ..|+||.+.+.+..+.+.+.|.+.++....|+......|-..+-   +.|
T Consensus        11 ~Vy~T~~~K~~Avv~ei~~~h~~-------GqPVLVGT~SVe~SE~lS~lL~~~gi~h~vLNAK~herEAeIIA---qAG   80 (219)
T d1nkta4          11 LIYKTEEAKYIAVVDDVAERYAK-------GQPVLIGTTSVERSEYLSRQFTKRRIPHNVLNAKYHEQEATIIA---VAG   80 (219)
T ss_dssp             EEESCHHHHHHHHHHHHHHHHHT-------TCCEEEEESCHHHHHHHHHHHHHTTCCCEEECSSCHHHHHHHHH---TTT
T ss_pred             eEEcCHHHHHHHHHHHHHHHHhc-------CCCEEEeeCcHHHHHHHHHHHHHhccchhccchhhHHHHHHHHH---hcc
Confidence            34556778888888888776644       34699999999999999999999999999999976543333222   345


Q ss_pred             C-CcEEEEccccccCCCCCC----------------------------------------------------CCEEEEcc
Q 010709          424 S-TNILVATDVASRGLDVMG----------------------------------------------------VAHVVNLD  450 (503)
Q Consensus       424 ~-~~vLvaT~~~~~Gldip~----------------------------------------------------v~~VI~~~  450 (503)
                      . -.|-|||++++||.||-=                                                    ==+||-..
T Consensus        81 ~~GaVTIATNMAGRGTDI~LGgn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~GGL~VIGTE  160 (219)
T d1nkta4          81 RRGGVTVATNMAGRGTDIVLGGNVDFLTDQRLRERGLDPVETPEEYEAAWHSELPIVKEEASKEAKEVIEAGGLYVLGTE  160 (219)
T ss_dssp             STTCEEEEETTCSTTCCCCTTCCHHHHHHHHHHHTTCCTTTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHTTSEEEEECS
T ss_pred             cCCcEEeeccccCCCCceeecCchhhhhHHHhhhcccCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcEEEecc
Confidence            4 568999999999999941                                                    12688888


Q ss_pred             CCCChhHHHHhhCcceee
Q 010709          451 LPKVLLAASESLCTTSFN  468 (503)
Q Consensus       451 ~p~s~~~~~Qr~GR~gR~  468 (503)
                      ...|..-=.|-.||+||.
T Consensus       161 rHeSrRIDnQLRGRsGRQ  178 (219)
T d1nkta4         161 RHESRRIDNQLRGRSGRQ  178 (219)
T ss_dssp             CCSSHHHHHHHHHTSSGG
T ss_pred             cccccccccccccccccc
Confidence            888887777888888874

>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=97.64  E-value=4.9e-05  Score=69.66  Aligned_cols=70  Identities=24%  Similarity=0.169  Sum_probs=51.3

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      +++|-|.+++..  ....++|.|+.|||||.+.+. -+.+++....   .+..+++++++|+.+|..+.+.+.++.
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~-rv~~ll~~~~---~~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITN-KIAHLIRGCG---YQARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHH-HHHHHHHHHC---CCGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHH-HHHHHHHhcC---CChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            467889999975  345699999999999987533 3334433211   124579999999999999888887765

>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=97.35  E-value=0.00028  Score=64.87  Aligned_cols=70  Identities=26%  Similarity=0.218  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHHHHhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          143 RPTSIQAQAMPVALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      .+++-|.+++..  .+..++|.|+.|||||++.+- -+.+++...   .....+++++++++.++..+...+....
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~-ri~~ll~~~---~~~p~~il~lt~t~~aa~~~~~~~~~~~   80 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTH-RIAYLMAEK---HVAPWNILAITFTNKAAREMRERVQSLL   80 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHH-HHHHHHHTT---CCCGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHH-HHHHHHHcC---CCCHHHeEeEeccHHHHHHHHHHHHhhc
Confidence            478889999985  355799999999999987643 333444332   1123579999999999999998887665

>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=97.33  E-value=0.00051  Score=58.34  Aligned_cols=131  Identities=17%  Similarity=0.183  Sum_probs=66.4

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc--ccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA--PTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQ  238 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~--Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (503)
                      ++++||||+|||+...- +..++..+       +.++.+++  ..|.-|.++.+.+.+..    ++.+............
T Consensus        13 i~lvGp~GvGKTTTiaK-LA~~~~~~-------g~kV~lit~Dt~R~gA~eQL~~~a~~l----~v~~~~~~~~~~~~~~   80 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAK-LALYYKGK-------GRRPLLVAADTQRPAAREQLRLLGEKV----GVPVLEVMDGESPESI   80 (207)
T ss_dssp             EEEECCTTTTHHHHHHH-HHHHHHHT-------TCCEEEEECCSSCHHHHHHHHHHHHHH----TCCEEECCTTCCHHHH
T ss_pred             EEEECCCCCCHHHHHHH-HHHHHHHC-------CCcEEEEecccccchHHHHHHHHHHhc----CCccccccccchhhHH
Confidence            67799999999986432 22233322       34455555  35555554444444433    3444444333332221


Q ss_pred             HHHhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHHhhC-CCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHH
Q 010709          239 RSELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRMLDM-GFEPQIREVMQNLPDKHQTLLFSATMPVEIEAL  317 (503)
Q Consensus       239 ~~~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~  317 (503)
                      ....              ...     ..+.++++|+||=+-+.-.. .....+.++....++..-++.++|+...+....
T Consensus        81 ~~~~--------------~~~-----~~~~~~d~vlIDTaGr~~~d~~~~~el~~~~~~~~~~~~llv~~a~~~~~~~~~  141 (207)
T d1ls1a2          81 RRRV--------------EEK-----ARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSV  141 (207)
T ss_dssp             HHHH--------------HHH-----HHHHTCCEEEEECCCCSSCCHHHHHHHHHHHHHHCCSEEEEEEEGGGTHHHHHH
T ss_pred             HHHH--------------HHH-----HhhccCcceeecccccchhhhhhHHHHHHHHhhcCCceEEEEeccccchhHHHH
Confidence            1000              000     01233455666655432211 123445556666666666788899888776666


Q ss_pred             HHHhc
Q 010709          318 AQEYL  322 (503)
Q Consensus       318 ~~~~~  322 (503)
                      +..|+
T Consensus       142 ~~~f~  146 (207)
T d1ls1a2         142 ARAFD  146 (207)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66653

>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=97.13  E-value=0.00071  Score=57.72  Aligned_cols=43  Identities=14%  Similarity=0.190  Sum_probs=28.8

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      ...+.+++||||+|.|... -...+.+++...++...+++.+-.
T Consensus       105 ~~~~~kviIide~d~l~~~-a~n~Llk~lEep~~~~~fIl~t~~  147 (207)
T d1a5ta2         105 RLGGAKVVWVTDAALLTDA-AANALLKTLEEPPAETWFFLATRE  147 (207)
T ss_dssp             TTSSCEEEEESCGGGBCHH-HHHHHHHHHTSCCTTEEEEEEESC
T ss_pred             ccCccceEEechhhhhhhh-hhHHHHHHHHhhcccceeeeeecC
Confidence            3456889999999987543 355666777776666655554433

>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=97.06  E-value=0.0023  Score=56.14  Aligned_cols=73  Identities=18%  Similarity=0.263  Sum_probs=63.3

Q ss_pred             cEEEEEcchhhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          376 LTIVFVERKTRCDEVSEALVA----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       376 ~~lIF~~~~~~~~~l~~~L~~----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      ++++.+++.--+.+.++.+.+    .|+.+..+||+++..+|.+++....+|+.+|+|+|- ++...+.+.++.+||.
T Consensus       134 q~~~m~Pt~~La~Qh~~~~~~~f~~~~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~~~~f~~Lglvii  211 (264)
T d1gm5a3         134 QTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQEDVHFKNLGLVII  211 (264)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTCSSCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHHCCCCSCCCEEEE
T ss_pred             ceeEEeehHhhhHHHHHHHHHhhhhccccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcCCCCccccceeee
Confidence            599999999888887777665    378999999999999999999999999999999995 5556788888888775

>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=96.86  E-value=0.0031  Score=53.24  Aligned_cols=52  Identities=19%  Similarity=0.103  Sum_probs=28.9

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEc-c-cHHHHHHHHHHHHHHh
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLA-P-TRELAQQIEKEVKALS  218 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~-P-tr~La~q~~~~~~~~~  218 (503)
                      +-++++||||+|||+... -+..++...       +.++.+++ - .|.-|.++.+.+.+..
T Consensus         7 ~vi~lvGptGvGKTTTia-KLA~~~~~~-------g~kV~lit~Dt~R~gA~eQL~~~a~~l   60 (207)
T d1okkd2           7 RVVLVVGVNGVGKTTTIA-KLGRYYQNL-------GKKVMFCAGDTFRAAGGTQLSEWGKRL   60 (207)
T ss_dssp             SEEEEECSTTSSHHHHHH-HHHHHHHTT-------TCCEEEECCCCSSTTHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHH-HHHHHHHHC-------CCcEEEEEeccccccchhhHhhccccc
Confidence            447889999999998643 232333222       34455554 3 4555544444444433

>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=96.80  E-value=0.0079  Score=50.67  Aligned_cols=15  Identities=33%  Similarity=0.501  Sum_probs=13.1

Q ss_pred             eEEEccCCCchhHHh
Q 010709          161 LLGCAETGSGKTAAF  175 (503)
Q Consensus       161 vii~~~TGsGKTl~~  175 (503)
                      ++++||||+|||+..
T Consensus        12 i~lvGptGvGKTTTi   26 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTI   26 (211)
T ss_dssp             EEEECCTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            667999999999864

>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=96.67  E-value=0.0037  Score=52.55  Aligned_cols=43  Identities=16%  Similarity=0.278  Sum_probs=31.4

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATM  310 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  310 (503)
                      ..+.+++||||||+|-.. ....+.+++..-++...++++|..+
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            456789999999987533 4556777777777777777766655

>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=96.67  E-value=0.0036  Score=53.37  Aligned_cols=45  Identities=18%  Similarity=0.242  Sum_probs=27.1

Q ss_pred             CCccEEEecchhHHhhC-CCHHHHHHHHHhCC-CCCcEEEEEeeCCH
Q 010709          268 SRVSFVILDEADRMLDM-GFEPQIREVMQNLP-DKHQTLLFSATMPV  312 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~~  312 (503)
                      ...++|+||++|.+.+. .....+..++..+. .+.++|+.|...|.
T Consensus        96 ~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~  142 (213)
T d1l8qa2          96 KSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQ  142 (213)
T ss_dssp             HTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGG
T ss_pred             hhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcch
Confidence            35789999999987654 23444555555443 34555555554443

>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=96.66  E-value=0.009  Score=51.21  Aligned_cols=75  Identities=11%  Similarity=0.160  Sum_probs=65.5

Q ss_pred             CCcEEEEEcchhhHHHHHHHHHH----CCCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-ccccCCCCCCCCEEEE
Q 010709          374 FPLTIVFVERKTRCDEVSEALVA----EGLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-VASRGLDVMGVAHVVN  448 (503)
Q Consensus       374 ~~~~lIF~~~~~~~~~l~~~L~~----~~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-~~~~Gldip~v~~VI~  448 (503)
                      +.++++.+|+.--+.++++.+++    .+.++..+||.++..+|..+++.+.+|+.+|||.|. ++...+.++++..||.
T Consensus       104 g~qv~~l~Pt~~La~Q~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~~~~~f~~LgLiIi  183 (233)
T d2eyqa3         104 HKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIV  183 (233)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHHSTTTTCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHHSCCCCSSEEEEEE
T ss_pred             CCceEEEccHHHhHHHHHHHHHHHHhhCCCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhccCCccccccceee
Confidence            34699999999999999999886    477899999999999999999999999999999996 5555788888887775

>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=96.50  E-value=0.002  Score=60.64  Aligned_cols=66  Identities=30%  Similarity=0.374  Sum_probs=49.7

Q ss_pred             CCcHHHHHHHHHHhc----C-CCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVALS----G-RDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~~----~-~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .|..-|-+||..+.+    | ++.++.|-||||||+.. ..++.. .         +..+|||+|+..+|.|+++.++.+
T Consensus        11 ~p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~i-A~l~~~-~---------~rp~LVVt~n~~~A~qL~~dL~~~   79 (413)
T d1t5la1          11 EPQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTI-SNVIAQ-V---------NKPTLVIAHNKTLAGQLYSELKEF   79 (413)
T ss_dssp             CCCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHH-HHHHHH-H---------TCCEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHH-HHHHHH-h---------CCCEEEEeCCHHHHHHHHHHHHHH
Confidence            566678777776653    4 45889999999999743 223332 2         234899999999999999999998


Q ss_pred             hc
Q 010709          218 SR  219 (503)
Q Consensus       218 ~~  219 (503)
                      ..
T Consensus        80 l~   81 (413)
T d1t5la1          80 FP   81 (413)
T ss_dssp             CT
T ss_pred             cC
Confidence            74

>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=96.47  E-value=0.015  Score=49.11  Aligned_cols=15  Identities=27%  Similarity=0.505  Sum_probs=13.2

Q ss_pred             eEEEccCCCchhHHh
Q 010709          161 LLGCAETGSGKTAAF  175 (503)
Q Consensus       161 vii~~~TGsGKTl~~  175 (503)
                      ++++||||+|||+..
T Consensus        14 i~lvGptGvGKTTTi   28 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSC   28 (213)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            678999999999864

>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=96.20  E-value=0.017  Score=50.11  Aligned_cols=52  Identities=13%  Similarity=0.057  Sum_probs=28.5

Q ss_pred             CCcccCCCCHHHHHHHHHCCCCCCcHHHHHHHHHHh--cCCCeEEEccCCCchhHHh
Q 010709          121 ESFTDMCLHPSIMKDIEFHEYTRPTSIQAQAMPVAL--SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       121 ~~~~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~i~--~~~~vii~~~TGsGKTl~~  175 (503)
                      .+|+++.-.+...+.|...  ..+ ..+.+.+...-  ..+.+++.||+|+|||+.+
T Consensus         6 ~~~~di~G~~~~k~~l~~~--i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           6 VTFKDVAGAEEAKEELKEI--VEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             CCGGGCCSCHHHHHHHHHH--HHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CcHHHHccHHHHHHHHHHH--HHH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            5688886566666665421  000 00111122211  1245999999999999743

>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=96.14  E-value=0.044  Score=47.21  Aligned_cols=40  Identities=15%  Similarity=0.245  Sum_probs=26.1

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEe
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSA  308 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SA  308 (503)
                      .+.+++||||+|.|... ....+.+++...++...+++.+-
T Consensus       114 ~~~kviiIde~d~l~~~-~q~~Llk~lE~~~~~~~~il~tn  153 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLATT  153 (239)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CCCEEEEEECcccCCHH-HHHHHHHHHhcCCCCeEEEEEcC
Confidence            45789999999987432 34456677766555665555443

>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=95.96  E-value=0.0043  Score=54.29  Aligned_cols=39  Identities=18%  Similarity=0.359  Sum_probs=26.4

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      ..++++||||+|.+... ....+.+++...++...+|+.+
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            45679999999986433 4455677777777666555544

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.90  E-value=0.0055  Score=47.65  Aligned_cols=37  Identities=14%  Similarity=0.122  Sum_probs=25.4

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      -+++||+.||||.-. +-.+......       +.+++++-|...
T Consensus         5 ~li~GpMfsGKTt~L-i~~~~~~~~~-------g~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKSTEL-MRRVRRFQIA-------QYKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHHTT-------TCCEEEEEETTC
T ss_pred             EEEEecccCHHHHHH-HHHHHHHHHc-------CCcEEEEecccc
Confidence            578999999999853 4444433332       567899988753

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.89  E-value=0.0088  Score=46.84  Aligned_cols=87  Identities=18%  Similarity=0.142  Sum_probs=51.0

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRS  240 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (503)
                      -++.||+.||||.-. +-.+......       +.+++++-|...--         +..   .+  ... .|.       
T Consensus         5 ~~i~GpMfsGKTteL-i~~~~~~~~~-------~~kv~~ikp~~D~R---------~~~---~i--~s~-~g~-------   54 (139)
T d2b8ta1           5 EFITGPMFAGKTAEL-IRRLHRLEYA-------DVKYLVFKPKIDTR---------SIR---NI--QSR-TGT-------   54 (139)
T ss_dssp             EEEECSTTSCHHHHH-HHHHHHHHHT-------TCCEEEEEECCCGG---------GCS---SC--CCC-CCC-------
T ss_pred             EEEEccccCHHHHHH-HHHHHHHHHC-------CCcEEEEEEccccc---------ccc---eE--Ecc-cCc-------
Confidence            478899999999854 4344443332       56799999985421         110   11  001 111       


Q ss_pred             HhhCCCcEEEECcHHHHHHHHcCCCCCCCccEEEecchhHH
Q 010709          241 ELRGGVSIVVATPGRFLDHLQQGNTSLSRVSFVILDEADRM  281 (503)
Q Consensus       241 ~~~~~~~Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~l  281 (503)
                         .-..+.+.....+...+.... ...++++|.|||++-+
T Consensus        55 ---~~~~~~~~~~~~~~~~~~~~~-~~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          55 ---SLPSVEVESAPEILNYIMSNS-FNDETKVIGIDEVQFF   91 (139)
T ss_dssp             ---SSCCEEESSTHHHHHHHHSTT-SCTTCCEEEECSGGGS
T ss_pred             ---eeeeEEeccchhhHHHHHhhc-cccCcCEEEechhhhc
Confidence               113455666666666665433 3468899999999965

>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=95.85  E-value=0.0062  Score=52.65  Aligned_cols=49  Identities=24%  Similarity=0.319  Sum_probs=28.5

Q ss_pred             CCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHH
Q 010709          268 SRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMPVEIEAL  317 (503)
Q Consensus       268 ~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~  317 (503)
                      ...+++|+||+|.+... ....+..++........+++.+......+..+
T Consensus       107 ~~~~viiiDe~d~l~~~-~~~~l~~~~~~~~~~~~~i~~~~~~~~~~~~l  155 (237)
T d1sxjd2         107 PPYKIIILDEADSMTAD-AQSALRRTMETYSGVTRFCLICNYVTRIIDPL  155 (237)
T ss_dssp             CSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEESCGGGSCHHH
T ss_pred             cCceEEEEecccccCHH-HHHHHhhccccccccccccccccccccccccc
Confidence            35678999999987543 23345555666555555555444443333333

>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=95.84  E-value=0.0098  Score=51.02  Aligned_cols=43  Identities=21%  Similarity=0.349  Sum_probs=28.0

Q ss_pred             CCCCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEE
Q 010709          264 NTSLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFS  307 (503)
Q Consensus       264 ~~~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~S  307 (503)
                      .....+.+++|+||+|.+... ....+..++....+...+++.+
T Consensus        94 ~~~~~~~kiiiiDe~d~~~~~-~~~~Ll~~le~~~~~~~~~~~~  136 (227)
T d1sxjc2          94 QIFSKGFKLIILDEADAMTNA-AQNALRRVIERYTKNTRFCVLA  136 (227)
T ss_dssp             CSSSCSCEEEEETTGGGSCHH-HHHHHHHHHHHTTTTEEEEEEE
T ss_pred             cccCCCeEEEEEeccccchhh-HHHHHHHHhhhcccceeecccc
Confidence            344556789999999976543 3455667777766665444443

>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=95.83  E-value=0.0075  Score=51.72  Aligned_cols=44  Identities=23%  Similarity=0.254  Sum_probs=28.9

Q ss_pred             CCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEeeCC
Q 010709          267 LSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSATMP  311 (503)
Q Consensus       267 l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  311 (503)
                      ..+.+++|+||+|++... ....+...+...+....+++.+....
T Consensus        99 ~~~~kviiiDe~d~~~~~-~~~~ll~~~e~~~~~~~~i~~~~~~~  142 (224)
T d1sxjb2          99 PGKHKIVILDEADSMTAG-AQQALRRTMELYSNSTRFAFACNQSN  142 (224)
T ss_dssp             TTCCEEEEEESGGGSCHH-HHHTTHHHHHHTTTTEEEEEEESCGG
T ss_pred             CcceEEEEEecccccchh-HHHHHhhhccccccceeeeeccCchh
Confidence            446789999999987644 23345556666666666666665553

>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=95.80  E-value=0.016  Score=48.29  Aligned_cols=91  Identities=16%  Similarity=0.206  Sum_probs=68.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++.||+|..+-....++.++++.   ++.++.+++|.....+....+    .+..+|+|||.     .+.. .++..+
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~---p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIEv-GiDvpn  101 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIET-GIDIPT  101 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHC---TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTGG-GSCCTT
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhC---CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhhh-ccCCCC
Confidence            7889999999988888888887775   467899999988876544333    35699999993     3333 567889


Q ss_pred             ccEEEecchhHHhhCCCHHHHHHHHHhC
Q 010709          270 VSFVILDEADRMLDMGFEPQIREVMQNL  297 (503)
Q Consensus       270 ~~~vViDEaH~l~~~~~~~~~~~il~~~  297 (503)
                      ..++||..|+++.    ..++.++--+.
T Consensus       102 A~~iiI~~a~rfG----LaQLhQLRGRV  125 (211)
T d2eyqa5         102 ANTIIIERADHFG----LAQLHQLRGRV  125 (211)
T ss_dssp             EEEEEETTTTSSC----HHHHHHHHTTC
T ss_pred             CcEEEEecchhcc----cccccccccee
Confidence            9999999999864    45566665554

>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=95.79  E-value=0.018  Score=48.39  Aligned_cols=53  Identities=17%  Similarity=0.307  Sum_probs=27.2

Q ss_pred             CccEEEecchhHHhhCC---CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHHHHh
Q 010709          269 RVSFVILDEADRMLDMG---FEPQIREVMQNLPDKHQTLLFSATMPVEIEALAQEY  321 (503)
Q Consensus       269 ~~~~vViDEaH~l~~~~---~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~~~~  321 (503)
                      ++++|+||=+=+.-...   ....+.++....++.-.++.++|+...+....+..+
T Consensus        94 ~~d~IlIDTaGr~~~~~~~~~~~el~~~~~~~~~~~~~LVl~a~~~~~~~~~~~~~  149 (211)
T d1j8yf2          94 KMEIIIVDTAGRHGYGEEAALLEEMKNIYEAIKPDEVTLVIDASIGQKAYDLASKF  149 (211)
T ss_dssp             TCSEEEEECCCSCCTTCHHHHHHHHHHHHHHHCCSEEEEEEEGGGGGGHHHHHHHH
T ss_pred             CCceEEEecCCcCccchhhHHHHHHHHHHhhcCCceEEEEEecccCcchHHHHhhh
Confidence            45566666553211000   123455555556665567788888865544443333

>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=95.60  E-value=0.026  Score=48.34  Aligned_cols=43  Identities=19%  Similarity=0.265  Sum_probs=25.6

Q ss_pred             CCCCccEEEecchhHHhhCCCHHHHHHHHHhCCCCCcEEEEEee
Q 010709          266 SLSRVSFVILDEADRMLDMGFEPQIREVMQNLPDKHQTLLFSAT  309 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  309 (503)
                      ...+..++++||+|.+... ....+..++........+++.+..
T Consensus       106 ~~~~~~iilide~d~~~~~-~~~~ll~~l~~~~~~~~~i~~~n~  148 (231)
T d1iqpa2         106 GGASFKIIFLDEADALTQD-AQQALRRTMEMFSSNVRFILSCNY  148 (231)
T ss_dssp             GGCSCEEEEEETGGGSCHH-HHHHHHHHHHHTTTTEEEEEEESC
T ss_pred             cCCCceEEeehhhhhcchh-HHHHHhhhcccCCcceEEEeccCC
Confidence            3456779999999976533 233455566655555544444333

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=95.45  E-value=0.016  Score=45.34  Aligned_cols=37  Identities=19%  Similarity=0.161  Sum_probs=25.3

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHH
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRE  205 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~  205 (503)
                      -+++||+.||||+-. +-.+......       +.+++++-|...
T Consensus        10 ~lI~GpMfSGKTteL-i~~~~~~~~~-------g~~vl~i~~~~D   46 (141)
T d1xx6a1          10 EVIVGPMYSGKSEEL-IRRIRRAKIA-------KQKIQVFKPEID   46 (141)
T ss_dssp             EEEECSTTSSHHHHH-HHHHHHHHHT-------TCCEEEEEEC--
T ss_pred             EEEEeccccHHHHHH-HHHHHHhhhc-------CCcEEEEEeccc
Confidence            578999999999854 4444443332       567999999854

>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=95.14  E-value=0.13  Score=44.35  Aligned_cols=16  Identities=38%  Similarity=0.231  Sum_probs=13.9

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+++.||+|+|||..+
T Consensus        42 ~vLL~GppGtGKT~la   57 (246)
T d1d2na_          42 SVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECcCCCCHHHHH
Confidence            4999999999999743

>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=94.78  E-value=0.014  Score=52.82  Aligned_cols=64  Identities=19%  Similarity=0.292  Sum_probs=38.0

Q ss_pred             HHHHHCCCCC---CcHHHHHHHHH-HhcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHH
Q 010709          134 KDIEFHEYTR---PTSIQAQAMPV-ALSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTREL  206 (503)
Q Consensus       134 ~~l~~~~~~~---~~~~Q~~~i~~-i~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~L  206 (503)
                      ..+...|+..   ..+.+...+.. +..+++++|+|+||||||+. +-.++.+ .       +...+++.+--+.||
T Consensus       138 ~~l~~~g~~~~~~~~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~-i-------~~~~rivtiEd~~El  205 (323)
T d1g6oa_         138 SFFEEQGFYNLLDNKEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEF-I-------PKEERIISIEDTEEI  205 (323)
T ss_dssp             HHHHHTTTTTTCSSHHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGG-S-------CTTCCEEEEESSCCC
T ss_pred             HHHHHHhhhcccccHHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhh-c-------ccccceeeccchhhh
Confidence            4444444433   23444444444 44678999999999999984 2323222 1       124567777777776

>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=94.47  E-value=0.031  Score=52.21  Aligned_cols=66  Identities=30%  Similarity=0.415  Sum_probs=48.1

Q ss_pred             CCcHHHHHHHHHHh----cCCC-eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHHHHHHHHHHH
Q 010709          143 RPTSIQAQAMPVAL----SGRD-LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQQIEKEVKAL  217 (503)
Q Consensus       143 ~~~~~Q~~~i~~i~----~~~~-vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~q~~~~~~~~  217 (503)
                      .|+.-|-+||..+.    .|+. +.+.|-+||||++.  ++.+.....         ..+|||+|+...|.++++.++.+
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~--~A~l~~~~~---------rp~LvVt~~~~~A~~l~~dL~~~   76 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVT--MAKVIEALG---------RPALVLAPNKILAAQLAAEFREL   76 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHH--HHHHHHHHT---------CCEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHH--HHHHHHHhC---------CCEEEEeCCHHHHHHHHHHHHHh
Confidence            55666766776654    4544 78999999999974  333333222         34899999999999999999988


Q ss_pred             hc
Q 010709          218 SR  219 (503)
Q Consensus       218 ~~  219 (503)
                      ..
T Consensus        77 l~   78 (408)
T d1c4oa1          77 FP   78 (408)
T ss_dssp             CT
T ss_pred             cC
Confidence            63

>d1jbka_ c.37.1.20 (A:) ClpB, 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: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=94.43  E-value=0.05  Score=44.84  Aligned_cols=120  Identities=16%  Similarity=0.182  Sum_probs=62.1

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCC-CCCCCCCeEEEEcccHHHH-----HHHHHHHHHHhccC--CCceEEEE
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTP-VGRGDGPLALVLAPTRELA-----QQIEKEVKALSRSL--DSFKTAIV  229 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~-~~~~~~~~~lil~Ptr~La-----~q~~~~~~~~~~~~--~~~~~~~~  229 (503)
                      .+|++++|++|.|||...  --+.+.+.... +..-.+.+++-+-..+-+|     -++.++++.+....  ..-.+.++
T Consensus        43 k~n~lLvG~pGVGKTalv--~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILf  120 (195)
T d1jbka_          43 KNNPVLIGEPGVGKTAIV--EGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILF  120 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH--HHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEE
T ss_pred             CCCeEEEecCCcccHHHH--HHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEE
Confidence            346999999999999743  33333333222 2223345555555544332     25666666554322  11122322


Q ss_pred             EC-------------CccHHHHHH-Hhh-CCCc-EEEECcHHHHHHHHcCCCCCCCccEEEecchh
Q 010709          230 VG-------------GTNIAEQRS-ELR-GGVS-IVVATPGRFLDHLQQGNTSLSRVSFVILDEAD  279 (503)
Q Consensus       230 ~~-------------~~~~~~~~~-~~~-~~~~-Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH  279 (503)
                      .+             +....+... .+. +... |.-+||+.+.+.+.+..-..+.|..|-|+|-.
T Consensus       121 IDeih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~aL~rrF~~I~V~Ep~  186 (195)
T d1jbka_         121 IDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPS  186 (195)
T ss_dssp             EETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHHHHTTEEEEECCCCC
T ss_pred             cchHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHHHHhcCCEeecCCCC
Confidence            22             111112111 111 2334 44567787777766654456678888888865

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

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: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=94.26  E-value=0.032  Score=52.25  Aligned_cols=38  Identities=21%  Similarity=0.266  Sum_probs=26.9

Q ss_pred             cHHHHHHHHHHhcCCC--eEEEccCCCchhHHhHHHHHHHH
Q 010709          145 TSIQAQAMPVALSGRD--LLGCAETGSGKTAAFTIPMIQHC  183 (503)
Q Consensus       145 ~~~Q~~~i~~i~~~~~--vii~~~TGsGKTl~~~lp~l~~~  183 (503)
                      .+.|.+.+..+.....  +|++||||||||+.. ..++.++
T Consensus       143 ~~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~  182 (401)
T d1p9ra_         143 TAHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQEL  182 (401)
T ss_dssp             CHHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHH
T ss_pred             cHHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhh
Confidence            3456666666665544  999999999999864 4466654

>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=93.92  E-value=0.3  Score=39.15  Aligned_cols=76  Identities=17%  Similarity=0.255  Sum_probs=59.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.|+++.-+..+++.+.+.     ++++..++|+....+....+    .+..+|+|+|     +.+.. .++..+
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT-----~v~~~-GiDip~   99 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGI-----NLLRE-GLDIPE   99 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEES-----CCCCT-TCCCTT
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEee-----eeeee-eccCCC
Confidence            678999999999999988888875     48899999998876554433    3679999999     33333 567889


Q ss_pred             ccEEEecchhH
Q 010709          270 VSFVILDEADR  280 (503)
Q Consensus       270 ~~~vViDEaH~  280 (503)
                      +++||+=.++.
T Consensus       100 V~~Vi~~~~~~  110 (174)
T d1c4oa2         100 VSLVAILDADK  110 (174)
T ss_dssp             EEEEEETTTTS
T ss_pred             CcEEEEecccc
Confidence            99999876664

>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=93.62  E-value=0.12  Score=44.89  Aligned_cols=122  Identities=19%  Similarity=0.164  Sum_probs=64.1

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHH-----HHHHHHHHHHhccCCC-ceEEEEEC
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELA-----QQIEKEVKALSRSLDS-FKTAIVVG  231 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La-----~q~~~~~~~~~~~~~~-~~~~~~~~  231 (503)
                      .+|++++||.|.|||... -.+...+....-+....+..++.+-+.+-++     -++.++++.+...... -.+.++.+
T Consensus        39 k~n~lLVG~~GvGKTalv-~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiD  117 (268)
T d1r6bx2          39 KNNPLLVGESGVGKTAIA-EGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFID  117 (268)
T ss_dssp             SCEEEEECCTTSSHHHHH-HHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEET
T ss_pred             cCCcEEECCCCCcHHHHH-HHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhccCCceEEec
Confidence            356999999999999743 2233333332222223345566655555443     2345555544432211 12333322


Q ss_pred             C-----------ccHHHHHHHhh-----CCCc-EEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          232 G-----------TNIAEQRSELR-----GGVS-IVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       232 ~-----------~~~~~~~~~~~-----~~~~-Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      .           ....+....+.     +... |.-+||+.+...+.+..-..+.|..|-|+|-+.
T Consensus       118 eih~l~~~g~~~g~~~d~a~~Lkp~L~rg~i~vIgatT~eey~~~~e~d~al~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         118 EIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSI  183 (268)
T ss_dssp             TTTTTTTSCCSSSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCH
T ss_pred             chHHHhcCCCCCCccccHHHHhhHHHhCCCCeEEEeCCHHHHHHHHhhcHHHHhhhcccccCCCCH
Confidence            1           11122233332     2233 456678888766666555677899999999983

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

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: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.12  E-value=0.41  Score=37.53  Aligned_cols=53  Identities=17%  Similarity=0.221  Sum_probs=40.0

Q ss_pred             CCCCccEEEecchhHHhhCC--CHHHHHHHHHhCCCCCcEEEEEeeCCHHHHHHH
Q 010709          266 SLSRVSFVILDEADRMLDMG--FEPQIREVMQNLPDKHQTLLFSATMPVEIEALA  318 (503)
Q Consensus       266 ~l~~~~~vViDEaH~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~~~~~~  318 (503)
                      .-..+++||+||+-..++.+  -...+..+++..|+..-+|+..-.+|+++.+.+
T Consensus        91 ~~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~A  145 (157)
T d1g5ta_          91 ADPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLA  145 (157)
T ss_dssp             TCTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHC
T ss_pred             hcCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhc
Confidence            34568999999999888877  456778888887777777766666777766543

>d1um8a_ c.37.1.20 (A:) ClpX {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: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=93.07  E-value=0.043  Score=50.48  Aligned_cols=17  Identities=41%  Similarity=0.446  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .+++.+||||+|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999743

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

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: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=92.82  E-value=0.041  Score=49.50  Aligned_cols=18  Identities=33%  Similarity=0.423  Sum_probs=15.6

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      .+.++++||||+|||+.+
T Consensus        49 ~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          49 PKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999744

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {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: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=92.60  E-value=0.62  Score=42.68  Aligned_cols=121  Identities=20%  Similarity=0.197  Sum_probs=60.2

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH-----HHHHHHHHHhccCC--CceEEEEE
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ-----QIEKEVKALSRSLD--SFKTAIVV  230 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~-----q~~~~~~~~~~~~~--~~~~~~~~  230 (503)
                      .+|++++|+.|.|||.... -+...+....-+..-.+.+++-+-+.+-+|-     ++.+.++.+.....  .-.+.++.
T Consensus        43 k~n~llvG~~GvGKtaiv~-~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfi  121 (387)
T d1qvra2          43 KNNPVLIGEPGVGKTAIVE-GLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFI  121 (387)
T ss_dssp             CCCCEEEECTTSCHHHHHH-HHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEE
T ss_pred             CCCCeEECCCCCCHHHHHH-HHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEe
Confidence            3569999999999997432 2333333332233334566666666655542     55666655543210  11222222


Q ss_pred             CCc-------------cHHHHH-HHh-hCCCc-EEEECcHHHHHHHHcCCCCCCCccEEEecchhH
Q 010709          231 GGT-------------NIAEQR-SEL-RGGVS-IVVATPGRFLDHLQQGNTSLSRVSFVILDEADR  280 (503)
Q Consensus       231 ~~~-------------~~~~~~-~~~-~~~~~-Ilv~Tp~~l~~~l~~~~~~l~~~~~vViDEaH~  280 (503)
                      +..             +..... -.+ ++... |.-+||+-+. .+.+..-..+.|..|-|+|-+.
T Consensus       122 de~h~l~~~g~~~g~~d~a~~Lkp~L~rg~~~~I~~tT~~ey~-~~e~d~al~rrF~~v~v~ep~~  186 (387)
T d1qvra2         122 DELHTVVGAGKAEGAVDAGNMLKPALARGELRLIGATTLDEYR-EIEKDPALERRFQPVYVDEPTV  186 (387)
T ss_dssp             CCC-------------------HHHHHTTCCCEEEEECHHHHH-HHTTCTTTCSCCCCEEECCCCH
T ss_pred             ccHHHHhcCCCCCCcccHHHHHHHHHhCCCcceeeecCHHHHH-HhcccHHHHHhcccccCCCCcH
Confidence            211             110100 111 23344 5566777775 4566555667899999999883

>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=92.08  E-value=0.17  Score=41.07  Aligned_cols=76  Identities=21%  Similarity=0.315  Sum_probs=58.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.++++.-+..++..+++.     ++.+..++|+....+....+    .+..+|+|+|     +.+.+ .++..+
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaT-----dv~~r-GiDip~   99 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGI-----NLLRE-GLDIPE   99 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEES-----CCCSS-SCCCTT
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEeh-----hHHHc-cCCCCC
Confidence            567999999999988888777765     48899999999876654444    2679999999     33333 568889


Q ss_pred             ccEEEecchhH
Q 010709          270 VSFVILDEADR  280 (503)
Q Consensus       270 ~~~vViDEaH~  280 (503)
                      +++||.-++..
T Consensus       100 v~~VI~~d~p~  110 (181)
T d1t5la2         100 VSLVAILDADK  110 (181)
T ss_dssp             EEEEEETTTTS
T ss_pred             CCEEEEecCCc
Confidence            99999887764

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

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: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=91.89  E-value=0.062  Score=50.74  Aligned_cols=27  Identities=22%  Similarity=0.306  Sum_probs=19.7

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      ..+|+|+.||||+|||+.  .-.|..++.
T Consensus        48 ~ksNILliGPTGvGKTlL--Ar~LAk~l~   74 (443)
T d1g41a_          48 TPKNILMIGPTGVGKTEI--ARRLAKLAN   74 (443)
T ss_dssp             CCCCEEEECCTTSSHHHH--HHHHHHHTT
T ss_pred             ccccEEEECCCCCCHHHH--HHHHHHHhC
Confidence            356899999999999974  334555443

>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=91.34  E-value=0.6  Score=36.89  Aligned_cols=73  Identities=18%  Similarity=0.302  Sum_probs=54.3

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      ..++||.|.++.-+.++++.+...     ++.+..++|+....+....+    .+..+|+|+|.     .+.+ .+++.+
T Consensus        27 ~~k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v~~r-GiDi~~   95 (162)
T d1fuka_          27 VTQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLAR-GIDVQQ   95 (162)
T ss_dssp             CSCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GGTT-TCCCCS
T ss_pred             CCcEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----cccc-cccCCC
Confidence            456999999999999988877664     47788899988876554433    25688999994     3333 567888


Q ss_pred             ccEEEecc
Q 010709          270 VSFVILDE  277 (503)
Q Consensus       270 ~~~vViDE  277 (503)
                      +++||.=+
T Consensus        96 v~~VI~~d  103 (162)
T d1fuka_          96 VSLVINYD  103 (162)
T ss_dssp             CSEEEESS
T ss_pred             ceEEEEec
Confidence            88888744

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=91.31  E-value=0.059  Score=42.78  Aligned_cols=19  Identities=21%  Similarity=0.335  Sum_probs=16.1

Q ss_pred             CCCeEEEccCCCchhHHhH
Q 010709          158 GRDLLGCAETGSGKTAAFT  176 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~  176 (503)
                      .+++++.|++|+|||+.+.
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4689999999999998653

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

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: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=91.24  E-value=0.065  Score=47.02  Aligned_cols=15  Identities=27%  Similarity=0.224  Sum_probs=12.2

Q ss_pred             eEEEccCCCchhHHh
Q 010709          161 LLGCAETGSGKTAAF  175 (503)
Q Consensus       161 vii~~~TGsGKTl~~  175 (503)
                      ++++||+|+|||++.
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            356799999999864

>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=91.21  E-value=0.21  Score=42.56  Aligned_cols=37  Identities=24%  Similarity=0.364  Sum_probs=24.2

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      |.-++|.|++|+|||+..+ -++......       +..+++++-
T Consensus        26 gsl~li~G~pGsGKT~l~~-qia~~~~~~-------~~~~~~is~   62 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVS-RFVENACAN-------KERAILFAY   62 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHH-HHHHHHHTT-------TCCEEEEES
T ss_pred             CeEEEEEeCCCCCHHHHHH-HHHHHHHHh-------ccccceeec
Confidence            4569999999999997543 333333332       455777763

>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=91.13  E-value=0.096  Score=42.37  Aligned_cols=26  Identities=19%  Similarity=0.190  Sum_probs=18.6

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      ++++|.||+|+|||+.. ..++..+..
T Consensus         2 k~v~ItG~~GtGKTtl~-~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLI-HKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHHH-HHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHH-HHHHHHHHH
Confidence            67999999999999843 334444433

>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=90.50  E-value=0.76  Score=35.89  Aligned_cols=72  Identities=15%  Similarity=0.301  Sum_probs=51.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||-|+++.-+.++++.+++.     ++.+..++++....+....+    .+...|+|+|.     .+.+ .+++..
T Consensus        28 ~~k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-----~~~~-Gid~~~   96 (155)
T d1hv8a2          28 EFYGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSR-GIDVND   96 (155)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHH-HCCCSC
T ss_pred             CCCEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehh-----HHhh-hhhhcc
Confidence            456899999999999888888765     36788888887765544333    35689999993     2222 456777


Q ss_pred             ccEEEec
Q 010709          270 VSFVILD  276 (503)
Q Consensus       270 ~~~vViD  276 (503)
                      +++||.=
T Consensus        97 v~~Vi~~  103 (155)
T d1hv8a2          97 LNCVINY  103 (155)
T ss_dssp             CSEEEES
T ss_pred             CcEEEEe
Confidence            8887753

>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=90.50  E-value=0.57  Score=38.76  Aligned_cols=71  Identities=18%  Similarity=0.218  Sum_probs=55.0

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc-----cc-ccCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD-----VA-SRGLDVMG  442 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~-~~Gldip~  442 (503)
                      ...++||.|++++.|.++.+.+...    +..+..++|+.+..++.+.++     ..+|||+|.     .+ ...+++.+
T Consensus        71 ~~~~~lil~pt~~l~~q~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~l~-----~~~IlV~TP~~l~~~l~~~~~~~~~  145 (208)
T d1hv8a1          71 NGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK-----NANIVVGTPGRILDHINRGTLNLKN  145 (208)
T ss_dssp             SSCCEEEECSCHHHHHHHHHHHHHHHCSSCCCEEEECTTSCHHHHHHHHH-----TCSEEEECHHHHHHHHHTTCSCTTS
T ss_pred             cCcceEEEeeccccchhhhhhhhhhcccCCeEEEEeeCCCChHHHHHhcC-----CCCEEEEChHHHHHHHHcCCCCccc
Confidence            4457999999999999988887653    678889999998877665543     368999993     23 44668899


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      ++++|.
T Consensus       146 l~~lVi  151 (208)
T d1hv8a1         146 VKYFIL  151 (208)
T ss_dssp             CCEEEE
T ss_pred             CcEEEE
Confidence            998875

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal 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: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.13  E-value=0.35  Score=45.79  Aligned_cols=61  Identities=15%  Similarity=0.076  Sum_probs=40.3

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHhcCCC----CCCCCCeEEEEcccHHHHHHHHHHHHHHh
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVAQTPV----GRGDGPLALVLAPTRELAQQIEKEVKALS  218 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~----~~~~~~~~lil~Ptr~La~q~~~~~~~~~  218 (503)
                      ...+||.|.-|||||.+..--++..+......    ..-....+|+|+=|+..|..+.+++....
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L   80 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI   80 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHH
Confidence            44689999999999987544444443332111    11123459999999988888888775543

>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=89.64  E-value=0.86  Score=38.08  Aligned_cols=72  Identities=15%  Similarity=0.235  Sum_probs=55.7

Q ss_pred             CCCcEEEEEcchhhHHHHHHHHHHC----CCeEEEEcCCCCHHHHHHHHHHHhcCCCcEEEEcc------ccccCCCCCC
Q 010709          373 PFPLTIVFVERKTRCDEVSEALVAE----GLHAVALHGGRNQSDRESALRDFRNGSTNILVATD------VASRGLDVMG  442 (503)
Q Consensus       373 ~~~~~lIF~~~~~~~~~l~~~L~~~----~~~v~~lh~~~~~~~r~~~~~~f~~g~~~vLvaT~------~~~~Gldip~  442 (503)
                      ....++|++++++.|.++++.+...    ++.+..++|+.+..+....++.    ...|||+|.      +-...+++.+
T Consensus        84 ~~~~~lil~PtreLa~Qi~~~~~~l~~~~~i~~~~~~g~~~~~~~~~~l~~----~~~Ilv~TPgrl~~~~~~~~~~~~~  159 (222)
T d2j0sa1          84 RETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY----GQHVVAGTPGRVFDMIRRRSLRTRA  159 (222)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTTCCEEEECTTSCHHHHHHHHHH----CCSEEEECHHHHHHHHHTTSSCCTT
T ss_pred             cCceeEEecchHHHHHHHHHHHHHHhCccceeEEEEeecccchhhHHHhcc----CCeEEeCCCCcHHhccccccccccc
Confidence            3446999999999999999888654    5788899999987776655542    368999993      2256778889


Q ss_pred             CCEEEE
Q 010709          443 VAHVVN  448 (503)
Q Consensus       443 v~~VI~  448 (503)
                      ++++|.
T Consensus       160 l~~lVl  165 (222)
T d2j0sa1         160 IKMLVL  165 (222)
T ss_dssp             CCEEEE
T ss_pred             ceeeee
Confidence            999884

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {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: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=89.35  E-value=0.27  Score=41.75  Aligned_cols=17  Identities=29%  Similarity=0.315  Sum_probs=14.9

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||..+
T Consensus        36 ~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2          36 DHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CCEEEESSTTSSHHHHH
T ss_pred             CeEEEECCCCCcHHHHH
Confidence            46999999999999854

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {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: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=89.13  E-value=0.076  Score=41.65  Aligned_cols=16  Identities=31%  Similarity=0.277  Sum_probs=13.5

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      -++++|++|||||+.+
T Consensus         4 lIii~G~pGsGKTTla   19 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999843

>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=88.92  E-value=1.1  Score=35.55  Aligned_cols=75  Identities=15%  Similarity=0.195  Sum_probs=55.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.|.++.-+..++..+...+     +.+..++|+....+....+    .+..+|+|+|.     .+. ..+++..
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~~g-----~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td-----~~~-~Gid~~~  100 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITDLG-----YSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD-----LLT-RGIDIQA  100 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHHT-----CCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS-----CSS-SSCCCTT
T ss_pred             CCceEEEEeeeehhhHhHHhhhccc-----ccccccccccchhhhhhhhhhcccCccccccchh-----Hhh-hccccce
Confidence            5679999999999988888887763     7788888888765544333    25689999994     222 3567888


Q ss_pred             ccEEEecchh
Q 010709          270 VSFVILDEAD  279 (503)
Q Consensus       270 ~~~vViDEaH  279 (503)
                      +++||.=++.
T Consensus       101 v~~VI~~d~p  110 (171)
T d1s2ma2         101 VNVVINFDFP  110 (171)
T ss_dssp             EEEEEESSCC
T ss_pred             eEEEEecCCc
Confidence            8888866554

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=88.78  E-value=0.084  Score=42.40  Aligned_cols=18  Identities=33%  Similarity=0.505  Sum_probs=15.3

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      +.++++.|++|+|||+++
T Consensus         5 ~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           5 GINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHH
Confidence            456999999999999854

>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=88.67  E-value=0.18  Score=47.35  Aligned_cols=45  Identities=20%  Similarity=0.349  Sum_probs=32.0

Q ss_pred             hcCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcccHHHHH
Q 010709          156 LSGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAPTRELAQ  208 (503)
Q Consensus       156 ~~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~Ptr~La~  208 (503)
                      ...++++|.|+||+|||..+ ..++..+..+       +..++|+=|.-++..
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~~~-------g~~~iiiD~kge~~~   92 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGLLR-------GDRMVIVDPNGDMLS   92 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHHHT-------TCEEEEEEETTHHHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHHhC-------CCCEEEEeCChhHHH
Confidence            35678999999999999764 4455555553       455777778877643

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=88.29  E-value=0.12  Score=41.20  Aligned_cols=17  Identities=29%  Similarity=0.311  Sum_probs=14.6

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .+++++|++|||||+.+
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46899999999999854

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=87.96  E-value=0.1  Score=41.78  Aligned_cols=16  Identities=19%  Similarity=0.245  Sum_probs=13.8

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      -+++.|++|+|||+.+
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999854

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=87.93  E-value=0.075  Score=42.79  Aligned_cols=19  Identities=37%  Similarity=0.454  Sum_probs=15.7

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|+-+++.|++|||||+.+
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4566889999999999853

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

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: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=87.77  E-value=0.13  Score=44.52  Aligned_cols=17  Identities=24%  Similarity=0.286  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||.+.
T Consensus        44 ~~lll~GppGtGKT~l~   60 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTL   60 (276)
T ss_dssp             CEEEEECCTTSSHHHHH
T ss_pred             CceEEECCCCCCHHHHH
Confidence            46999999999999754

>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=87.63  E-value=0.66  Score=36.91  Aligned_cols=74  Identities=14%  Similarity=0.112  Sum_probs=53.0

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.|+++.-+..+.+.+.+.     ++.+..++|+....+....+    .+..+|+|+|.     .+. ..+.+..
T Consensus        27 ~~k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~-----~~~-~Gid~~~   95 (168)
T d1t5ia_          27 FNQVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LFG-RGMDIER   95 (168)
T ss_dssp             CSSEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-----CCS-TTCCGGG
T ss_pred             CCeEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeeccc-----ccc-chhhccc
Confidence            457999999999888888777664     36788899988776554433    25688999993     222 2556777


Q ss_pred             ccEEEecch
Q 010709          270 VSFVILDEA  278 (503)
Q Consensus       270 ~~~vViDEa  278 (503)
                      +++||.=+.
T Consensus        96 ~~~vi~~~~  104 (168)
T d1t5ia_          96 VNIAFNYDM  104 (168)
T ss_dssp             CSEEEESSC
T ss_pred             chhhhhhhc
Confidence            887776554

>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=87.59  E-value=0.8  Score=37.59  Aligned_cols=71  Identities=18%  Similarity=0.249  Sum_probs=51.4

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||-++|+.-+..++..++..     ++.+..++|+....+....+    .+..+|+|+|.     .+.. .+++.+
T Consensus        30 ~~~~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~~~~-GiD~p~   98 (200)
T d1oywa3          30 GKSGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AFGM-GINKPN   98 (200)
T ss_dssp             TCCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TSCT-TTCCTT
T ss_pred             CCCEEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----hhhh-ccCCCC
Confidence            456999999999999888877764     47788889988765543333    25688999993     2222 566778


Q ss_pred             ccEEEe
Q 010709          270 VSFVIL  275 (503)
Q Consensus       270 ~~~vVi  275 (503)
                      +++||.
T Consensus        99 v~~VI~  104 (200)
T d1oywa3          99 VRFVVH  104 (200)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            888874

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {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: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=87.35  E-value=0.15  Score=43.47  Aligned_cols=17  Identities=35%  Similarity=0.346  Sum_probs=14.8

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      .++++.||+|+|||+.+
T Consensus        36 ~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2          36 EHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            46999999999999854

>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=87.26  E-value=1  Score=35.73  Aligned_cols=74  Identities=15%  Similarity=0.269  Sum_probs=54.9

Q ss_pred             CCeEEEEcccHHHHHHHHHHHHHHhccCCCceEEEEECCccHHHHHHHh----hCCCcEEEECcHHHHHHHHcCCCCCCC
Q 010709          194 GPLALVLAPTRELAQQIEKEVKALSRSLDSFKTAIVVGGTNIAEQRSEL----RGGVSIVVATPGRFLDHLQQGNTSLSR  269 (503)
Q Consensus       194 ~~~~lil~Ptr~La~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ilv~Tp~~l~~~l~~~~~~l~~  269 (503)
                      +.++||.|.++.-+..+++.++..+     +.+..++|+....+....+    .+..+|+|+|.     .+.+ .+++.+
T Consensus        34 ~~k~iiF~~~~~~~~~~~~~l~~~~-----~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td-----~~~r-GiDi~~  102 (168)
T d2j0sa2          34 ITQAVIFCNTKRKVDWLTEKMREAN-----FTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VWAR-GLDVPQ  102 (168)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT-----CCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GGSS-SCCCTT
T ss_pred             CCceEEEeeeHHHHHHHHHHhhhcc-----cchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc-----hhcc-cccccC
Confidence            4679999999999998888887753     6678888888776554433    35689999993     3433 667888


Q ss_pred             ccEEEecch
Q 010709          270 VSFVILDEA  278 (503)
Q Consensus       270 ~~~vViDEa  278 (503)
                      +++||.=++
T Consensus       103 v~~VIn~d~  111 (168)
T d2j0sa2         103 VSLIINYDL  111 (168)
T ss_dssp             EEEEEESSC
T ss_pred             cceEEEecC
Confidence            888886444

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=87.20  E-value=0.083  Score=42.88  Aligned_cols=18  Identities=17%  Similarity=0.193  Sum_probs=15.2

Q ss_pred             CCCeEEEccCCCchhHHh
Q 010709          158 GRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~  175 (503)
                      -+.+++.|++|+|||+.+
T Consensus         7 ~K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLV   24 (192)
T ss_dssp             CEEEEEECCTTSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            356999999999999843

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {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 C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.55  E-value=0.48  Score=40.43  Aligned_cols=52  Identities=13%  Similarity=0.079  Sum_probs=28.3

Q ss_pred             CcccCCCCHHHHHHHHHCCCCCCcHHH-HHHHHH-----HhcCCCeEEEccCCCchhHHh
Q 010709          122 SFTDMCLHPSIMKDIEFHEYTRPTSIQ-AQAMPV-----ALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~~~~~~~~~Q-~~~i~~-----i~~~~~vii~~~TGsGKTl~~  175 (503)
                      +|+++-..+...+.|...--.  +... ...+..     ....+.+++.||+|+|||+++
T Consensus        12 ~~~dlig~~~~~~~L~~~l~~--~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2          12 NLQQVCGNKGSVMKLKNWLAN--WENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             SGGGCCSCHHHHHHHHHHHHT--HHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             CHHHhcCCHHHHHHHHHHHHh--hhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            578887778777776542000  0000 000000     001245999999999999854

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=86.35  E-value=0.13  Score=41.12  Aligned_cols=19  Identities=16%  Similarity=0.270  Sum_probs=15.5

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .++-++++|++|+|||+.+
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456889999999999854

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=86.11  E-value=0.16  Score=40.33  Aligned_cols=25  Identities=16%  Similarity=0.219  Sum_probs=18.0

Q ss_pred             CCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          159 RDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      +++++.|++|+|||+..  -++...+.
T Consensus         1 k~I~liG~~GsGKsTi~--k~La~~l~   25 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLA--RALAKDLD   25 (161)
T ss_dssp             CCEEEECCTTSCHHHHH--HHHHHHHT
T ss_pred             CcEEEECCCCCCHHHHH--HHHHHHhC
Confidence            57899999999999854  34444333

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=85.50  E-value=0.36  Score=38.81  Aligned_cols=26  Identities=12%  Similarity=0.181  Sum_probs=18.3

Q ss_pred             CCCeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          158 GRDLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      ++-+++.|++|+|||+.  .-.|...+.
T Consensus         1 ~kiI~i~G~~GsGKsT~--~~~L~~~l~   26 (190)
T d1khta_           1 NKVVVVTGVPGVGSTTS--SQLAMDNLR   26 (190)
T ss_dssp             CCEEEEECCTTSCHHHH--HHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHH--HHHHHHHHH
Confidence            35589999999999984  334444443

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

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: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=85.12  E-value=0.37  Score=41.91  Aligned_cols=39  Identities=18%  Similarity=0.184  Sum_probs=25.0

Q ss_pred             cCCCeEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          157 SGRDLLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      .|.-+++.|+||+|||...+-.+++....+       +.+++++..
T Consensus        34 ~G~l~vi~G~~G~GKT~~~~~la~~~a~~~-------g~~v~~~s~   72 (277)
T d1cr2a_          34 GGEVIMVTSGSGMGKSTFVRQQALQWGTAM-------GKKVGLAML   72 (277)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHHHTS-------CCCEEEEES
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHhhhhhc-------ccceeEeee
Confidence            566699999999999964433223222232       456777764

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=85.03  E-value=0.12  Score=41.55  Aligned_cols=19  Identities=26%  Similarity=0.219  Sum_probs=15.8

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|..++++|.+|+|||+.+
T Consensus         5 ~g~~I~l~G~~GsGKTTia   23 (183)
T d1m8pa3           5 QGFTIFLTGYMNSGKDAIA   23 (183)
T ss_dssp             CCEEEEEECSTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            4556889999999999865

>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=84.98  E-value=0.29  Score=39.20  Aligned_cols=24  Identities=25%  Similarity=0.371  Sum_probs=17.1

Q ss_pred             CeEEEccCCCchhHHhHHHHHHHHHh
Q 010709          160 DLLGCAETGSGKTAAFTIPMIQHCVA  185 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~lp~l~~~~~  185 (503)
                      .++|.||+|+|||+  ++-.+...+.
T Consensus         2 ki~I~G~~G~GKST--Ll~~i~~~l~   25 (178)
T d1ye8a1           2 KIIITGEPGVGKTT--LVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHH--HHHHHHHHHG
T ss_pred             EEEEECCCCcHHHH--HHHHHHhcCC
Confidence            37899999999998  3444444443

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {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: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=84.38  E-value=0.2  Score=39.92  Aligned_cols=15  Identities=33%  Similarity=0.377  Sum_probs=13.5

Q ss_pred             eEEEccCCCchhHHh
Q 010709          161 LLGCAETGSGKTAAF  175 (503)
Q Consensus       161 vii~~~TGsGKTl~~  175 (503)
                      ++++|++|||||+.+
T Consensus         9 ivl~G~~GsGKsT~a   23 (171)
T d1knqa_           9 YVLMGVSGSGKSAVA   23 (171)
T ss_dssp             EEEECSTTSCHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999999864

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=84.21  E-value=0.19  Score=43.64  Aligned_cols=16  Identities=38%  Similarity=0.405  Sum_probs=13.8

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+++.||+|+|||..+
T Consensus        34 ~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEECCTTSCTHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3899999999999843

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {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: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=83.48  E-value=0.58  Score=36.81  Aligned_cols=34  Identities=26%  Similarity=0.255  Sum_probs=21.3

Q ss_pred             eEEEccCCCchhHHhHHHHHHHHHhcCCCCCCCCCeEEEEcc
Q 010709          161 LLGCAETGSGKTAAFTIPMIQHCVAQTPVGRGDGPLALVLAP  202 (503)
Q Consensus       161 vii~~~TGsGKTl~~~lp~l~~~~~~~~~~~~~~~~~lil~P  202 (503)
                      +.|+|+.|||||+.. --++.++..+       |.++.++..
T Consensus         5 i~itG~~GSGKTTL~-~~L~~~l~~~-------g~~v~v~~~   38 (170)
T d1np6a_           5 LAFAAWSGTGKTTLL-KKLIPALCAR-------GIRPGLIKH   38 (170)
T ss_dssp             EEEECCTTSCHHHHH-HHHHHHHHHT-------TCCEEEEEE
T ss_pred             EEEEcCCCCCHHHHH-HHHHHHHHHC-------CCeEEEecc
Confidence            689999999999843 3344443332       445555543

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=83.07  E-value=0.32  Score=39.62  Aligned_cols=19  Identities=21%  Similarity=0.242  Sum_probs=15.5

Q ss_pred             CCCeEEEccCCCchhHHhH
Q 010709          158 GRDLLGCAETGSGKTAAFT  176 (503)
Q Consensus       158 ~~~vii~~~TGsGKTl~~~  176 (503)
                      |-.+++.||+|||||+++-
T Consensus         3 ~~riil~G~pGSGKsT~a~   21 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAP   21 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHH
Confidence            4468889999999999653

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=82.75  E-value=0.38  Score=38.37  Aligned_cols=17  Identities=18%  Similarity=0.221  Sum_probs=14.7

Q ss_pred             CCeEEEccCCCchhHHh
Q 010709          159 RDLLGCAETGSGKTAAF  175 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~~  175 (503)
                      +.+++.|++|+|||+++
T Consensus         3 ~~Iil~G~~GsGKSTia   19 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVG   19 (170)
T ss_dssp             CCEEEESCTTSSHHHHH
T ss_pred             CCEEEECCCCCCHHHHH
Confidence            56889999999999854

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {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: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.34  E-value=0.27  Score=39.52  Aligned_cols=14  Identities=21%  Similarity=0.432  Sum_probs=12.9

Q ss_pred             eEEEccCCCchhHH
Q 010709          161 LLGCAETGSGKTAA  174 (503)
Q Consensus       161 vii~~~TGsGKTl~  174 (503)
                      +|++|++|||||+.
T Consensus        17 iil~G~pGsGKST~   30 (172)
T d1yj5a2          17 VVAVGFPGAGKSTF   30 (172)
T ss_dssp             EEEECCTTSSHHHH
T ss_pred             EEEECCCCCCHHHH
Confidence            89999999999974

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=82.31  E-value=0.32  Score=39.60  Aligned_cols=17  Identities=18%  Similarity=0.241  Sum_probs=14.5

Q ss_pred             CeEEEccCCCchhHHhH
Q 010709          160 DLLGCAETGSGKTAAFT  176 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~  176 (503)
                      .+++.||+|||||+.+.
T Consensus         5 ~I~i~GppGsGKsT~a~   21 (189)
T d1zaka1           5 KVMISGAPASGKGTQCE   21 (189)
T ss_dssp             CEEEEESTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            48899999999998653

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.28  E-value=0.48  Score=39.99  Aligned_cols=19  Identities=21%  Similarity=0.113  Sum_probs=15.6

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|+-+++.|++|+|||+..
T Consensus        33 ~G~~~li~G~pGsGKT~l~   51 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLC   51 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHH
Confidence            4567999999999999743

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=82.27  E-value=0.31  Score=39.21  Aligned_cols=17  Identities=24%  Similarity=0.294  Sum_probs=14.4

Q ss_pred             CeEEEccCCCchhHHhH
Q 010709          160 DLLGCAETGSGKTAAFT  176 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~  176 (503)
                      +++|.||+|||||+.+.
T Consensus         2 ~I~i~G~pGSGKsT~a~   18 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAE   18 (182)
T ss_dssp             EEEEECSTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            37899999999999653

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.22  E-value=0.25  Score=39.97  Aligned_cols=17  Identities=24%  Similarity=0.280  Sum_probs=14.4

Q ss_pred             CeEEEccCCCchhHHhH
Q 010709          160 DLLGCAETGSGKTAAFT  176 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~~  176 (503)
                      ++++.||+|||||+++-
T Consensus         2 ~I~i~G~pGsGKsT~a~   18 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAV   18 (181)
T ss_dssp             EEEEECCTTSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999999653

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=81.72  E-value=0.34  Score=39.66  Aligned_cols=21  Identities=19%  Similarity=0.232  Sum_probs=16.9

Q ss_pred             HhcCCCeEEEccCCCchhHHh
Q 010709          155 ALSGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       155 i~~~~~vii~~~TGsGKTl~~  175 (503)
                      +...+-+++.||+|||||+++
T Consensus         5 ~~~~~iI~l~G~pGSGKsT~a   25 (194)
T d3adka_           5 LKKSKIIFVVGGPGSGKGTQC   25 (194)
T ss_dssp             HHTSCEEEEEECTTSSHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHH
Confidence            345566889999999999865

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=81.57  E-value=0.38  Score=38.84  Aligned_cols=16  Identities=19%  Similarity=0.289  Sum_probs=13.9

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+++.||+|||||+++
T Consensus         2 ~I~i~G~pGSGKsT~a   17 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQA   17 (182)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999965

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {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: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.51  E-value=0.29  Score=40.07  Aligned_cols=16  Identities=19%  Similarity=0.270  Sum_probs=13.8

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      -+++.||+|||||+++
T Consensus        10 iI~i~GppGSGKsT~a   25 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQC   25 (196)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3888999999999865

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {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: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=81.49  E-value=0.28  Score=39.53  Aligned_cols=16  Identities=13%  Similarity=0.098  Sum_probs=13.9

Q ss_pred             CeEEEccCCCchhHHh
Q 010709          160 DLLGCAETGSGKTAAF  175 (503)
Q Consensus       160 ~vii~~~TGsGKTl~~  175 (503)
                      .+++.||+|||||+++
T Consensus         2 ~I~i~G~pGSGKsT~~   17 (179)
T d1e4va1           2 RIILLGAPVAGKGTQA   17 (179)
T ss_dssp             EEEEEESTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4788999999999965

>d1tf7a1 c.37.1.11 (A:14-255) 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=81.25  E-value=0.69  Score=38.67  Aligned_cols=19  Identities=37%  Similarity=0.448  Sum_probs=15.8

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|.-++|.|++|+|||..+
T Consensus        25 ~G~~~~I~G~~G~GKT~la   43 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFS   43 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHH
Confidence            4566999999999999754

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {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: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=80.95  E-value=0.55  Score=39.86  Aligned_cols=19  Identities=32%  Similarity=0.128  Sum_probs=15.7

Q ss_pred             cCCCeEEEccCCCchhHHh
Q 010709          157 SGRDLLGCAETGSGKTAAF  175 (503)
Q Consensus       157 ~~~~vii~~~TGsGKTl~~  175 (503)
                      .|+-++|.|++|+|||+..
T Consensus        35 ~G~~~li~G~pGsGKT~~~   53 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLA   53 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHH
Confidence            3456999999999999744

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {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: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.55  E-value=0.37  Score=39.17  Aligned_cols=16  Identities=25%  Similarity=0.511  Sum_probs=14.0

Q ss_pred             CCeEEEccCCCchhHH
Q 010709          159 RDLLGCAETGSGKTAA  174 (503)
Q Consensus       159 ~~vii~~~TGsGKTl~  174 (503)
                      +-++++||+|+|||..
T Consensus         2 rpIvl~GpsG~GK~tl   17 (186)
T d1gkya_           2 RPIVISGPSGTGKSTL   17 (186)
T ss_dssp             CCEEEECCTTSSHHHH
T ss_pred             CeEEEECCCCCCHHHH
Confidence            4589999999999983

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.35  E-value=0.57  Score=41.84  Aligned_cols=24  Identities=29%  Similarity=0.457  Sum_probs=19.7

Q ss_pred             HHHHHhcCCC--eEEEccCCCchhHH
Q 010709          151 AMPVALSGRD--LLGCAETGSGKTAA  174 (503)
Q Consensus       151 ~i~~i~~~~~--vii~~~TGsGKTl~  174 (503)
                      .+..+++|.+  ++..|+||||||..
T Consensus        67 lv~~~l~G~n~~i~aYGqtgSGKTyT   92 (323)
T d1bg2a_          67 IVKDVLEGYNGTIFAYGQTSSGKTHT   92 (323)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHH
T ss_pred             HHHHHHcCCCcceeeecccCCCCcee
Confidence            3556678887  89999999999965

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=80.29  E-value=0.41  Score=39.02  Aligned_cols=15  Identities=27%  Similarity=0.355  Sum_probs=13.4

Q ss_pred             eEEEccCCCchhHHh
Q 010709          161 LLGCAETGSGKTAAF  175 (503)
Q Consensus       161 vii~~~TGsGKTl~~  175 (503)
                      +++.||+|||||+.+
T Consensus         9 I~i~G~pGSGKsT~a   23 (194)
T d1qf9a_           9 VFVLGGPGSGKGTQC   23 (194)
T ss_dssp             EEEEESTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            788999999999864

>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=80.14  E-value=0.81  Score=39.21  Aligned_cols=50  Identities=18%  Similarity=0.238  Sum_probs=26.5

Q ss_pred             CcccCCCCHHHHHHHHHC--CCCCCcHHHHHHHHHHhcCCCeEEEccCCCchhHH
Q 010709          122 SFTDMCLHPSIMKDIEFH--EYTRPTSIQAQAMPVALSGRDLLGCAETGSGKTAA  174 (503)
Q Consensus       122 ~~~~~~l~~~l~~~l~~~--~~~~~~~~Q~~~i~~i~~~~~vii~~~TGsGKTl~  174 (503)
                      +|+++.-.+...+.+...  -+..+..+|...   +-..+.+++.||+|+|||+.
T Consensus        10 t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~l   61 (256)
T d1lv7a_          10 TFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLL   61 (256)
T ss_dssp             CGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHH
T ss_pred             CHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHH
Confidence            577876666666555321  011111111110   01235699999999999974